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Hartig F, Abrego N, Bush A, Chase JM, Guillera-Arroita G, Leibold MA, Ovaskainen O, Pellissier L, Pichler M, Poggiato G, Pollock L, Si-Moussi S, Thuiller W, Viana DS, Warton DI, Zurell D, Yu DW. Novel community data in ecology-properties and prospects. Trends Ecol Evol 2024; 39:280-293. [PMID: 37949795 DOI: 10.1016/j.tree.2023.09.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 09/28/2023] [Accepted: 09/29/2023] [Indexed: 11/12/2023]
Abstract
New technologies for monitoring biodiversity such as environmental (e)DNA, passive acoustic monitoring, and optical sensors promise to generate automated spatiotemporal community observations at unprecedented scales and resolutions. Here, we introduce 'novel community data' as an umbrella term for these data. We review the emerging field around novel community data, focusing on new ecological questions that could be addressed; the analytical tools available or needed to make best use of these data; and the potential implications of these developments for policy and conservation. We conclude that novel community data offer many opportunities to advance our understanding of fundamental ecological processes, including community assembly, biotic interactions, micro- and macroevolution, and overall ecosystem functioning.
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Affiliation(s)
- Florian Hartig
- Theoretical Ecology, University of Regensburg, Regensburg, Germany.
| | - Nerea Abrego
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35 (Survontie 9C), FI-40014 Jyväskylä, Finland
| | - Alex Bush
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
| | - Jonathan M Chase
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | | | | | - Otso Ovaskainen
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35 (Survontie 9C), FI-40014 Jyväskylä, Finland; Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, P.O. Box 65, Helsinki 00014, Finland
| | - Loïc Pellissier
- Ecosystems and Landscape Evolution, Institute of Terrestrial Ecosystems, Department of Environmental Systems Science, ETH Zürich, 8092 Zurich, Switzerland; Unit of Land Change Science, Swiss Federal Research Institute for Forest, Snow and Landscape Research (WSL), 8903 Birmensdorf, Switzerland
| | | | - Giovanni Poggiato
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, F38000, Grenoble, France
| | - Laura Pollock
- Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Sara Si-Moussi
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, F38000, Grenoble, France
| | - Wilfried Thuiller
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, F38000, Grenoble, France
| | | | | | | | - Douglas W Yu
- Kunming Institute of Zoology; Yunnan, China; University of East Anglia, Norfolk, UK
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2
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Li Z, Linard B, Vogler AP, Yu DW, Wang Z. Phylogenetic diversity only weakly mitigates climate-change-driven biodiversity loss in insect communities. Mol Ecol 2023; 32:6147-6160. [PMID: 36271787 DOI: 10.1111/mec.16747] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 09/28/2022] [Accepted: 10/06/2022] [Indexed: 11/30/2022]
Abstract
To help address the underrepresentation of arthropods and Asian biodiversity from climate-change assessments, we carried out year-long, weekly sampling campaigns with Malaise traps at different elevations and latitudes in Gaoligongshan National Park in southwestern China. From these 623 samples, we barcoded 10,524 beetles and compared scenarios of climate-change-induced biodiversity loss, by designating seasonal, elevational, and latitudinal subsets of beetles as communities that plausibly could go extinct as a group, which we call "loss sets". The availability of a published mitochondrial-genome-based phylogeny of the Coleoptera allowed us to compare the loss of species diversity with and without accounting for phylogenetic relatedness. We hypothesised that phylogenetic relatedness would mitigate extinction, since the extinction of any loss set would result in the disappearance of all its species but only part of its evolutionary history, which is still extant in the remaining loss sets. We found different patterns of community clustering by season and latitude, depending on whether phylogenetic information was incorporated. However, accounting for phylogeny only slightly mitigated the amount of biodiversity loss under climate change scenarios, against our expectations: there is no phylogenetic "escape clause" for biodiversity conservation. We achieve the same results whether phylogenetic information was derived from the mitogenome phylogeny or from a de novo barcode-gene tree. We encourage interested researchers to use this data set to study lineage-specific community assembly patterns in conjunction with life-history traits and environmental covariates.
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Affiliation(s)
- Zongxu Li
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Benjamin Linard
- LIRMM, University of Montpellier, CNRS, Montpellier, France
- SPYGEN, Le Bourget-du-Lac, France
| | - Alfried P Vogler
- Department of Life Sciences, Natural History Museum, London, UK
- Department of Life Sciences, Imperial College London, Ascot, UK
| | - Douglas W Yu
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Zhengyang Wang
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts, USA
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3
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Luo M, Ji Y, Warton D, Yu DW. Extracting abundance information from
DNA
‐based data. Mol Ecol Resour 2022; 23:174-189. [PMID: 35986714 PMCID: PMC10087802 DOI: 10.1111/1755-0998.13703] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 07/31/2022] [Accepted: 08/16/2022] [Indexed: 11/26/2022]
Abstract
The accurate extraction of species-abundance information from DNA-based data (metabarcoding, metagenomics) could contribute usefully to diet analysis and food-web reconstruction, the inference of species interactions, the modelling of population dynamics and species distributions, the biomonitoring of environmental state and change, and the inference of false positives and negatives. However, multiple sources of bias and noise in sampling and processing combine to inject error into DNA-based data sets. To understand how to extract abundance information, it is useful to distinguish two concepts. (i) Within-sample across-species quantification describes relative species abundances in one sample. (ii) Across-sample within-species quantification describes how the abundance of each individual species varies from sample to sample, such as over a time series, an environmental gradient or different experimental treatments. First, we review the literature on methods to recover across-species abundance information (by removing what we call "species pipeline biases") and within-species abundance information (by removing what we call "pipeline noise"). We argue that many ecological questions can be answered with just within-species quantification, and we therefore demonstrate how to use a "DNA spike-in" to correct for pipeline noise and recover within-species abundance information. We also introduce a model-based estimator that can be used on data sets without a physical spike-in to approximate and correct for pipeline noise.
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Affiliation(s)
- Mingjie Luo
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong MountainKunming Institute of Zoology, Chinese Academy of SciencesKunmingYunnanChina
- Kunming College of Life SciencesUniversity of Chinese Academy of SciencesKunmingYunnanChina
| | - Yinqiu Ji
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong MountainKunming Institute of Zoology, Chinese Academy of SciencesKunmingYunnanChina
| | - David Warton
- School of Mathematics and StatisticsUNSW SydneySydneyNew South WalesAustralia
- Evolution and Ecology Research Centre, UNSW SydneySydneyNew South WalesAustralia
| | - Douglas W. Yu
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong MountainKunming Institute of Zoology, Chinese Academy of SciencesKunmingYunnanChina
- Center for Excellence in Animal Evolution and GeneticsChinese Academy of SciencesKunmingYunnanChina
- School of Biological SciencesUniversity of East Anglia, Norwich Research ParkNorwichNorfolkUK
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4
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Bohmann K, Elbrecht V, Carøe C, Bista I, Leese F, Bunce M, Yu DW, Seymour M, Dumbrell AJ, Creer S. Strategies for sample labelling and library preparation in DNA metabarcoding studies. Mol Ecol Resour 2022; 22:1231-1246. [PMID: 34551203 PMCID: PMC9293284 DOI: 10.1111/1755-0998.13512] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 09/07/2021] [Accepted: 09/14/2021] [Indexed: 11/26/2022]
Abstract
Metabarcoding of DNA extracted from environmental or bulk specimen samples is increasingly used to profile biota in basic and applied biodiversity research because of its targeted nature that allows sequencing of genetic markers from many samples in parallel. To achieve this, PCR amplification is carried out with primers designed to target a taxonomically informative marker within a taxonomic group, and sample-specific nucleotide identifiers are added to the amplicons prior to sequencing. The latter enables assignment of the sequences back to the samples they originated from. Nucleotide identifiers can be added during the metabarcoding PCR and during "library preparation", that is, when amplicons are prepared for sequencing. Different strategies to achieve this labelling exist. All have advantages, challenges and limitations, some of which can lead to misleading results, and in the worst case compromise the fidelity of the metabarcoding data. Given the range of questions addressed using metabarcoding, ensuring that data generation is robust and fit for the chosen purpose is critically important for practitioners seeking to employ metabarcoding for biodiversity assessments. Here, we present an overview of the three main workflows for sample-specific labelling and library preparation in metabarcoding studies on Illumina sequencing platforms; one-step PCR, two-step PCR, and tagged PCR. Further, we distill the key considerations for researchers seeking to select an appropriate metabarcoding strategy for their specific study. Ultimately, by gaining insights into the consequences of different metabarcoding workflows, we hope to further consolidate the power of metabarcoding as a tool to assess biodiversity across a range of applications.
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Affiliation(s)
- Kristine Bohmann
- Faculty of Health and Medical SciencesSection for Evolutionary GenomicsGlobe InstituteUniversity of CopenhagenCopenhagenDenmark
| | - Vasco Elbrecht
- Department of Environmental Systems ScienceETH ZurichZürichSwitzerland
| | - Christian Carøe
- Faculty of Health and Medical SciencesSection for Evolutionary GenomicsGlobe InstituteUniversity of CopenhagenCopenhagenDenmark
| | - Iliana Bista
- Department of GeneticsUniversity of CambridgeCambridgeUK
- Tree of LifeWellcome Sanger InstituteHinxtonUK
| | - Florian Leese
- Aquatic Ecosystem ResearchFaculty of BiologyUniversity of Duisburg‐EssenEssenGermany
| | - Michael Bunce
- Trace and Environmental DNA (TrEnD) LaboratorySchool of Molecular and Life SciencesCurtin UniversityPerthWAAustralia
| | - Douglas W. Yu
- State Key Laboratory of Genetic Resources and EvolutionKunming Institute of ZoologyChinese Academy of SciencesKunmingChina
- School of Biological SciencesNorwich Research ParkUniversity of East AngliaNorwichUK
- Center for Excellence in Animal Evolution and GeneticsChinese Academy of SciencesKunming YunnanChina
| | - Mathew Seymour
- Department of EcologySwedish University of Agricultural SciencesUppsalaSweden
| | | | - Simon Creer
- Molecular Ecology and Evolution GroupSchool of Natural SciencesBangor UniversityGwyneddUK
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5
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Ji Y, Baker CCM, Popescu VD, Wang J, Wu C, Wang Z, Li Y, Wang L, Hua C, Yang Z, Yang C, Xu CCY, Diana A, Wen Q, Pierce NE, Yu DW. Measuring protected-area effectiveness using vertebrate distributions from leech iDNA. Nat Commun 2022; 13:1555. [PMID: 35322033 PMCID: PMC8943135 DOI: 10.1038/s41467-022-28778-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 01/31/2022] [Indexed: 11/09/2022] Open
Abstract
Protected areas are key to meeting biodiversity conservation goals, but direct measures of effectiveness have proven difficult to obtain. We address this challenge by using environmental DNA from leech-ingested bloodmeals to estimate spatially-resolved vertebrate occupancies across the 677 km2 Ailaoshan reserve in Yunnan, China. From 30,468 leeches collected by 163 park rangers across 172 patrol areas, we identify 86 vertebrate species, including amphibians, mammals, birds and squamates. Multi-species occupancy modelling shows that species richness increases with elevation and distance to reserve edge. Most large mammals (e.g. sambar, black bear, serow, tufted deer) follow this pattern; the exceptions are the three domestic mammal species (cows, sheep, goats) and muntjak deer, which are more common at lower elevations. Vertebrate occupancies are a direct measure of conservation outcomes that can help guide protected-area management and improve the contributions that protected areas make towards global biodiversity goals. Here, we show the feasibility of using invertebrate-derived DNA to estimate spatially-resolved vertebrate occupancies across entire protected areas. Invertebrate-derived eDNA (iDNA) is an emerging tool for taxonomic and spatial biodiversity monitoring. Here, the authors use metabarcoding of leech-derived iDNA to estimate vertebrate occupancy over an entire protected area, the Ailaoshan Nature Reserve, China.
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Affiliation(s)
- Yinqiu Ji
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, 650223, Kunming, Yunnan, China
| | - Christopher C M Baker
- Museum of Comparative Zoology and Department of Organismic & Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA. .,US Army ERDC Cold Regions Research and Engineering Laboratory, 72 Lyme Road, Hanover, NH, 03755, USA.
| | - Viorel D Popescu
- Department of Biological Sciences and Sustainability Studies Theme, Ohio University, 107 Irvine Hall, Athens, OH, 45701, USA.,Center for Environmental Studies (CCMESI), University of Bucharest, 1 N. Balcescu Blvd., Bucharest, Romania
| | - Jiaxin Wang
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, 650223, Kunming, Yunnan, China
| | - Chunying Wu
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, 650223, Kunming, Yunnan, China
| | - Zhengyang Wang
- Museum of Comparative Zoology and Department of Organismic & Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
| | - Yuanheng Li
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, 650223, Kunming, Yunnan, China.,Museum of Comparative Zoology and Department of Organismic & Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
| | - Lin Wang
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, 666303, Mengla, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, 666303, Mengla, China
| | - Chaolang Hua
- Yunnan Forestry Survey and Planning Institute, 289 Renmin E Rd, 650028, Kunming, Yunnan, China
| | - Zhongxing Yang
- Yunnan Forestry Survey and Planning Institute, 289 Renmin E Rd, 650028, Kunming, Yunnan, China
| | - Chunyan Yang
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, 650223, Kunming, Yunnan, China
| | - Charles C Y Xu
- Redpath Museum and Department of Biology, McGill University, 859 Sherbrooke Street West, Montreal, PQ, H3A2K6, Canada
| | - Alex Diana
- School of Mathematics, Statistics and Actuarial Science, University of Kent, Sibson Building, Canterbury, Kent, CT27FS, UK
| | - Qingzhong Wen
- Yunnan Forestry Survey and Planning Institute, 289 Renmin E Rd, 650028, Kunming, Yunnan, China
| | - Naomi E Pierce
- Museum of Comparative Zoology and Department of Organismic & Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA.
| | - Douglas W Yu
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, 650223, Kunming, Yunnan, China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650201, Kunming, Yunnan, China. .,School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR47TJ, UK.
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6
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Sire L, Yáñez PS, Wang C, Bézier A, Courtial B, Cours J, Fontaneto D, Larrieu L, Bouget C, Thorn S, Müller J, Yu DW, Monaghan MT, Herniou EA, Lopez-Vaamonde C. Climate-induced forest dieback drives compositional changes in insect communities that are more pronounced for rare species. Commun Biol 2022; 5:57. [PMID: 35042989 PMCID: PMC8766456 DOI: 10.1038/s42003-021-02968-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 12/07/2021] [Indexed: 12/26/2022] Open
Abstract
Species richness, abundance and biomass of insects have recently undergone marked declines in Europe. We metabarcoded 211 Malaise-trap samples to investigate whether drought-induced forest dieback and subsequent salvage logging had an impact on ca. 3000 species of flying insects in silver fir Pyrenean forests. While forest dieback had no measurable impact on species richness, there were significant changes in community composition that were consistent with those observed during natural forest succession. Importantly, most observed changes were driven by rare species. Variation was explained primarily by canopy openness at the local scale, and the tree-related microhabitat diversity and deadwood amount at landscape scales. The levels of salvage logging in our study did not explain compositional changes. We conclude that forest dieback drives changes in species assemblages that mimic natural forest succession, and markedly increases the risk of catastrophic loss of rare species through homogenization of environmental conditions.
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Affiliation(s)
- Lucas Sire
- Institut de Recherche sur la Biologie de l'Insecte (IRBI), UMR 7261, CNRS-Université de Tours, Tours, France.
| | - Paul Schmidt Yáñez
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301, 12587, Berlin, Germany
| | - Cai Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, China
| | - Annie Bézier
- Institut de Recherche sur la Biologie de l'Insecte (IRBI), UMR 7261, CNRS-Université de Tours, Tours, France
| | | | - Jérémy Cours
- INRAE 'Forest Ecosystems' Research Unit - Biodiversity team Domaine des Barres, F-45290, Nogent-sur-Vernisson, France
| | - Diego Fontaneto
- Water Research Institute, National Research Council of Italy, CNR-IRSA, Largo Tonolli 50, 28922, Verbania Pallanza, Italy
| | - Laurent Larrieu
- Université de Toulouse, INRAE, UMR DYNAFOR, Castanet-Tolosan, France
- CRPF Occitanie, Tarbes, France
| | - Christophe Bouget
- INRAE 'Forest Ecosystems' Research Unit - Biodiversity team Domaine des Barres, F-45290, Nogent-sur-Vernisson, France
| | - Simon Thorn
- Field Station Fabrikschleichach, Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Glashüttenstraße 5, 96181, Rauhenebrach, Germany
| | - Jörg Müller
- Field Station Fabrikschleichach, Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Glashüttenstraße 5, 96181, Rauhenebrach, Germany
- Bavarian Forest National Park, Freyunger Str. 2, 94481, Grafenau, Germany
| | - Douglas W Yu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR47TJ, UK
| | - Michael T Monaghan
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301, 12587, Berlin, Germany
- Institut für Biologie, Freie Universität Berlin, Königin-Luise-Straße. 1-3, 12489, Berlin, Germany
| | - Elisabeth A Herniou
- Institut de Recherche sur la Biologie de l'Insecte (IRBI), UMR 7261, CNRS-Université de Tours, Tours, France
| | - Carlos Lopez-Vaamonde
- Institut de Recherche sur la Biologie de l'Insecte (IRBI), UMR 7261, CNRS-Université de Tours, Tours, France
- INRAE, Zoologie Forestière, F-45075, Orléans, France
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7
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Worsley SF, Innocent TM, Holmes NA, Al-Bassam MM, Schiøtt M, Wilkinson B, Murrell JC, Boomsma JJ, Yu DW, Hutchings MI. Competition-based screening helps to secure the evolutionary stability of a defensive microbiome. BMC Biol 2021; 19:205. [PMID: 34526023 PMCID: PMC8444595 DOI: 10.1186/s12915-021-01142-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 09/03/2021] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND The cuticular microbiomes of Acromyrmex leaf-cutting ants pose a conundrum in microbiome biology because they are freely colonisable, and yet the prevalence of the vertically transmitted bacteria Pseudonocardia, which contributes to the control of Escovopsis fungus garden disease, is never compromised by the secondary acquisition of other bacterial strains. Game theory suggests that competition-based screening can allow the selective recruitment of antibiotic-producing bacteria from the environment, by providing abundant resources to foment interference competition between bacterial species and by using Pseudonocardia to bias the outcome of competition in favour of antibiotic producers. RESULTS Here, we use RNA-stable isotope probing (RNA-SIP) to confirm that Acromyrmex ants can maintain a range of microbial symbionts on their cuticle by supplying public resources. We then used RNA sequencing, bioassays, and competition experiments to show that vertically transmitted Pseudonocardia strains produce antibacterials that differentially reduce the growth rates of other microbes, ultimately biassing the bacterial competition to allow the selective establishment of secondary antibiotic-producing strains while excluding non-antibiotic-producing strains that would parasitise the symbiosis. CONCLUSIONS Our findings are consistent with the hypothesis that competition-based screening is a plausible mechanism for maintaining the integrity of the co-adapted mutualism between the leaf-cutting ant farming symbiosis and its defensive microbiome. Our results have broader implications for explaining the stability of other complex symbioses involving horizontal acquisition.
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Affiliation(s)
- Sarah F Worsley
- School of Biological Sciences, Norwich Research Park, University of East Anglia, Norwich, Norfolk, NR4 7TJ, UK
| | - Tabitha M Innocent
- Centre for Social Evolution, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Neil A Holmes
- School of Biological Sciences, Norwich Research Park, University of East Anglia, Norwich, Norfolk, NR4 7TJ, UK
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, Norfolk, NR4 7UH, UK
| | - Mahmoud M Al-Bassam
- School of Biological Sciences, Norwich Research Park, University of East Anglia, Norwich, Norfolk, NR4 7TJ, UK
| | - Morten Schiøtt
- Centre for Social Evolution, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Barrie Wilkinson
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, Norfolk, NR4 7UH, UK
| | - J Colin Murrell
- School of Environmental Sciences, Norwich Research Park, University of East Anglia, Norwich, Norfolk, NR4 7TJ, UK
| | - Jacobus J Boomsma
- Centre for Social Evolution, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Douglas W Yu
- School of Biological Sciences, Norwich Research Park, University of East Anglia, Norwich, Norfolk, NR4 7TJ, UK.
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China.
| | - Matthew I Hutchings
- School of Biological Sciences, Norwich Research Park, University of East Anglia, Norwich, Norfolk, NR4 7TJ, UK.
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, Norfolk, NR4 7UH, UK.
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8
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Yang C, Bohmann K, Wang X, Cai W, Wales N, Ding Z, Gopalakrishnan S, Yu DW. Biodiversity Soup II: A bulk‐sample metabarcoding pipeline emphasizing error reduction. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13602] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Chunyan Yang
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyChinese Academy of Sciences Kunming China
| | - Kristine Bohmann
- Section for Evolutionary Genomics Globe Institute Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark
| | - Xiaoyang Wang
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyChinese Academy of Sciences Kunming China
| | - Wang Cai
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyChinese Academy of Sciences Kunming China
| | - Nathan Wales
- Section for Evolutionary Genomics Globe Institute Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark
- Department of Archaeology University of York York UK
| | - Zhaoli Ding
- Biodiversity Genomics Center Kunming Institute of Zoology Chinese Academy of Sciences Kunming China
| | - Shyam Gopalakrishnan
- Section for Evolutionary Genomics Globe Institute Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark
| | - Douglas W. Yu
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyChinese Academy of Sciences Kunming China
- School of Biological Sciences University of East AngliaNorwich Research Park Norwich UK
- Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences Kunming China
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9
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Arribas P, Andújar C, Bidartondo MI, Bohmann K, Coissac É, Creer S, deWaard JR, Elbrecht V, Ficetola GF, Goberna M, Kennedy S, Krehenwinkel H, Leese F, Novotny V, Ronquist F, Yu DW, Zinger L, Creedy TJ, Meramveliotakis E, Noguerales V, Overcast I, Morlon H, Vogler AP, Papadopoulou A, Emerson BC. Connecting high-throughput biodiversity inventories: Opportunities for a site-based genomic framework for global integration and synthesis. Mol Ecol 2021; 30:1120-1135. [PMID: 33432777 PMCID: PMC7986105 DOI: 10.1111/mec.15797] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 12/21/2020] [Accepted: 01/05/2021] [Indexed: 01/03/2023]
Abstract
High-throughput sequencing (HTS) is increasingly being used for the characterization and monitoring of biodiversity. If applied in a structured way, across broad geographical scales, it offers the potential for a much deeper understanding of global biodiversity through the integration of massive quantities of molecular inventory data generated independently at local, regional and global scales. The universality, reliability and efficiency of HTS data can potentially facilitate the seamless linking of data among species assemblages from different sites, at different hierarchical levels of diversity, for any taxonomic group and regardless of prior taxonomic knowledge. However, collective international efforts are required to optimally exploit the potential of site-based HTS data for global integration and synthesis, efforts that at present are limited to the microbial domain. To contribute to the development of an analogous strategy for the nonmicrobial terrestrial domain, an international symposium entitled "Next Generation Biodiversity Monitoring" was held in November 2019 in Nicosia (Cyprus). The symposium brought together evolutionary geneticists, ecologists and biodiversity scientists involved in diverse regional and global initiatives using HTS as a core tool for biodiversity assessment. In this review, we summarize the consensus that emerged from the 3-day symposium. We converged on the opinion that an effective terrestrial Genomic Observatories network for global biodiversity integration and synthesis should be spatially led and strategically united under the umbrella of the metabarcoding approach. Subsequently, we outline an HTS-based strategy to collectively build an integrative framework for site-based biodiversity data generation.
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Affiliation(s)
- Paula Arribas
- Island Ecology and Evolution Research GroupInstituto de Productos Naturales y Agrobiología (IPNA‐CSIC)San Cristóbal de la LagunaSpain
| | - Carmelo Andújar
- Island Ecology and Evolution Research GroupInstituto de Productos Naturales y Agrobiología (IPNA‐CSIC)San Cristóbal de la LagunaSpain
| | - Martin I. Bidartondo
- Department of Life SciencesImperial College LondonLondonUK
- Comparative Plant and Fungal BiologyRoyal Botanic GardensLondonUK
| | - Kristine Bohmann
- Section for Evolutionary Genomics, Faculty of Health and Medical Sciences, Globe InstituteUniversity of CopenhagenCopenhagenDenmark
| | - Éric Coissac
- Université Grenoble Alpes, CNRS, Université Savoie Mont BlancLECA, Laboratoire d’Ecologie AlpineGrenobleFrance
| | - Simon Creer
- School of Natural SciencesBangor UniversityGwyneddUK
| | - Jeremy R. deWaard
- Centre for Biodiversity GenomicsUniversity of GuelphGuelphCanada
- School of Environmental SciencesUniversity of GuelphGuelphCanada
| | - Vasco Elbrecht
- Centre for Biodiversity Monitoring (ZBM)Zoological Research Museum Alexander KoenigBonnGermany
| | - Gentile F. Ficetola
- Université Grenoble Alpes, CNRS, Université Savoie Mont BlancLECA, Laboratoire d’Ecologie AlpineGrenobleFrance
- Department of Environmental Sciences and PolicyUniversity of MilanoMilanoItaly
| | - Marta Goberna
- Department of Environment and AgronomyINIAMadridSpain
| | - Susan Kennedy
- Biodiversity and Biocomplexity UnitOkinawa Institute of Science and Technology Graduate UniversityOnna‐sonJapan
- Department of BiogeographyTrier UniversityTrierGermany
| | | | - Florian Leese
- Aquatic Ecosystem Research, Faculty of BiologyUniversity of Duisburg‐EssenEssenGermany
- Centre for Water and Environmental Research (ZWU) EssenUniversity of Duisburg‐EssenEssenGermany
| | - Vojtech Novotny
- Biology Centre, Institute of EntomologyCzech Academy of SciencesCeske BudejoviceCzech Republic
- Faculty of ScienceUniversity of South BohemiaCeske BudejoviceCzech Republic
| | - Fredrik Ronquist
- Department of Bioinformatics and GeneticsSwedish Museum of Natural HistoryStockholmSweden
| | - Douglas W. Yu
- State Key Laboratory of Genetic Resources and EvolutionKunming Institute of Zoology, Chinese Academy of SciencesKunmingChina
- Center for Excellence in Animal Evolution and GeneticsChinese Academy of SciencesKunmingChina
- School of Biological SciencesUniversity of East AngliaNorwichUK
| | - Lucie Zinger
- Institut de Biologie de l’ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERMUniversité PSLParisFrance
| | | | | | | | - Isaac Overcast
- Institut de Biologie de l’ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERMUniversité PSLParisFrance
- Division of Vertebrate ZoologyAmerican Museum of Natural HistoryNew YorkUSA
| | - Hélène Morlon
- Institut de Biologie de l’ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERMUniversité PSLParisFrance
| | - Alfried P. Vogler
- Department of Life SciencesImperial College LondonLondonUK
- Department of Life SciencesNatural History MuseumLondonUK
| | | | - Brent C. Emerson
- Island Ecology and Evolution Research GroupInstituto de Productos Naturales y Agrobiología (IPNA‐CSIC)San Cristóbal de la LagunaSpain
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10
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Lynggaard C, Yu DW, Oliveira G, Caldeira CF, Ramos SJ, Ellegaard MR, Gilbert MTP, Gastauer M, Bohmann K. DNA-Based Arthropod Diversity Assessment in Amazonian Iron Mine Lands Show Ecological Succession Towards Undisturbed Reference Sites. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.590976] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Human activities change natural landscapes, and in doing so endanger biodiversity and associated ecosystem services. To reduce the net impacts of these activities, such as mining, disturbed areas are rehabilitated and restored. During this process, monitoring is important to ensure that desired trajectories are maintained. In the Carajás region of the Brazilian Amazon, exploration for iron ores has transformed the original ecosystem; natural forest and a savanna formation with lateritic iron duricrust outcrops named canga. Here, native vegetation is logged and topsoil removed and deposited in waste piles along with mine waste. During rehabilitation, these waste piles are hydroseeded with non-native plant species to achieve rapid revegetation. Further, seeds of native canga and forest plant species are planted to point ecological succession towards natural ecosystems. In this study, we investigate diversity and composition of the arthropod community along a post-mining rehabilitation and restoration gradient, taking seasonality and primer bias into account. We use DNA metabarcoding of bulk arthropod samples collected in both the dry and rainy seasons from waste-pile benches at various stages of revegetation: non-revegetated exposed soils, initial stage with one-to-three-year-old stands, intermediate stage with four-to-five-year-old stands, and advanced stage with six-to-seven-year-old stands. We use samples from undisturbed cangas and forests as reference sites. In addition, we vegetation diversity and structure were measured to investigate relations between arthropod community and vegetation structure. Our results show that, over time, the arthropod community composition of the waste piles becomes more similar to the reference forests, but not to the reference cangas. Nevertheless, even the communities in the advanced-stage waste piles are different from the reference forests, and full restoration in these highly diverse ecosystems is not achieved, even after 6 to 7 years. Finally, our results show seasonal variation in arthropod communities and primer bias.
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11
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Hughes AC, Lechner AM, Chitov A, Horstmann A, Hinsley A, Tritto A, Chariton A, Li BV, Ganapin D, Simonov E, Morton K, Toktomushev K, Foggin M, Tan-Mullins M, Orr MC, Griffiths R, Nash R, Perkin S, Glémet R, Kim M, Yu DW. Horizon Scan of the Belt and Road Initiative. Trends Ecol Evol 2020; 35:583-593. [PMID: 32521242 DOI: 10.1016/j.tree.2020.02.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 01/29/2020] [Accepted: 02/11/2020] [Indexed: 10/24/2022]
Abstract
The Belt and Road Initiative (BRI) represents the largest infrastructure and development project in human history, and presents risks and opportunities for ecosystems, economies, and communities. Some risks (habitat fragmentation, roadkill) are obvious, however, many of the BRI's largest challenges for development and conservation are not obvious and require extensive consideration to identify. In this first BRI Horizon Scan, we identify 11 frontier issues that may have large environmental and social impacts but are not yet recognised. More generally, the BRI will increase China's participation in international environmental governance. Thus, new cooperative modes of governance are needed to balance geopolitical, societal, and environmental interests. Upgrading and standardising global environmental standards is essential to safeguard ecological systems and human societies.
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Affiliation(s)
- Alice C Hughes
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan 666303, China; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, Yunnan 666303, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Alex M Lechner
- School of Environmental and Geographical Sciences, University of Nottingham Malaysia, 43500 Semenyih, Malaysia
| | - Alexander Chitov
- Faculty of Law, University of Chiang Mai, Chiang Mai 50200, Thailand
| | | | - Amy Hinsley
- WildCRU, Department of Zoology, University of Oxford, OX1 3SZ, UK
| | - Angela Tritto
- Institute of Emerging Market Studies, The Hong Kong University of Science and Technology, Hong Kong, HK-SAR, China
| | - Anthony Chariton
- Department of Biological Sciences, Macquarie University, NSW, Australia
| | - Binbin V Li
- Environmental Research Center, Duke Kunshan University, Kunshan, Jiangsu, China; Nicholas School of the Environment, Duke University, Durham, North, Carolina, NC 27708, USA
| | - Delfin Ganapin
- World Wide Fund for Nature (WWF) International, 1196 Gland, Switzerland
| | - Eugene Simonov
- Rivers without Boundaries International Coalition, Dalian 116650, China; Daursky Biosphere Reserve, Nizhny Tsasuchei, Zabaikalsky Province, Russia
| | - Katherine Morton
- School of East Asian Studies, University of Sheffield, Sheffield, S10 2TD, UK; Schwarzman College, Tsinghua University, Beijing, China
| | - Kemel Toktomushev
- Mountain Societies Research Institute, University of Central Asia, Bishkek 720002, Kyrgyz Republic
| | - Marc Foggin
- Institute of Asian Research, School of Public Policy and Global Affairs, University of British Columbia, Vancouver, BC, Canada
| | - May Tan-Mullins
- School of International Studies, Institute of Asia and Pacific Studies, University of Nottingham, Ningbo, China
| | - Michael C Orr
- Key Laboratory of Zoological Systematics, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Richard Griffiths
- International Institute for Asian Studies, 2311, GJ, Leiden, The Netherlands
| | - Richard Nash
- Rivers without Boundaries International Coalition, Dalian 116650, China
| | - Scott Perkin
- IUCN Asia Regional Office, Watthana, Bangkok 10110, Thailand
| | - Raphaël Glémet
- IUCN Asia Regional Office, Watthana, Bangkok 10110, Thailand
| | - Minsun Kim
- IUCN Asia Regional Office, Watthana, Bangkok 10110, Thailand
| | - Douglas W Yu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
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12
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Pochardt M, Allen JM, Hart T, Miller SDL, Yu DW, Levi T. Environmental DNA facilitates accurate, inexpensive, and multiyear population estimates of millions of anadromous fish. Mol Ecol Resour 2019; 20:457-467. [DOI: 10.1111/1755-0998.13123] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 12/02/2019] [Accepted: 12/02/2019] [Indexed: 11/28/2022]
Affiliation(s)
- Meredith Pochardt
- Department of Fisheries and Wildlife Oregon State University Corvallis OR USA
- Chilkoot Indian Association Haines AK USA
- Takshanuk Watershed Council Haines AK USA
| | - Jennifer M. Allen
- Department of Fisheries and Wildlife Oregon State University Corvallis OR USA
| | - Ted Hart
- Chilkoot Indian Association Haines AK USA
| | - Sophie D. L. Miller
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming China
| | - Douglas W. Yu
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming China
- Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences Kunming China
- School of Biological Sciences University of East Anglia Norwich UK
| | - Taal Levi
- Department of Fisheries and Wildlife Oregon State University Corvallis OR USA
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13
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Wang X, Hua F, Wang L, Wilcove DS, Yu DW. The biodiversity benefit of native forests and mixed‐species plantations over monoculture plantations. DIVERS DISTRIB 2019. [DOI: 10.1111/ddi.12972] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Xiaoyang Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology Chinese Academy of Sciences Kunming China
- Kunming College of Life Sciences University of Chinese Academy of Sciences Kunming China
| | - Fangyuan Hua
- Conservation Science Group, Department of Zoology University of Cambridge Cambridge UK
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany Chinese Academy of Sciences Kunming China
| | - Lin Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology Chinese Academy of Sciences Kunming China
| | - David S. Wilcove
- Department of Ecology and Evolutionary Biology Princeton University Princeton NJ USA
- Program in Science, Technology and Environmental Policy, School of Public and International Affairs Princeton University Princeton NJ USA
| | - Douglas W. Yu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology Chinese Academy of Sciences Kunming China
- Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences Kunming China
- School of Biological Sciences University of East Anglia, Norwich Research Park Norwich UK
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14
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Ji Y, Huotari T, Roslin T, Schmidt NM, Wang J, Yu DW, Ovaskainen O. SPIKEPIPE: A metagenomic pipeline for the accurate quantification of eukaryotic species occurrences and intraspecific abundance change using DNA barcodes or mitogenomes. Mol Ecol Resour 2019; 20:256-267. [PMID: 31293086 DOI: 10.1111/1755-0998.13057] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 06/15/2019] [Accepted: 07/03/2019] [Indexed: 11/24/2022]
Abstract
The accurate quantification of eukaryotic species abundances from bulk samples remains a key challenge for community ecology and environmental biomonitoring. We resolve this challenge by combining shotgun sequencing, mapping to reference DNA barcodes or to mitogenomes, and three correction factors: (a) a percent-coverage threshold to filter out false positives, (b) an internal-standard DNA spike-in to correct for stochasticity during sequencing, and (c) technical replicates to correct for stochasticity across sequencing runs. The SPIKEPIPE pipeline achieves a strikingly high accuracy of intraspecific abundance estimates (in terms of DNA mass) from samples of known composition (mapping to barcodes R2 = .93, mitogenomes R2 = .95) and a high repeatability across environmental-sample replicates (barcodes R2 = .94, mitogenomes R2 = .93). As proof of concept, we sequence arthropod samples from the High Arctic, systematically collected over 17 years, detecting changes in species richness, species-specific abundances, and phenology. SPIKEPIPE provides cost-efficient and reliable quantification of eukaryotic communities.
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Affiliation(s)
- Yinqiu Ji
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Tea Huotari
- Department of Agricultural Sciences, Spatial Foodweb Ecology Group, University of Helsinki, Helsinki, Finland
| | - Tomas Roslin
- Department of Agricultural Sciences, Spatial Foodweb Ecology Group, University of Helsinki, Helsinki, Finland.,Department of Ecology, Spatial Foodweb Ecology Group, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Niels Martin Schmidt
- Arctic Research Centre, Aarhus University, Aarhus, Denmark.,Department of Bioscience, Aarhus University, Roskilde, Denmark
| | - Jiaxin Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Douglas W Yu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,School of Biological Sciences, University of East Anglia, Norfolk, UK.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Otso Ovaskainen
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland.,Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
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15
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Peel N, Dicks LV, Clark MD, Heavens D, Percival‐Alwyn L, Cooper C, Davies RG, Leggett RM, Yu DW. Semi‐quantitative characterisation of mixed pollen samples using MinION sequencing and Reverse Metagenomics (RevMet). Methods Ecol Evol 2019. [DOI: 10.1111/2041-210x.13265] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Ned Peel
- Earlham Institute Norwich UK
- University of East Anglia Norwich UK
| | | | | | | | | | | | | | | | - Douglas W. Yu
- University of East Anglia Norwich UK
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology, Chinese Academy of Sciences Kunming China
- Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences Kunming China
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16
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Boza G, Worsley SF, Yu DW, Scheuring I. Efficient assembly and long-term stability of defensive microbiomes via private resources and community bistability. PLoS Comput Biol 2019; 15:e1007109. [PMID: 31150382 PMCID: PMC6576795 DOI: 10.1371/journal.pcbi.1007109] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 06/17/2019] [Accepted: 05/15/2019] [Indexed: 11/19/2022] Open
Abstract
Understanding the mechanisms that promote the assembly and maintenance of host-beneficial microbiomes is an open problem. Empirical evidence supports the idea that animal and plant hosts can combine 'private resources' with the ecological phenomenon known as 'community bistability' to favour some microbial strains over others. We briefly review evidence showing that hosts can: (i) protect the growth of beneficial strains in an isolated habitat, (ii) use antibiotics to suppress non-beneficial, competitor strains, and (iii) provide resources that only beneficial strains are able to translate into an increased rate of growth, reproduction, or antibiotic production. We then demonstrate in a spatially explicit, individual-based model that these three mechanisms act similarly by selectively promoting the initial proliferation of preferred strains, that is, by acting as a private resource. The faster early growth of preferred strains, combined with the phenomenon of 'community bistability,' allows those strains to continue to dominate the microbiome even after the private resource is withdrawn or made public. This is because after a beneficial colony reaches a sufficiently large size, it can resist invasion by parasites without further private support from the host. We further explicitly model localized microbial interactions and diffusion dynamics, and we show that an intermediate level of antibiotic diffusion is the most efficient mechanism in promoting preferred strains and that there is a wide range of parameters under which hosts can promote the assembly of a self-sustaining defensive microbiome. This in turn supports the idea that hosts readily evolve to promote host-beneficial defensive microbiomes.
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Affiliation(s)
- Gergely Boza
- Evolutionary Systems Research Group, MTA Centre for Ecological Research, Hungarian Academy of Sciences, Tihany, Hungary
- International Institute for Applied Systems Analysis (IIASA), Laxenburg, Austria
- * E-mail: , (GB); (IS)
| | - Sarah F. Worsley
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Douglas W. Yu
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - István Scheuring
- Evolutionary Systems Research Group, MTA Centre for Ecological Research, Hungarian Academy of Sciences, Tihany, Hungary
- MTA-ELTE Theoretical Biology and Evolutionary Ecology Research Group, Hungarian Academy of Sciences, Budapest, Hungary
- * E-mail: , (GB); (IS)
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17
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Abrams JF, Hörig LA, Brozovic R, Axtner J, Crampton‐Platt A, Mohamed A, Wong ST, Sollmann R, Yu DW, Wilting A. Shifting up a gear with
iDNA
: From mammal detection events to standardised surveys. J Appl Ecol 2019. [DOI: 10.1111/1365-2664.13411] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jesse F. Abrams
- Leibniz Institute for Zoo and Wildlife Research Berlin Germany
| | - Lisa A. Hörig
- Leibniz Institute for Zoo and Wildlife Research Berlin Germany
| | - Robert Brozovic
- Leibniz Institute for Zoo and Wildlife Research Berlin Germany
| | - Jan Axtner
- Leibniz Institute for Zoo and Wildlife Research Berlin Germany
| | | | - Azlan Mohamed
- Leibniz Institute for Zoo and Wildlife Research Berlin Germany
| | - Seth T. Wong
- Leibniz Institute for Zoo and Wildlife Research Berlin Germany
| | - Rahel Sollmann
- Department of Wildlife, Fish, and Conservation Biology University of California Davis Davis California
| | - Douglas W. Yu
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming Yunnan China
- School of Biological Sciences University of East AngliaNorwich Research Park Norwich Norfolk UK
- Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences Kunming China
| | - Andreas Wilting
- Leibniz Institute for Zoo and Wildlife Research Berlin Germany
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18
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Levi T, Allen JM, Bell D, Joyce J, Russell JR, Tallmon DA, Vulstek SC, Yang C, Yu DW. Environmental DNA for the enumeration and management of Pacific salmon. Mol Ecol Resour 2019; 19:597-608. [DOI: 10.1111/1755-0998.12987] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 11/14/2018] [Accepted: 12/03/2018] [Indexed: 01/22/2023]
Affiliation(s)
- Taal Levi
- Department of Fisheries and Wildlife Oregon State University Corvallis Oregon
| | - Jennifer M. Allen
- Department of Fisheries and Wildlife Oregon State University Corvallis Oregon
| | - Donovan Bell
- Auke Bay Laboratories National Oceanic and Atmospheric Administration Juneau, Alaska
| | - John Joyce
- Auke Bay Laboratories National Oceanic and Atmospheric Administration Juneau, Alaska
| | - Joshua R. Russell
- Auke Bay Laboratories National Oceanic and Atmospheric Administration Juneau, Alaska
| | - David A. Tallmon
- Biology and Marine Biology Program University of Alaska Southeast Juneau, Alaska
| | - Scott C. Vulstek
- Auke Bay Laboratories National Oceanic and Atmospheric Administration Juneau, Alaska
| | - Chunyan Yang
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology, Chinese Academy of Sciences Kunming China
| | - Douglas W. Yu
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology, Chinese Academy of Sciences Kunming China
- Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences Kunming China
- School of Biological Sciences University of East Anglia Norwich UK
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19
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Axtner J, Crampton-Platt A, Hörig LA, Mohamed A, Xu CCY, Yu DW, Wilting A. An efficient and robust laboratory workflow and tetrapod database for larger scale environmental DNA studies. Gigascience 2019; 8:giz029. [PMID: 30997489 PMCID: PMC6461710 DOI: 10.1093/gigascience/giz029] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 10/12/2018] [Accepted: 03/07/2019] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND The use of environmental DNA for species detection via metabarcoding is growing rapidly. We present a co-designed lab workflow and bioinformatic pipeline to mitigate the 2 most important risks of environmental DNA use: sample contamination and taxonomic misassignment. These risks arise from the need for polymerase chain reaction (PCR) amplification to detect the trace amounts of DNA combined with the necessity of using short target regions due to DNA degradation. FINDINGS Our high-throughput workflow minimizes these risks via a 4-step strategy: (i) technical replication with 2 PCR replicates and 2 extraction replicates; (ii) using multi-markers (12S,16S,CytB); (iii) a "twin-tagging," 2-step PCR protocol; and (iv) use of the probabilistic taxonomic assignment method PROTAX, which can account for incomplete reference databases. Because annotation errors in the reference sequences can result in taxonomic misassignment, we supply a protocol for curating sequence datasets. For some taxonomic groups and some markers, curation resulted in >50% of sequences being deleted from public reference databases, owing to (i) limited overlap between our target amplicon and reference sequences, (ii) mislabelling of reference sequences, and (iii) redundancy. Finally, we provide a bioinformatic pipeline to process amplicons and conduct PROTAX assignment and tested it on an invertebrate-derived DNA dataset from 1,532 leeches from Sabah, Malaysia. Twin-tagging allowed us to detect and exclude sequences with non-matching tags. The smallest DNA fragment (16S) amplified most frequently for all samples but was less powerful for discriminating at species rank. Using a stringent and lax acceptance criterion we found 162 (stringent) and 190 (lax) vertebrate detections of 95 (stringent) and 109 (lax) leech samples. CONCLUSIONS Our metabarcoding workflow should help research groups increase the robustness of their results and therefore facilitate wider use of environmental and invertebrate-derived DNA, which is turning into a valuable source of ecological and conservation information on tetrapods.
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Affiliation(s)
- Jan Axtner
- Leibniz Institute for Zoo and Wildlife Research, Department of Ecological Dynamics, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
| | - Alex Crampton-Platt
- Leibniz Institute for Zoo and Wildlife Research, Department of Ecological Dynamics, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
| | - Lisa A Hörig
- Leibniz Institute for Zoo and Wildlife Research, Department of Ecological Dynamics, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
| | - Azlan Mohamed
- Leibniz Institute for Zoo and Wildlife Research, Department of Ecological Dynamics, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
| | - Charles C Y Xu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang East Rd, Kunming, Yunnan 650223, China
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, P.O. Box 11103, 9700 CC Groningen, The Netherlands
- Redpath Museum and Department of Biology, McGill University 859 Sherbooke Street West, Montreal, PQ, Canada H3A 2K6
| | - Douglas W Yu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang East Rd, Kunming, Yunnan 650223, China
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR47TJ, UK
| | - Andreas Wilting
- Leibniz Institute for Zoo and Wildlife Research, Department of Ecological Dynamics, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
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20
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Kocher SD, Mallarino R, Rubin BER, Yu DW, Hoekstra HE, Pierce NE. The genetic basis of a social polymorphism in halictid bees. Nat Commun 2018; 9:4338. [PMID: 30337532 PMCID: PMC6194137 DOI: 10.1038/s41467-018-06824-8] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 09/17/2018] [Indexed: 11/09/2022] Open
Abstract
The emergence of eusociality represents a major evolutionary transition from solitary to group reproduction. The most commonly studied eusocial species, honey bees and ants, represent the behavioral extremes of social evolution but lack close relatives that are non-social. Unlike these species, the halictid bee Lasioglossum albipes produces both solitary and eusocial nests and this intraspecific variation has a genetic basis. Here, we identify genetic variants associated with this polymorphism, including one located in the intron of syntaxin 1a (syx1a), a gene that mediates synaptic vesicle release. We show that this variant can alter gene expression in a pattern consistent with differences between social and solitary bees. Surprisingly, syx1a and several other genes associated with sociality in L. albipes have also been implicated in autism spectrum disorder in humans. Thus, genes underlying behavioral variation in L. albipes may also shape social behaviors across a wide range of taxa, including humans. The halictid bee Lasioglossum albipes has both solitary and eusocial individuals, making it a model for social evolution. Here, Kocher et al. identify a genetic variation associated with this social polymorphism, including a variant that can regulate the expression of an autism-associated gene, syntaxin 1a.
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Affiliation(s)
- Sarah D Kocher
- Department of Ecology and Evoutionary Biology, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08544, USA. .,Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, 28 Oxford St, Cambridge, MA, 02138, USA.
| | - Ricardo Mallarino
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, 28 Oxford St, Cambridge, MA, 02138, USA.,Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, Harvard University, 52 Oxford St, Cambridge, MA, 01238, USA.,Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Benjamin E R Rubin
- Department of Ecology and Evoutionary Biology, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08544, USA
| | - Douglas W Yu
- Kunming Institute for Zoology, 32 Jiaochang Donglu, Kunming, Yunnan, 650223, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 32 Jiaochang Donglu, Kunming, Yunnan, 650223, China.,School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Hopi E Hoekstra
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, 28 Oxford St, Cambridge, MA, 02138, USA.,Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, Harvard University, 52 Oxford St, Cambridge, MA, 01238, USA
| | - Naomi E Pierce
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, 28 Oxford St, Cambridge, MA, 02138, USA.
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21
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Andújar C, Arribas P, Yu DW, Vogler AP, Emerson BC. Why the COI barcode should be the community DNA metabarcode for the metazoa. Mol Ecol 2018; 27:3968-3975. [PMID: 30129071 DOI: 10.1111/mec.14844] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 07/21/2018] [Accepted: 08/03/2018] [Indexed: 12/25/2022]
Abstract
Metabarcoding of complex metazoan communities is increasingly being used to measure biodiversity in terrestrial, freshwater and marine ecosystems, revolutionizing our ability to observe patterns and infer processes regarding the origin and conservation of biodiversity. A fundamentally important question is which genetic marker to amplify, and although the mitochondrial cytochrome oxidase subunit I (COI) gene is one of the more widely used markers in metabarcoding for the Metazoa, doubts have recently been raised about its suitability. We argue that (a) the extensive coverage of reference sequence databases for COI; (b) the variation it presents; (c) the comparative advantages for denoising protein-coding genes; and (d) recent advances in DNA sequencing protocols argue in favour of standardizing for the use of COI for metazoan community samples. We also highlight where research efforts should focus to maximize the utility of metabarcoding.
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Affiliation(s)
- Carmelo Andújar
- Grupo de Ecología y Evolución en Islas, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), San Cristóbal de la Laguna, Spain
| | - Paula Arribas
- Grupo de Ecología y Evolución en Islas, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), San Cristóbal de la Laguna, Spain
| | - Douglas W Yu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- School of Biological Sciences, University of East Anglia, Norwich, Norfolk, UK
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming Yunnan, China
| | - Alfried P Vogler
- Department of Life Sciences, Natural History Museum, London, UK
- Department of Life Sciences, Imperial College London, Ascot, UK
| | - Brent C Emerson
- Grupo de Ecología y Evolución en Islas, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), San Cristóbal de la Laguna, Spain
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22
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Schnell IB, Bohmann K, Schultze SE, Richter SR, Murray DC, Sinding MHS, Bass D, Cadle JE, Campbell MJ, Dolch R, Edwards DP, Gray TNE, Hansen T, Hoa ANQ, Noer CL, Heise-Pavlov S, Sander Pedersen AF, Ramamonjisoa JC, Siddall ME, Tilker A, Traeholt C, Wilkinson N, Woodcock P, Yu DW, Bertelsen MF, Bunce M, Gilbert MTP. Debugging diversity - a pan-continental exploration of the potential of terrestrial blood-feeding leeches as a vertebrate monitoring tool. Mol Ecol Resour 2018; 18:1282-1298. [PMID: 29877042 DOI: 10.1111/1755-0998.12912] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 04/09/2018] [Accepted: 04/18/2018] [Indexed: 01/31/2023]
Abstract
The use of environmental DNA (eDNA) has become an applicable noninvasive tool with which to obtain information about biodiversity. A subdiscipline of eDNA is iDNA (invertebrate-derived DNA), where genetic material ingested by invertebrates is used to characterize the biodiversity of the species that served as hosts. While promising, these techniques are still in their infancy, as they have only been explored on limited numbers of samples from only a single or a few different locations. In this study, we investigate the suitability of iDNA extracted from more than 3,000 haematophagous terrestrial leeches as a tool for detecting a wide range of terrestrial vertebrates across five different geographical regions on three different continents. These regions cover almost the full geographical range of haematophagous terrestrial leeches, thus representing all parts of the world where this method might apply. We identify host taxa through metabarcoding coupled with high-throughput sequencing on Illumina and IonTorrent sequencing platforms to decrease economic costs and workload and thereby make the approach attractive for practitioners in conservation management. We identified hosts in four different taxonomic vertebrate classes: mammals, birds, reptiles and amphibians, belonging to at least 42 different taxonomic families. We find that vertebrate blood ingested by haematophagous terrestrial leeches throughout their distribution is a viable source of DNA with which to examine a wide range of vertebrates. Thus, this study provides encouraging support for the potential of haematophagous terrestrial leeches as a tool for detecting and monitoring terrestrial vertebrate biodiversity.
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Affiliation(s)
- Ida Baerholm Schnell
- Section for EvoGenomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,Center for Zoo and Wild Animal Health, Copenhagen Zoo, Frederiksberg, Denmark
| | - Kristine Bohmann
- Section for EvoGenomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Sebastian E Schultze
- Section for EvoGenomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Stine R Richter
- Section for EvoGenomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Dáithí C Murray
- Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, Perth, Western Australia, Australia
| | - Mikkel-Holger S Sinding
- Section for EvoGenomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,Greenland Institute of Natural Resources, Nuuk, Greenland
| | - David Bass
- Department of Life Sciences, The Natural History Museum, London, UK.,Cefas, Weymouth, Dorset, UK
| | - John E Cadle
- Centre ValBio, Ranomafana, Ifanadiana, Fianarantsoa, Madagascar
| | - Mason J Campbell
- Centre for Tropical Environmental and Sustainability Science (TESS) and College of Science and Engineering, James Cook University, Cairns, Queensland, Australia
| | | | - David P Edwards
- Centre for Tropical Environmental and Sustainability Science (TESS) and College of Science and Engineering, James Cook University, Cairns, Queensland, Australia.,Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | | | - Teis Hansen
- Section for EvoGenomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | | | - Christina Lehmkuhl Noer
- Section for EvoGenomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,Center for Zoo and Wild Animal Health, Copenhagen Zoo, Frederiksberg, Denmark
| | - Sigrid Heise-Pavlov
- Centre for Rainforest Studies at the School for Field Studies, Yungaburra, Queensland, Australia
| | - Adam F Sander Pedersen
- Department of Immunology and Microbiology, Centre for Medical Parasitology, University of Copenhagen, Copenhagen, Denmark
| | | | - Mark E Siddall
- Division of Invertebrate Zoology, Sackler Institute of Comparative Genomics, American Museum of Natural History, New York, New York
| | - Andrew Tilker
- Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany.,Global Wildlife Conservation, Austin, Texas
| | - Carl Traeholt
- Center for Zoo and Wild Animal Health, Copenhagen Zoo, Frederiksberg, Denmark
| | | | | | - Douglas W Yu
- School of Biological Sciences, University of East Anglia, Norwich, UK.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | | | - Michael Bunce
- Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, Perth, Western Australia, Australia
| | - M Thomas P Gilbert
- Section for EvoGenomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, Perth, Western Australia, Australia.,NTNU University Museum, Trondheim, Norway
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23
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Heine D, Holmes NA, Worsley SF, Santos ACA, Innocent TM, Scherlach K, Patrick EH, Yu DW, Murrell JC, Vieria PC, Boomsma JJ, Hertweck C, Hutchings MI, Wilkinson B. Chemical warfare between leafcutter ant symbionts and a co-evolved pathogen. Nat Commun 2018; 9:2208. [PMID: 29880868 PMCID: PMC5992151 DOI: 10.1038/s41467-018-04520-1] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 04/24/2018] [Indexed: 11/14/2022] Open
Abstract
Acromyrmex leafcutter ants form a mutually beneficial symbiosis with the fungus Leucoagaricus gongylophorus and with Pseudonocardia bacteria. Both are vertically transmitted and actively maintained by the ants. The fungus garden is manured with freshly cut leaves and provides the sole food for the ant larvae, while Pseudonocardia cultures are reared on the ant-cuticle and make antifungal metabolites to help protect the cultivar against disease. If left unchecked, specialized parasitic Escovopsis fungi can overrun the fungus garden and lead to colony collapse. We report that Escovopsis upregulates the production of two specialized metabolites when it infects the cultivar. These compounds inhibit Pseudonocardia and one, shearinine D, also reduces worker behavioral defenses and is ultimately lethal when it accumulates in ant tissues. Our results are consistent with an active evolutionary arms race between Pseudonocardia and Escovopsis, which modifies both bacterial and behavioral defenses such that colony collapse is unavoidable once Escovopsis infections escalate. Acromyrmex ants cultivate fungus gardens that can be parasitized by Escovopsis sp., leading to colony collapse. Here, Heine et al. identify two secondary metabolites produced by Escovopsis that accumulate in Acromyrmex tissue, reduce behavioural defenses and suppress symbiotic Pseudonocardia bacteria.
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Affiliation(s)
- Daniel Heine
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, Norfolk, NR4 7UH, UK
| | - Neil A Holmes
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK
| | - Sarah F Worsley
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK
| | - Ana Carolina A Santos
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstraße 11a, Jena, 07745, Germany.,Friedrich Schiller University, Jena, Germany.,Departmento de Química, Universidade Federal de São Carlos, UFSCar, Via Washington Luiz KM 235, CP 676, São Carlos, SP, Brazil
| | - Tabitha M Innocent
- Department of Biology, Centre for Social Evolution, University of Copenhagen, Universitetsparken 15, Copenhagen, 2100, Denmark
| | - Kirstin Scherlach
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstraße 11a, Jena, 07745, Germany
| | - Elaine H Patrick
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK
| | - Douglas W Yu
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK
| | - J Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK
| | - Paulo C Vieria
- Departmento de Química, Universidade Federal de São Carlos, UFSCar, Via Washington Luiz KM 235, CP 676, São Carlos, SP, Brazil
| | - Jacobus J Boomsma
- Department of Biology, Centre for Social Evolution, University of Copenhagen, Universitetsparken 15, Copenhagen, 2100, Denmark
| | - Christian Hertweck
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstraße 11a, Jena, 07745, Germany.,Friedrich Schiller University, Jena, Germany
| | - Matthew I Hutchings
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK.
| | - Barrie Wilkinson
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, Norfolk, NR4 7UH, UK.
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24
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Affiliation(s)
- Michael Tessler
- Richard Gilder Graduate School, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
- Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
- Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
| | - Sarah R. Weiskopf
- Department of Entomology and Wildlife Ecology, University of Delaware, 531 South College Avenue, Newark, DE 19716, USA
| | - Lily Berniker
- Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
| | - Rebecca Hersch
- Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
| | - Kyle P. Mccarthy
- Department of Entomology and Wildlife Ecology, University of Delaware, 531 South College Avenue, Newark, DE 19716, USA
| | - Douglas W. Yu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, 32 Jiaochang Dong Lu, Kunming, Yunnan 650223, China
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, UK
| | - Mark E. Siddall
- Richard Gilder Graduate School, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
- Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
- Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
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25
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Andújar C, Arribas P, Gray C, Bruce C, Woodward G, Yu DW, Vogler AP. Metabarcoding of freshwater invertebrates to detect the effects of a pesticide spill. Mol Ecol 2017; 27:146-166. [DOI: 10.1111/mec.14410] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 10/09/2017] [Accepted: 10/16/2017] [Indexed: 12/22/2022]
Affiliation(s)
- Carmelo Andújar
- Department of Life Sciences; Natural History Museum; London UK
- Department of Life Sciences; Imperial College London; Ascot UK
- Grupo de Ecología y Evolución en Islas; Instituto de Productos Naturales y Agrobiología (IPNA-CSIC); San Cristóbal de la Laguna Spain
| | - Paula Arribas
- Department of Life Sciences; Natural History Museum; London UK
- Department of Life Sciences; Imperial College London; Ascot UK
- Grupo de Ecología y Evolución en Islas; Instituto de Productos Naturales y Agrobiología (IPNA-CSIC); San Cristóbal de la Laguna Spain
| | - Clare Gray
- Department of Life Sciences; Imperial College London; Ascot UK
| | | | - Guy Woodward
- Department of Life Sciences; Imperial College London; Ascot UK
| | - Douglas W. Yu
- State Key Laboratory of Genetic Resources and Evolution; Kunming Institute of Zoology; Chinese Academy of Sciences; Kunming Yunnan China
- School of Biological Sciences; University of East Anglia; Norwich Norfolk UK
| | - Alfried P. Vogler
- Department of Life Sciences; Natural History Museum; London UK
- Department of Life Sciences; Imperial College London; Ascot UK
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26
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Rodgers TW, Xu CCY, Giacalone J, Kapheim KM, Saltonstall K, Vargas M, Yu DW, Somervuo P, McMillan WO, Jansen PA. Carrion fly-derived DNA metabarcoding is an effective tool for mammal surveys: Evidence from a known tropical mammal community. Mol Ecol Resour 2017; 17:e133-e145. [PMID: 28758342 DOI: 10.1111/1755-0998.12701] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 07/11/2017] [Accepted: 07/25/2017] [Indexed: 11/28/2022]
Abstract
Metabarcoding of vertebrate DNA derived from carrion flies has been proposed as a promising tool for biodiversity monitoring. To evaluate its efficacy, we conducted metabarcoding surveys of carrion flies on Barro Colorado Island (BCI), Panama, which has a well-known mammal community, and compared our results against diurnal transect counts and camera trapping. We collected 1,084 flies in 29 sampling days, conducted metabarcoding with mammal-specific (16S) and vertebrate-specific (12S) primers, and sequenced amplicons on Illumina MiSeq. For taxonomic assignment, we compared blast with the new program protax, and we found that protax improved species identifications. We detected 20 mammal, four bird, and one lizard species from carrion fly metabarcoding, all but one of which are known from BCI. Fly metabarcoding detected more mammal species than concurrent transect counts (29 sampling days, 13 species) and concurrent camera trapping (84 sampling days, 17 species), and detected 67% of the number of mammal species documented by 8 years of transect counts and camera trapping combined, although fly metabarcoding missed several abundant species. This study demonstrates that carrion fly metabarcoding is a powerful tool for mammal biodiversity surveys and has the potential to detect a broader range of species than more commonly used methods.
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Affiliation(s)
- Torrey W Rodgers
- Department of Wildland Resources, Utah State University, Logan, UT, USA.,Smithsonian Tropical Research Institute, Balboa, Panama
| | - Charles C Y Xu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands.,Redpath Museum and Department of Biology, McGill University, Montreal, QC, Canada
| | - Jacalyn Giacalone
- College of Science and Mathematics, Montclair State University, Montclair, NJ, USA
| | - Karen M Kapheim
- Smithsonian Tropical Research Institute, Balboa, Panama.,Department of Biology, Utah State University, Logan, UT, USA
| | | | - Marta Vargas
- Smithsonian Tropical Research Institute, Balboa, Panama
| | - Douglas W Yu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk, UK
| | - Panu Somervuo
- Department of Biosciences, University of Helsinki, Helsinki, Finland
| | | | - Patrick A Jansen
- Smithsonian Tropical Research Institute, Balboa, Panama.,Department of Environmental Sciences, Wageningen University, Wageningen, The Netherlands
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27
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Somervuo P, Yu DW, Xu CC, Ji Y, Hultman J, Wirta H, Ovaskainen O. Quantifying uncertainty of taxonomic placement in
DNA
barcoding and metabarcoding. Methods Ecol Evol 2017. [DOI: 10.1111/2041-210x.12721] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Panu Somervuo
- Department of Biosciences University of Helsinki P.O. Box 65 Helsinki FI‐00014 Finland
| | - Douglas W. Yu
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences 32 Jiaochang East Road Kunming Yunnan 650223 China
- School of Biological Sciences University of East Anglia Norwich Research Park Norwich Norfolk NR47TJ UK
| | - Charles C.Y. Xu
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences 32 Jiaochang East Road Kunming Yunnan 650223 China
- Groningen Institute for Evolutionary Life Sciences University of Groningen P.O. Box 11103 9700 CC Groningen The Netherlands
| | - Yinqiu Ji
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences 32 Jiaochang East Road Kunming Yunnan 650223 China
| | - Jenni Hultman
- Department of Food and Environmental Sciences University of Helsinki P.O. Box 56 Helsinki FI‐00014 Finland
| | - Helena Wirta
- Department of Agricultural Sciences University of Helsinki P.O. Box 27 Helsinki FI‐00014 Finland
| | - Otso Ovaskainen
- Department of Biosciences University of Helsinki P.O. Box 65 Helsinki FI‐00014 Finland
- Centre for Biodiversity Dynamics Department of Biology Norwegian University of Science and Technology N‐7491 Trondheim Norway
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28
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Hudson LN, Newbold T, Contu S, Hill SLL, Lysenko I, De Palma A, Phillips HRP, Alhusseini TI, Bedford FE, Bennett DJ, Booth H, Burton VJ, Chng CWT, Choimes A, Correia DLP, Day J, Echeverría‐Londoño S, Emerson SR, Gao D, Garon M, Harrison MLK, Ingram DJ, Jung M, Kemp V, Kirkpatrick L, Martin CD, Pan Y, Pask‐Hale GD, Pynegar EL, Robinson AN, Sanchez‐Ortiz K, Senior RA, Simmons BI, White HJ, Zhang H, Aben J, Abrahamczyk S, Adum GB, Aguilar‐Barquero V, Aizen MA, Albertos B, Alcala EL, del Mar Alguacil M, Alignier A, Ancrenaz M, Andersen AN, Arbeláez‐Cortés E, Armbrecht I, Arroyo‐Rodríguez V, Aumann T, Axmacher JC, Azhar B, Azpiroz AB, Baeten L, Bakayoko A, Báldi A, Banks JE, Baral SK, Barlow J, Barratt BIP, Barrico L, Bartolommei P, Barton DM, Basset Y, Batáry P, Bates AJ, Baur B, Bayne EM, Beja P, Benedick S, Berg Å, Bernard H, Berry NJ, Bhatt D, Bicknell JE, Bihn JH, Blake RJ, Bobo KS, Bóçon R, Boekhout T, Böhning‐Gaese K, Bonham KJ, Borges PAV, Borges SH, Boutin C, Bouyer J, Bragagnolo C, Brandt JS, Brearley FQ, Brito I, Bros V, Brunet J, Buczkowski G, Buddle CM, Bugter R, Buscardo E, Buse J, Cabra‐García J, Cáceres NC, Cagle NL, Calviño‐Cancela M, Cameron SA, Cancello EM, Caparrós R, Cardoso P, Carpenter D, Carrijo TF, Carvalho AL, Cassano CR, Castro H, Castro‐Luna AA, Rolando CB, Cerezo A, Chapman KA, Chauvat M, Christensen M, Clarke FM, Cleary DF, Colombo G, Connop SP, Craig MD, Cruz‐López L, Cunningham SA, D'Aniello B, D'Cruze N, da Silva PG, Dallimer M, Danquah E, Darvill B, Dauber J, Davis ALV, Dawson J, de Sassi C, de Thoisy B, Deheuvels O, Dejean A, Devineau J, Diekötter T, Dolia JV, Domínguez E, Dominguez‐Haydar Y, Dorn S, Draper I, Dreber N, Dumont B, Dures SG, Dynesius M, Edenius L, Eggleton P, Eigenbrod F, Elek Z, Entling MH, Esler KJ, de Lima RF, Faruk A, Farwig N, Fayle TM, Felicioli A, Felton AM, Fensham RJ, Fernandez IC, Ferreira CC, Ficetola GF, Fiera C, Filgueiras BKC, Fırıncıoğlu HK, Flaspohler D, Floren A, Fonte SJ, Fournier A, Fowler RE, Franzén M, Fraser LH, Fredriksson GM, Freire GB, Frizzo TLM, Fukuda D, Furlani D, Gaigher R, Ganzhorn JU, García KP, Garcia‐R JC, Garden JG, Garilleti R, Ge B, Gendreau‐Berthiaume B, Gerard PJ, Gheler‐Costa C, Gilbert B, Giordani P, Giordano S, Golodets C, Gomes LGL, Gould RK, Goulson D, Gove AD, Granjon L, Grass I, Gray CL, Grogan J, Gu W, Guardiola M, Gunawardene NR, Gutierrez AG, Gutiérrez‐Lamus DL, Haarmeyer DH, Hanley ME, Hanson T, Hashim NR, Hassan SN, Hatfield RG, Hawes JE, Hayward MW, Hébert C, Helden AJ, Henden J, Henschel P, Hernández L, Herrera JP, Herrmann F, Herzog F, Higuera‐Diaz D, Hilje B, Höfer H, Hoffmann A, Horgan FG, Hornung E, Horváth R, Hylander K, Isaacs‐Cubides P, Ishida H, Ishitani M, Jacobs CT, Jaramillo VJ, Jauker B, Hernández FJ, Johnson MF, Jolli V, Jonsell M, Juliani SN, Jung TS, Kapoor V, Kappes H, Kati V, Katovai E, Kellner K, Kessler M, Kirby KR, Kittle AM, Knight ME, Knop E, Kohler F, Koivula M, Kolb A, Kone M, Kőrösi Á, Krauss J, Kumar A, Kumar R, Kurz DJ, 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F, Collen B, Ewers RM, Mace GM, Purves DW, Scharlemann JPW, Purvis A. The database of the PREDICTS (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems) project. Ecol Evol 2017; 7:145-188. [PMID: 28070282 PMCID: PMC5215197 DOI: 10.1002/ece3.2579] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 09/10/2016] [Accepted: 09/22/2016] [Indexed: 11/29/2022] Open
Abstract
The PREDICTS project-Projecting Responses of Ecological Diversity In Changing Terrestrial Systems (www.predicts.org.uk)-has collated from published studies a large, reasonably representative database of comparable samples of biodiversity from multiple sites that differ in the nature or intensity of human impacts relating to land use. We have used this evidence base to develop global and regional statistical models of how local biodiversity responds to these measures. We describe and make freely available this 2016 release of the database, containing more than 3.2 million records sampled at over 26,000 locations and representing over 47,000 species. We outline how the database can help in answering a range of questions in ecology and conservation biology. To our knowledge, this is the largest and most geographically and taxonomically representative database of spatial comparisons of biodiversity that has been collated to date; it will be useful to researchers and international efforts wishing to model and understand the global status of biodiversity.
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Affiliation(s)
| | - Tim Newbold
- United Nations Environment Programme World Conservation Monitoring CentreCambridgeUK
- Department of Genetics, Evolution and EnvironmentCentre for Biodiversity and EnvironmentResearchUniversity College LondonLondonUK
| | - Sara Contu
- Department of Life SciencesNatural History MuseumLondonUK
| | - Samantha L. L. Hill
- Department of Life SciencesNatural History MuseumLondonUK
- United Nations Environment Programme World Conservation Monitoring CentreCambridgeUK
| | - Igor Lysenko
- Department of Life SciencesImperial College LondonAscotUK
| | - Adriana De Palma
- Department of Life SciencesNatural History MuseumLondonUK
- Department of Life SciencesImperial College LondonAscotUK
| | - Helen R. P. Phillips
- Department of Life SciencesNatural History MuseumLondonUK
- Department of Life SciencesImperial College LondonAscotUK
| | | | | | | | - Hollie Booth
- United Nations Environment Programme World Conservation Monitoring CentreCambridgeUK
- Frankfurt Zoological SocietyAfrica Regional OfficeArushaTanzania
| | - Victoria J. Burton
- Department of Life SciencesNatural History MuseumLondonUK
- Science and Solutions for a Changing Planet DTP and the Department of Life SciencesImperial College LondonSouth KensingtonLondonUK
| | | | - Argyrios Choimes
- Department of Life SciencesNatural History MuseumLondonUK
- Department of Life SciencesImperial College LondonAscotUK
| | | | - Julie Day
- Department of Life SciencesImperial College LondonAscotUK
| | - Susy Echeverría‐Londoño
- Department of Life SciencesNatural History MuseumLondonUK
- Department of Life SciencesImperial College LondonAscotUK
| | | | - Di Gao
- Department of Life SciencesNatural History MuseumLondonUK
| | - Morgan Garon
- Department of Life SciencesImperial College LondonAscotUK
| | | | | | - Martin Jung
- School of Life SciencesUniversity of SussexBrightonUK
| | - Victoria Kemp
- School of Biological and Chemical SciencesQueen Mary University of LondonLondonUK
| | - Lucinda Kirkpatrick
- School of Biological and Ecological SciencesUniversity of StirlingStirlingUK
| | - Callum D. Martin
- School of Biological SciencesRoyal Holloway University of LondonEgham, SurreyUK
| | - Yuan Pan
- Department of Animal and Plant SciencesUniversity of SheffieldWestern BankSheffieldUK
| | | | - Edwin L. Pynegar
- School of EnvironmentNatural Resources and GeographyBangor UniversityBangorGwyneddUK
| | | | | | - Rebecca A. Senior
- Department of Animal and Plant SciencesUniversity of SheffieldWestern BankSheffieldUK
| | | | - Hannah J. White
- School of Biological SciencesQueen's University BelfastBelfastUK
| | | | - Job Aben
- Institute of Biological and Environmental SciencesUniversity of AberdeenAberdeenUK
- Evolutionary Ecology GroupUniversity of AntwerpAntwerpBelgium
| | | | - Gilbert B. Adum
- Wildlife and Range Management DepartmentFaculty of Renewable Natural Resources (FRNR)College of Agriculture and Natural Resources (CANR)Kwame Nkrumah University of Science and Technology (KNUST)KumasiGhana
- SAVE THE FROGS! GhanaAdum‐KumasiGhana
| | | | - Marcelo A. Aizen
- Laboratorio Ecotono‐CRUBUniversidad Nacional del Comahue and INIBIOMARío NegroArgentina
| | - Belén Albertos
- Departamento de BotánicaFacultad de FarmaciaUniversidad de ValenciaBurjassot, ValenciaSpain
| | - E. L. Alcala
- Marine LaboratorySilliman University‐Angelo King Center for Research and Environmental ManagementSilliman UniversityDumaguete CityPhilippines
| | - Maria del Mar Alguacil
- Department of Soil and Water ConservationCSIC‐Centro de Edafología y Biología Aplicada del SeguraMurciaSpain
| | - Audrey Alignier
- INRAUR 0980 SAD‐PaysageRennes CedexFrance
- INRAUMR 1201 DYNAFORCastanet Tolosan CedexFrance
| | - Marc Ancrenaz
- HUTAN – Kinabatangan Orang‐utan Conservation ProgrammeKota KinabaluMalaysia
- Borneo FuturesKota KinabaluMalaysia
| | | | - Enrique Arbeláez‐Cortés
- Museo de ZoologíaFacultad de CienciasUniversidad Nacional Autónoma de MéxicoMéxico D.F.Mexico
- Colección de TejidosInstituto de Investigación de Recursos Biológicos Alexander von HumboldtValle del CaucaColombia
| | | | - Víctor Arroyo‐Rodríguez
- Instituto de Investigaciones en Ecosistemas y SustentabilidadUniversidad Nacional Autónoma de MéxicoMoreliaMexico
| | - Tom Aumann
- College of Science, Engineering & HealthRMIT UniversityMelbourneVic.Australia
| | - Jan C. Axmacher
- UCL Department of GeographyUniversity College LondonLondonUK
| | - Badrul Azhar
- Biodiversity UnitInstitute of BioscienceUniversiti Putra MalaysiaSerdangMalaysia
- Faculty of ForestryUniversiti Putra MalaysiaSerdangMalaysia
| | - Adrián B. Azpiroz
- Departamento de Biodiversidad y GenéticaInstituto de Investigaciones Biológicas Clemente EstableMontevideoUruguay
| | - Lander Baeten
- Forest & Nature LabDepartment of Forest and Water ManagementGhent UniversityGontrodeBelgium
- Terrestrial Ecology UnitDepartment of BiologyGhent UniversityGhentBelgium
| | - Adama Bakayoko
- UFR Science de la NatureUniversité Naangui AbrogouaAbidjanIvory Coast
- Centre Suisse de Recherches Scientifiques en Côte d'IvoireAbidjanIvory Coast
| | - András Báldi
- MTA Centre for Ecological ResearchVácrátótHungary
| | | | | | - Jos Barlow
- Lancaster Environment CentreLancaster UniversityLancasterUK
- MCT/Museu Paraense Emílio GoeldiBelémBrazil
| | | | - Lurdes Barrico
- Centre for Functional EcologyDepartment of Life SciencesUniversity of CoimbraCoimbraPortugal
| | | | - Diane M. Barton
- AgResearch LimitedInvermay Agricultural CentrePuddle Alley, MosgielNew Zealand
| | - Yves Basset
- Smithsonian Tropical Research InstituteBalboaAnconPanama CityRepublic of Panama
| | - Péter Batáry
- AgroecologyDepartment of Crop SciencesGeorg‐August UniversityGöttingenGermany
| | - Adam J. Bates
- BiosciencesSchool of Science & TechnologyNottingham Trent UniversityClifton, NottinghamUK
- University of BirminghamEdgbaston, BirminghamUK
| | - Bruno Baur
- Section of Conservation BiologyDepartment of Environmental SciencesUniversity of BaselBaselSwitzerland
| | - Erin M. Bayne
- Department of Biological SciencesUniversity of AlbertaEdmontonABCanada
| | - Pedro Beja
- CIBIO/InBioCentro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do PortoVairãoPortugal
| | - Suzan Benedick
- Faculty of Sustainable AgricultureUniversiti Malaysia SabahSandakanMalaysia
| | - Åke Berg
- The Swedish University of Agricultural SciencesThe Swedish Biodiversity CentreUppsalaSweden
| | - Henry Bernard
- Institute for Tropical Biology and ConservationUniversiti Malaysia Sabah, Jalan UMSKota KinabaluMalaysia
| | | | - Dinesh Bhatt
- Department of Zoology & Environmental ScienceGurukula Kangri UniversityHaridwarIndia
| | - Jake E. Bicknell
- Durrell Institute of Conservation and Ecology (DICE)School of Anthropology and ConservationUniversity of KentCanterburyUK
- Iwokrama International Centre for Rainforest Conservation and DevelopmentGeorgetownGuyana
| | - Jochen H. Bihn
- Department of Ecology‐Animal EcologyFaculty of BiologyPhilipps‐Universität MarburgMarburgGermany
| | - Robin J. Blake
- Compliance Services InternationalPentlands Science ParkPenicuik, EdinburghUK
- Centre for Agri‐Environmental ResearchSchool of Agriculture, Policy and DevelopmentUniversity of ReadingReadingUK
| | - Kadiri S. Bobo
- School for the Training of Wildlife Specialists GarouaGarouaCameroon
- Department of ForestryFaculty of Agronomy and Agricultural SciencesUniversity of DschangDschangCameroon
| | - Roberto Bóçon
- Mater Natura – Instituto de Estudos AmbientaisCuritibaBrazil
| | - Teun Boekhout
- CBS Fungal Biodiversity Centre (CBS‐KNAW)UtrechtThe Netherlands
| | - Katrin Böhning‐Gaese
- Senckenberg Biodiversity and Climate Research Centre (BiK‐F)Frankfurt am MainGermany
- Institute for Ecology, Evolution & DiversityGoethe University FrankfurtBiologicum, Frankfurt am MainGermany
| | - Kevin J. Bonham
- School of Land and FoodUniversity of TasmaniaSandy BayTas.Australia
| | - Paulo A. V. Borges
- Departamento de Ciências AgráriascE3c – Centre for Ecology, Evolution and Environmental Changes/Azorean Biodiversity Group and Universidade dos AçoresAngra do Heroísmo, AçoresPortugal
| | | | - Céline Boutin
- Environment and Climate Change Canada, Science & Technology BranchCarleton UniversityOttawaONCanada
| | - Jérémy Bouyer
- Unité Mixte de Recherche Contrôle des Maladies Animales Exotiques et EmergentesCentre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD)MontpellierFrance
- Unité Mixte de Recherche 1309 Contrôle des Maladies Animales Exotiques et EmergentesInstitut national de la recherche agronomique (INRA)MontpellierFrance
| | - Cibele Bragagnolo
- Departamento de ZoologiaInstituto de BiociênciasUniversidade de São PauloSão PauloBrazil
| | - Jodi S. Brandt
- Human Environment Systems CenterBoise State UniversityBoiseIDUSA
| | - Francis Q. Brearley
- School of Science and the EnvironmentManchester Metropolitan UniversityManchesterUK
| | | | - Vicenç Bros
- Natural Parks Technical OfficeDiputació de BarcelonaBarcelonaSpain
- Natural History Museum of BarcelonaBarcelona, CataloniaSpain
| | - Jörg Brunet
- Swedish University of Agricultural SciencesSouthern Swedish Forest Research CentreAlnarpSweden
| | | | | | - Rob Bugter
- Alterra, part of Wageningen University and ResearchRB WageningenThe Netherlands
| | - Erika Buscardo
- Departamento de Ciências da VidaCentro de Ecologia FuncionalUniversidade de CoimbraCoimbraPortugal
- Departamento de Biologia VegetalInstituto de BiologiaUniversidade Estadual de CampinasCampinasBrazil
- Department of BotanySchool of Natural SciencesTrinity College DublinDublin 2Ireland
| | - Jörn Buse
- Institute for Environmental SciencesUniversity Koblenz‐LandauLandauGermany
| | - Jimmy Cabra‐García
- Departamento de ZoologiaInstituto de BiociênciasUniversidade de São PauloSão PauloBrazil
- Departamento de BiologíaGrupo de investigación en BiologíaEcología y Manejo de HormigasSección de EntomologíaUniversidad del ValleCaliColombia
| | - Nilton C. Cáceres
- Department of BiologyFederal University of Santa Maria, CCNESanta MariaBrazil
| | | | - María Calviño‐Cancela
- Department of Ecology and Animal BiologyFaculty of SciencesUniversity of VigoVigoSpain
| | - Sydney A. Cameron
- Department of EntomologyUniversity of IllinoisUrbanaILUSA
- Program in Ecology, Evolution and Conservation BiologyUniversity of IllinoisUrbanaILUSA
| | | | - Rut Caparrós
- Departamento de BotánicaFacultad de FarmaciaUniversidad de ValenciaBurjassot, ValenciaSpain
- Departamento de Biología (Botánica)Facultad de CienciasUniversidad Autonoma de MadridMadridSpain
| | - Pedro Cardoso
- Departamento de Ciências AgráriascE3c – Centre for Ecology, Evolution and Environmental Changes/Azorean Biodiversity Group and Universidade dos AçoresAngra do Heroísmo, AçoresPortugal
- Finnish Museum of Natural HistoryUniversity of HelsinkiHelsinkiFinland
| | - Dan Carpenter
- Parks and CountrysideBracknell Forest CouncilBracknellUK
- Soil Biodiversity GroupLife Sciences DepartmentNatural History MuseumLondonUK
| | | | | | - Camila R. Cassano
- Laboratório de Ecologia Aplicada à ConservaçãoUniversidade Estadual de Santa CruzIlhéusBrazil
| | - Helena Castro
- Centre for Functional EcologyDepartment of Life SciencesUniversity of CoimbraCoimbraPortugal
| | | | - Cerda B. Rolando
- Centro Agronómico Tropical de Investigación y Enseñanza (CATIE)Tropical Agricultural Research and Higher Education CenterTurrialbaCosta Rica
| | - Alexis Cerezo
- Department of Quantitative Methods and Information SystemsFaculty of AgronomyUniversity of Buenos AiresBuenos AiresArgentina
| | | | - Matthieu Chauvat
- Normandie UnivEA 1293 ECODIV‐RouenSFR SCALEUFR Sciences et TechniquesMont Saint Aignan CedexFrance
| | | | - Francis M. Clarke
- Institute of Biological and Environmental SciencesUniversity of AberdeenAberdeenUK
| | | | - Giorgio Colombo
- Dipartimento di BiologiaUniversità degli Studi di MilanoMilanoItaly
| | - Stuart P. Connop
- Sustainability Research InstituteUniversity of East LondonLondonUK
| | - Michael D. Craig
- Centre of Excellence for Environmental DecisionsSchool of Plant BiologyUniversity of Western AustraliaNedlandsWAAustralia
- School of Veterinary and Life SciencesMurdoch UniversityMurdochWAAustralia
| | - Leopoldo Cruz‐López
- Grupo Ecología de Artrópodos y Manejo de PlagasEl Colegio de la Frontera SurTapachulaMexico
| | | | - Biagio D'Aniello
- Dipartimento di BiologiaUniversità di Napoli Federico IINapoliItaly
| | - Neil D'Cruze
- Wildlife Conservation Research UnitDepartment of ZoologyUniversity of OxfordRecanati‐Kaplan CentreTubneyUK
| | - Pedro Giovâni da Silva
- Programa de Pós‐Graduação em EcologiaUniversidade Federal de Santa CatarinaFlorianópolisBrazil
| | - Martin Dallimer
- Sustainability Research InstituteSchool of Earth and EnvironmentUniversity of LeedsLeedsUK
| | - Emmanuel Danquah
- Wildlife and Range Management DepartmentFaculty of Renewable Natural Resources (FRNR)College of Agriculture and Natural Resources (CANR)Kwame Nkrumah University of Science and Technology (KNUST)KumasiGhana
| | | | - Jens Dauber
- Thünen Institute of BiodiversityBraunschweigGermany
| | - Adrian L. V. Davis
- Scarab Research GroupDepartment of Zoology & EntomologyUniversity of PretoriaHatfieldSouth Africa
| | - Jeff Dawson
- Durrell Wildlife Conservation TrustTrinityJersey
| | | | | | - Olivier Deheuvels
- CIRADUMR SystemMontpellierFrance
- ICRAFRegional Office for Latin AmericaLimaPeru
| | - Alain Dejean
- UPSINPLaboratoire Écologie Fonctionnelle et EnvironnementUniversité de ToulouseToulouseFrance
- CNRS – UMR 5245EcolabToulouseFrance
- CNRS – UMR 8172Écologie des Forêts de GuyaneKourou cedexFrance
| | | | - Tim Diekötter
- Department of Landscape EcologyInstitute of Natural Resource ConservationKiel UniversityKielGermany
- Department of Biology, Nature ConservationUniversity MarburgMarburgGermany
- Institute of Integrative BiologyETH ZürichZürichSwitzerland
| | - Jignasu V. Dolia
- Post Graduate Program in Wildlife Biology and ConservationNational Centre for Biological SciencesBangaloreIndia
- Wildlife Conservation Society (India Program)Centre for Wildlife StudiesBangaloreIndia
| | - Erwin Domínguez
- Instituto de Investigaciones Agropecuarias – INIA – CRI – KampenaikePunta ArenasChile
| | | | - Silvia Dorn
- Applied EntomologyETH ZürichZürichSwitzerland
| | - Isabel Draper
- Departamento de Biología (Botánica)Facultad de CienciasUniversidad Autonoma de MadridMadridSpain
| | - Niels Dreber
- Unit for Environmental Sciences and ManagementNorth‐West UniversityPotchefstroomSouth Africa
- Department of Ecosystem ModellingBüsgen‐InstituteGeorg‐August‐University of GöttingenGöttingenGermany
| | | | - Simon G. Dures
- Department of Life SciencesImperial College LondonAscotUK
- Institute of ZoologyZoological Society of London, Regents ParkLondonUK
| | - Mats Dynesius
- Department of Ecology and Environmental ScienceUmeå UniversityUmeåSweden
| | - Lars Edenius
- Department of Wildlife, Fish and Environmental StudiesSwedish University of Agricultural SciencesUmeaSweden
| | - Paul Eggleton
- Department of Life SciencesNatural History MuseumLondonUK
| | - Felix Eigenbrod
- Centre for Biological SciencesUniversity of SouthamptonSouthamptonUK
| | - Zoltán Elek
- MTA‐ELTE‐MTM Ecology Research GroupHungarian Academy of Sciencesc/o Biological InstituteEötvös Lóránd UniversityBudapestHungary
- Hungarian Natural History MuseumBudapestHungary
| | - Martin H. Entling
- Institute for Environmental SciencesUniversity of Koblenz‐LandauLandauGermany
| | - Karen J. Esler
- Department of Conservation Ecology and EntomologyStellenbosch UniversityMatielandSouth Africa
- Centre for Invasion BiologyStellenbosch UniversityMatielandSouth Africa
| | - Ricardo F. de Lima
- CE3C – Centre for Ecology, Evolution and Environmental ChangesFaculdade de CiênciasUniversidade de LisboaLisboaPortugal
- Associação Monte PicoMonte CaféMé ZóchiSão Tomé and Príncipe
| | - Aisyah Faruk
- Kew GardensWakehurstArdingly, Haywards Heath, SussexUK
- Wild AsiaUpper PenthouseWisma RKTKuala LumpurMalaysia
| | - Nina Farwig
- Conservation EcologyFaculty of BiologyPhilipps‐Universität MarburgMarburgGermany
| | - Tom M. Fayle
- Department of Life SciencesImperial College LondonAscotUK
- Institute of EntomologyBiology Centre of Academy of Sciences Czech RepublicČeské BudějoviceCzech Republic
- Institute for Tropical Biology and ConservationUniversiti Malaysia SabahKota KinabaluMalaysia
| | | | | | - Roderick J. Fensham
- Department of Biological SciencesUniversity of QueenslandSt LuciaQldAustralia
- Queensland Herbarium (DSITIA)ToowongQldAustralia
| | | | | | | | - Cristina Fiera
- Institute of Biology Bucharest of Romanian AcademyBucharestRomania
| | | | | | - David Flaspohler
- School of Forest Resources and Environmental ScienceMichigan Technological UniversityHoughtonMIUSA
| | - Andreas Floren
- Department of Animal Ecology and Tropical BiologyBiocenterUniversity of WürzburgWürzburgGermany
| | - Steven J. Fonte
- Department of Plant SciencesUniversity of CaliforniaDavisCAUSA
- Department of Soil and Crop SciencesColorado State UniversityFort CollinsCOUSA
| | | | | | - Markus Franzén
- Department of Community EcologyUFZHelmholtz Centre for Environmental ResearchHalleGermany
| | - Lauchlan H. Fraser
- Department of Natural Resource SciencesThompson Rivers UniversityKamloopsBCCanada
| | - Gabriella M. Fredriksson
- Institute for Biodiversity and Ecosystem Dynamics (IBED)University of AmsterdamGE AmsterdamThe Netherlands
- PanEco/Yayasan Ekosistem LestariSumatran Orangutan Conservation ProgrammeMedanIndonesia
| | - Geraldo B. Freire
- Programa de Pós Graduação em EcologiaUniversidade de BrasíliaBrasília, Distrito FederalBrazil
| | - Tiago L. M. Frizzo
- Programa de Pós Graduação em EcologiaUniversidade de BrasíliaBrasília, Distrito FederalBrazil
| | | | - Dario Furlani
- Dipartimento di BiologiaUniversità degli Studi di MilanoMilanoItaly
| | - René Gaigher
- Department of Conservation Ecology and EntomologyStellenbosch UniversityMatielandSouth Africa
| | | | - Karla P. García
- Departamento de ZoologíaFacultad de Ciencias Naturales y OceanográficasUniversidad de ConcepciónConcepciónChile
- Departamento de Planificación TerritorialFacultad de Ciencias AmbientalesCentro EULA‐ChileUniversidad de ConcepciónConcepciónChile
| | | | - Jenni G. Garden
- Seed Consulting ServicesAdelaideSAAustralia
- Environmental Futures Research InstituteGriffith UniversityBrisbaneQldAustralia
- Barbara Hardy InstituteUniversity of South AustraliaMawson LakesSAAustralia
| | - Ricardo Garilleti
- Departamento de BotánicaFacultad de FarmaciaUniversidad de ValenciaBurjassot, ValenciaSpain
| | - Bao‐Ming Ge
- Jiangsu Key Laboratory for Bioresources of Saline SoilsYancheng Teachers UniversityYanchengChina
| | - Benoit Gendreau‐Berthiaume
- Département des sciences biologiquesCentre d’études de la forêt Université du Québec à Montréal Succursale Centre‐villeMontréalQCCanada
| | | | - Carla Gheler‐Costa
- Ecologia Aplicada/Applied EcologyUniversidade Sagrado Coração (USC)BauruBrazil
| | - Benjamin Gilbert
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoONCanada
| | | | | | | | | | - Rachelle K. Gould
- Rubenstein School of Natural ResourcesUniversity of VermontBurlingtonVTUSA
| | - Dave Goulson
- School of Life SciencesUniversity of SussexBrightonUK
| | - Aaron D. Gove
- Astron Environmental ServicesEast PerthWAAustralia
- Department of Environment and AgricultureCurtin UniversityPerthWAAustralia
| | - Laurent Granjon
- Centre de Biologie pour la Gestion des Populations (CBGP)INRAIRDCIRADSUPAGROMontferrier‐sur‐Lez cedexFrance
| | - Ingo Grass
- AgroecologyDepartment of Crop SciencesGeorg‐August UniversityGöttingenGermany
- Conservation EcologyFaculty of BiologyPhilipps‐Universität MarburgMarburgGermany
| | - Claudia L. Gray
- School of Life SciencesUniversity of SussexBrightonUK
- Department of ZoologyUniversity of OxfordOxfordUK
| | - James Grogan
- Department of Biological SciencesMount Holyoke CollegeSouth HadleyMAUSA
| | - Weibin Gu
- China International Engineering Consulting CorporationHaidian DistrictBeijingChina
| | | | | | - Alvaro G. Gutierrez
- Departamento de Ciencias Ambientales y Recursos Naturales RenovablesFacultad de Ciencias AgronómicasUniversidad de ChileLa PintanaChile
| | | | - Daniela H. Haarmeyer
- Biodiversity, Evolution and Ecology of Plants (BEE)Biocentre Klein Flottbek and Botanical GardenUniversity of HamburgHamburgGermany
| | - Mick E. Hanley
- School of Biological ScienceUniversity of PlymouthPlymouthUK
| | | | - Nor R. Hashim
- International University of Malaya‐Wales, Jalan Tun IsmailKuala LumpurMalaysia
| | - Shombe N. Hassan
- Department of Wildlife ManagementSokoine University of AgricultureMorogoroTanzania
| | | | - Joseph E. Hawes
- Animal & Environment Research GroupDepartment of Life SciencesAnglia Ruskin UniversityCambridgeUK
| | - Matt W. Hayward
- Walter Sisulu UniversityMthatha, TranskeiSouth Africa
- Centre for African Conservation EcologyNelson Mandela Metropolitan UniversityPort ElizabethSouth Africa
- College of Natural SciencesBangor UniversityBangor, GwyneddUK
| | - Christian Hébert
- Natural Resources CanadaCanadian Forest ServiceLaurentian Forestry CentreQuébecQCCanada
| | - Alvin J. Helden
- Animal & Environment Research GroupDepartment of Life SciencesAnglia Ruskin UniversityCambridgeUK
| | - John‐André Henden
- Department of Arctic and Marine BiologyUniversity of TromsøTromsøNorway
| | | | - Lionel Hernández
- Universidad Nacional Experimental de GuayanaPuerto OrdazVenezuela
| | - James P. Herrera
- Richard Gilder Graduate SchoolAmerican Museum of Natural HistoryNew YorkNYUSA
| | - Farina Herrmann
- AgroecologyDepartment of Crop SciencesGeorg‐August UniversityGöttingenGermany
| | | | | | - Branko Hilje
- Earth and Atmospheric Sciences DepartmentUniversity of AlbertaEdmontonABCanada
| | - Hubert Höfer
- State Museum of Natural History Karlsruhe (SMNK)BiosciencesKarlsruheGermany
| | - Anke Hoffmann
- Museum für Naturkunde – Leibniz Institute for Evolution and Biodiversity ScienceBerlinGermany
| | - Finbarr G. Horgan
- University of Technology SydneySydneyNSWAustralia
- University of New BrunswickFrederictonNBCanada
| | - Elisabeth Hornung
- Department of EcologyFaculty of Veterinary ScienceSZIE UniversityBudapestHungary
| | - Roland Horváth
- Department of EcologyUniversity of DebrecenDebrecenHungary
| | - Kristoffer Hylander
- Department of Ecology, Environment and Plant SciencesStockholm UniversityStockholmSweden
| | - Paola Isaacs‐Cubides
- Instituto de Investigaciones y Recursos Biológicos Alexander von HumboldtBogotá, Colombia
| | - Hiroaki Ishida
- Institute of Natural and Environmental SciencesUniversity of HyogoHyogoJapan
| | | | - Carmen T. Jacobs
- Scarab Research GroupDepartment of Zoology & EntomologyUniversity of PretoriaHatfieldSouth Africa
| | - Víctor J. Jaramillo
- Instituto de Investigaciones en Ecosistemas y SustentabilidadUniversidad Nacional Autónoma de MéxicoMoreliaMéxico C.P.Mexico
| | - Birgit Jauker
- Department of Animal EcologyJustus‐Liebig‐UniversityGiessenGermany
| | | | | | - Virat Jolli
- Biodiversity and Environmental SustainabilityRohiniIndia
- Department of Environmental StudiesShivaji College (University of Delhi)New DelhiIndia
| | - Mats Jonsell
- Department of EcologySwedish University of Agricultural SciencesUppsalaSweden
| | - S. Nur Juliani
- School of Biological SciencesUniversiti Sains MalaysiaMindenMalaysia
| | | | | | - Heike Kappes
- Cologne BiocenterZoological InstituteUniversity of CologneKölnGermany
| | - Vassiliki Kati
- Department of Environmental & Natural Resources ManagementUniversity of PatrasAgrinioGreece
| | - Eric Katovai
- Centre for Tropical Environmental and Sustainability Science (TESS) & College of Marine and Environmental SciencesJames Cook UniversityCairnsQldAustralia
- School of Science and TechnologyPacific Adventist UniversityPort MoresbyPapua New Guinea
| | - Klaus Kellner
- Unit for Environmental Sciences and ManagementNorth‐West UniversityPotchefstroomSouth Africa
| | - Michael Kessler
- Department of Systematic and Evolutionary BotanyUniversity of ZürichZürichSwitzerland
| | - Kathryn R. Kirby
- Department of Ecology and Evolutionary Biology and Department of Geography and PlanningUniversity of TorontoTorontoONCanada
| | | | | | - Eva Knop
- Institute of Ecology and EvolutionUniversity of BernBernSwitzerland
| | - Florian Kohler
- Section EnvironnementDéveloppement durable et TerritoireDivision Environnement et TerritoireBundesamt für StatistikNeuchâtelSwitzerland
| | - Matti Koivula
- School of Forest SciencesUniversity of Eastern FinlandJoensuuFinland
| | - Annette Kolb
- Institute of Ecology, FB2University of BremenBremenGermany
| | - Mouhamadou Kone
- Université Peleforo Gon CoulibalyKorhogoIvory Coast
- Station d'Ecologie de LamtoN'DouciIvory Coast
| | - Ádám Kőrösi
- MTA‐ELTE‐MTM Ecology Research GroupHungarian Academy of Sciencesc/o Biological InstituteEötvös Lóránd UniversityBudapestHungary
- Theoretical Evolutionary Ecology GroupDepartment of Animal Ecology and Tropical BiologyBiocenterUniversity of WürzburgWürzburgGermany
| | - Jochen Krauss
- Department of Animal Ecology and Tropical BiologyBiocenterUniversity of WürzburgWürzburgGermany
| | - Ajith Kumar
- Wildlife Conservation Society‐IndiaNational Centre for Biological SciencesBangaloreIndia
| | | | - David J. Kurz
- Department of Environmental Science, Policy, and ManagementUniversity of CaliforniaBerkeleyCAUSA
| | - Alex S. Kutt
- School of BioSciencesUniversity of MelbourneMelbourneVic.Australia
| | - Thibault Lachat
- School of Agricultural, Forest and Food Sciences HAFLBern University of Applied SciencesZollikofenSwitzerland
- Swiss Federal Institute for ForestSnow and Landscape Research WSLBirmensdorfSwitzerland
| | - Victoria Lantschner
- Instituto Nacional de Tecnología AgropecuariaEEA BarilocheBarilocheArgentina
| | - Francisco Lara
- Departamento de Biología (Botánica)Facultad de CienciasUniversidad Autonoma de MadridMadridSpain
| | - Jesse R. Lasky
- Department of BiologyPennsylvania State UniversityUniversity ParkPAUSA
| | | | - William F. Laurance
- Centre for Tropical Environmental and Sustainability SciencesCollege of Marine and Environmental ScienceJames Cook UniversityCairnsQldAustralia
| | - Patrick Lavelle
- Université Pierre‐et‐Marie‐CurieParisFrance
- Institute of Ecology and Environmental SciencesParisFrance
| | | | - Gretchen LeBuhn
- Department of BiologySan Francisco State UniversitySan FranciscoCAUSA
| | - Jean‐Philippe Légaré
- Laboratoire de diagnostic en phytoprotectionMinistère de l'agriculture, des pêcheries et de l'alimentation du QuébecVille de QuébecQCCanada
| | - Valérie Lehouck
- Research Unit Terrestrial EcologyGhent UniversityGhentBelgium
| | - María V. Lencinas
- Laboratorio de Recursos AgroforestalesCentro Austral de Investigaciones Científicas (CADIC)Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)UshuaiaArgentina
| | - Pia E. Lentini
- School of BiosciencesUniversity of MelbourneParkvilleVic.Australia
| | | | - Qi Li
- Institute of Applied EcologyChinese Academy of SciencesShenyangChina
| | - Simon A. Litchwark
- School of Biological SciencesUniversity of CanterburyChristchurchNew Zealand
| | | | - Yunhui Liu
- College of Resources and Environmental SciencesChina Agricultural UniversityBeijingChina
| | | | | | - Mounir Louhaichi
- International Center for Agricultural Research in the Dry Areas (ICARDA)Amman OfficeAmmanJordan
- Animal and Rangeland Sciences DepartmentOregon State UniversityCorvallisORUSA
| | - Gabor L. Lövei
- Department of AgroecologyFlakkebjerg Research CentreAarhus UniversitySlagelseDenmark
| | - Manuel Esteban Lucas‐Borja
- Department of Agroforestry Technology and Science and GeneticsSchool of Advanced Agricultural EngineeringCastilla La Mancha UniversityAlbaceteSpain
| | - Victor H. Luja
- Unidad Académica de TurismoCoordinación de Investigación y PosgradoUniversidad Autónoma de NayaritTepicMexico
| | - Matthew S. Luskin
- Department of Environmental Science, Policy, and ManagementUniversity of CaliforniaBerkeleyCAUSA
| | | | - Kaoru Maeto
- Graduate School of Agricultural ScienceKobe UniversityKobeJapan
| | - Tibor Magura
- Department of EcologyUniversity of DebrecenDebrecenHungary
| | - Neil Aldrin Mallari
- Center for Conservation InnovationSan Jose Tagaytay CityPhilippines
- Biology DepartmentDe La Salle UniversityManilaPhilippines
| | - Louise A. Malone
- The New Zealand Institute for Plant & Food Research LimitedAucklandNew Zealand
| | | | - Jagoba Malumbres‐Olarte
- Center for Macroecology, Evolution and ClimateNatural History Museum of DenmarkUniversity of CopenhagenCopenhagen ØDenmark
| | - Salvador Mandujano
- Red de Biología y Conservación de VertebradosInstituto de Ecología A.C.XalapaMexico
| | | | | | | | | | - Eliana Martínez
- Universidad Nacional de Colombia, Ciudad UniversitariaBogotáColombia
| | - Guillermo Martínez Pastur
- Laboratorio de Recursos AgroforestalesCentro Austral de Investigaciones Científicas (CADIC)Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)UshuaiaArgentina
| | | | | | - Vicente Mazimpaka
- Departamento de Biología (Botánica)Facultad de CienciasUniversidad Autonoma de MadridMadridSpain
| | | | - Kyle P. McCarthy
- Department of Entomology and Wildlife EcologyUniversity of DelawareNewarkDEUSA
| | | | - Sean McNamara
- Centre for Mined Land RehabilitationThe University of QueenslandBrisbaneQldAustralia
| | - Nagore G. Medina
- Departamento de Biología (Botánica)Facultad de CienciasUniversidad Autonoma de MadridMadridSpain
- Departamento de Biogeografía y Cambio GlobalMuseo Nacional de Ciencias Naturales (CSIC)MadridSpain
| | - Rafael Medina
- Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsCTUSA
| | - Jose L. Mena
- Museo de Historia Natural “Vera Alleman Haeghebaert”Universidad Ricardo PalmaLima 33Peru
| | - Estefania Mico
- Centro Iberoamericano de la Biodiversidad (CIBIO)Universidad de AlicanteAlicanteSpain
| | - Grzegorz Mikusinski
- Department of EcologySwedish University of Agricultural Sciences, Grimsö Wildlife Research StationRiddarhyttanSweden
| | - Jeffrey C. Milder
- Rainforest AllianceNew YorkNYUSA
- Department of Natural ResourcesCornell UniversityIthacaNYUSA
| | - James R. Miller
- Department of Natural Resources & Environmental SciencesUniversity of IllinoisUrbanaILUSA
| | | | - Melinda L. Moir
- School of BiosciencesUniversity of MelbourneParkvilleVic.Australia
- School of Plant BiologyUniversity of Western AustraliaCrawleyWAAustralia
| | - Carolina L. Morales
- Lab. EcotonoINIBIOMA (Universidad Nacional del Comahue‐CONICET)BarilocheArgentina
| | | | - Muchai Muchane
- Department of Wildlife ManagementUniversity of EldoretEldoretKenya
| | - Sonja Mudri‐Stojnic
- Department of Biology and EcologyFaculty of SciencesUniversity of Novi SadNovi SadSerbia
| | - A. Nur Munira
- School of Biological SciencesUniversiti Sains MalaysiaPenangMalaysia
| | - Antonio Muoñz‐Alonso
- El Colegio de la Frontera SurEcología Evolutiva y ConservaciónSan Cristóbal de las CasasMexico
| | | | | | - A. Naithani
- Independent Research ScholarNew DelhiIndia
- Avian Diversity and Bioacoustic LabDepartment of ZoologyGurukula Kangri UniversityHaridwarIndia
| | - Michiko Nakagawa
- Graduate School of Bioagricultural SciencesNagoya UniversityNagoyaJapan
| | - Akihiro Nakamura
- Key Laboratory of Tropical Forest EcologyXishuangbanna Tropical Botanical GardenChinese Academy of SciencesMenglunChina
- Environmental Futures Research Institute, and Griffith School of EnvironmentGriffith UniversityNathanBrisbaneQldAustralia
| | | | - Shoji Naoe
- Forestry and Forest Products Research InstituteTsukubaJapan
| | - Guiomar Nates‐Parra
- Laboratorio de Investigaciones en Abejas (Departamento de Biología)Universidad Nacional de ColombiaBogotáColombia
| | | | | | - Paul K. Ndang'ang'a
- BirdLife International – Africa Partnership SecretariatNairobiKenya
- Ornithology SectionNational Museums of KenyaNairobiKenya
| | - Eike L. Neuschulz
- Senckenberg Biodiversity and Climate Research Centre (BiK‐F)Frankfurt am MainGermany
| | | | - Violaine Nicolas
- Institut de Systématique, Évolution, BiodiversitéISYEB – UMR 7205 – CNRS, MNHN, UPMC, EPHEMuséum national d'Histoire naturelleSorbonne UniversitésParisFrance
| | | | - Norbertas Noreika
- Department of BiosciencesUniversity of HelsinkiHelsinkiFinland
- Department of Environmental SciencesUniversity of HelsinkiHelsinkiFinland
| | - Olivia Norfolk
- School of BiologyThe University of NottinghamUniversity ParkNottinghamUK
| | - Jorge Ari Noriega
- Laboratorio de Zoología y Ecología Acuática – LAZOEAUniversidad de Los AndesBogotáColombia
| | - David A. Norton
- School of ForestryUniversity of CanterburyChristchurchNew Zealand
| | | | - A. Justin Nowakowski
- Department of Wildlife, Fish and Conservation BiologyUniversity of California, DavisDavisCAUSA
| | - Catherine Numa
- IUCN‐Centre for Mediterranean CooperationCampanillas, MálagaSpain
| | - Niall O'Dea
- Oxford University Centre for the EnvironmentUniversity of OxfordOxfordUK
| | - Patrick J. O'Farrell
- Natural Resources and the EnvironmentCSIRStellenboschSouth Africa
- Plant Conservation UnitBiological SciencesUniversity of Cape TownRondeboschSouth Africa
| | - William Oduro
- Wildlife and Range Management DepartmentFaculty of Renewable Natural Resources (FRNR)College of Agriculture and Natural Resources (CANR)Kwame Nkrumah University of Science and Technology (KNUST)KumasiGhana
- International Programme Office (IPO)Vice Chancellor's OfficeKwame Nkrumah University of Science and Technology (KNUST)KumasiGhana
| | - Sabine Oertli
- Naturschutz – Planung und BeratungWiesendangenSwitzerland
| | - Caleb Ofori‐Boateng
- Department of Wildlife and Range ManagementKwame Nkrumah University of Science and TechnologyKumasiGhana
- Forestry Research Institute of GhanaKumasiGhana
| | | | - Vicencio Oostra
- Department of Genetics, Evolution and EnvironmentUniversity College LondonLondonUK
| | | | - Samuel Eduardo Otavo
- Laboratorio de Ecología del PaisajeFacultad de Ciencias ForestalesUniversidad de ConcepciónConcepciónChile
| | | | - Juan Paritsis
- Laboratorio EcotonoCONICET–INIBIOMAUniversidad Nacional del ComahueBarilocheArgentina
| | - Alejandro Parra‐H
- Laboratorio de Investigaciones en AbejasLABUNUniversidad Nacional de ColombiaBogotá D.C.Colombia
| | - Luke Parry
- Lancaster Environment CentreLancaster UniversityLancasterUK
- Universidade Federal do Pará (UFPA)Núcleo de Altos Estudos Amazonicos (NAEA)BelémBrazil
| | - Guy Pe'er
- Department of Community EcologyUFZHelmholtz Centre for Environmental ResearchHalleGermany
- German Centre for Integrative Biodiversity Research (iDiv)Halle‐Jena‐LeipzigLeipzigGermany
| | - Peter B. Pearman
- Department of Plant Biology and EcologyFaculty of Science and TechnologyUniversity of the Basque CountryLeioaSpain
- IKERBASQUE. Basque Foundation for ScienceBilbaoSpain
| | - Nicolás Pelegrin
- Instituto de Diversidad y Ecología Animal (IDEA, CONICET‐UNC) and Centro de Zoología AplicadaFCEFyNUniversidad Nacional de CórdobaCórdobaArgentina
| | - Raphaël Pélissier
- IRDUMR AMAPTA A51/PS2Montpellier cedex 05France
- French Institute of PondicherryUMIFRE 21 CNRS‐MAEEPuducherryIndia
| | - Carlos A. Peres
- School of Environmental SciencesUniversity of East AngliaNorwichUK
| | - Pablo L. Peri
- National Institute of Agricultural Technology (INTA)Río GallegosArgentina
- National University of Southern Patagonia (UNPA)Río GallegosArgentina
- National Commission of Scientist Research and Technology (CONICET)Buenos Aires, Argentina
| | | | - Theodora Petanidou
- Laboratory of Biogeography & EcologyDepartment of GeographyUniversity of the AegeanMytileneGreece
| | - Marcell K. Peters
- Department of Animal Ecology and Tropical BiologyBiocenterUniversity of WürzburgWürzburgGermany
| | | | - Ben Phalan
- Conservation Science GroupDepartment of ZoologyUniversity of CambridgeCambridgeUK
| | - T. Keith Philips
- Systematics and Evolution LaboratoryDepartment of BiologyWestern Kentucky UniversityBowling GreenKYUSA
| | - Finn C. Pillsbury
- Department of Natural Resource Ecology and ManagementIowa State UniversityAmesIAUSA
| | - Jimmy Pincheira‐Ulbrich
- Departamento de ZoologíaFacultad de Ciencias Naturales y OceanográficasUniversidad de ConcepciónConcepciónChile
- Facultad de Recursos NaturalesEscuela de Ciencias AmbientalesLaboratorio de Planificación TerritorialUniversidad Católica de TemucoTemucoChile
| | - Eduardo Pineda
- Biología y Conservación de VertebradosInstituto de Ecología A.C.El Haya, XalapaMexico
| | - Joan Pino
- CREAFCerdanyola del Vallès, CataloniaSpain
- Universitat Autònoma de BarcelonaCerdanyola del VallèsSpain
| | - Jaime Pizarro‐Araya
- Laboratorio de Entomología EcológicaDepartamento de BiologíaFacultad de CienciasUniversidad de La SerenaLa SerenaChile
| | - A. J. Plumptre
- Albertine Rift ProgramWildlife Conservation SocietyKampalaUganda
| | - Santiago L. Poggio
- IFEVA/Cátedra de Producción VegetalDepartamento de Producción VegetalFacultad de AgronomíaUniversidad de Buenos Aires/CONICET.Buenos AiresArgentina
| | - Natalia Politi
- Directora del Programa Conservación de Biodiversidad en Bosques SubtropicalesCátedra de Desarrollo Sustentable y BiodiversidadFacultad de Ciencias AgrariasUniversidad Nacional de JujuyCIT‐Jujuy CONICET, Fundaciòn CEBioSan Salvador de Jujuy, Argentina
| | - Pere Pons
- Departament de Ciències AmbientalsUniversitat de GironaGironaSpain
| | | | - Eileen F. Power
- BotanySchool of Natural SciencesTrinity College DublinDublin 2Ireland
| | - Steven J. Presley
- Center for Environmental Sciences and Engineering & Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsCTUSA
| | - Vânia Proença
- MARETEC, Instituto Superior TécnicoUniversidade de LisboaLisbonPortugal
| | - Marino Quaranta
- CREA‐ABP, Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Centro di ricerca per l'agrobiologia e la pedologiaFirenzeItaly
| | - Carolina Quintero
- Laboratorio EcotonoCONICET–INIBIOMAUniversidad Nacional del ComahueBarilocheArgentina
| | - Romina Rader
- Ecosystem Management, School of Environment and Rural ScienceUniversity of New EnglandArmidaleNSWAustralia
| | - B. R. Ramesh
- French Institute of PondicherryUMIFRE 21 CNRS‐MAEEPuducherryIndia
| | | | - Jai Ranganathan
- National Center for Ecological Analysis and SynthesisUniversity of California, Santa BarbaraSanta BarbaraCAUSA
| | | | | | - J. Leighton Reid
- Center for Conservation and Sustainable DevelopmentMissouri Botanical GardenSaint LouisMOUSA
| | - Yana T. Reis
- Departamento de BiologiaUniversidade Federal de SergipeSão Cristóvão/SeBrazil
| | | | - Juan Carlos Rey‐Velasco
- Entomology Colletion, Systematics and Biogeography LaboratorySchool of BiologyIndustrial University of SantanderBucaramangaColombia
| | - Chevonne Reynolds
- Percy FitzPatrick Institute of African OrnithologyDST/NRF Centre of ExcellenceUniversity of Cape TownRondeboschCape TownSouth Africa
- School of Animal, Plant and Environmental SciencesUniversity of the WitwatersrandWitsSouth Africa
| | - Danilo Bandini Ribeiro
- Centro de Ciências Biológicas e da SaúdeUniversidade Federal de Mato Grosso do SulCampo GrandeBrazil
| | | | - Barbara A. Richardson
- EdinburghUK
- Luquillo LTER, Institute for Tropical Ecosystem Studies, College of Natural SciencesUniversity of Puerto Rico at Rio PiedrasSan JuanPRUSA
| | - Michael J. Richardson
- EdinburghUK
- Luquillo LTER, Institute for Tropical Ecosystem Studies, College of Natural SciencesUniversity of Puerto Rico at Rio PiedrasSan JuanPRUSA
| | - Rodrigo Macip Ríos
- Escuela Nacional de Estudios SuperioresUniversidad Nacional Autónoma de MéxicoMoreliaMexico
| | - Richard Robinson
- Science and Conservation DivisionDepartment of Parks and WildlifeManjimupWAAustralia
| | - Carolina A. Robles
- PROPLAME‐PRHIDEB‐CONICETDepartamento de Biodiversidad y Biología ExperimentalFacultad de Ciencias Exactas y NaturalesUniversidad de Buenos Aires, Ciudad Universitaria(CP1428EHA) Ciudad Autónoma de Buenos AiresArgentina
| | - Jörg Römbke
- ECT Oekotoxikologie GmbHFlörsheim am MainGermany
- LOEWE Biodiversity and Climate Research Centre BiK‐FFrankfurt/MainGermany
| | - Luz Piedad Romero‐Duque
- Facultad de Ciencias AmbientalesUniversidad de Ciencias Aplicadas y Ambientales U.D.C.ABogotáColombia
| | - Matthias Rös
- Catedras CONACYTCIIDIR, Unidad Oaxaca, IPNSanta Cruz Xoxocotlán, Mexico
| | - Loreta Rosselli
- Universidad de Ciencias Aplicadas y Ambientales U.D.C.A.BogotáColombia
| | - Stephen J. Rossiter
- School of Biological and Chemical SciencesQueen Mary University of LondonLondonUK
| | - Dana S. Roth
- School of Natural Resources and EnvironmentUniversity of MichiganAnn ArborMIUSA
| | - T'ai H. Roulston
- Department of Environmental SciencesUniversity of VirginiaCharlottesvilleVAUSA
- Blandy Experimental FarmBoyceVAUSA
| | - Laurent Rousseau
- Département des sciences biologiques (SB)Universitédu Québec à Montréal (UQÀM)MontréalQCCanada
| | | | | | - Jonathan P. Sadler
- School of Geography, Earth and Environmental SciencesUniversity of BirminghamBirminghamUK
| | - Szabolcs Sáfián
- Institute of Silviculture and Forest ProtectionUniversity of West HungarySopronHungary
| | - Romeo A. Saldaña‐Vázquez
- Red de Ecología FuncionalInstituto de Ecología A.C. Carretera antigua a CoatepecEl Haya, XalapaMexico
| | - Katerina Sam
- Environmental Futures Research InstituteGriffith UniversityBrisbaneQldAustralia
- Biology Centre CASInstitute of EntomologyCeske BudejoviceCzech Republic
- Faculty of ScienceUniversity of South BohemiaCeske BudejoviceCzech Republic
| | - Ulrika Samnegård
- Department of Ecology, Environment and Plant SciencesStockholm UniversityStockholmSweden
- Department of Biology/BiodiversityLund UniversityLundSweden
| | - Joana Santana
- CIBIO/InBioCentro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do PortoVairãoPortugal
| | - Xavier Santos
- CIBIO/InBioCentro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do PortoVairãoPortugal
| | | | | | - Menno Schilthuizen
- Naturalis Biodiversity CenterCR LeidenThe Netherlands
- Institute for Tropical Biology and ConservationUniversiti Malaysia Sabah, Jalan UMSKota KinabaluMalaysia
| | - Ute Schmiedel
- Biocentre Klein Flottbek & Botanical GardenUniversity of HamburgHamburgGermany
| | - Christine B. Schmitt
- Center for Development Research (ZEF)University of BonnBonnGermany
- Chair for Landscape ManagementUniversity of FreiburgFreiburgGermany
| | - Nicole L. Schon
- AgResearch LimitedLincoln Research CentreChristchurchNew Zealand
| | - Christof Schüepp
- Institute of Ecology and EvolutionUniversity of BernBernSwitzerland
| | - Katharina Schumann
- Institute for Ecology, Evolution and DiversityGoethe University FrankfurtFrankfurt am MainGermany
| | - Oliver Schweiger
- Department of Community EcologyUFZHelmholtz Centre for Environmental ResearchHalleGermany
| | - Dawn M. Scott
- Biology and Biomedical Sciences DivisionUniversity of BrightonBrightonUK
| | | | | | - Steven S. Seefeldt
- School of Natural Resources and ExtensionUniversity of Alaska FairbanksFairbanksAKUSA
| | | | - Graeme Shannon
- College of Natural SciencesBangor UniversityBangor, GwyneddUK
- School of Life SciencesUniversity of KwaZulu‐NatalDurbanSouth Africa
| | - Douglas Sheil
- Department of Ecology and Natural Resource Management (INA)Norwegian University of Life Sciences (NMBU)ÅsNorway
| | - Frederick H. Sheldon
- Museum of Natural Science and Department of Biological SciencesLouisiana State UniversityBaton RougeLAUSA
- Baton RougeLAUSA
| | - Eyal Shochat
- Department of Life SciencesBen‐Gurion University of the NegevBe'er ShevaIsrael
- The Yerucham Center of Ornithology and EcologyYeruchamIsrael
| | - Stefan J. Siebert
- Unit for Environmental Sciences and ManagementNorth‐West UniversityPotchefstroomSouth Africa
| | | | | | | | - Jo Smith
- Organic Research CentreElm FarmNewburyUK
| | - Allan H. Smith‐Pardo
- United States Department of AgricultureSouth San FranciscoCAUSA
- Universidad Nacional de ColombiaSede MedellinMedellinColombia
| | - Navjot S. Sodhi
- Department of Biological SciencesNational University of SingaporeSingaporeSingapore
| | - Eduardo J. Somarriba
- Centro Agronómico Tropical de Investigación y Enseñanza (CATIE)Tropical Agricultural Research and Higher Education CenterTurrialbaCosta Rica
| | - Ramón A. Sosa
- Ecología de Comunidades Ãridas y Semiaridas (EComAS)Departamento de RecursosFacultad de Ciencias Exactas y NaturalesUNLPam.Santa rosaLa PampaUruguay
| | - Grimaldo Soto Quiroga
- Centro Agronómico Tropical de Investigación y Enseñanza (CATIE)Tropical Agricultural Research and Higher Education CenterTurrialbaCosta Rica
- Gobierno Autónomo Departamental Santa CruzSanta Cruz de la SierraBolivia
| | - Martin‐Hugues St‐Laurent
- Université du Québec à RimouskiCentre for Northern Research, Centre for Forest StudiesRimouskiQCCanada
| | | | - Constanti Stefanescu
- CREAFCerdanyola del Vallès, CataloniaSpain
- Universitat Autònoma de BarcelonaCerdanyola del VallèsSpain
- Museu de Ciències Naturals de GranollersGranollersBarcelonaSpain
| | - Ingolf Steffan‐Dewenter
- Department of Animal Ecology and Tropical BiologyBiocenterUniversity of WürzburgWürzburgGermany
| | - Philip C. Stouffer
- School of Renewable Natural ResourcesLouisiana State University Agricultural CenterBaton RougeLAUSA
- Biological Dynamics of Forest Fragments ProjectInstituto Nacional de Pesquisas da AmazôniaManausBrazil
| | - Jane C. Stout
- BotanySchool of Natural SciencesTrinity College DublinDublin 2Ireland
| | - Ayron M. Strauch
- Department of Natural Resources and Environmental ManagementUniversity of HawaiiManoaHonoluluHIUSA
| | - Matthew J. Struebig
- Durrell Institute of Conservation and Ecology (DICE)School of Anthropology and ConservationUniversity of KentCanterburyUK
| | - Zhimin Su
- Key Laboratory of Zoological Systematics and EvolutionInstitute of ZoologyChinese Academy of SciencesChaoyang DistrictBeijingChina
- State Key Laboratory of Urban and Regional EcologyResearch Center for Eco‐Environmental SciencesChinese Academy of SciencesHaidian DistrictBeijingChina
| | - Marcela Suarez‐Rubio
- Institute of ZoologyUniversity of Natural Resources and Life SciencesViennaAustria
| | - Shinji Sugiura
- Graduate School of Agricultural ScienceKobe UniversityKobeJapan
| | | | - Yik‐Hei Sung
- Department of BiologyHong Kong Baptist UniversityKowloon Tong, Hong Kong SARChina
| | - Hari Sutrisno
- Zoological DivisionResearch Center For BiologyThe Indonesian Institute of SciencesCibinongBogorIndonesia
| | - Jens‐Christian Svenning
- Section for Ecoinformatics & BiodiversityDepartment of BioscienceAarhus UniversityAarhus CDenmark
| | - Tiit Teder
- Department of Zoology, Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | - Caragh G. Threlfall
- School of Ecosystem and Forest Science, Faculty of ScienceThe University of MelbourneRichmondVic.Australia
| | - Anu Tiitsaar
- Department of Zoology, Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | - Jacqui H. Todd
- The New Zealand Institute for Plant & Food Research LimitedAucklandNew Zealand
| | | | - Ignasi Torre
- Museu de Ciències Naturals de GranollersGranollersBarcelonaSpain
| | - Béla Tóthmérész
- MTA‐DE Biodiversity and Ecosystem Services Research GroupDebrecenHungary
| | - Teja Tscharntke
- AgroecologyDepartment of Crop SciencesGeorg‐August UniversityGöttingenGermany
| | - Edgar C. Turner
- Insect Ecology GroupDepartment of ZoologyUniversity of CambridgeCambridgeUK
| | - Jason M. Tylianakis
- Department of Life SciencesImperial College LondonAscotUK
- Centre for Integrative Ecology, School of Biological SciencesUniversity of CanterburyChristchurchNew Zealand
| | | | - Nicolas Urbina‐Cardona
- Department of Ecology and TerritorySchool of Environmental and Rural StudiesPontificia Universidad JaverianaBogotaColombia
| | - Denis Vallan
- Naturhistorisches Museum BaselLeiter BiowissenschaftenBaselSwitzerland
| | | | | | - Kiril Vassilev
- Institute of Biodiversity and Ecosystem ResearchBulgarian Academy of ScienceSofiaBulgaria
| | - Hans A. F. Verboven
- Division Forest, Nature, and LandscapeDepartment of Earth & Environmental SciencesKU LeuvenLeuvenBelgium
| | - Maria João Verdasca
- Museu Nacional de História Natural e da CiênciaBorboletário – Depart. ZoologiaLisboaPortugal
| | - José R. Verdú
- Centro Iberoamericano de la Biodiversidad (CIBIO)Universidad de AlicanteAlicanteSpain
| | - Carlos H. Vergara
- Departamento de Ciencias Químico‐BiológicasUniversidad de las Américas PueblaCholulaMexico
| | - Pablo M. Vergara
- Departamento de Gestión AgrariaUniversidad de Santiago de ChileSantiagoChile
| | | | | | - Lien Van Vu
- Vietnam National Museum of NatureVietnam Academy of Science and TechnologyCau GiayHanoiVietnam
| | | | - Tony R. Walker
- School of BiologyThe University of NottinghamUniversity ParkNottinghamUK
- School for Resource and Environmental StudiesFaculty of ManagementDalhousie UniversityHalifaxNSCanada
| | - Hua‐Feng Wang
- Key Laboratory of Protection and Development Utilization of Tropical Crop Germplasm Resource, Ministry of Education, College of Horticulture and Landscape AgricultureHainan UniversityHaikouChina
| | - Yanping Wang
- College of Life SciencesZhejiang UniversityHangzhouChina
| | - James I. Watling
- Department of BiologyJohn Carroll UniversityUniversity HeightsOHUSA
| | - Britta Weller
- Biocentre GrindelUniversity of HamburgHamburgGermany
| | - Konstans Wells
- The Environment Institute and School of Earth and Environmental SciencesThe University of AdelaideAdelaideSAAustralia
- Environmental Futures Research InstituteGriffith UniversityBrisbaneQldAustralia
| | - Catrin Westphal
- AgroecologyDepartment of Crop SciencesGeorg‐August UniversityGöttingenGermany
| | - Edward D. Wiafe
- Department of Environmental and Natural ResourcesPresbyterian University CollegeAkropong AkuapemGhana
| | | | - Michael R. Willig
- Center for Environmental Sciences & EngineeringUniversity of ConnecticutStorrsCTUSA
- Department of Ecology & Evolutionary BiologyUniversity of ConnecticutStorrsCTUSA
| | | | - Jan H. D. Wolf
- Institute for Biodiversity and Ecosystem Dynamics (IBED)University of AmsterdamGE AmsterdamThe Netherlands
| | - Volkmar Wolters
- Department of Animal EcologyJustus‐Liebig‐UniversityGiessenGermany
| | - Ben A. Woodcock
- NERC Centre for Ecology & HydrologyCrowmarsh GiffordWallingfordUK
| | - Jihua Wu
- Institute of Biodiversity Science, School of Life SciencesFudan UniversityShanghaiChina
| | - Joseph M. Wunderle
- International Institute of Tropical ForestryUSDA Forest Service, Sabana Field Research StationLuquilloPRUSA
| | - Yuichi Yamaura
- Forestry and Forest Products Research InstituteTsukubaJapan
| | | | - Douglas W. Yu
- School of Biological SciencesUniversity of East AngliaNorwich Research ParkNorwichUK
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
| | - Andrey S. Zaitsev
- Department of Animal EcologyJustus‐Liebig‐UniversityGiessenGermany
- A. N. Severtsov Institute of Ecology and EvolutionMoscowRussia
| | - Juliane Zeidler
- Integrated Environmental Consultants Namibia (IECN)WindhoekNamibia
| | - Fasheng Zou
- Guangdong Entomological Institute/South China Institute of Endangered AnimalsGuangzhouChina
| | - Ben Collen
- Department of Genetics, Evolution and EnvironmentCentre for Biodiversity and EnvironmentResearchUniversity College LondonLondonUK
| | - Rob M. Ewers
- Department of Life SciencesImperial College LondonAscotUK
| | - Georgina M. Mace
- Department of Genetics, Evolution and EnvironmentCentre for Biodiversity and EnvironmentResearchUniversity College LondonLondonUK
| | - Drew W. Purves
- Computational Ecology and Environmental ScienceMicrosoft ResearchCambridgeUK
| | - Jörn P. W. Scharlemann
- United Nations Environment Programme World Conservation Monitoring CentreCambridgeUK
- School of Life SciencesUniversity of SussexBrightonUK
| | - Andy Purvis
- Department of Life SciencesNatural History MuseumLondonUK
- Department of Life SciencesImperial College LondonAscotUK
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Holmes NA, Innocent TM, Heine D, Bassam MA, Worsley SF, Trottmann F, Patrick EH, Yu DW, Murrell JC, Schiøtt M, Wilkinson B, Boomsma JJ, Hutchings MI. Genome Analysis of Two Pseudonocardia Phylotypes Associated with Acromyrmex Leafcutter Ants Reveals Their Biosynthetic Potential. Front Microbiol 2016; 7:2073. [PMID: 28082956 PMCID: PMC5183585 DOI: 10.3389/fmicb.2016.02073] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Accepted: 12/08/2016] [Indexed: 11/13/2022] Open
Abstract
The attine ants of South and Central America are ancient farmers, having evolved a symbiosis with a fungal food crop >50 million years ago. The most evolutionarily derived attines are the Atta and Acromyrmex leafcutter ants, which harvest fresh leaves to feed their fungus. Acromyrmex and many other attines vertically transmit a mutualistic strain of Pseudonocardia and use antifungal compounds made by these bacteria to protect their fungal partner against co-evolved fungal pathogens of the genus Escovopsis. Pseudonocardia mutualists associated with the attines Apterostigma dentigerum and Trachymyrmex cornetzi make novel cyclic depsipeptide compounds called gerumycins, while a mutualist strain isolated from derived Acromyrmex octospinosus makes an unusual polyene antifungal called nystatin P1. The novelty of these antimicrobials suggests there is merit in exploring secondary metabolites of Pseudonocardia on a genome-wide scale. Here, we report a genomic analysis of the Pseudonocardia phylotypes Ps1 and Ps2 that are consistently associated with Acromyrmex ants collected in Gamboa, Panama. These were previously distinguished solely on the basis of 16S rRNA gene sequencing but genome sequencing of five Ps1 and five Ps2 strains revealed that the phylotypes are distinct species and each encodes between 11 and 15 secondary metabolite biosynthetic gene clusters (BGCs). There are signature BGCs for Ps1 and Ps2 strains and some that are conserved in both. Ps1 strains all contain BGCs encoding nystatin P1-like antifungals, while the Ps2 strains encode novel nystatin-like molecules. Strains show variations in the arrangement of these BGCs that resemble those seen in gerumycin gene clusters. Genome analyses and invasion assays support our hypothesis that vertically transmitted Ps1 and Ps2 strains have antibacterial activity that could help shape the cuticular microbiome. Thus, our work defines the Pseudonocardia species associated with Acromyrmex ants and supports the hypothesis that Pseudonocardia species could provide a valuable source of new antimicrobials.
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Affiliation(s)
- Neil A Holmes
- School of Biological Sciences, University of East Anglia (UEA) Norwich, UK
| | - Tabitha M Innocent
- Centre for Social Evolution, University of Copenhagen Copenhagen, Denmark
| | - Daniel Heine
- Department of Molecular Microbiology, John Innes Centre Norwich, UK
| | - Mahmoud Al Bassam
- School of Biological Sciences, University of East Anglia (UEA) Norwich, UK
| | - Sarah F Worsley
- School of Biological Sciences, University of East Anglia (UEA) Norwich, UK
| | - Felix Trottmann
- Department of Molecular Microbiology, John Innes Centre Norwich, UK
| | - Elaine H Patrick
- School of Biological Sciences, University of East Anglia (UEA) Norwich, UK
| | - Douglas W Yu
- School of Biological Sciences, University of East Anglia (UEA)Norwich, UK; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of ZoologyKunming, China
| | - J C Murrell
- School of Environmental Sciences, University of East Anglia (UEA) Norwich, UK
| | - Morten Schiøtt
- Centre for Social Evolution, University of Copenhagen Copenhagen, Denmark
| | - Barrie Wilkinson
- Department of Molecular Microbiology, John Innes Centre Norwich, UK
| | - Jacobus J Boomsma
- Centre for Social Evolution, University of Copenhagen Copenhagen, Denmark
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30
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Orkin JD, Yang Y, Yang C, Yu DW, Jiang X. Cost-effective scat-detection dogs: unleashing a powerful new tool for international mammalian conservation biology. Sci Rep 2016; 6:34758. [PMID: 27721442 PMCID: PMC5056371 DOI: 10.1038/srep34758] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 09/19/2016] [Indexed: 11/30/2022] Open
Abstract
Recently, detection dogs have been utilized to collect fecal samples from cryptic and rare mammals. Despite the great promise of this technique for conservation biology, its broader application has been limited by the high cost (tens to hundreds of thousands of dollars) and logistical challenges of employing a scat-detection dog team while conducting international, collaborative research. Through an international collaboration of primatologists and the Chinese Ministry of Public Security, we trained and used a detection dog to find scat from three species of unhabituated, free-ranging primates, for less than $3,000. We collected 137 non-human primate fecal samples that we confirmed by sequencing taxonomically informative genetic markers. Our detection dog team had a 92% accuracy rate, significantly outperforming our human-only team. Our results demonstrate that detection dogs can locate fecal samples from unhabituated primates with variable diets, locomotion, and grouping patterns, despite challenging field conditions. We provide a model for in-country training, while also building local capacity for conservation and genetic monitoring. Unlike previous efforts, our approach will allow for the wide adoption of scat-detection dogs in international conservation biology.
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Affiliation(s)
- Joseph D. Orkin
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang Donglu, Kunming, Yunnan 650223, China
- Department of Anthropology, Washington University in St. Louis, 1 Brookings Drive, St. Louis, MO 63130, USA
- Department of Anthropology and Archaeology, University of Calgary, 2500 University Drive N.W., Calgary, Alberta, T2N 1N4, Canada
| | - Yuming Yang
- Kunming Police Dog Training Base, Chinese Ministry of Security, 579 Baiyunlu Kunming, Yunnan, 650204, China
| | - Chunyan Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang Donglu, Kunming, Yunnan 650223, China
| | - Douglas W. Yu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang Donglu, Kunming, Yunnan 650223, China
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR47TJ, UK
| | - Xuelong Jiang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang Donglu, Kunming, Yunnan 650223, China
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31
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Zhang K, Lin S, Ji Y, Yang C, Wang X, Yang C, Wang H, Jiang H, Harrison RD, Yu DW. Plant diversity accurately predicts insect diversity in two tropical landscapes. Mol Ecol 2016; 25:4407-19. [PMID: 27474399 DOI: 10.1111/mec.13770] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 06/11/2016] [Accepted: 07/13/2016] [Indexed: 11/29/2022]
Abstract
Plant diversity surely determines arthropod diversity, but only moderate correlations between arthropod and plant species richness had been observed until Basset et al. (Science, 338, 2012 and 1481) finally undertook an unprecedentedly comprehensive sampling of a tropical forest and demonstrated that plant species richness could indeed accurately predict arthropod species richness. We now require a high-throughput pipeline to operationalize this result so that we can (i) test competing explanations for tropical arthropod megadiversity, (ii) improve estimates of global eukaryotic species diversity, and (iii) use plant and arthropod communities as efficient proxies for each other, thus improving the efficiency of conservation planning and of detecting forest degradation and recovery. We therefore applied metabarcoding to Malaise-trap samples across two tropical landscapes in China. We demonstrate that plant species richness can accurately predict arthropod (mostly insect) species richness and that plant and insect community compositions are highly correlated, even in landscapes that are large, heterogeneous and anthropogenically modified. Finally, we review how metabarcoding makes feasible highly replicated tests of the major competing explanations for tropical megadiversity.
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Affiliation(s)
- Kai Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China
| | - Siliang Lin
- School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Yinqiu Ji
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Chenxue Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Xiaoyang Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China
| | - Chunyan Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Hesheng Wang
- Hainan Yinggeling National Nature Reserve, Baisha, 572800, China
| | - Haisheng Jiang
- School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Rhett D Harrison
- World Agroforestry Center, East and Central Asia Regional Office, Kunming, 650201, China.,Center for Mountain Ecosystem Studies (CMES), Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Douglas W Yu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR47TJ, UK
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32
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Yang C, Schaefer DA, Liu W, Popescu VD, Yang C, Wang X, Wu C, Yu DW. Higher fungal diversity is correlated with lower CO2 emissions from dead wood in a natural forest. Sci Rep 2016; 6:31066. [PMID: 27553882 PMCID: PMC4995510 DOI: 10.1038/srep31066] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 07/13/2016] [Indexed: 11/20/2022] Open
Abstract
Wood decomposition releases almost as much CO2 to the atmosphere as does fossil-fuel combustion, so the factors regulating wood decomposition can affect global carbon cycling. We used metabarcoding to estimate the fungal species diversities of naturally colonized decomposing wood in subtropical China and, for the first time, compared them to concurrent measures of CO2 emissions. Wood hosting more diverse fungal communities emitted less CO2, with Shannon diversity explaining 26 to 44% of emissions variation. Community analysis supports a ‘pure diversity’ effect of fungi on decomposition rates and thus suggests that interference competition is an underlying mechanism. Our findings extend the results of published experiments using low-diversity, laboratory-inoculated wood to a high-diversity, natural system. We hypothesize that high levels of saprotrophic fungal biodiversity could be providing globally important ecosystem services by maintaining dead-wood habitats and by slowing the atmospheric contribution of CO2 from the world’s stock of decomposing wood. However, large-scale surveys and controlled experimental tests in natural settings will be needed to test this hypothesis.
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Affiliation(s)
- Chunyan Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang East Rd., Kunming, Yunnan 650223, China
| | - Douglas A Schaefer
- Key Laboratory of Tropical Forest Ecology, Chinese Academy of Sciences, Xishuangbanna Tropical Botanical Garden, Menglun, Mengla, Yunnan 666303, China
| | - Weijie Liu
- Key Laboratory of Tropical Forest Ecology, Chinese Academy of Sciences, Xishuangbanna Tropical Botanical Garden, Menglun, Mengla, Yunnan 666303, China
| | - Viorel D Popescu
- Ohio University, Department of Biological Sciences, 107 Irvine Hall, Athens OH, 45701, USA.,University of Bucharest, Centre for Environmental Research (CCMESI), 1 N Balcescu Blvd., Bucharest, Romania
| | - Chenxue Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang East Rd., Kunming, Yunnan 650223, China
| | - Xiaoyang Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang East Rd., Kunming, Yunnan 650223, China
| | - Chunying Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang East Rd., Kunming, Yunnan 650223, China
| | - Douglas W Yu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang East Rd., Kunming, Yunnan 650223, China.,School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR47TJ, UK
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Abstract
‘Mitochondrial metagenomics’ (MMG) is a methodology for shotgun sequencing of total DNA from specimen mixtures and subsequent bioinformatic extraction of mitochondrial sequences. The approach can be applied to phylogenetic analysis of taxonomically selected taxa, as an economical alternative to mitogenome sequencing from individual species, or to environmental samples of mixed specimens, such as from mass trapping of invertebrates. The routine generation of mitochondrial genome sequences has great potential both for systematics and community phylogenetics. Mapping of reads from low-coverage shotgun sequencing of environmental samples also makes it possible to obtain data on spatial and temporal turnover in whole-community phylogenetic and species composition, even in complex ecosystems where species-level taxonomy and biodiversity patterns are poorly known. In addition, read mapping can produce information on species biomass, and potentially allows quantification of within-species genetic variation. The success of MMG relies on the formation of numerous mitochondrial genome contigs, achievable with standard genome assemblers, but various challenges for the efficiency of assembly remain, particularly in the face of variable relative species abundance and intra-specific genetic variation. Nevertheless, several studies have demonstrated the power of mitogenomes from MMG for accurate phylogenetic placement, evolutionary analysis of species traits, biodiversity discovery and the establishment of species distribution patterns; it offers a promising avenue for unifying the ecological and evolutionary understanding of species diversity.
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Affiliation(s)
- Alex Crampton-Platt
- Department of Life Sciences, Natural History Museum, London, SW7 5BD UK ; Department of Genetics, Evolution and Environment, University College London, Gower Street, London, WC1E 6BT UK
| | - Douglas W Yu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Kunming, Yunnan Province 650223 China ; School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ UK
| | - Xin Zhou
- China National GeneBank, BGI-Shenzhen, Shenzhen, Guangdong Province 518083 China
| | - Alfried P Vogler
- Department of Life Sciences, Natural History Museum, London, SW7 5BD UK ; Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, SL5 7PY UK
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34
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Zheng JM, Cui JL, He WT, Yu DW, Gao Y, Wang L, Chen ZK, Zhou HM. Construction and characterization of recombinant adenovirus carrying a mouse TIGIT-GFP gene. Genet Mol Res 2015; 14:18650-61. [PMID: 26782515 DOI: 10.4238/2015.december.28.14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Recombinant adenovirus vector systems have been used extensively in protein research and gene therapy. However, the construction and characterization of recombinant adenovirus is a tedious and time-consuming process. TIGIT is a recently discovered immunosuppressive molecule that plays an important role in maintaining immunological balance. The construction of recombinant adenovirus mediating TIGIT expression must be simplified to facilitate its use in the study of TIGIT. In this study, the TIGIT gene was combined with green fluorescent protein (GFP); the TIGIT-GFP gene was inserted into a gateway plasmid to construct a TIGIT-GFP adenovirus. HEK 293A cells were infected with the adenovirus, which was then purified and subjected to virus titering. TIGIT-GFP adenovirus was characterized by flow cytometry and immunofluorescence, and its expression in mouse liver was detected by infection through caudal vein injection. The results showed the successful construction of the TIGIT-GFP adenovirus (5 x 10(10) PFU/mL). Co-expression of TIGIT and GFP was identified in 293A and liver cells; synthesis and positioning of TIGIT-GFP was viewed under a fluorescence microscope. TIGIT-GFP was highly expressed on liver cells 1 day (25.53%) after infection and faded 3 days (11.36%) after injection. In conclusion, the fusion of TIGIT with GFP allows easy, rapid, and uncomplicated detection of TIGIT translation. The construction of a TIGIT-GFP adenovirus, mediating TIGIT expression in vitro and in vivo, lays the foundation for further research into TIGIT function and gene therapy. Moreover, the TIGIT-GFP adenovirus is a helpful tool for studying other proteins (which could replace the TIGIT gene).
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Affiliation(s)
- J M Zheng
- Department of Cardio-Thoracic Surgery, Zhongshan City People Hospital, Zhongshan, Guangdong, China
| | - J L Cui
- Department of Cardio-Thoracic Surgery, Hospital of Traditional Chinese Medicine of Zhongshan, Guangdong, China
| | - W T He
- Department of Endocrinology, Tongji Hospital, Tongji Medical College, Hua zhong University of Science and Technology, Wuhan, China
| | - D W Yu
- Institute of Organ Transplantation, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Key Laboratory of Ministry of Health, Key Laboratory of Ministry of Education, Wuhan, China
| | - Y Gao
- Institute of Organ Transplantation, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Key Laboratory of Ministry of Health, Key Laboratory of Ministry of Education, Wuhan, China
| | - L Wang
- Institute of Organ Transplantation, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Key Laboratory of Ministry of Health, Key Laboratory of Ministry of Education, Wuhan, China
| | - Z K Chen
- Institute of Organ Transplantation, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Key Laboratory of Ministry of Health, Key Laboratory of Ministry of Education, Wuhan, China
| | - H M Zhou
- Department of Cardio-Thoracic Surgery, Tongji Hospital, Tongji Medical College, Hua zhong University of Science and Technology, Wuhan, China
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35
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Kocher SD, Li C, Yang W, Tan H, Yi SV, Yang X, Hoekstra HE, Zhang G, Pierce NE, Yu DW. Erratum to: The draft genome of a socially polymorphic halictid bee, Lasioglossum albipes. Genome Biol 2015; 16:34. [PMID: 25723594 PMCID: PMC4326530 DOI: 10.1186/s13059-014-0574-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 12/16/2014] [Indexed: 11/23/2022] Open
Abstract
During the type-setting of the final version of the article [1] some of the additional files were swapped, and several were completely replaced. The correct files are republished in this Erratum.
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36
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Ren G, Young SS, Wang L, Wang W, Long Y, Wu R, Li J, Zhu J, Yu DW. Effectiveness of China's National Forest Protection Program and nature reserves. Conserv Biol 2015; 29:1368-77. [PMID: 26171762 DOI: 10.1111/cobi.12561] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 11/25/2014] [Indexed: 05/27/2023]
Abstract
There is profound interest in knowing the degree to which China's institutions are capable of protecting its natural forests and biodiversity in the face of economic and political change. China's 2 most important forest-protection policies are its National Forest Protection Program (NFPP) and its national-level nature reserves (NNRs). The NFPP was implemented in 2000 in response to deforestation-caused flooding. We undertook the first national, quantitative assessment of the NFPP and NNRs to examine whether the NFPP achieved its deforestation-reduction target and whether the NNRs deter deforestation altogether. We used MODIS data to estimate forest cover and loss across mainland China (2000-2010). We also assembled the first-ever polygon dataset for China's forested NNRs (n = 237, 74,030 km(2) in 2000) and used both conventional and covariate-matching approaches to compare deforestation rates inside and outside NNRs (2000-2010). In 2000, 1.765 million km(2) or 18.7% of mainland China was forested (12.3% with canopy cover of ≥70%)) or woodland (6.4% with canopy cover <70% and tree plus shrub cover ≥40%). By 2010, 480,203 km(2) of forest and woodland had been lost, an annual deforestation rate of 2.7%. Forest-only loss was 127,473 km(2) (1.05% annually). In the NFPP provinces, the forest-only loss rate was 0.62%, which was 3.3 times lower than in the non-NFPP provinces. Moreover, the Landsat data suggest that these loss rates are overestimates due to large MODIS pixel size. Thus, China appears to have achieved, and even exceeded, its target of reducing deforestation to 1.1% annually in the NFPP provinces. About two-thirds of China's NNRs were effective in protecting forest cover (prevented loss 4073 km(2) unmatched approach; 3148 km(2) matched approach), and within-NNR deforestation rates were higher in provinces with higher overall deforestation. Our results indicate that China's existing institutions can protect domestic forest cover.
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Affiliation(s)
- Guopeng Ren
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Stephen S Young
- Department of Geography, Salem State University, Salem, MA, 01970, U.S.A
| | - Lin Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Wei Wang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Yongcheng Long
- China Program, The Nature Conservancy, Kunming, Yunnan, 650031, China
| | - Ruidong Wu
- Yunnan Key Laboratory of International Rivers and Transboundary Eco-Security, Yunnan University, Kunming, Yunnan, China
| | - Junsheng Li
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Jianguo Zhu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Douglas W Yu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR47TJ, United Kingdom
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Schnell IB, Sollmann R, Calvignac-Spencer S, Siddall ME, Yu DW, Wilting A, Gilbert MTP. iDNA from terrestrial haematophagous leeches as a wildlife surveying and monitoring tool - prospects, pitfalls and avenues to be developed. Front Zool 2015; 12:24. [PMID: 26430464 PMCID: PMC4589908 DOI: 10.1186/s12983-015-0115-z] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 09/05/2015] [Indexed: 11/10/2022] Open
Abstract
Invertebrate-derived DNA (iDNA) from terrestrial haematophagous leeches has recently been proposed as a powerful non-invasive tool with which to detect vertebrate species and thus to survey their populations. However, to date little attention has been given to whether and how this, or indeed any other iDNA-derived data, can be combined with state-of-the-art analytical tools to estimate wildlife abundances, population dynamics and distributions. In this review, we discuss the challenges that face the application of existing analytical methods such as site-occupancy and spatial capture-recapture (SCR) models to terrestrial leech iDNA, in particular, possible violations of key assumptions arising from factors intrinsic to invertebrate parasite biology. Specifically, we review the advantages and disadvantages of terrestrial leeches as a source of iDNA and summarize the utility of leeches for presence, occupancy, and spatial capture-recapture models. The main source of uncertainty that attends species detections derived from leech gut contents is attributable to uncertainty about the spatio-temporal sampling frame, since leeches retain host-blood for months and can move after feeding. Subsequently, we briefly address how the analytical challenges associated with leeches may apply to other sources of iDNA. Our review highlights that despite the considerable potential of leech (and indeed any) iDNA as a new survey tool, further pilot studies are needed to assess how analytical methods can overcome or not the potential biases and assumption violations of the new field of iDNA. Specifically we argue that studies to compare iDNA sampling with standard survey methods such as camera trapping, and those to improve our knowledge on leech (and other invertebrate parasite) physiology, taxonomy, and ecology will be of immense future value.
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Affiliation(s)
- Ida Bærholm Schnell
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark ; Center for Zoo and Wild Animal Health, Copenhagen Zoo, Frederiksberg, Denmark
| | - Rahel Sollmann
- Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany ; Department of Forestry and Environmental Resources, North Carolina State University, North Carolina, Raleigh USA ; Present address: US Forest Service, Pacific Southwest 17 Research Station, 1731 Research Park Drive, Davis, CA 95618 USA
| | | | - Mark E Siddall
- Sackler Institute of Comparative Genomics and Division of Invertebrate Zoology, American Museum of Natural History, New York, USA
| | - Douglas W Yu
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK ; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan China
| | - Andreas Wilting
- Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - M Thomas P Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark ; Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, Perth, Western Australia Australia
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Tang M, Hardman CJ, Ji Y, Meng G, Liu S, Tan M, Yang S, Moss ED, Wang J, Yang C, Bruce C, Nevard T, Potts SG, Zhou X, Yu DW. High-throughput monitoring of wild bee diversity and abundance via mitogenomics. Methods Ecol Evol 2015; 6:1034-1043. [PMID: 27867467 PMCID: PMC5111398 DOI: 10.1111/2041-210x.12416] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 05/28/2015] [Indexed: 12/26/2022]
Abstract
Bee populations and other pollinators face multiple, synergistically acting threats, which have led to population declines, loss of local species richness and pollination services, and extinctions. However, our understanding of the degree, distribution and causes of declines is patchy, in part due to inadequate monitoring systems, with the challenge of taxonomic identification posing a major logistical barrier. Pollinator conservation would benefit from a high-throughput identification pipeline.We show that the metagenomic mining and resequencing of mitochondrial genomes (mitogenomics) can be applied successfully to bulk samples of wild bees. We assembled the mitogenomes of 48 UK bee species and then shotgun-sequenced total DNA extracted from 204 whole bees that had been collected in 10 pan-trap samples from farms in England and been identified morphologically to 33 species. Each sample data set was mapped against the 48 reference mitogenomes.The morphological and mitogenomic data sets were highly congruent. Out of 63 total species detections in the morphological data set, the mitogenomic data set made 59 correct detections (93·7% detection rate) and detected six more species (putative false positives). Direct inspection and an analysis with species-specific primers suggested that these putative false positives were most likely due to incorrect morphological IDs. Read frequency significantly predicted species biomass frequency (R2 = 24·9%). Species lists, biomass frequencies, extrapolated species richness and community structure were recovered with less error than in a metabarcoding pipeline.Mitogenomics automates the onerous task of taxonomic identification, even for cryptic species, allowing the tracking of changes in species richness and distributions. A mitogenomic pipeline should thus be able to contain costs, maintain consistently high-quality data over long time series, incorporate retrospective taxonomic revisions and provide an auditable evidence trail. Mitogenomic data sets also provide estimates of species counts within samples and thus have potential for tracking population trajectories.
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Affiliation(s)
- Min Tang
- China National GeneBank BGI-Shenzhen Shenzhen Guangdong 518083 China
| | - Chloe J Hardman
- Centre for Agri Environmental Research School of Agriculture Policy and Development University of Reading Reading RG66AR UK
| | - Yinqiu Ji
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences, Kunming Yunnan 650223 China
| | - Guanliang Meng
- China National GeneBank BGI-Shenzhen Shenzhen Guangdong 518083 China
| | - Shanlin Liu
- China National GeneBank BGI-Shenzhen Shenzhen Guangdong 518083 China
| | - Meihua Tan
- China National GeneBank BGI-Shenzhen Shenzhen Guangdong 518083 China; University of Chinese Academy of Sciences Beijing 100094 China
| | - Shenzhou Yang
- China National GeneBank BGI-Shenzhen Shenzhen Guangdong 518083 China
| | - Ellen D Moss
- School of Biological, Biomedical and Environmental Sciences University of Hull Hull HU67RX UK
| | - Jiaxin Wang
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences, Kunming Yunnan 650223 China
| | - Chenxue Yang
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences, Kunming Yunnan 650223 China
| | - Catharine Bruce
- School of Biological Sciences University of East Anglia Norwich Research Park Norwich Norfolk NR47TJ UK
| | - Tim Nevard
- Conservation Grade Ltd.St Neots Cambridgeshire PE196TY UK; Charles Darwin University Darwin NTNT0909 Australia
| | - Simon G Potts
- Centre for Agri Environmental Research School of Agriculture Policy and Development University of Reading Reading RG66AR UK
| | - Xin Zhou
- China National GeneBank BGI-Shenzhen Shenzhen Guangdong 518083 China
| | - Douglas W Yu
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences, Kunming Yunnan 650223 China; School of Biological Sciences University of East Anglia Norwich Research Park Norwich Norfolk NR47TJ UK
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Hudson LN, Newbold T, Contu S, Hill SLL, Lysenko I, De Palma A, Phillips HRP, Senior RA, Bennett DJ, Booth H, Choimes A, Correia DLP, Day J, Echeverría-Londoño S, Garon M, Harrison MLK, Ingram DJ, Jung M, Kemp V, Kirkpatrick L, Martin CD, Pan Y, White HJ, Aben J, Abrahamczyk S, Adum GB, Aguilar-Barquero V, Aizen MA, Ancrenaz M, Arbeláez-Cortés E, Armbrecht I, Azhar B, Azpiroz AB, Baeten L, Báldi A, Banks JE, Barlow J, Batáry P, Bates AJ, Bayne EM, Beja P, Berg Å, Berry NJ, Bicknell JE, Bihn JH, Böhning-Gaese K, Boekhout T, Boutin C, Bouyer J, Brearley FQ, Brito I, Brunet J, Buczkowski G, Buscardo E, Cabra-García J, Calviño-Cancela M, Cameron SA, Cancello EM, Carrijo TF, Carvalho AL, Castro H, Castro-Luna AA, Cerda R, Cerezo A, Chauvat M, Clarke FM, Cleary DFR, Connop SP, D'Aniello B, da Silva PG, Darvill B, Dauber J, Dejean A, Diekötter T, Dominguez-Haydar Y, Dormann CF, Dumont B, Dures SG, Dynesius M, Edenius L, Elek Z, Entling MH, Farwig N, Fayle TM, Felicioli A, Felton AM, Ficetola GF, Filgueiras BKC, Fonte SJ, Fraser LH, Fukuda D, Furlani D, Ganzhorn JU, Garden JG, Gheler-Costa C, Giordani P, Giordano S, Gottschalk MS, Goulson D, Gove AD, Grogan J, Hanley ME, Hanson T, Hashim NR, Hawes JE, Hébert C, Helden AJ, Henden JA, Hernández L, Herzog F, Higuera-Diaz D, Hilje B, Horgan FG, Horváth R, Hylander K, Isaacs-Cubides P, Ishitani M, Jacobs CT, Jaramillo VJ, Jauker B, Jonsell M, Jung TS, Kapoor V, Kati V, Katovai E, Kessler M, Knop E, Kolb A, Kőrösi Á, Lachat T, Lantschner V, Le Féon V, LeBuhn G, Légaré JP, Letcher SG, Littlewood NA, López-Quintero CA, Louhaichi M, Lövei GL, Lucas-Borja ME, Luja VH, Maeto K, Magura T, Mallari NA, Marin-Spiotta E, Marshall EJP, Martínez E, Mayfield MM, Mikusinski G, Milder JC, Miller JR, Morales CL, Muchane MN, Muchane M, Naidoo R, Nakamura A, Naoe S, Nates-Parra G, Navarrete Gutierrez DA, Neuschulz EL, Noreika N, Norfolk O, Noriega JA, Nöske NM, O'Dea N, Oduro W, Ofori-Boateng C, Oke CO, Osgathorpe LM, Paritsis J, Parra-H A, Pelegrin N, Peres CA, Persson AS, Petanidou T, Phalan B, Philips TK, Poveda K, Power EF, Presley SJ, Proença V, Quaranta M, Quintero C, Redpath-Downing NA, Reid JL, Reis YT, Ribeiro DB, Richardson BA, Richardson MJ, Robles CA, Römbke J, Romero-Duque LP, Rosselli L, Rossiter SJ, Roulston TH, Rousseau L, Sadler JP, Sáfián S, Saldaña-Vázquez RA, Samnegård U, Schüepp C, Schweiger O, Sedlock JL, Shahabuddin G, Sheil D, Silva FAB, Slade EM, Smith-Pardo AH, Sodhi NS, Somarriba EJ, Sosa RA, Stout JC, Struebig MJ, Sung YH, Threlfall CG, Tonietto R, Tóthmérész B, Tscharntke T, Turner EC, Tylianakis JM, Vanbergen AJ, Vassilev K, Verboven HAF, Vergara CH, Vergara PM, Verhulst J, Walker TR, Wang Y, Watling JI, Wells K, Williams CD, Willig MR, Woinarski JCZ, Wolf JHD, Woodcock BA, Yu DW, Zaitsev AS, Collen B, Ewers RM, Mace GM, Purves DW, Scharlemann JPW, Purvis A. The PREDICTS database: a global database of how local terrestrial biodiversity responds to human impacts. Ecol Evol 2014; 4:4701-35. [PMID: 25558364 PMCID: PMC4278822 DOI: 10.1002/ece3.1303] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Revised: 09/30/2014] [Accepted: 09/30/2014] [Indexed: 11/25/2022] Open
Abstract
Biodiversity continues to decline in the face of increasing anthropogenic pressures such as habitat destruction, exploitation, pollution and introduction of alien species. Existing global databases of species’ threat status or population time series are dominated by charismatic species. The collation of datasets with broad taxonomic and biogeographic extents, and that support computation of a range of biodiversity indicators, is necessary to enable better understanding of historical declines and to project – and avert – future declines. We describe and assess a new database of more than 1.6 million samples from 78 countries representing over 28,000 species, collated from existing spatial comparisons of local-scale biodiversity exposed to different intensities and types of anthropogenic pressures, from terrestrial sites around the world. The database contains measurements taken in 208 (of 814) ecoregions, 13 (of 14) biomes, 25 (of 35) biodiversity hotspots and 16 (of 17) megadiverse countries. The database contains more than 1% of the total number of all species described, and more than 1% of the described species within many taxonomic groups – including flowering plants, gymnosperms, birds, mammals, reptiles, amphibians, beetles, lepidopterans and hymenopterans. The dataset, which is still being added to, is therefore already considerably larger and more representative than those used by previous quantitative models of biodiversity trends and responses. The database is being assembled as part of the PREDICTS project (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems – http://www.predicts.org.uk). We make site-level summary data available alongside this article. The full database will be publicly available in 2015.
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Affiliation(s)
- Lawrence N Hudson
- Department of Life Sciences, Natural History Museum Cromwell Road, London, SW7 5BD, U.K
| | - Tim Newbold
- United Nations Environment Programme World Conservation Monitoring Centre 219 Huntingdon Road, Cambridge, CB3 0DL, U.K ; Computational Ecology and Environmental Science, Microsoft Research 21 Station Road, Cambridge, CB1 2FB, U.K
| | - Sara Contu
- Department of Life Sciences, Natural History Museum Cromwell Road, London, SW7 5BD, U.K
| | - Samantha L L Hill
- Department of Life Sciences, Natural History Museum Cromwell Road, London, SW7 5BD, U.K ; United Nations Environment Programme World Conservation Monitoring Centre 219 Huntingdon Road, Cambridge, CB3 0DL, U.K
| | - Igor Lysenko
- Imperial College London Silwood Park Campus, Buckhurst Road, Ascot, SL5 7PY, U.K
| | - Adriana De Palma
- Department of Life Sciences, Natural History Museum Cromwell Road, London, SW7 5BD, U.K ; Imperial College London Silwood Park Campus, Buckhurst Road, Ascot, SL5 7PY, U.K
| | - Helen R P Phillips
- Department of Life Sciences, Natural History Museum Cromwell Road, London, SW7 5BD, U.K ; Imperial College London Silwood Park Campus, Buckhurst Road, Ascot, SL5 7PY, U.K
| | - Rebecca A Senior
- United Nations Environment Programme World Conservation Monitoring Centre 219 Huntingdon Road, Cambridge, CB3 0DL, U.K
| | - Dominic J Bennett
- Imperial College London Silwood Park Campus, Buckhurst Road, Ascot, SL5 7PY, U.K
| | - Hollie Booth
- United Nations Environment Programme World Conservation Monitoring Centre 219 Huntingdon Road, Cambridge, CB3 0DL, U.K ; Frankfurt Zoological Society, Africa Regional Office PO Box 14935, Arusha, Tanzania
| | - Argyrios Choimes
- Department of Life Sciences, Natural History Museum Cromwell Road, London, SW7 5BD, U.K ; Imperial College London Silwood Park Campus, Buckhurst Road, Ascot, SL5 7PY, U.K
| | - David L P Correia
- Department of Life Sciences, Natural History Museum Cromwell Road, London, SW7 5BD, U.K
| | - Julie Day
- Imperial College London Silwood Park Campus, Buckhurst Road, Ascot, SL5 7PY, U.K
| | - Susy Echeverría-Londoño
- Department of Life Sciences, Natural History Museum Cromwell Road, London, SW7 5BD, U.K ; Imperial College London Silwood Park Campus, Buckhurst Road, Ascot, SL5 7PY, U.K
| | - Morgan Garon
- Imperial College London Silwood Park Campus, Buckhurst Road, Ascot, SL5 7PY, U.K
| | | | - Daniel J Ingram
- School of Life Sciences, University of Sussex Brighton, BN1 9QG, U.K
| | - Martin Jung
- Center for Macroecology, Climate and Evolution, the Natural History Museum of Denmark Universitetsparken 15, 2100, Copenhagen, Denmark
| | - Victoria Kemp
- Imperial College London Silwood Park Campus, Buckhurst Road, Ascot, SL5 7PY, U.K
| | - Lucinda Kirkpatrick
- School of Biological and Ecological Sciences, University of Stirling Bridge of Allan, Stirling, FK9 4LA, U.K
| | - Callum D Martin
- Imperial College London Silwood Park Campus, Buckhurst Road, Ascot, SL5 7PY, U.K
| | - Yuan Pan
- Department of Animal and Plant Sciences, University of Sheffield Alfred Denny Building, Western Bank, Sheffield, S10 2TN, U.K
| | - Hannah J White
- School of Biological Sciences, Queen's University Belfast 97 Lisburn Road, Belfast, BT9 7BL, U.K
| | - Job Aben
- Evolutionary Ecology Group, University of Antwerp Groenenborgerlaan 171, 2020, Antwerp, Belgium
| | - Stefan Abrahamczyk
- Nees Institute for Plant Biodiversity, University of Bonn Meckenheimer Allee 170, 53113, Bonn, Germany
| | - Gilbert B Adum
- Department of Wildlife and Range Management, FRNR, CANR, KNUST Kumasi, Ghana ; SAVE THE FROGS! Ghana Box KS 15924, Adum-Kumasi, Ghana
| | | | - Marcelo A Aizen
- CONICET, Lab. INIBIOMA (Universidad Nacional del Comahue-CONICET) Pasaje Gutierrez 1125, 8400, Bariloche, Rio Negro, Argentina
| | - Marc Ancrenaz
- HUTAN - Kinabatangan Orang-utan Conservation Programme PO Box 17793, 88874, Kota Kinabalu, Sabah, Malaysia
| | - Enrique Arbeláez-Cortés
- Museo de Zoología, Facultad de Ciencias, Universidad Nacional Autónoma de México México D.F, Mexico ; Colección de Tejidos, Instituto de Investigación de Recursos Biológicos Alexander von Humboldt Km 17 Cali-Palmira, Valle del Cauca, Colombia
| | - Inge Armbrecht
- Department of Biology, Universidad del Valle Calle 13 #100-00, Cali, Colombia
| | - Badrul Azhar
- Biodiversity Unit, Institute of Bioscience, Universiti Putra Malaysia 43400, Serdang, Selangor, Malaysia ; Faculty of Forestry, Universiti Putra Malaysia 43400, Serdang, Selangor, Malaysia
| | - Adrián B Azpiroz
- Laboratorio de Genética de la Conservación, Instituto de Investigaciones Biológicas Clemente Estable Montevideo, Uruguay
| | - Lander Baeten
- Department of Forest and Water Management, Forest & Nature Lab, Ghent University Geraardsbergsesteenweg 267, 9090, Gontrode, Belgium ; Terrestrial Ecology Unit Department of Biology, Ghent University K. L. Ledeganckstraat 35, 9000, Gent, Belgium
| | - András Báldi
- MTA Centre for Ecological Research Alkotmány u. 2-4, 2163, Vácrátót, Hungary
| | - John E Banks
- University of Washington 1900 Commerce Street, Tacoma, Washington, 98402, U.K
| | - Jos Barlow
- Lancaster Environment Centre, Lancaster University Lancaster, LA1 4YQ, U.K ; MCT/Museu Paraense Emílio Goeldi Belém, Pará, Brazil
| | - Péter Batáry
- Agroecology, Georg-August University Grisebachstrasse 6, 37077, Göttingen, Germany
| | - Adam J Bates
- University of Birmingham Edgbaston, Birmingham, B15 2TT, U.K
| | - Erin M Bayne
- Department of Biological Sciences, University of Alberta CW 405 - Biological Sciences Centre, Edmonton, AB, T6G 2E9, Canada
| | - Pedro Beja
- EDP Biodiversity Chair, CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto Campus Agrário de Vairão, 4485-601, Vairão, Portugal
| | - Åke Berg
- The Swedish University of Agricultural Sciences, The Swedish Biodiversity Centre SE 750 07, Uppsala, Sweden
| | - Nicholas J Berry
- University of Edinburgh, School of GeoSciences Crew Building, King's Buildings, West Mains Road, Edinburgh, EH9 3JN, U.K
| | - Jake E Bicknell
- Durrell Institute of Conservation and Ecology (DICE), School of Anthropology and Conservation, University of Kent Canterbury, CT2 7NR, U.K ; Iwokrama International Centre for Rainforest Conservation and Development 77 High Street, Georgetown, Guyana
| | - Jochen H Bihn
- Department of Animal Ecology, Philipps-University Marburg Karl-von-Frisch Strasse 8, 35032, Marburg, Germany
| | - Katrin Böhning-Gaese
- Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung Senckenberganlage 25, 60325, Frankfurt am Main, Germany ; Institute for Ecology, Evolution & Diversity, Biologicum, Goethe University Frankfurt Max von Laue St. 13, D 60439, Frankfurt am Main, Germany
| | - Teun Boekhout
- CBS-KNAW Fungal Biodiversity Centre Utrecht, The Netherlands
| | - Céline Boutin
- Environment Canada, Science & Technology Branch, Carleton University 1125 Colonel By Drive, Raven Road, Ottawa, ON, K1A 0H3, Canada
| | - Jérémy Bouyer
- Unité Mixte de Recherche Contrôle des Maladies Animales Exotiques et Emergentes, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD) 34398, Montpellier, France ; Unité Mixte de Recherche 1309 Contrôle des Maladies Animales Exotiques et Emergentes, Institut national de la recherche agronomique (INRA) 34398, Montpellier, France
| | - Francis Q Brearley
- School of Science and the Environment, Manchester Metropolitan University Chester Street, Manchester, M1 5GD, U.K
| | - Isabel Brito
- University of Évora - ICAAMA, Apartado 94 7002-554, Évora, Portugal
| | - Jörg Brunet
- Southern Swedish Forest Research Centre, Swedish University of Agricultural Sciences Box 49, 230 53, Alnarp, Sweden
| | - Grzegorz Buczkowski
- Department of Entomology, Purdue University 901 W. State Street, West Lafayette, 47907, Indiana, Portugal
| | - Erika Buscardo
- Centro de Ecologia Funcional, Departamento de Ciências da Vida, Universidade de Coimbra Calçada Martim de Freitas, 3000-456, Coimbra, Portugal ; Escritório Central do LBA, Instituto Nacional de Pesquisa da Amazônia Av. André Araújo, 2936, Campus II, Aleixo, CEP 69060-001, Manaus, AM, Brazil ; Department of Botany, School of Natural Sciences, Trinity College Dublin College Green, Dublin 2, Ireland
| | - Jimmy Cabra-García
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo São Paulo, SP, 05508-090, Brazil
| | - María Calviño-Cancela
- Department of Ecology and Animal Biology, Faculty of Sciences, University of Vigo 36310, Vigo, Spain
| | - Sydney A Cameron
- Department of Entomology, University of Illinois Urbana, Illinois, 61801, Brazil
| | - Eliana M Cancello
- Museu de Zoologia da Universidade de São Paulo Av. Nazaré 481, 04263-000, São Paulo, SP, Brazil
| | - Tiago F Carrijo
- Museu de Zoologia da Universidade de São Paulo Av. Nazaré 481, 04263-000, São Paulo, SP, Brazil
| | - Anelena L Carvalho
- Instituto Nacional de Pesquisas da Amazônia Av. André Araújo, 2.936, Petrópolis, CEP 69067-375, Manaus, AM, Brazil
| | - Helena Castro
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra Calçada Martim de Freitas, 3000-456, Coimbra, Portugal
| | - Alejandro A Castro-Luna
- Instituto de Biotecnologia y Ecologia Aplicada (INBIOTECA), Universidad Veracruzana Av. de las Culturas Veracruzanas, 101, Col. Emiliano Zapata, CP 91090, Xalapa, Veracruz, Mexico
| | - Rolando Cerda
- Centro Agronómico Tropical de Investigación y Enseñanza (CATIE), Tropical Agricultural Research and Higher Education Center 7170, Cartago, Turrialba, 30501, Costa Rica
| | - Alexis Cerezo
- Department of Quantitative Methods and Information Systems, Faculty of Agronomy, University of Buenos Aires Av. San Martín 4453, Ciudad Autónoma de Buenos Aires, Argentina, C.P. 1417, Argentina
| | - Matthieu Chauvat
- Normandie Univ., EA 1293 ECODIV-Rouen, SFR SCALE, UFR Sciences et Techniques 76821, Mont Saint Aignan Cedex, France
| | | | - Daniel F R Cleary
- Department of Biology, CESAM, Universidade de Aveiro Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Stuart P Connop
- Sustainability Research Institute, University of East London 4-6 University Way, London, E16 2RD, U.K
| | - Biagio D'Aniello
- Department of Biology, University of Naples "Federico II" Naples, Italy
| | - Pedro Giovâni da Silva
- Programa de Pós-graduação em Ecologia, Universidade Federal de Santa Catarina Florianópolis, Santa Catarina, CEP 88040-900, Brazil
| | - Ben Darvill
- British Trust for Ornithology, University of Stirling Stirling, FK9 4LA, U.K
| | - Jens Dauber
- Thünen Institute of Biodiversity Bundesallee 50, 38116, Braunschweig, Germany
| | - Alain Dejean
- CNRS, Écologie des Forêts de Guyane (UMR-CNRS 8172) BP 316, 97379, Kourou cedex, France ; Université de Toulouse, UPS, INP, Laboratoire Écologie Fonctionnelle et Environnement (Ecolab) 118 route de Narbonne, 31062, Toulouse, France
| | - Tim Diekötter
- Department of Landscape Ecology, Institute for Nature and Resource Conservation, Kiel University Olshausenstrasse 75, 24098, Kiel, Germany ; Department of Biology, Nature Conservation, University Marburg Marburg, Germany ; Institute of Integrative Biology ETH Zurich, Switzerland
| | | | - Carsten F Dormann
- Biometry and Environmental System Analysis, University of Freiburg Tennenbacher Strasse 4, 79106, Freiburg, Germany
| | - Bertrand Dumont
- INRA, UMR1213 Herbivores 63122, Saint-Genès-Champanelle, France
| | - Simon G Dures
- Imperial College London Silwood Park Campus, Buckhurst Road, Ascot, SL5 7PY, U.K ; Institute of Zoology, Zoological Society of London Nuffield Building, Regents Park, London, NW1 4RY, U.K
| | - Mats Dynesius
- Department of Ecology and Environmental Science, Umeå University 901 87, Umeå, Sweden
| | - Lars Edenius
- Wildlife, Fish and Environmental Studies, Swedish University of Agricultural Sciences 901 83, Umeå, Sweden
| | - Zoltán Elek
- MTA-ELTE-MTM Ecology Research Group, Hungarian Academy of Sciences, c/o Biological Institute, Eötvös Lóránd University Pázmány Péter sétány 1/C., 1117, Budapest, Hungary
| | - Martin H Entling
- University of Koblenz-Landau, Institute for Environmental Sciences Fortstr. 7, 76829, Landau, Germany
| | - Nina Farwig
- Department of Ecology - Conservation Ecology, Faculty of Biology, Philipps-Universität Marburg Karl-von-Frisch-Street 8, 35032, Marburg, Germany
| | - Tom M Fayle
- Imperial College London Silwood Park Campus, Buckhurst Road, Ascot, SL5 7PY, U.K ; Faculty of Science, University of South Bohemia and Institute of Entomology, Biology Centre of Academy of Sciences Czech Republic Branišovská 31, 370 05, České Budějovice, Czech Republic ; Institute for Tropical Biology and Conservation, Universiti Malaysia Sabah 88999, Kota Kinabalu, Sabah, Malaysia
| | - Antonio Felicioli
- Dipartimento di Scienze Veterinarie, Università di Pisa Viale delle Piagge, n°2, 56124, Pisa, Italy
| | - Annika M Felton
- The Southern Swedish Forest Research Centre, The Swedish University of Agricultural Sciences PO Box 49, 23453, Alnarp, Sweden
| | - Gentile F Ficetola
- Laboratoire d'Ecologie Alpine (LECA), Université Grenoble Alpes F-38000, Grenoble, France
| | - Bruno K C Filgueiras
- Programa de Pós-Graduação em Biologia Animal, Universidade Federal de Pernambuco Recife, PE 50670-901, Brazil
| | - Steven J Fonte
- Department of Plant Sciences, University of California Davis, California, 95616, Canada
| | - Lauchlan H Fraser
- Department of Natural Resource Sciences, Thompson Rivers University 900 McGill Road, Kamloops, BC, V2C 0C8, Canada
| | - Daisuke Fukuda
- IDEA Consultants Inc Okinawa Branch Office, Aja 2-6-19, Naha, Okinawa, 900-0003, Japan
| | - Dario Furlani
- Carl Zeiss Microscopy GmbH Königsallee 9 - 21, 37081, Göttingen, Germany
| | - Jörg U Ganzhorn
- University of Hamburg, Biocentre Grindel Martin-Luther-King Platz 3, 20146, Hamburg, Germany
| | - Jenni G Garden
- Seed Consulting Services 106 Gilles Street, Adelaide, 5000, SA, Australia ; School of Geography, Planning and Environmental Management, The University of Queensland St Lucia, 4072, Qld, Australia
| | - Carla Gheler-Costa
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| | - Paolo Giordani
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| | - Marco S Gottschalk
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| | - Dave Goulson
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| | - Aaron D Gove
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| | - James Grogan
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| | - Thor Hanson
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| | - Joseph E Hawes
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| | - Finbarr G Horgan
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| | - Paola Isaacs-Cubides
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| | - Mats Jonsell
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| | - Vena Kapoor
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| | - Neil Aldrin Mallari
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| | - Erika Marin-Spiotta
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| | - E J P Marshall
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| | - Eliana Martínez
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| | - Margaret M Mayfield
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| | - Grzegorz Mikusinski
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| | - Jeffrey C Milder
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| | - Mary N Muchane
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| | - Guiomar Nates-Parra
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| | | | - Niall O'Dea
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| | - Juan Paritsis
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| | - Alejandro Parra-H
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| | - Nicolás Pelegrin
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| | - Carlos A Peres
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| | - Anna S Persson
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| | - Theodora Petanidou
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| | - Ben Phalan
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| | - Marino Quaranta
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| | - Carolina Quintero
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| | - J Leighton Reid
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| | - Michael J Richardson
- 165 Braid Road, Edinburgh, EH10 6JE, U.K ; Associate Scientist, Luquillo LTER, Institute for Tropical Ecosystem Studies, College of Natural Sciences, University of Puerto Rico at Rio Piedras P.O. Box 70377, San Juan, Puerto Rico, 00936-8377, Argentina
| | - Carolina A Robles
- PROPLAME-PRHIDEB-CONICET, Departamento de Biodiversidad y Biología Experimental, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria PB II, 4to piso, (CP1428EHA), Ciudad Autónoma de Buenos Aires, Argentina
| | - Jörg Römbke
- Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung Senckenberganlage 25, 60325, Frankfurt am Main, Germany ; ECT Oekotoxikologie GmbH Böttgerstr. 2-14, 65439, Flörsheim, Germany
| | | | - Loreta Rosselli
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| | - Stephen J Rossiter
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| | - T'ai H Roulston
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| | - Laurent Rousseau
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| | - Jonathan P Sadler
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| | - Szabolcs Sáfián
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| | - Romeo A Saldaña-Vázquez
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| | - Ulrika Samnegård
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| | - Christof Schüepp
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| | - Oliver Schweiger
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| | - Jodi L Sedlock
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| | - Douglas Sheil
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| | - Jane C Stout
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| | - Matthew J Struebig
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| | - Yik-Hei Sung
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| | - Caragh G Threlfall
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| | - Rebecca Tonietto
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| | - Béla Tóthmérész
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| | - Teja Tscharntke
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| | - Edgar C Turner
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| | - Jason M Tylianakis
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| | - Adam J Vanbergen
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| | - Kiril Vassilev
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| | - Carlos H Vergara
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| | - Pablo M Vergara
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| | - Jort Verhulst
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| | - Tony R Walker
- School of Biology, The University of Nottingham University Park, Nottingham, NG7 2RD, U.K ; Dillon Consulting Limited 137 Chain Lake Drive, Halifax, NS, B3S 1B3, Canada
| | - Yanping Wang
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| | - James I Watling
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| | - Christopher D Williams
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| | - Michael R Willig
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| | | | - Jan H D Wolf
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| | - Ben A Woodcock
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| | - Douglas W Yu
- University of East Anglia Norwich Research Park, Norwich, Norfolk,, NR4 7TJ, U.K ; Kunming Institute of Zoology Kunming, Yunnan,, 650023, China
| | - Andrey S Zaitsev
- Institute of Animal Ecology, Justus-Liebig-University Heinrich-Buff-Ring 26, 35392, Giessen, Germany ; A. N. Severtsov Institute of Ecology and Evolution Leninsky Prospekt 33, 119071, Moscow, Russia
| | - Ben Collen
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| | - Rob M Ewers
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| | - Georgina M Mace
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| | - Drew W Purves
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| | - Jörn P W Scharlemann
- United Nations Environment Programme World Conservation Monitoring Centre 219 Huntingdon Road, Cambridge, CB3 0DL, U.K ; School of Life Sciences, University of Sussex Brighton, BN1 9QG, U.K
| | - Andy Purvis
- Department of Life Sciences, Natural History Museum Cromwell Road, London, SW7 5BD, U.K ; Imperial College London Silwood Park Campus, Buckhurst Road, Ascot, SL5 7PY, U.K
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Harris RB, Jiake Z, Yinqiu J, Kai Z, Chunyan Y, Yu DW. Evidence that the Tibetan fox is an obligate predator of the plateau pika: conservation implications. J Mammal 2014. [DOI: 10.1644/14-mamm-a-021] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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He D, Wu R, Feng Y, Li Y, Ding C, Wang W, Yu DW. China's transboundary waters: new paradigms for water and ecological security through applied ecology. J Appl Ecol 2014; 51:1159-1168. [PMID: 25558084 PMCID: PMC4278448 DOI: 10.1111/1365-2664.12298] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 05/28/2014] [Indexed: 11/27/2022]
Abstract
China is Asia's most important upstream riparian country, sharing 110 rivers and lakes with 18 downstream countries. Consequently, China's management of transboundary water resources must consider both environmental and geopolitical risks. The major threats to and conflicts over international rivers in China revolve around biotic homogenisation due to the installation of transport links, water allocation, water pollution, alteration of natural flow patterns and disruption of fisheries due to the installation of hydropower dams, and droughts and floods exacerbated by climate change. Because these problems have an international component, they fall under China's Peaceful Rise strategy, mandating that transboundary conflicts be resolved amicably as part of the overarching goal of increasing regional economic growth with as little conflict as possible. Science‐backed policy is more likely to result in long term, mutually agreeable solutions; the results of applied ecological research have already resulted in a number of mitigation measures, including setting operational thresholds to reduce the downstream impact of dams, designating protected areas along key river stretches where dams cannot be installed (one dam in a critical location has been cancelled), and the installation of terrestrial protected‐area networks. Synthesis and applications. Applied ecology will continue to play an important role in the diagnosis and resolution of environmental threats to China's transboundary waters. More importantly, applied ecology can inform the development of a transboundary environmental compensation mechanism and regional consultative mechanisms that support informed, cooperative decision‐making for China and its riparian neighbours.
Applied ecology will continue to play an important role in the diagnosis and resolution of environmental threats to China's transboundary waters. More importantly, applied ecology can inform the development of a transboundary environmental compensation mechanism and regional consultative mechanisms that support informed, cooperative decision‐making for China and its riparian neighbours.
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Affiliation(s)
- Daming He
- Yunnan Key Laboratory of International Rivers and Transboundary Eco-Security, Yunnan University 2 North Road of the Green Lake, Kunming, Yunnan, 650091, China
| | - Ruidong Wu
- Yunnan Key Laboratory of International Rivers and Transboundary Eco-Security, Yunnan University 2 North Road of the Green Lake, Kunming, Yunnan, 650091, China
| | - Yan Feng
- Yunnan Key Laboratory of International Rivers and Transboundary Eco-Security, Yunnan University 2 North Road of the Green Lake, Kunming, Yunnan, 650091, China
| | - Yungang Li
- Yunnan Key Laboratory of International Rivers and Transboundary Eco-Security, Yunnan University 2 North Road of the Green Lake, Kunming, Yunnan, 650091, China
| | - Chengzhi Ding
- Yunnan Key Laboratory of International Rivers and Transboundary Eco-Security, Yunnan University 2 North Road of the Green Lake, Kunming, Yunnan, 650091, China
| | - Wenling Wang
- Yunnan Key Laboratory of International Rivers and Transboundary Eco-Security, Yunnan University 2 North Road of the Green Lake, Kunming, Yunnan, 650091, China
| | - Douglas W Yu
- Ecology, Conservation, & Environment Center (ECEC), Kunming Institute of Zoology 32 Jiaochang East Road, Kunming, Yunnan, 650223, China ; School of Biological Sciences, University of East Anglia, Norwich Research Park Norwich, Norfolk, NR7TJ, UK
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Bohmann K, Evans A, Gilbert MTP, Carvalho GR, Creer S, Knapp M, Yu DW, de Bruyn M. Environmental DNA for wildlife biology and biodiversity monitoring. Trends Ecol Evol 2014; 29:358-67. [DOI: 10.1016/j.tree.2014.04.003] [Citation(s) in RCA: 515] [Impact Index Per Article: 51.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 04/08/2014] [Accepted: 04/09/2014] [Indexed: 01/07/2023]
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Gao H, Grüschow S, Barke J, Seipke RF, Hill LM, Orivel J, Yu DW, Hutchings M, Goss RJM. Filipins: the first antifungal “weed killers” identified from bacteria isolated from the trap-ant. RSC Adv 2014. [DOI: 10.1039/c4ra09875g] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Allomerus ants cultivate fungus to fabricate their insect traps. Speculation is that the ants employ actinomycetes to help achieve fungal monoculture. From an associated actinomycete we identify the first antifungal compounds and encoding genes.
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Affiliation(s)
- Hong Gao
- School of Chemistry
- University of St. Andrews
- St. Andrews, UK KY16 9ST
- School of Chemistry
- University of East Anglia
| | - Sabine Grüschow
- School of Chemistry
- University of St. Andrews
- St. Andrews, UK KY16 9ST
- School of Chemistry
- University of East Anglia
| | - Jörg Barke
- School of Biological Sciences
- University of East Anglia
- Norwich, UK NR4 7TJ
| | - Ryan F. Seipke
- School of Biological Sciences
- University of East Anglia
- Norwich, UK NR4 7TJ
| | | | - Jérôme Orivel
- CNRS
- UMR Ecologie des Forêts de Guyane
- Campus Agronomique
- 97379 Kourou Cedex, France
| | - Douglas W. Yu
- School of Biological Sciences
- University of East Anglia
- Norwich, UK NR4 7TJ
- State Key Laboratory of Genetic Resources and Evolution
- Kunming Institute of Zoology
| | - Matthew Hutchings
- School of Biological Sciences
- University of East Anglia
- Norwich, UK NR4 7TJ
| | - Rebecca J. M. Goss
- School of Chemistry
- University of St. Andrews
- St. Andrews, UK KY16 9ST
- School of Chemistry
- University of East Anglia
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Edwards DP, Magrach A, Woodcock P, Ji Y, Lim NTL, Edwards FA, Larsen TH, Hsu WW, Benedick S, Khen CV, Chung AYC, Reynolds G, Fisher B, Laurance WF, Wilcove DS, Hamer KC, Yu DW. Selective‐logging and oil palm: multitaxon impacts, biodiversity indicators, and trade‐offs for conservation planning. Ecol Appl 2014; 24:2029-2049. [PMID: 29185670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Strong global demand for tropical timber and agricultural products has driven large-scale logging and subsequent conversion of tropical forests. Given that the majority of tropical landscapes have been or will likely be logged, the protection of biodiversity within tropical forests thus depends on whether species can persist in these economically exploited lands, and if species cannot persist, whether we can protect enough primary forest from logging and conversion. However, our knowledge of the impact of logging and conversion on biodiversity is limited to a few taxa, often sampled in different locations with complex land-use histories, hampering attempts to plan cost-effective conservation strategies and to draw conclusions across taxa. Spanning a land-use gradient of primary forest, once- and twice-logged forests, and oil palm plantations, we used traditional sampling and DNA metabarcoding to compile an extensive data set in Sabah, Malaysian Borneo for nine vertebrate and invertebrate taxa to quantify the biological impacts of logging and oil palm, develop cost-effective methods of protecting biodiversity, and examine whether there is congruence in response among taxa. Logged forests retained high species richness, including, on average, 70% of species found in primary forest. In contrast, conversion to oil palm dramatically reduces species richness, with significantly fewer primary-forest species than found on logged forest transects for seven taxa. Using a systematic conservation planning analysis, we show that efficient protection of primary-forest species is achieved with land portfolios that include a large proportion of logged-forest plots. Protecting logged forests is thus a cost-effective method of protecting an ecologically and taxonomically diverse range of species, particularly when conservation budgets are limited. Six indicator groups (birds, leaf-litter ants, beetles, aerial hymenopterans, flies, and true bugs) proved to be consistently good predictors of the response of the other taxa to logging and oil palm. Our results confidently establish the high conservation value of logged forests and the low value of oil palm. Cross-taxon congruence in responses to disturbance also suggests that the practice of focusing on key indicator taxa yields important information of general biodiversity in studies of logging and oil palm.
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Kocher SD, Li C, Yang W, Tan H, Yi SV, Yang X, Hoekstra HE, Zhang G, Pierce NE, Yu DW. The draft genome of a socially polymorphic halictid bee, Lasioglossum albipes. Genome Biol 2013; 14:R142. [PMID: 24359881 PMCID: PMC4062844 DOI: 10.1186/gb-2013-14-12-r142] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 12/20/2013] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Taxa that harbor natural phenotypic variation are ideal for ecological genomic approaches aimed at understanding how the interplay between genetic and environmental factors can lead to the evolution of complex traits. Lasioglossum albipes is a polymorphic halictid bee that expresses variation in social behavior among populations, and common-garden experiments have suggested that this variation is likely to have a genetic component. RESULTS We present the L. albipes genome assembly to characterize the genetic and ecological factors associated with the evolution of social behavior. The de novo assembly is comparable to other published social insect genomes, with an N50 scaffold length of 602 kb. Gene families unique to L. albipes are associated with integrin-mediated signaling and DNA-binding domains, and several appear to be expanded in this species, including the glutathione-s-transferases and the inositol monophosphatases. L. albipes has an intact DNA methylation system, and in silico analyses suggest that methylation occurs primarily in exons. Comparisons to other insect genomes indicate that genes associated with metabolism and nucleotide binding undergo accelerated evolution in the halictid lineage. Whole-genome resequencing data from one solitary and one social L. albipes female identify six genes that appear to be rapidly diverging between social forms, including a putative odorant receptor and a cuticular protein. CONCLUSIONS L. albipes represents a novel genetic model system for understanding the evolution of social behavior. It represents the first published genome sequence of a primitively social insect, thereby facilitating comparative genomic studies across the Hymenoptera as a whole.
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Affiliation(s)
- Sarah D Kocher
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, 26 Oxford St, Cambridge, MA 02138, USA
- China National GeneBank, BGI-Shenzhen, Shenzen 518083, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Kunming, Yunnan 650223, China
| | - Cai Li
- China National GeneBank, BGI-Shenzhen, Shenzen 518083, China
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, Copenhagen 1350, Denmark
| | - Wei Yang
- China National GeneBank, BGI-Shenzhen, Shenzen 518083, China
| | - Hao Tan
- China National GeneBank, BGI-Shenzhen, Shenzen 518083, China
| | - Soojin V Yi
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Xingyu Yang
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Hopi E Hoekstra
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, 26 Oxford St, Cambridge, MA 02138, USA
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, Harvard University, 26 Oxford St, Cambridge, MA 02138, USA
| | - Guojie Zhang
- China National GeneBank, BGI-Shenzhen, Shenzen 518083, China
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, Copenhagen DK-2100, Denmark
| | - Naomi E Pierce
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, 26 Oxford St, Cambridge, MA 02138, USA
| | - Douglas W Yu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Kunming, Yunnan 650223, China
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR47TJ, UK
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Liu S, Li Y, Lu J, Su X, Tang M, Zhang R, Zhou L, Zhou C, Yang Q, Ji Y, Yu DW, Zhou X. SOAP
B
arcode: revealing arthropod biodiversity through assembly of Illumina shotgun sequences of PCR amplicons. Methods Ecol Evol 2013. [DOI: 10.1111/2041-210x.12120] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Shanlin Liu
- China National GeneBank BGI‐Shenzhen Beishan Industrial Zone Yantian District Shenzhen Guangdong Province 518083 China
| | - Yiyuan Li
- China National GeneBank BGI‐Shenzhen Beishan Industrial Zone Yantian District Shenzhen Guangdong Province 518083 China
| | - Jianliang Lu
- China National GeneBank BGI‐Shenzhen Beishan Industrial Zone Yantian District Shenzhen Guangdong Province 518083 China
| | - Xu Su
- China National GeneBank BGI‐Shenzhen Beishan Industrial Zone Yantian District Shenzhen Guangdong Province 518083 China
| | - Min Tang
- China National GeneBank BGI‐Shenzhen Beishan Industrial Zone Yantian District Shenzhen Guangdong Province 518083 China
| | - Rui Zhang
- China National GeneBank BGI‐Shenzhen Beishan Industrial Zone Yantian District Shenzhen Guangdong Province 518083 China
| | - Lili Zhou
- China National GeneBank BGI‐Shenzhen Beishan Industrial Zone Yantian District Shenzhen Guangdong Province 518083 China
| | - Chengran Zhou
- China National GeneBank BGI‐Shenzhen Beishan Industrial Zone Yantian District Shenzhen Guangdong Province 518083 China
- College of Life Sciences Sichuan University Chengdu Sichuan Province 610000 China
| | - Qing Yang
- China National GeneBank BGI‐Shenzhen Beishan Industrial Zone Yantian District Shenzhen Guangdong Province 518083 China
| | - Yinqiu Ji
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming Yunnan 650223 China
| | - Douglas W. Yu
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming Yunnan 650223 China
- School of Biological Sciences University of East Anglia Norwich Research Park Norwich Norfolk NR4 7TJ UK
| | - Xin Zhou
- China National GeneBank BGI‐Shenzhen Beishan Industrial Zone Yantian District Shenzhen Guangdong Province 518083 China
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Ji Y, Ashton L, Pedley SM, Edwards DP, Tang Y, Nakamura A, Kitching R, Dolman PM, Woodcock P, Edwards FA, Larsen TH, Hsu WW, Benedick S, Hamer KC, Wilcove DS, Bruce C, Wang X, Levi T, Lott M, Emerson BC, Yu DW. Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding. Ecol Lett 2013; 16:1245-57. [DOI: 10.1111/ele.12162] [Citation(s) in RCA: 414] [Impact Index Per Article: 37.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Revised: 04/11/2013] [Accepted: 07/01/2013] [Indexed: 11/29/2022]
Affiliation(s)
- Yinqiu Ji
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming Yunnan 650223 China
| | - Louise Ashton
- Environmental Futures Centre and Griffith School of Environment Griffith University Nathan Queensland 4111 Australia
| | - Scott M. Pedley
- School of Environmental Sciences University of East Anglia Norwich Research Park Norwich Norfolk NR47TJ UK
| | - David P. Edwards
- Woodrow Wilson School of Public and International Affairs Princeton University Princeton New Jersey 08544 USA
- Centre for Tropical Environmental and Sustainability Science (TESS) School of Marine and Tropical Biology James Cook University Cairns Queensland 4878 Australia
- Department of Ecology and Evolutionary Biology Princeton University Princeton New Jersey 08544 USA
| | - Yong Tang
- Xishuangbanna Tropical Botanical Garden Chinese Academy of Sciences Meng La Yunnan 666303 China
| | - Akihiro Nakamura
- Environmental Futures Centre and Griffith School of Environment Griffith University Nathan Queensland 4111 Australia
- Queensland Museum South Brisbane Queensland 4101 Australia
| | - Roger Kitching
- Environmental Futures Centre and Griffith School of Environment Griffith University Nathan Queensland 4111 Australia
| | - Paul M. Dolman
- School of Environmental Sciences University of East Anglia Norwich Research Park Norwich Norfolk NR47TJ UK
| | - Paul Woodcock
- Institute of Integrative and Comparative Biology and Faculty of Biological Sciences University of Leeds Leeds West Yorkshire LS29JT UK
| | - Felicity A. Edwards
- Institute of Integrative and Comparative Biology and Faculty of Biological Sciences University of Leeds Leeds West Yorkshire LS29JT UK
| | - Trond H. Larsen
- The Betty and Gordon Moore Center for Ecosystem Science and Economics Conservation International Arlington Virginia 22202 USA
| | - Wayne W. Hsu
- Department of Ecology Evolution, and Environmental Biology Columbia University New York City New York 10027 USA
| | - Suzan Benedick
- School of Sustainable Agriculture Universiti Malaysia Sabah Sandakan Sabah 9000 Malaysia
| | - Keith C. Hamer
- Institute of Integrative and Comparative Biology and Faculty of Biological Sciences University of Leeds Leeds West Yorkshire LS29JT UK
| | - David S. Wilcove
- Woodrow Wilson School of Public and International Affairs Princeton University Princeton New Jersey 08544 USA
- Department of Ecology and Evolutionary Biology Princeton University Princeton New Jersey 08544 USA
| | - Catharine Bruce
- School of Biological Sciences University of East Anglia Norwich Research Park Norwich Norfolk NR47TJ UK
| | - Xiaoyang Wang
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming Yunnan 650223 China
| | - Taal Levi
- Cary Institute of Ecosystem Studies Millbrook New York 12545 USA
- Department of Biology University of Florida Gainesville Florida 32611 USA
| | - Martin Lott
- School of Computing Sciences University of East Anglia Norwich Research Park Norwich Norfolk NR47TJ UK
| | - Brent C. Emerson
- Island Ecology and Evolution Research Group IPNA‐CSIC Tenerife Canary Islands 38206 Spain
| | - Douglas W. Yu
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming Yunnan 650223 China
- School of Biological Sciences University of East Anglia Norwich Research Park Norwich Norfolk NR47TJ UK
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Ramirez-Gonzalez R, Yu DW, Bruce C, Heavens D, Caccamo M, Emerson BC. PyroClean: denoising pyrosequences from protein-coding amplicons for the recovery of interspecific and intraspecific genetic variation. PLoS One 2013; 8:e57615. [PMID: 23469211 PMCID: PMC3585932 DOI: 10.1371/journal.pone.0057615] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Accepted: 01/24/2013] [Indexed: 01/24/2023] Open
Abstract
High-throughput parallel sequencing is a powerful tool for the quantification of microbial diversity through the amplification of nuclear ribosomal gene regions. Recent work has extended this approach to the quantification of diversity within otherwise difficult-to-study metazoan groups. However, nuclear ribosomal genes present both analytical challenges and practical limitations that are a consequence of the mutational properties of nuclear ribosomal genes. Here we exploit useful properties of protein-coding genes for cross-species amplification and denoising of 454 flowgrams. We first use experimental mixtures of species from the class Collembola to amplify and pyrosequence the 5′ region of the COI barcode, and we implement a new algorithm called PyroClean for the denoising of Roche GS FLX pyrosequences. Using parameter values from the analysis of experimental mixtures, we then analyse two communities sampled from field sites on the island of Tenerife. Cross-species amplification success of target mitochondrial sequences in experimental species mixtures is high; however, there is little relationship between template DNA concentrations and pyrosequencing read abundance. Homopolymer error correction and filtering against a consensus reference sequence reduced the volume of unique sequences to approximately 5% of the original unique raw reads. Filtering of remaining non-target sequences attributed to PCR error, sequencing error, or numts further reduced unique sequence volume to 0.8% of the original raw reads. PyroClean reduces or eliminates the need for an additional, time-consuming step to cluster reads into Operational Taxonomic Units, which facilitates the detection of intraspecific DNA sequence variation. PyroCleaned sequence data from field sites in Tenerife demonstrate the utility of our approach for quantifying evolutionary diversity and its spatial structure. Comparison of our sequence data to public databases reveals that we are able to successfully recover both interspecific and intraspecific sequence diversity.
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Affiliation(s)
| | - Douglas W. Yu
- Ecology, Conservation, and Environment Center, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, People’s Republic of China
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Catharine Bruce
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Darren Heavens
- The Genome Analysis Centre, Norwich Research Park, Norwich, United Kingdom
| | - Mario Caccamo
- The Genome Analysis Centre, Norwich Research Park, Norwich, United Kingdom
| | - Brent C. Emerson
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
- * E-mail:
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Seipke RF, Barke J, Heavens D, Yu DW, Hutchings MI. Analysis of the bacterial communities associated with two ant-plant symbioses. Microbiologyopen 2013; 2:276-83. [PMID: 23417898 PMCID: PMC3633351 DOI: 10.1002/mbo3.73] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Revised: 01/07/2013] [Accepted: 01/08/2013] [Indexed: 02/01/2023] Open
Abstract
Insect fungiculture is practiced by ants, termites, beetles, and gall midges and it has been suggested to be widespread among plant–ants. Some of the insects engaged in fungiculture, including attine ants and bark beetles, are known to use symbiotic antibiotic-producing actinobacteria to protect themselves and their fungal cultivars against infection. In this study, we analyze the bacterial communities on the cuticles of the plant–ant genera Allomerus and Tetraponera using deep sequencing of 16S rRNA. Allomerus ants cultivate fungus as a building material to strengthen traps for prey, while Tetraponera ants cultivate fungus as a food source. We report that Allomerus and Tetraponera microbiomes contain >75% Proteobacteria and remarkably the bacterial phyla that dominate their cuticular microbiomes are very similar despite their geographic separation (South America and Africa, respectively). Notably, antibiotic-producing actinomycete bacteria represent a tiny fraction of the cuticular microbiomes of both Allomerus and Tetraponera spp. and instead they are dominated by γ-proteobacteria Erwinia and Serratia spp. Both these phyla are known to contain antibiotic-producing species which might therefore play a protective role in these ant–plant systems.
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Affiliation(s)
- Ryan F Seipke
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom.
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