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Santos-Perdomo I, Suárez D, Moraza ML, Arribas P, Andújar C. Towards a Canary Islands barcode database for soil biodiversity: revealing cryptic and unrecorded mite species diversity within insular soils. Biodivers Data J 2024; 12:e113301. [PMID: 38314123 PMCID: PMC10838043 DOI: 10.3897/bdj.12.e113301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 12/23/2023] [Indexed: 02/06/2024] Open
Abstract
Soil arthropod diversity contributes to a high proportion of the total biodiversity on Earth. However, most soil arthropods are still undescribed, hindering our understanding of soil functioning and global biodiversity estimations. Inventorying soil arthropods using conventional taxonomical approaches is particularly difficult and costly due to the great species richness, abundance and local-scale heterogeneity of mesofauna communities and the poor taxonomic background knowledge of most lineages. To alleviate this situation, we have designed and implemented a molecular barcoding framework adapted to soil fauna. This pipeline includes different steps, starting with a morphology-based selection of specimens which are imaged. Then, DNA is extracted non-destructively. Both images and voucher specimens are used to assign a taxonomic identification, based on morphology that is further checked for consistency with molecular information. Using this procedure, we studied 239 specimens of mites from the Canary Islands including representatives of Mesostigmata, Sarcoptiformes and Trombidiformes, of which we recovered barcode sequences for 168 specimens that were morphologically identified to 49 species, with nine specimens that could only be identified at the genus or family levels. Multiple species delimitation analyses were run to compare molecular delimitations with morphological identifications, including ASAP, mlPTP, BINs and 3% and 8% genetic distance thresholds. Additionally, a species-level search was carried out at the Biodiversity Databank of the Canary Islands (BIOTA) to evaluate the number of species in our dataset that were not previously recorded in the archipelago. In parallel, a sequence-level search of our sequences was performed against BOLD Systems. Our results reveal that multiple morphologically identified species correspond to different molecular lineages, which points to significant levels of unknown cryptic diversity within the archipelago. In addition, we evidenced that multiple species in our dataset constituted new records for the Canary Islands fauna and that the information for these lineages within online genetic repositories is very incomplete. Our study represents the first systematic effort to catalogue the soil arthropod mesofauna of the Canary Islands and establishes the basis for the Canary Islands Soil Biodiversity barcode database. This resource will constitute a step forward in the knowledge of these arthropods in a region of special interest.
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Affiliation(s)
- Irene Santos-Perdomo
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), 38206, La Laguna, Spain Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), 38206 La Laguna Spain
- School of Doctoral and Postgraduate Studies, University of La Laguna, 38206, La Laguna, Spain School of Doctoral and Postgraduate Studies, University of La Laguna, 38206 La Laguna Spain
| | - Daniel Suárez
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), 38206, La Laguna, Spain Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), 38206 La Laguna Spain
- School of Doctoral and Postgraduate Studies, University of La Laguna, 38206, La Laguna, Spain School of Doctoral and Postgraduate Studies, University of La Laguna, 38206 La Laguna Spain
| | - María L Moraza
- Universidad de Navarra, Instituto de Biodiversidad y Medioambiente BIOMA, Irunlarrea 1, 31008, Pamplona, Spain Universidad de Navarra, Instituto de Biodiversidad y Medioambiente BIOMA, Irunlarrea 1, 31008 Pamplona Spain
| | - Paula Arribas
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), 38206, La Laguna, Spain Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), 38206 La Laguna Spain
| | - Carmelo Andújar
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), 38206, La Laguna, Spain Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), 38206 La Laguna Spain
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Emerson BC, Borges PAV, Cardoso P, Convey P, deWaard JR, Economo EP, Gillespie RG, Kennedy S, Krehenwinkel H, Meier R, Roderick GK, Strasberg D, Thébaud C, Traveset A, Creedy TJ, Meramveliotakis E, Noguerales V, Overcast I, Morlon H, Papadopoulou A, Vogler AP, Arribas P, Andújar C. Collective and harmonized high throughput barcoding of insular arthropod biodiversity: Toward a Genomic Observatories Network for islands. Mol Ecol 2023; 32:6161-6176. [PMID: 36156326 DOI: 10.1111/mec.16683] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 08/11/2022] [Accepted: 08/19/2022] [Indexed: 12/01/2022]
Abstract
Current understanding of ecological and evolutionary processes underlying island biodiversity is heavily shaped by empirical data from plants and birds, although arthropods comprise the overwhelming majority of known animal species, and as such can provide key insights into processes governing biodiversity. Novel high throughput sequencing (HTS) approaches are now emerging as powerful tools to overcome limitations in the availability of arthropod biodiversity data, and hence provide insights into these processes. Here, we explored how these tools might be most effectively exploited for comprehensive and comparable inventory and monitoring of insular arthropod biodiversity. We first reviewed the strengths, limitations and potential synergies among existing approaches of high throughput barcode sequencing. We considered how this could be complemented with deep learning approaches applied to image analysis to study arthropod biodiversity. We then explored how these approaches could be implemented within the framework of an island Genomic Observatories Network (iGON) for the advancement of fundamental and applied understanding of island biodiversity. To this end, we identified seven island biology themes at the interface of ecology, evolution and conservation biology, within which collective and harmonized efforts in HTS arthropod inventory could yield significant advances in island biodiversity research.
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Affiliation(s)
- Brent C Emerson
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), San Cristóbal de la Laguna, Spain
| | - Paulo A V Borges
- Centre for Ecology, Evolution and Environmental Changes (cE3c)/Azorean Biodiversity Group, Faculty of Agricultural Sciences and Environment, CHANGE - Global Change and Sustainability Institute, University of the Azores, Angra do Heroísmo, Portugal
| | - Pedro Cardoso
- Centre for Ecology, Evolution and Environmental Changes (cE3c)/Azorean Biodiversity Group, Faculty of Agricultural Sciences and Environment, CHANGE - Global Change and Sustainability Institute, University of the Azores, Angra do Heroísmo, Portugal
- Laboratory for Integrative Biodiversity Research (LIBRe), Finnish Museum of Natural History Luomus, University of Helsinki, Helsinki, Finland
| | - Peter Convey
- British Antarctic Survey, NERC, Cambridge, UK
- Department of Zoology, University of Johannesburg, Auckland Park, South Africa
| | - Jeremy R deWaard
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Canada
- School of Environmental Sciences, University of Guelph, Guelph, Canada
| | - Evan P Economo
- Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
- Radcliffe Institute for Advanced Study, Harvard University, Cambridge, Massachusetts, USA
| | - Rosemary G Gillespie
- Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, California, USA
| | - Susan Kennedy
- Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | | | - Rudolf Meier
- Center for Integrative Biodiversity Discovery, Leibniz Institute for Evolution and Biodiversity Science, Museum für Naturkunde, Berlin, Germany
- Department of Biological Sciences, National University of Singapore, Singapore City, Singapore
| | - George K Roderick
- Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, California, USA
| | | | - Christophe Thébaud
- UMR 5174 EDB Laboratoire Évolution & Diversité Biologique, Université Paul Sabatier Toulouse III, CNRS, IRD, Toulouse, France
| | - Anna Traveset
- Global Change Research Group, Mediterranean Institut of Advanced Studies (CSIC-UIB), Mallorca, Spain
| | - Thomas J Creedy
- Department of Life Sciences, Natural History Museum, London, UK
| | | | - Víctor Noguerales
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), San Cristóbal de la Laguna, Spain
| | - Isaac Overcast
- Département de Biologie, École normale supérieure, Institut de Biologie de l'ENS (IBENS), CNRS, INSERM, Université PSL, Paris, France
| | - Hélène Morlon
- Département de Biologie, École normale supérieure, Institut de Biologie de l'ENS (IBENS), CNRS, INSERM, Université PSL, Paris, France
| | - Anna Papadopoulou
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Alfried P Vogler
- Department of Life Sciences, Natural History Museum, London, UK
- Department of Life Sciences, Imperial College London, London, UK
| | - Paula Arribas
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), San Cristóbal de la Laguna, Spain
| | - Carmelo Andújar
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), San Cristóbal de la Laguna, Spain
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Arjona Y, Arribas P, Salces-Castellano A, López H, Emerson BC, Andújar C. Metabarcoding for biodiversity inventory blind spots: A test case using the beetle fauna of an insular cloud forest. Mol Ecol 2023; 32:6130-6146. [PMID: 36197789 DOI: 10.1111/mec.16716] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 09/24/2022] [Accepted: 09/28/2022] [Indexed: 11/28/2022]
Abstract
Soils harbour a rich arthropod fauna, but many species are still not formally described (Linnaean shortfall) and the distribution of those already described is poorly understood (Wallacean shortfall). Metabarcoding holds much promise to fill this gap, however, nuclear copies of mitochondrial genes, and other artefacts lead to taxonomic inflation, which compromise the reliability of biodiversity inventories. Here, we explore the potential of a bioinformatic approach to jointly "denoise" and filter nonauthentic mitochondrial sequences from metabarcode reads to obtain reliable soil beetle inventories and address open questions in soil biodiversity research, such as the scale of dispersal constraints in different soil layers. We sampled cloud forest arthropod communities from 49 sites in the Anaga peninsula of Tenerife (Canary Islands). We performed whole organism community DNA (wocDNA) metabarcoding, and built a local reference database with COI barcode sequences of 310 species of Coleoptera for filtering reads and the identification of metabarcoded species. This resulted in reliable haplotype data after considerably reducing nuclear mitochondrial copies and other artefacts. Comparing our results with previous beetle inventories, we found: (i) new species records, potentially representing undescribed species; (ii) new distribution records, and (iii) validated phylogeographic structure when compared with traditional sequencing approaches. Analyses also revealed evidence for higher dispersal constraint within deeper soil beetle communities, compared to those closer to the surface. The combined power of barcoding and metabarcoding contribute to mitigate the important shortfalls associated with soil arthropod diversity data, and thus address unresolved questions for this vast biodiversity fraction.
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Affiliation(s)
- Yurena Arjona
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), La Laguna, Tenerife, Canary Islands, Spain
| | - Paula Arribas
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), La Laguna, Tenerife, Canary Islands, Spain
| | - Antonia Salces-Castellano
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), La Laguna, Tenerife, Canary Islands, Spain
- Department of Biology, Ecology and Evolution, University of Liege, Liege, Belgium
| | - Heriberto López
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), La Laguna, Tenerife, Canary Islands, Spain
| | - Brent C Emerson
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), La Laguna, Tenerife, Canary Islands, Spain
| | - Carmelo Andújar
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), La Laguna, Tenerife, Canary Islands, Spain
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Guo M, Yuan C, Tao L, Cai Y, Zhang W. Life barcoded by DNA barcodes. CONSERV GENET RESOUR 2022; 14:351-365. [PMID: 35991367 PMCID: PMC9377290 DOI: 10.1007/s12686-022-01291-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 08/05/2022] [Indexed: 11/15/2022]
Abstract
The modern concept of DNA-based barcoding for cataloguing biodiversity was proposed in 2003 by first adopting an approximately 600 bp fragment of the mitochondrial COI gene to compare via nucleotide alignments with known sequences from specimens previously identified by taxonomists. Other standardized regions meeting barcoding criteria then are also evolving as DNA barcodes for fast, reliable and inexpensive assessment of species composition across all forms of life, including animals, plants, fungi, bacteria and other microorganisms. Consequently, global DNA barcoding campaigns have resulted in the formation of many online workbenches and databases, such as BOLD system, as barcode references, and facilitated the development of mini-barcodes and metabarcoding strategies as important extensions of barcode techniques. Here we intend to give an overview of the characteristics and features of these barcode markers and major reference libraries existing for barcoding the planet’s life, as well as to address the limitations and opportunities of DNA barcodes to an increasingly broader community of science and society.
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Ross GM, Berg MP, Salmon S, Nielsen UN. Phylogenies of traits and functions in soil invertebrate assemblages. AUSTRAL ECOL 2022. [DOI: 10.1111/aec.13153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Giles M. Ross
- Hawkesbury Institute for the Environment Western Sydney University Locked Bag 1797 Penrith NSW 2751 Australia
| | - Matty P. Berg
- Department of Ecological Science Vrije Universiteit Amsterdam, De Boelelaan 1085 Amsterdam HV 1081 The Netherlands
- Community and Conservation Ecology Group, Groningen Institute for Evolutionary Life Sciences University of Groningen Nijenborgh 7 Groningen AG 9747 The Netherlands
| | - Sandrine Salmon
- Department of Living Adaptations UMR 7179 MECADEV, Muséum National d'Histoire Naturelle 1 Avenue du Petit Château, Brunoy Paris 91800 France
| | - Uffe N. Nielsen
- Hawkesbury Institute for the Environment Western Sydney University Locked Bag 1797 Penrith NSW 2751 Australia
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Majoros SE, Adamowicz SJ. Phylogenetic signal of sub-arctic beetle communities. Ecol Evol 2022; 12:e8520. [PMID: 35222946 PMCID: PMC8848465 DOI: 10.1002/ece3.8520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 11/30/2021] [Accepted: 12/14/2021] [Indexed: 11/07/2022] Open
Abstract
Postglacial dispersal and colonization processes have shaped community patterns in sub-Arctic regions such as Churchill, Manitoba, and Canada. This study investigates evolutionary community structure within the beetle (Coleoptera) families of Churchill and tests whether biological traits have played a role in governing colonization patterns from refugial and southerly geographic regions. This study quantifies sub-Arctic beetle phylogenetic community structure for each family using the net relatedness index (NRI) and nearest taxon index (NTI), calculated using publicly available data from the Barcode of Life Data Systems (BOLD); compares patterns across families with different traits (habitat, diet) using standard statistical analysis (ANOVA) as well as phylogenetic generalized least squares (PGLS) using a family-level beetle phylogeny obtained from the literature; and compares community structure in Churchill with a region in southern Canada (Guelph, Ontario). These analyses were also repeated at a genus level. The dominant pattern detected in our study was that aquatic families were much better represented in Churchill compared to terrestrial families, when compared against richness sampled from across Canada and Alaska. Individually, most families showed significant phylogenetic clustering in Churchill, likely due to the strong environmental filtering present in Arctic environments. There was no significant difference in phylogenetic structure between Churchill and Guelph but with a trend toward stronger clustering in the North. Fungivores were significantly more overdispersed than other feeding modes, predators were significantly more clustered, and aquatic families showed significantly stronger clustering compared to terrestrial. This study contributes to our understanding of the traits and processes structuring insect biodiversity and macroecological trends in the sub-Arctic.
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OUP accepted manuscript. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Khater EIM, Baig F, Kamal HA, Powell JR, Saleh AA. Molecular Phylogenetics and Population Genetics of the Dengue Vector Aedes aegypti From the Arabian Peninsula. JOURNAL OF MEDICAL ENTOMOLOGY 2021; 58:2161-2176. [PMID: 34313761 DOI: 10.1093/jme/tjab112] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Indexed: 06/13/2023]
Abstract
Aedes aegypti mosquito is the principal dengue vector in the Kingdom of Saudi Arabia (KSA); however, no study has addressed its ecology and population structure yet. Therefore, we report on Ae. aegypti phylo- and population genetics using three DNA markers: COI, ND4, and rDNA-ITS2. Sampling the immature stages of Ae. aegypti revealed that water storage tanks (34.3% of habitats) were the most productive and contained 33% of immatures stages. Other important habitats included containers for wastewater drainage (including air-conditioning and water cooler trays) and containers associated with ornamentation. Shallow water leakage spots (2.7% of habitats, 8% of immatures) can be considered rare-but-epidemiologically-important containers. Neighbor-joining (NJ) phylogenetic analysis of Ae. aegypti identified 8, 14, and 9 haplotypes of COI, ND4, and ITS2, respectively, and revealed high levels of genetic variation in Ae. aegypti populations of KSA. Global distribution of haplotypes also indicated multiple gene introductions into these populations, with high levels of intra-population genetic variation and continuous gene exchange. The neutrality values indicated a deficiency of alleles and suggested that the KSA Ae. aegypti loci tested did not follow a neutral model of molecular evolution. Fst values and AMOVA indicated that most of the genetic variation in the KSA Ae. aegypti populations is due to intra- rather than inter-population differences. This is the first comprehensive report on the phylo- and population genetics of Ae. aegypti from the Arabian Peninsula. This information expands our understanding of the ecology and population dynamics of this important arboviral vector for informed control efforts.
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Affiliation(s)
- Emad I M Khater
- Plant Protection Department, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
- Department of Entomology, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Farrukh Baig
- Plant Protection Department, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Hany A Kamal
- Department of Pest Control Projects, Dallah Establishment, Jeddah, Saudi Arabia
| | - Jeffery R Powell
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Amgad A Saleh
- Plant Protection Department, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
- Agricultural Genetic Engineering Research Institute, Agriculture Research Center, Giza, Egypt
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Abrego N. Wood-inhabiting fungal communities: Opportunities for integration of empirical and theoretical community ecology. FUNGAL ECOL 2021. [DOI: 10.1016/j.funeco.2021.101112] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Antich A, Palacin C, Wangensteen OS, Turon X. To denoise or to cluster, that is not the question: optimizing pipelines for COI metabarcoding and metaphylogeography. BMC Bioinformatics 2021; 22:177. [PMID: 33820526 PMCID: PMC8020537 DOI: 10.1186/s12859-021-04115-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 03/30/2021] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND The recent blooming of metabarcoding applications to biodiversity studies comes with some relevant methodological debates. One such issue concerns the treatment of reads by denoising or by clustering methods, which have been wrongly presented as alternatives. It has also been suggested that denoised sequence variants should replace clusters as the basic unit of metabarcoding analyses, missing the fact that sequence clusters are a proxy for species-level entities, the basic unit in biodiversity studies. We argue here that methods developed and tested for ribosomal markers have been uncritically applied to highly variable markers such as cytochrome oxidase I (COI) without conceptual or operational (e.g., parameter setting) adjustment. COI has a naturally high intraspecies variability that should be assessed and reported, as it is a source of highly valuable information. We contend that denoising and clustering are not alternatives. Rather, they are complementary and both should be used together in COI metabarcoding pipelines. RESULTS Using a COI dataset from benthic marine communities, we compared two denoising procedures (based on the UNOISE3 and the DADA2 algorithms), set suitable parameters for denoising and clustering, and applied these steps in different orders. Our results indicated that the UNOISE3 algorithm preserved a higher intra-cluster variability. We introduce the program DnoisE to implement the UNOISE3 algorithm taking into account the natural variability (measured as entropy) of each codon position in protein-coding genes. This correction increased the number of sequences retained by 88%. The order of the steps (denoising and clustering) had little influence on the final outcome. CONCLUSIONS We highlight the need for combining denoising and clustering, with adequate choice of stringency parameters, in COI metabarcoding. We present a program that uses the coding properties of this marker to improve the denoising step. We recommend researchers to report their results in terms of both denoised sequences (a proxy for haplotypes) and clusters formed (a proxy for species), and to avoid collapsing the sequences of the latter into a single representative. This will allow studies at the cluster (ideally equating species-level diversity) and at the intra-cluster level, and will ease additivity and comparability between studies.
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Affiliation(s)
- Adrià Antich
- Department of Marine Ecology, Centre for Advanced Studies of Blanes (CEAB-CSIC), Blanes (Girona), Catalonia, Spain
| | - Creu Palacin
- Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona and Research Institute of Biodiversity (IRBIO), Barcelona, Catalonia, Spain
| | - Owen S Wangensteen
- Norwegian College of Fishery Science, UiT The Arctic University of Norway, Tromsö, Norway.
| | - Xavier Turon
- Department of Marine Ecology, Centre for Advanced Studies of Blanes (CEAB-CSIC), Blanes (Girona), Catalonia, Spain.
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Guzik MT, Stevens MI, Cooper SJB, Humphreys WF, Austin AD. Extreme genetic diversity among springtails (Collembola) in subterranean calcretes of arid Australia. Genome 2020; 64:181-195. [PMID: 32552081 DOI: 10.1139/gen-2019-0199] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The subterranean islands hypothesis for calcretes of the Yilgarn region in Western Australia applies to many stygobitic (subterranean-aquatic) species that are "trapped" evolutionarily within isolated aquifers due to their aquatic lifestyles. In contrast, little is known about the distribution of terrestrial-subterranean invertebrates associated with the calcretes. We used subterranean Collembola from the Yilgarn calcretes to test the hypothesis that troglobitic species, those inhabiting the subterranean unsaturated (non-aquatic) zone of calcretes, are also restricted in their distribution and represent reciprocally monophyletic and endemic lineages. We used the barcoding fragment of the mtDNA cytochrome c oxidase subunit 1 (COI) gene from 183 individuals to reconstruct the phylogenetic history of the genus Pseudosinella Schäffer (Collembola, Lepidocyrtidae) from 10 calcretes in the Yilgarn. These calcretes represent less than 5% of the total possible calcretes in this region, yet we show that their diversity for subterranean Collembola comprises a minimum of 25 new species. Regionally, multiple levels of diversity exist in Pseudosinella, indicative of a complex evolutionary history for this genus in the Yilgarn. These species have probably been impacted by climatic oscillations, facilitating their dispersal across the landscape. The results represent a small proportion of the undiscovered diversity in Australia's arid zone.
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Affiliation(s)
- Michelle T Guzik
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, the University of Adelaide, SA 5005, Australia
| | - Mark I Stevens
- Biological and Earth Sciences, South Australian Museum, SA 5000, Australia.,University of South Australia, Clinical and Health Sciences, SA 5000, Australia
| | - Steven J B Cooper
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, the University of Adelaide, SA 5005, Australia.,South Australian Museum, North Terrace, Adelaide, SA 5000, Australia
| | - William F Humphreys
- Department of Terrestrial Zoology, Western Australian Museum, Locked Bag 49, Welshpool DC, Western Australia 6986, Australia, Affiliate.,School of Biological Sciences, University of Western Australia, Crawley, WA 6009, Australia
| | - Andrew D Austin
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, the University of Adelaide, SA 5005, Australia.,South Australian Museum, North Terrace, Adelaide, SA 5000, Australia
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Turon X, Antich A, Palacín C, Præbel K, Wangensteen OS. From metabarcoding to metaphylogeography: separating the wheat from the chaff. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2020; 30:e02036. [PMID: 31709684 PMCID: PMC7078904 DOI: 10.1002/eap.2036] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 07/31/2019] [Accepted: 10/03/2019] [Indexed: 05/31/2023]
Abstract
Metabarcoding is by now a well-established method for biodiversity assessment in terrestrial, freshwater, and marine environments. Metabarcoding data sets are usually used for α- and β-diversity estimates, that is, interspecies (or inter-MOTU [molecular operational taxonomic unit]) patterns. However, the use of hypervariable metabarcoding markers may provide an enormous amount of intraspecies (intra-MOTU) information-mostly untapped so far. The use of cytochrome oxidase (COI) amplicons is gaining momentum in metabarcoding studies targeting eukaryote richness. COI has been for a long time the marker of choice in population genetics and phylogeographic studies. Therefore, COI metabarcoding data sets may be used to study intraspecies patterns and phylogeographic features for hundreds of species simultaneously, opening a new field that we suggest to name metaphylogeography. The main challenge for the implementation of this approach is the separation of erroneous sequences from true intra-MOTU variation. Here, we develop a cleaning protocol based on changes in entropy of the different codon positions of the COI sequence, together with co-occurrence patterns of sequences. Using a data set of community DNA from several benthic littoral communities in the Mediterranean and Atlantic seas, we first tested by simulation on a subset of sequences a two-step cleaning approach consisting of a denoising step followed by a minimal abundance filtering. The procedure was then applied to the whole data set. We obtained a total of 563 MOTUs that were usable for phylogeographic inference. We used semiquantitative rank data instead of read abundances to perform AMOVAs and haplotype networks. Genetic variability was mainly concentrated within samples, but with an important between seas component as well. There were intergroup differences in the amount of variability between and within communities in each sea. For two species, the results could be compared with traditional Sanger sequence data available for the same zones, giving similar patterns. Our study shows that metabarcoding data can be used to infer intra- and interpopulation genetic variability of many species at a time, providing a new method with great potential for basic biogeography, connectivity and dispersal studies, and for the more applied fields of conservation genetics, invasion genetics, and design of protected areas.
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Affiliation(s)
- Xavier Turon
- Department of Marine EcologyCentre for Advanced Studies of Blanes (CEAB, CSIC)BlanesCataloniaSpain
| | - Adrià Antich
- Department of Marine EcologyCentre for Advanced Studies of Blanes (CEAB, CSIC)BlanesCataloniaSpain
| | - Creu Palacín
- Department of Evolutionary Biology, Ecology and Environmental Sciences, and Institute of Biodiversity Research (IRBio)University of BarcelonaBarcelonaCataloniaSpain
| | - Kim Præbel
- Norwegian College of Fishery ScienceUiT the Arctic University of NorwayTromsøNorway
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13
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Schäffer S, Kerschbaumer M, Koblmüller S. Multiple new species: Cryptic diversity in the widespread mite species Cymbaeremaeus cymba (Oribatida, Cymbaeremaeidae). Mol Phylogenet Evol 2019; 135:185-192. [PMID: 30898693 DOI: 10.1016/j.ympev.2019.03.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 03/15/2019] [Accepted: 03/16/2019] [Indexed: 10/27/2022]
Abstract
The absence of obvious morphological differences between species impedes species identification in many groups of organisms. Such cryptic species appear to be particularly common in small-bodied animals, impacting species richness estimates. In this study we aimed at characterizing the molecular diversity of the Palearctic arboreal oribatid mite species Cymbaeremaeus cymba across large parts of Europe. Phylogenetic analyses of three molecular markers, including the COI barcoding region, identified eight well supported, fairly divergent clades within C. cymba, which we consider to represent distinct species based on molecular species delimitation methods. Intraspecific variation of the COI gene was extremely low in all putative species, contradicting previous assumptions of high intraspecific diversity in oribatid mites. The frequent co-occurrence of two species on a single tree suggests an ecological micro-niche differentiation. Contrary to previous studies on oribatid mites, we find that COI is a good marker for species delimitation and its further use for barcoding of oribatids is highly recommended. Furthermore, we provide descriptions of six new Cymbaeremaeus species and designate a neotype of C. cymba.
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Affiliation(s)
- Sylvia Schäffer
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010 Graz, Austria.
| | | | - Stephan Koblmüller
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010 Graz, Austria.
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14
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New Insights Into Nematode DNA-metabarcoding as Revealed by the Characterization of Artificial and Spiked Nematode Communities. DIVERSITY-BASEL 2019. [DOI: 10.3390/d11040052] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Nematodes are ideal biological indicators to monitor soil biodiversity and ecosystem functioning. For this reason, they have been receiving increasing attention from a broad range of scientists. The main method to characterize soil nematode communities until at least genus level is still based on microscopic observations of nematode morphology. Such an approach is time-consuming, labor-intensive, and requires specialized personnel. The first studies on the potential use of DNA-metabarcoding to characterize nematode communities showed some shortcomings: under- or overestimation of species richness caused by failure to detect a number of nematode species or caused by intraspecific sequence variants increasing the number of OTUs (operational taxonomic units) or ‘molecular’ species, and flaws in quantification. We set up experiments to optimize this metabarcoding approach. Our results provided new insights such as the drastic effect of different DNA-extraction methods on nematode species richness due to variation in lysis efficacy. Our newly designed primer set (18S rRNA gene, V4-V5 region) showed in silico an improved taxonomic coverage compared with a published primer set (18S rRNA gene, V6-V8 region). However, results of DNA-metabarcoding with the new primer set showed less taxonomic coverage, and more non-nematode reads. Thus, the new primer set might be more suitable for whole soil faunal analysis. Species-specific correction factors calculated from a mock community with equal amounts of different nematode species were applied on another mock community with different amounts of the same nematode species and on a biological sample spiked with four selected nematode species. Results showed an improved molecular quantification. In conclusion, DNA-metabarcoding of soil nematode communities is useful for monitoring shifts in nematode composition but the technique still needs further optimization to enhance its precision.
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15
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Bocek M, Bocak L. The origins and dispersal history of the trichaline net-winged beetles in Southeast Asia, Wallacea, New Guinea and Australia. Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zly090] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Matej Bocek
- Laboratory of Molecular Systematics, Department of Zoology, Faculty of Science, Palacky University, 17. listopadu 50, 771 46 Olomouc, Czech Republic
| | - Ladislav Bocak
- Laboratory of Molecular Systematics, Department of Zoology, Faculty of Science, Palacky University, 17. listopadu 50, 771 46 Olomouc, Czech Republic
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16
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Sun X, Bedos A, Deharveng L. Unusually low genetic divergence at COI barcode locus between two species of intertidal Thalassaphorura (Collembola: Onychiuridae). PeerJ 2018; 6:e5021. [PMID: 29938135 PMCID: PMC6011825 DOI: 10.7717/peerj.5021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 05/29/2018] [Indexed: 01/30/2023] Open
Abstract
Species classification is challenging when taxa display limited morphological differences. In this paper, we combined morphology and DNA barcode data to investigate the complicated taxonomy of two Onychiurid Collembolan species. Thalassaphorura thalassophila and Thalassaphorura debilis are among the most common arthropod species in intertidal ecosystems and are often considered to be synonymous. Based on morphological and barcode analyses of fresh material collected in their type localities, we redescribed and compared the two species. However, their morphological distinctiveness was supported by a molecular divergence much smaller than previously reported at the interspecific level among Collembola. This divergence was even smaller than inter-population divergences recognized in the related edaphic species T. zschokkei, as well as those known between MOTUs within many Collembolan species. Our results may indicate a link between low genetic interspecific divergence and intertidal habitat, as the only biological peculiarity of the two species of interest compared to other Collembolan species analyzed to date is their strict intertidal life.
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Affiliation(s)
- Xin Sun
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China.,J.F. Blumenbach Institute of Zoology and Anthropology, University of Göttingen, Göttingen, Germany
| | - Anne Bedos
- Institut de Systématique, Evolution, Biodiversité, ISYEB-UMR 7205-CNRS, MNHN, UPMC, EPHE, Sorbonne Universités, Museum national d'Histoire naturelle, Paris, France
| | - Louis Deharveng
- Institut de Systématique, Evolution, Biodiversité, ISYEB-UMR 7205-CNRS, MNHN, UPMC, EPHE, Sorbonne Universités, Museum national d'Histoire naturelle, Paris, France
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17
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Reich M, Labes A. How to boost marine fungal research: A first step towards a multidisciplinary approach by combining molecular fungal ecology and natural products chemistry. Mar Genomics 2017; 36:57-75. [PMID: 29031541 DOI: 10.1016/j.margen.2017.09.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 09/22/2017] [Accepted: 09/23/2017] [Indexed: 12/30/2022]
Abstract
Marine fungi have attracted attention in recent years due to increased appreciation of their functional role in ecosystems and as important sources of new natural products. The concomitant development of various "omic" technologies has boosted fungal research in the fields of biodiversity, physiological ecology and natural product biosynthesis. Each of these research areas has its own research agenda, scientific language and quality standards, which have so far hindered an interdisciplinary exchange. Inter- and transdisciplinary interactions are, however, vital for: (i) a detailed understanding of the ecological role of marine fungi, (ii) unlocking their hidden potential for natural product discovery, and (iii) designing access routes for biotechnological production. In this review and opinion paper, we describe the two different "worlds" of marine fungal natural product chemists and marine fungal molecular ecologists. The individual scientific approaches and tools employed are summarised and explained, and enriched with a first common glossary. We propose a strategy to find a multidisciplinary approach towards a comprehensive view on marine fungi and their chemical potential.
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Affiliation(s)
- Marlis Reich
- University of Bremen, BreMarE, NW2 B3320, Leobener Str. 5, D-28359 Bremen, Germany.
| | - Antje Labes
- Flensburg University of Applied Sciences, Kanzleistr. 91-93, D-24943 Flensburg, Germany.
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18
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Cicconardi F, Borges PAV, Strasberg D, Oromí P, López H, Pérez-Delgado AJ, Casquet J, Caujapé-Castells J, Fernández-Palacios JM, Thébaud C, Emerson BC. MtDNA metagenomics reveals large-scale invasion of belowground arthropod communities by introduced species. Mol Ecol 2017; 26:3104-3115. [PMID: 28139037 DOI: 10.1111/mec.14037] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 12/12/2016] [Accepted: 12/24/2016] [Indexed: 11/26/2022]
Abstract
Using a series of standardized sampling plots within forest ecosystems in remote oceanic islands, we reveal fundamental differences between the structuring of aboveground and belowground arthropod biodiversity that are likely due to large-scale species introductions by humans. Species of beetle and spider were sampled almost exclusively from single islands, while soil-dwelling Collembola exhibited more than tenfold higher species sharing among islands. Comparison of Collembola mitochondrial metagenomic data to a database of more than 80 000 Collembola barcode sequences revealed almost 30% of sampled island species are genetically identical, or near identical, to individuals sampled from often very distant geographic regions of the world. Patterns of mtDNA relatedness among Collembola implicate human-mediated species introductions, with minimum estimates for the proportion of introduced species on the sampled islands ranging from 45% to 88%. Our results call for more attention to soil mesofauna to understand the global extent and ecological consequences of species introductions.
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Affiliation(s)
- Francesco Cicconardi
- Institute of Ecology, University of Innsbruck, Technikerstrasse 25, a-6020, Innsbruck, Austria
| | - Paulo A V Borges
- CE3C - Centre for Ecology, Evolution and Environmental Changes/Azorean Biodiversity Group and Departamento de Ciências Agrárias e Ambiente, Universidade dos Açores, Rua Capitão João d'Ávila s/n, 9700-042, Angra do Heroísmo, Açores, Portugal
| | - Dominique Strasberg
- UMR PVBMT, Peuplements Végétaux et Bio-agresseurs en Milieu Tropical, Université de La Réunion, 15 avenue René Cassin, CS 93002, 97 744, Saint Denis Cedex 9, Reunion Island, France
| | - Pedro Oromí
- Departamento de Biología Animal y Edafología y Geología, Universidad de La Laguna, C/Astrofísico Francisco Sánchez, 38206, La Laguna, Tenerife, Canary Islands, Spain
| | - Heriberto López
- Island Ecology and Evolution Research Group, IPNA-CSIC, 38206, La Laguna, Tenerife, Canary Islands, Spain
| | - Antonio J Pérez-Delgado
- Island Ecology and Evolution Research Group, IPNA-CSIC, 38206, La Laguna, Tenerife, Canary Islands, Spain
| | - Juliane Casquet
- Laboratoire Evolution & Diversité Biologique, UMR 5174 CNRS-Université Paul Sabatier-ENFA, 31062, Toulouse Cedex 9, France
| | - Juli Caujapé-Castells
- Departamento de Biodiversidad Molecular y Banco de ADN, Jardín Botánico Canario 'Viera y Clavijo' - Unidad Asociada CSIC, Cabildo de Gran Canaria, Camino del Palmeral 15 de Tafira Alta, 35017, Las Palmas de Gran Canaria, Spain
| | - José María Fernández-Palacios
- Island Ecology and Biogeography Research Group, Instituto de Enfermedades Tropicales y Salud Pública de Canarias (IUETSPC), Universidad de La Laguna, Tenerife, Canary Islands, 38206, Spain
| | - Christophe Thébaud
- Laboratoire Evolution & Diversité Biologique, UMR 5174 CNRS-Université Paul Sabatier-ENFA, 31062, Toulouse Cedex 9, France
| | - Brent C Emerson
- Island Ecology and Evolution Research Group, IPNA-CSIC, 38206, La Laguna, Tenerife, Canary Islands, Spain.,School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
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19
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Emerson BC, Casquet J, López H, Cardoso P, Borges PAV, Mollaret N, Oromí P, Strasberg D, Thébaud C. A combined field survey and molecular identification protocol for comparing forest arthropod biodiversity across spatial scales. Mol Ecol Resour 2016; 17:694-707. [PMID: 27768248 DOI: 10.1111/1755-0998.12617] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 09/02/2016] [Accepted: 09/16/2016] [Indexed: 11/28/2022]
Abstract
Obtaining fundamental biodiversity metrics such as alpha, beta and gamma diversity for arthropods is often complicated by a lack of prior taxonomic information and/or taxonomic expertise, which can result in unreliable morphologically based estimates. We provide a set of standardized ecological and molecular sampling protocols that can be employed by researchers whose taxonomic skills may be limited, and where there may be a lack of robust a priori information regarding the regional pool of species. These protocols combine mass sampling of arthropods, classification of samples into parataxonomic units (PUs) and selective sampling of individuals for mtDNA sequencing to infer biological species. We sampled ten lowland rainforest plots located on the volcanic oceanic island of Réunion (Mascarene archipelago) for spiders, a group with limited taxonomic and distributional data for this region. We classified adults and juveniles into PUs and then demonstrated the reconciliation of these units with presumed biological species using mtDNA sequence data, ecological data and distributional data. Because our species assignment protocol is not reliant upon prior taxonomic information, or taxonomic expertise, it minimizes the problem of the Linnean shortfall to yield diversity estimates that can be directly compared across independent studies. Field sampling can be extended to other arthropod groups and habitats by adapting our field sampling protocol accordingly.
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Affiliation(s)
- Brent C Emerson
- Island Ecology and Evolution Research Group, Instituto de Productos Naturales y Agrobiología, C/Astrofísico Francisco Sánchez 3, La Laguna, Tenerife, Canary Islands, 38206, Spain.,School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Juliane Casquet
- Laboratoire Evolution & Diversité Biologique, UMR 5174 CNRS-Université Paul Sabatier-ENFA, 31062, Toulouse Cedex 9, France
| | - Heriberto López
- Island Ecology and Evolution Research Group, Instituto de Productos Naturales y Agrobiología, C/Astrofísico Francisco Sánchez 3, La Laguna, Tenerife, Canary Islands, 38206, Spain
| | - Pedro Cardoso
- Finnish Museum of Natural History, University of Helsinki, P.O. Box 17, 00014, Helsinki, Finland.,Azorean Biodiversity Group, Departamento de Ciências e Engenharia do Ambiente, CE3C - Centre for Ecology, Evolution and Environmental Changes, Universidade dos Açores, Rua Capitão João d'Ávila s/n, 9700-042, Angra do Heroísmo, Açores, Portugal
| | - Paulo A V Borges
- Azorean Biodiversity Group, Departamento de Ciências e Engenharia do Ambiente, CE3C - Centre for Ecology, Evolution and Environmental Changes, Universidade dos Açores, Rua Capitão João d'Ávila s/n, 9700-042, Angra do Heroísmo, Açores, Portugal
| | - Noémy Mollaret
- Direction des collections, Invertébrés marins, Muséum National d'Histoire Naturelle, CP53, 61 rue Buffon, 75231, Paris Cedex 05, France
| | - Pedro Oromí
- Departamento de Biología Animal, Edafología y Geología, Universidad de La Laguna, C/Astrofísico Francisco Sánchez, 38206, La Laguna, Tenerife, Canary Islands, Spain
| | - Dominique Strasberg
- UMR PVBMT, Peuplements Végétaux et Bio-agresseurs en Milieu Tropical, Université de La Réunion, 15 Avenue René Cassin, CS 93002, 97 744, Saint Denis, Cedex 9, Reunion Island, France
| | - Christophe Thébaud
- Laboratoire Evolution & Diversité Biologique, UMR 5174 CNRS-Université Paul Sabatier-ENFA, 31062, Toulouse Cedex 9, France
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20
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von Saltzwedel H, Scheu S, Schaefer I. Founder events and pre-glacial divergences shape the genetic structure of European Collembola species. BMC Evol Biol 2016; 16:148. [PMID: 27423184 PMCID: PMC4947257 DOI: 10.1186/s12862-016-0719-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 07/04/2016] [Indexed: 11/19/2022] Open
Abstract
Background Climate oscillations in the Cenozoic reduced species richness and genetic diversity of terrestrial and aquatic animals and plants in central and northern Europe. The most abundant arthropods in temperate soils are Collembola that live in almost any soil-related habitat. Extant species show little morphological variation to Eocene fossils, suggesting persistence of species in stable habitats for millions of years. Collembola are able to evade adverse climatic conditions by moving into deeper soil layers and are tolerant to frost and draught. If these adaptations sufficed for surviving glacial periods remains open and needs to be investigated in a phylogeographic context, i.e. investigating spatial structure on molecular level. We investigated the molecular variation of three common species of Collembola at a pan-European scale to identify glacial refuges and post-glacial colonization patterns with three genetic markers. Results All genes revealed remarkable genetic structure between but not within populations, suggesting density dependent processes for establishment of populations (founder-takes-all principle), which is common for European animals and plants. In contrast to the post-glacial recolonization patterns of many aboveground organisms, divergence times of most geographic lineages indicate preservation of genetic structure since the Miocene. Conclusions Collembola survived severe climatic changes including those during Quatenary glaciation and kept high genetic variance across Europe. Likely the buffering of temperature oscilliations in soil and the ability to evade adverse climatic conditions due to cold-tolerance and horizontal migration enabled Collembola to evade strong selective pressure of abiotic forces. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0719-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Helge von Saltzwedel
- Johann Friedrich Blumenbach Institute of Zoology and Anthropology, Georg August University Göttingen, Berliner Strasse 28, 37073, Göttingen, Germany.
| | - Stefan Scheu
- Johann Friedrich Blumenbach Institute of Zoology and Anthropology, Georg August University Göttingen, Berliner Strasse 28, 37073, Göttingen, Germany
| | - Ina Schaefer
- Johann Friedrich Blumenbach Institute of Zoology and Anthropology, Georg August University Göttingen, Berliner Strasse 28, 37073, Göttingen, Germany
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21
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Giska I, Sechi P, Babik W. Deeply divergent sympatric mitochondrial lineages of the earthworm Lumbricus rubellus are not reproductively isolated. BMC Evol Biol 2015; 15:217. [PMID: 26438011 PMCID: PMC4595309 DOI: 10.1186/s12862-015-0488-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 09/14/2015] [Indexed: 11/10/2022] Open
Abstract
Background The accurate delimitation of species is essential to numerous areas of biological research. An unbiased assessment of the diversity, including the cryptic diversity, is of particular importance for the below ground fauna, a major component of global biodiversity. On the British Isles, the epigeic earthworm Lumbricus rubellus, which is a sentinel species in soil ecotoxicology, consists of two cryptic taxa that are differentiated in both the nuclear and the mitochondrial (mtDNA) genomes. Recently, several deeply divergent mtDNA lineages were detected in mainland Europe, but whether these earthworms also constitute cryptic species remains unclear. This information is important from an evolutionary perspective, but it is also essential for the interpretation and the design of ecotoxicological projects. In this study, we used genome-wide RADseq data to assess the reproductive isolation of the divergent mitochondrial lineages of L. rubellus that occur in sympatry in multiple localities in Central Europe. Results We identified five divergent (up to 16 % net p-distance) mitochondrial lineages of L. rubellus in sympatry. Because the clustering of the RADseq data was according to the population of origin and not the mtDNA lineage, reproductive isolation among the mtDNA lineages was not likely. Although each population contained multiple mtDNA lineages, subdivisions within the populations were not observed for the nuclear genome. The lack of fixed differences and sharing of the overwhelming majority of nuclear polymorphisms between localities, indicated that the populations did not constitute allopatric species. The nucleotide diversity within the populations was high, 0.7–0.8 %. Conclusions The deeply divergent mtDNA sympatric lineages of L. rubellus in Central Europe were not reproductively isolated groups. The earthworm L. rubellus, which is represented by several mtDNA lineages in continental Europe, apparently is a single highly polymorphic species rather than a complex of several cryptic species. This study demonstrated the critical importance of the use of multilocus nuclear data for the unbiased assessment of cryptic diversity and for the delimitation of species in soil invertebrates. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0488-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Iwona Giska
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland.
| | - Pierfrancesco Sechi
- Institute of Ecosystem Study, Sassari, National Research Council, Traversa La Crucca 3, Regione Baldinca, 07100, Sassari, Italy.
| | - Wiesław Babik
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland.
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22
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D'Amen M, Rahbek C, Zimmermann NE, Guisan A. Spatial predictions at the community level: from current approaches to future frameworks. Biol Rev Camb Philos Soc 2015; 92:169-187. [PMID: 26426308 DOI: 10.1111/brv.12222] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Revised: 09/02/2015] [Accepted: 09/09/2015] [Indexed: 12/22/2022]
Abstract
A fundamental goal of ecological research is to understand and model how processes generate patterns so that if conditions change, changes in the patterns can be predicted. Different approaches have been proposed for modelling species assemblage, but their use to predict spatial patterns of species richness and other community attributes over a range of spatial and temporal scales remains challenging. Different methods emphasize different processes of structuring communities and different goals. In this review, we focus on models that were developed for generating spatially explicit predictions of communities, with a particular focus on species richness, composition, relative abundance and related attributes. We first briefly describe the concepts and theories that span the different drivers of species assembly. A combination of abiotic processes and biotic mechanisms are thought to influence the community assembly process. In this review, we describe four categories of drivers: (i) historical and evolutionary, (ii) environmental, (iii) biotic, and (iv) stochastic. We discuss the different modelling approaches proposed or applied at the community level and examine them from different standpoints, i.e. the theoretical bases, the drivers included, the source data, and the expected outputs, with special emphasis on conservation needs under climate change. We also highlight the most promising novelties, possible shortcomings, and potential extensions of existing methods. Finally, we present new approaches to model and predict species assemblages by reviewing promising 'integrative frameworks' and views that seek to incorporate all drivers of community assembly into a unique modelling workflow. We discuss the strengths and weaknesses of these new solutions and how they may hasten progress in community-level modelling.
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Affiliation(s)
- Manuela D'Amen
- Department of Ecology and Evolution (DEE), University of Lausanne, Biophore, CH-1015, Lausanne, Switzerland
| | - Carsten Rahbek
- CMEC, Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100, Copenhagen, Denmark
| | - Niklaus E Zimmermann
- Dynamic Macroecology Group, WSL, Zuercherstrasse 111, CH-8903, Birmensdorf, Switzerland
| | - Antoine Guisan
- Department of Ecology and Evolution (DEE), University of Lausanne, Biophore, CH-1015, Lausanne, Switzerland.,Institute of Earth Surface Dynamics (IDYST), University of Lausanne, Geopolis, CH-1015, Lausanne, Switzerland
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23
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Liebeke M, Bruford MW, Donnelly RK, Ebbels TMD, Hao J, Kille P, Lahive E, Madison RM, Morgan AJ, Pinto-Juma GA, Spurgeon DJ, Svendsen C, Bundy JG. Identifying biochemical phenotypic differences between cryptic species. Biol Lett 2015; 10:rsbl.2014.0615. [PMID: 25252836 DOI: 10.1098/rsbl.2014.0615] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Molecular genetic methods can distinguish divergent evolutionary lineages in what previously appeared to be single species, but it is not always clear what functional differences exist between such cryptic species. We used a metabolomic approach to profile biochemical phenotype (metabotype) differences between two putative cryptic species of the earthworm Lumbricus rubellus. There were no straightforward metabolite biomarkers of lineage, i.e. no metabolites that were always at higher concentration in one lineage. Multivariate methods, however, identified a small number of metabolites that together helped distinguish the lineages, including uncommon metabolites such as Nε-trimethyllysine, which is not usually found at high concentrations. This approach could be useful for characterizing functional trait differences, especially as it is applicable to essentially any species group, irrespective of its genome sequencing status.
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Affiliation(s)
- Manuel Liebeke
- Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, UK
| | | | | | - Timothy M D Ebbels
- Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, UK
| | - Jie Hao
- Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, UK
| | - Peter Kille
- School of Biosciences, University of Cardiff, Cardiff, UK
| | - Elma Lahive
- NERC Centre for Ecology and Hydrology, Crowmarsh Gifford, Wallingford OX10 8BB, UK
| | - Rachael M Madison
- NERC Centre for Ecology and Hydrology, Crowmarsh Gifford, Wallingford OX10 8BB, UK
| | - A John Morgan
- School of Biosciences, University of Cardiff, Cardiff, UK
| | | | - David J Spurgeon
- NERC Centre for Ecology and Hydrology, Crowmarsh Gifford, Wallingford OX10 8BB, UK
| | - Claus Svendsen
- NERC Centre for Ecology and Hydrology, Crowmarsh Gifford, Wallingford OX10 8BB, UK
| | - Jacob G Bundy
- Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, UK
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24
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Andújar C, Arribas P, Ruzicka F, Crampton-Platt A, Timmermans MJ, Vogler AP. Phylogenetic community ecology of soil biodiversity using mitochondrial metagenomics. Mol Ecol 2015; 24:3603-17. [DOI: 10.1111/mec.13195] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Revised: 04/03/2015] [Accepted: 04/08/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Carmelo Andújar
- Department of Life Sciences; Natural History Museum; Cromwell Road London SW7 5BD UK
- Department of Life Sciences; Imperial College London; Silwood Park Campus Ascot SL5 7PY UK
| | - Paula Arribas
- Department of Life Sciences; Natural History Museum; Cromwell Road London SW7 5BD UK
- Department of Life Sciences; Imperial College London; Silwood Park Campus Ascot SL5 7PY UK
| | - Filip Ruzicka
- Department of Life Sciences; Natural History Museum; Cromwell Road London SW7 5BD UK
- Department of Genetics, Evolution and Environment; University College London; Gower Street London WC1E 6BT UK
| | - Alex Crampton-Platt
- Department of Life Sciences; Natural History Museum; Cromwell Road London SW7 5BD UK
- Department of Genetics, Evolution and Environment; University College London; Gower Street London WC1E 6BT UK
| | - Martijn J.T.N. Timmermans
- Department of Life Sciences; Natural History Museum; Cromwell Road London SW7 5BD UK
- Department of Life Sciences; Imperial College London; Silwood Park Campus Ascot SL5 7PY UK
| | - Alfried P. Vogler
- Department of Life Sciences; Natural History Museum; Cromwell Road London SW7 5BD UK
- Department of Life Sciences; Imperial College London; Silwood Park Campus Ascot SL5 7PY UK
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25
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Katz AD, Giordano R, Soto-Adames FN. Operational criteria for cryptic species delimitation when evidence is limited, as exemplified by North AmericanEntomobrya(Collembola: Entomobryidae). Zool J Linn Soc 2015. [DOI: 10.1111/zoj.12220] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Aron D. Katz
- Department of Entomology; University of Illinois; 320 Morrill Hall 505 South Goodwin Avenue Urbana IL 61801 USA
- Illinois Natural History Survey; University of Illinois; 1816 South Oak Street Champaign IL 61820 USA
| | - Rosanna Giordano
- Department of Entomology; University of Illinois; 320 Morrill Hall 505 South Goodwin Avenue Urbana IL 61801 USA
| | - Felipe N. Soto-Adames
- Illinois Natural History Survey; University of Illinois; 1816 South Oak Street Champaign IL 61820 USA
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26
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Paprocki H, França D. Brazilian Trichoptera Checklist II. Biodivers Data J 2014:e1557. [PMID: 25349524 PMCID: PMC4206778 DOI: 10.3897/bdj.2.e1557] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 10/02/2014] [Indexed: 11/17/2022] Open
Abstract
A second assessment of Brazilian Trichoptera species records is presented here. A total of 625 species were recorded for Brazil. This represents an increase of 65.34% new species recorded during the last decade. The Hydropsychidae (124 spp.), followed by the Hydroptilidae (102 spp.) and Polycentropodidae (97 spp.), are the families with the greatest richness recorded for Brazil. The knowledge on Trichoptera biodiversity in Brazil is geographically unequal. The majority of the species is recorded for the southeastern region.
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Affiliation(s)
- Henrique Paprocki
- Pontifícia Universidade Católica de Minas Gerais, Museu de Ciências Naturais, Coleção de Invertebrados. Av. Dom José Gaspar, 290, sala 104, Coração Eucarístico, CEP 30535-901, Belo Horizonte, Minas Gerais, Brazil, Belo Horizonte, Brazil
| | - Diogo França
- Pontifícia Universidade Católica de Minas Gerais, Museu de Ciências Naturais, Coleção de Invertebrados. Av. Dom José Gaspar, 290, sala 104, Coração Eucarístico, CEP 30535-901, Belo Horizonte, Minas Gerais, Brazil, Belo Horizonte, Brazil
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27
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Stockinger H, Peyret-Guzzon M, Koegel S, Bouffaud ML, Redecker D. The largest subunit of RNA polymerase II as a new marker gene to study assemblages of arbuscular mycorrhizal fungi in the field. PLoS One 2014; 9:e107783. [PMID: 25275381 PMCID: PMC4183475 DOI: 10.1371/journal.pone.0107783] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2014] [Accepted: 08/14/2014] [Indexed: 11/30/2022] Open
Abstract
Due to the potential of arbuscular mycorrhizal fungi (AMF, Glomeromycota) to improve plant growth and soil quality, the influence of agricultural practice on their diversity continues to be an important research question. Up to now studies of community diversity in AMF have exclusively been based on nuclear ribosomal gene regions, which in AMF show high intra-organism polymorphism, seriously complicating interpretation of these data. We designed specific PCR primers for 454 sequencing of a region of the largest subunit of RNA polymerase II gene, and established a new reference dataset comprising all major AMF lineages. This gene is known to be monomorphic within fungal isolates but shows an excellent barcode gap between species. We designed a primer set to amplify all known lineages of AMF and demonstrated its applicability in combination with high-throughput sequencing in a long-term tillage experiment. The PCR primers showed a specificity of 99.94% for glomeromycotan sequences. We found evidence of significant shifts of the AMF communities caused by soil management and showed that tillage effects on different AMF taxa are clearly more complex than previously thought. The high resolving power of high-throughput sequencing highlights the need for quantitative measurements to efficiently detect these effects.
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Affiliation(s)
- Herbert Stockinger
- Université de Bourgogne, UMR1347 Agroécologie, Dijon, France
- INRA, UMR1347 Agroécologie, Dijon, France
| | | | | | | | - Dirk Redecker
- Université de Bourgogne, UMR1347 Agroécologie, Dijon, France
- * E-mail:
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28
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Meyer-Wachsmuth I, Curini Galletti M, Jondelius U. Hyper-cryptic marine meiofauna: species complexes in Nemertodermatida. PLoS One 2014; 9:e107688. [PMID: 25225981 PMCID: PMC4166464 DOI: 10.1371/journal.pone.0107688] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2014] [Accepted: 08/08/2014] [Indexed: 01/30/2023] Open
Abstract
Nemertodermatida are microscopically small, benthic marine worms. Specimens of two nominal species, Sterreria psammicola and Nemertinoides elongatus from 33 locations worldwide were sequenced for three molecular markers. Species delimitation and validation was done using gene trees, haplotype networks and multilocus Bayesian analysis. We found 20 supported species of which nine: Nemertinoides glandulosum n.sp., N. wolfgangi n.sp., Sterreria boucheti n.sp., S. lundini n.sp., S. martindalei n.sp., S. monolithes n.sp., S. papuensis n.sp., S. variabilis n.sp. and S. ylvae n.sp., are described including nucleotide-based diagnoses. The distribution patterns indicate transoceanic dispersal in some of the species. Sympatric species were found in many cases. The high level of cryptic diversity in this meiofauna group implies that marine diversity may be higher than previously estimated.
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Affiliation(s)
- Inga Meyer-Wachsmuth
- Department of Zoology, Swedish Museum of Natural History, Stockholm, Sweden
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Marco Curini Galletti
- Dipartimento di Scienze della Natura e del Territorio, Università di Sassari, Sassari, Italy
| | - Ulf Jondelius
- Department of Zoology, Swedish Museum of Natural History, Stockholm, Sweden
- Department of Zoology, Stockholm University, Stockholm, Sweden
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29
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Chan YL, Schanzenbach D, Hickerson MJ. Detecting concerted demographic response across community assemblages using hierarchical approximate Bayesian computation. Mol Biol Evol 2014; 31:2501-15. [PMID: 24925925 PMCID: PMC4137712 DOI: 10.1093/molbev/msu187] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Methods that integrate population-level sampling from multiple taxa into a single community-level analysis are an essential addition to the comparative phylogeographic toolkit. Detecting how species within communities have demographically tracked each other in space and time is important for understanding the effects of future climate and landscape changes and the resulting acceleration of extinctions, biological invasions, and potential surges in adaptive evolution. Here, we present a statistical framework for such an analysis based on hierarchical approximate Bayesian computation (hABC) with the goal of detecting concerted demographic histories across an ecological assemblage. Our method combines population genetic data sets from multiple taxa into a single analysis to estimate: 1) the proportion of a community sample that demographically expanded in a temporally clustered pulse and 2) when the pulse occurred. To validate the accuracy and utility of this new approach, we use simulation cross-validation experiments and subsequently analyze an empirical data set of 32 avian populations from Australia that are hypothesized to have expanded from smaller refugia populations in the late Pleistocene. The method can accommodate data set heterogeneity such as variability in effective population size, mutation rates, and sample sizes across species and exploits the statistical strength from the simultaneous analysis of multiple species. This hABC framework used in a multitaxa demographic context can increase our understanding of the impact of historical climate change by determining what proportion of the community responded in concert or independently and can be used with a wide variety of comparative phylogeographic data sets as biota-wide DNA barcoding data sets accumulate.
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Affiliation(s)
- Yvonne L Chan
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Manoa
| | | | - Michael J Hickerson
- Biology Department, City College of New YorkThe Graduate Center, City University of New York
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30
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Adams M, Raadik TA, Burridge CP, Georges A. Global Biodiversity Assessment and Hyper-Cryptic Species Complexes: More Than One Species of Elephant in the Room? Syst Biol 2014; 63:518-33. [DOI: 10.1093/sysbio/syu017] [Citation(s) in RCA: 113] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Mark Adams
- Evolutionary Biology Unit, South Australian Museum, North Terrace, SA 5000, Australia
- School of Earth and Environmental Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Tarmo A. Raadik
- Aquatic Ecology Section, Arthur Rylah Institute for Environmental Research, Department of Environment and Primary Industries, 123 Brown Street, Heidelberg, VIC 3084, Australia
- Institute for Applied Ecology and Collaborative Research Network for Murray-Darling Futures, University of Canberra, ACT 2601, Australia and
| | - Christopher P. Burridge
- School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS 7001, Australia
| | - Arthur Georges
- Institute for Applied Ecology and Collaborative Research Network for Murray-Darling Futures, University of Canberra, ACT 2601, Australia and
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31
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Cicconardi F, Fanciulli PP, Emerson BC. Collembola, the biological species concept and the underestimation of global species richness. Mol Ecol 2013; 22:5382-96. [DOI: 10.1111/mec.12472] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Revised: 07/10/2013] [Accepted: 07/17/2013] [Indexed: 11/29/2022]
Affiliation(s)
- Francesco Cicconardi
- Department of Physics; University of Rome “La Sapienza”; P.le A. Moro 5 Rome 00185 Italy
- Smithsonian Tropical Research Institute; Apartado 0843-03092 Panamá, República de Panamá
| | - Pietro P. Fanciulli
- Department of Life Sciences; University of Siena; Via Aldo Moro 2 Siena 53100 Italy
| | - Brent C. Emerson
- Island Ecology and Evolution Research Group; IPNA-CSIC; La Laguna Tenerife 38206 Canary Islands Spain
- School of Biological Sciences; University of East Anglia; Norwich Research Park Norwich NR4 7TJ UK
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32
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Bourguignon T, Šobotník J, Hanus R, Krasulová J, Vrkoslav V, Cvačka J, Roisin Y. Delineating species boundaries using an iterative taxonomic approach: the case of soldierless termites (Isoptera, Termitidae, Apicotermitinae). Mol Phylogenet Evol 2013; 69:694-703. [PMID: 23891950 DOI: 10.1016/j.ympev.2013.07.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 07/01/2013] [Accepted: 07/09/2013] [Indexed: 10/26/2022]
Abstract
Species boundaries are traditionally inferred using morphological characters, although morphology sometimes fails to correctly delineate species. To overcome this limitation, researchers have widely taken advantage of alternative methods such as DNA barcoding or analysis of cuticular hydrocarbons (CHs) profiles, but rarely use them simultaneously in an iterative taxonomic approach. Here, we follow such an approach using morphology, DNA barcoding and CHs profiles to precisely discriminate species of soldierless termites, a diversified clade constituting about one-third of the Neotropical termite species richness, but poorly resolved taxonomically due to the paucity of useful characters. We sampled soldierless termites in various forest types of the Nouragues Nature Reserve, French Guiana. Our results show that morphological species determination generally matches DNA barcoding, which only suggests the existence of three cryptic species in the 31 morphological species. Among them, Longustitermes manni is the only species whose splitting is corroborated by ecological data, other widely distributed species being supported by DNA barcoding. On the contrary, although CHs profiles provide a certain taxonomic signal, they often suggest inconsistent groupings which are not supported by other methods. Overall, our data support DNA barcoding and morphology as two efficient methods to distinguish soldierless termite species.
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Affiliation(s)
- Thomas Bourguignon
- Evolutionary Biology and Ecology, CP 160/12, Université Libre de Bruxelles, Avenue F.D. Roosevelt 50, 1050 Brussels, Belgium; Department of Biological Sciences, National University of Singapore, 117543 Singapore, Singapore
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33
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Krasnov BR, Pilosof S, Stanko M, Morand S, Korallo-Vinarskaya NP, Vinarski MV, Poulin R. Co-occurrence and phylogenetic distance in communities of mammalian ectoparasites: limiting similarity versus environmental filtering. OIKOS 2013. [DOI: 10.1111/j.1600-0706.2013.00646.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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34
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Avoiding inaccuracies in tree calibration and phylogenetic community analysis using Phylocom 4.2. ECOL INFORM 2013. [DOI: 10.1016/j.ecoinf.2013.03.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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35
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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] [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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36
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Dawson MN, Algar AC, Antonelli A, Dávalos LM, Davis E, Early R, Guisan A, Jansson R, Lessard JP, Marske KA, McGuire JL, Stigall AL, Swenson NG, Zimmermann NE, Gavin DG. An horizon scan of biogeography. FRONTIERS OF BIOGEOGRAPHY 2013; 5:fb_18854. [PMID: 24707348 PMCID: PMC3972886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023] Open
Abstract
The opportunity to reflect broadly on the accomplishments, prospects, and reach of a field may present itself relatively infrequently. Each biennial meeting of the International Biogeography Society showcases ideas solicited and developed largely during the preceding year, by individuals or teams from across the breadth of the discipline. Here, we highlight challenges, developments, and opportunities in biogeography from that biennial synthesis. We note the realized and potential impact of rapid data accumulation in several fields, a renaissance for inter-disciplinary research, the importance of recognizing the evolution-ecology continuum across spatial and temporal scales and at different taxonomic, phylogenetic and functional levels, and re-exploration of classical assumptions and hypotheses using new tools. However, advances are taxonomically and geographically biased, and key theoretical frameworks await tools to handle, or strategies to simplify, the biological complexity seen in empirical systems. Current threats to biodiversity require unprecedented integration of knowledge and development of predictive capacity that may enable biogeography to unite its descriptive and hypothetico-deductive branches and establish a greater role within and outside academia.
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Affiliation(s)
- Michael N Dawson
- School of Natural Sciences, 5200 North Lake Road, University of California, Merced, CA 95343, USA
| | - Adam C. Algar
- School of Geography, University of Nottingham, Nottingham NG7 2RD UK
| | - Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - Liliana M. Dávalos
- Ecology and Evolution, and Consortium for Inter Disciplinary Environmental Research, Stony Brook University, NY, USA
| | - Edward Davis
- Department of Geological Sciences, Museum of Natural and Cultural History, University of Oregon, Eugene, OR 97403, USA
| | - Regan Early
- Cátedra Rui Nabeiro - Biodiversidade, Universidade de Évora, 7000-890 Évora, Portugal and Museo Nacional de Ciencias Naturales (CSIC), Calle José Gutiérrez Abascal, 2 28006, Madrid, Spain
| | - Antoine Guisan
- Department of Ecology and Evolution, and Institute of Earth Sciences, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Roland Jansson
- Department of Ecology and Environmental Science, Umeå University, SE-901 87 Umeå, Sweden
| | - Jean-Philippe Lessard
- Quebec Centre for Biodiversity Science, Department of Biology, McGill University, Canada
| | - Katharine A. Marske
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Jenny L. McGuire
- School of Environmental and Forest Sciences, University of Washington, Seattle, WA 98195, USA
| | - Alycia L. Stigall
- Department of Geological Sciences and OHIO Center for Ecology and Evolutionary Studies, Ohio University, USA
| | - Nathan G. Swenson
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Niklaus E. Zimmermann
- Landscape Dynamics Unit, Swiss Federal Research Institute WSL, CH-8903 Birmensdorf, Switzerland
| | - Daniel G. Gavin
- Department of Geography, University of Oregon, Eugene, OR 97403, USA
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37
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Yu DW, Ji Y, Emerson BC, Wang X, Ye C, Yang C, Ding Z. Biodiversity soup: metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring. Methods Ecol Evol 2012. [DOI: 10.1111/j.2041-210x.2012.00198.x] [Citation(s) in RCA: 440] [Impact Index Per Article: 36.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Douglas W. Yu
- Ecology, Conservation, and Environment Center (ECEC), 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
| | - Yinqiu Ji
- Ecology, Conservation, and Environment Center (ECEC), State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang East Rd., Kunming, Yunnan 650223, China
| | - Brent C. Emerson
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR47TJ, UK
| | - Xiaoyang Wang
- Ecology, Conservation, and Environment Center (ECEC), State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang East Rd., Kunming, Yunnan 650223, China
| | - Chengxi Ye
- Ecology, Conservation, and Environment Center (ECEC), State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang East Rd., Kunming, Yunnan 650223, China
| | - Chunyan Yang
- Ecology, Conservation, and Environment Center (ECEC), State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang East Rd., Kunming, Yunnan 650223, China
| | - Zhaoli Ding
- Kunming Biodiversity Large‐Apparatus Regional Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
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38
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Stone G, Lohse K, Nicholls J, Fuentes-Utrilla P, Sinclair F, Schönrogge K, Csóka G, Melika G, Nieves-Aldrey JL, Pujade-Villar J, Tavakoli M, Askew R, Hickerson M. Reconstructing Community Assembly in Time and Space Reveals Enemy Escape in a Western Palearctic Insect Community. Curr Biol 2012; 22:532-7. [PMID: 22405865 DOI: 10.1016/j.cub.2012.01.059] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Revised: 01/09/2012] [Accepted: 01/27/2012] [Indexed: 11/25/2022]
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39
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Marske KA, Leschen RAB, Buckley TR. CONCERTED VERSUS INDEPENDENT EVOLUTION AND THE SEARCH FOR MULTIPLE REFUGIA: COMPARATIVE PHYLOGEOGRAPHY OF FOUR FOREST BEETLES. Evolution 2012; 66:1862-77. [DOI: 10.1111/j.1558-5646.2011.01538.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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40
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Sequencing our way towards understanding global eukaryotic biodiversity. Trends Ecol Evol 2012; 27:233-43. [PMID: 22244672 DOI: 10.1016/j.tree.2011.11.010] [Citation(s) in RCA: 236] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2011] [Revised: 11/23/2011] [Accepted: 11/24/2011] [Indexed: 02/01/2023]
Abstract
Microscopic eukaryotes are abundant, diverse and fill critical ecological roles across every ecosystem on Earth, yet there is a well-recognized gap in understanding of their global biodiversity. Fundamental advances in DNA sequencing and bioinformatics now allow accurate en masse biodiversity assessments of microscopic eukaryotes from environmental samples. Despite a promising outlook, the field of eukaryotic marker gene surveys faces significant challenges: how to generate data that are most useful to the community, especially in the face of evolving sequencing technologies and bioinformatics pipelines, and how to incorporate an expanding number of target genes.
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41
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Jenkins DG, Ricklefs RE. Biogeography and ecology: two views of one world. Philos Trans R Soc Lond B Biol Sci 2011; 366:2331-5. [PMID: 21768149 DOI: 10.1098/rstb.2011.0064] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Both biogeography and ecology seek to understand the processes that determine patterns in nature, but do so at different spatial and temporal scales. The two disciplines were not always so different, and are recently converging again at regional spatial scales and broad temporal scales. In order to avoid confusion and to hasten progress at the converging margins of each discipline, the following papers were presented at a symposium in the International Biogeography Society's 2011 meeting, and are now published in this issue of the Philosophical Transactions of the Royal Society B. In a novel approach, groups of authors were paired to represent biogeographic and ecological perspectives on each of four topics: niche, comparative ecology and macroecology, community assembly, and diversity. Collectively, this compilation identifies points of agreement and disagreement between the two views on these central topics, and points to future research directions that may build on agreements and reconcile differences. We conclude this compilation with an overview on the integration of biogeography and ecology.
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Affiliation(s)
- David G Jenkins
- Department of Biology, University of Central Florida, Orlando, FL 32816-2368, USA.
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42
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Ricklefs RE, Jenkins DG. Biogeography and ecology: towards the integration of two disciplines. Philos Trans R Soc Lond B Biol Sci 2011; 366:2438-48. [PMID: 21768158 DOI: 10.1098/rstb.2011.0066] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Although ecology and biogeography had common origins in the natural history of the nineteenth century, they diverged substantially during the early twentieth century as ecology became increasingly hypothesis-driven and experimental. This mechanistic focus narrowed ecology's purview to local scales of time and space, and mostly excluded large-scale phenomena and historical explanations. In parallel, biogeography became more analytical with the acceptance of plate tectonics and the development of phylogenetic systematics, and began to pay more attention to ecological factors that influence large-scale distributions. This trend towards unification exposed problems with terms such as 'community' and 'niche,' in part because ecologists began to view ecological communities as open systems within the contexts of history and geography. The papers in this issue represent biogeographic and ecological perspectives and address the general themes of (i) the niche, (ii) comparative ecology and macroecology, (iii) community assembly, and (iv) diversity. The integration of ecology and biogeography clearly is a natural undertaking that is based on evolutionary biology, has developed its own momentum, and which promises novel, synthetic approaches to investigating ecological systems and their variation over the surface of the Earth. We offer suggestions on future research directions at the intersection of biogeography and ecology.
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Affiliation(s)
- Robert E Ricklefs
- Department of Biology, University of Missouri-Saint Louis, One University Boulevard, Saint Louis, MO 63121-4499, USA.
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43
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Weiher E, Freund D, Bunton T, Stefanski A, Lee T, Bentivenga S. Advances, challenges and a developing synthesis of ecological community assembly theory. Philos Trans R Soc Lond B Biol Sci 2011; 366:2403-13. [PMID: 21768155 DOI: 10.1098/rstb.2011.0056] [Citation(s) in RCA: 250] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Ecological approaches to community assembly have emphasized the interplay between neutral processes, niche-based environmental filtering and niche-based species sorting in an interactive milieu. Recently, progress has been made in terms of aligning our vocabulary with conceptual advances, assessing how trait-based community functional parameters differ from neutral expectation and assessing how traits vary along environmental gradients. Experiments have confirmed the influence of these processes on assembly and have addressed the role of dispersal in shaping local assemblages. Community phylogenetics has forged common ground between ecologists and biogeographers, but it is not a proxy for trait-based approaches. Community assembly theory is in need of a comparative synthesis that addresses how the relative importance of niche and neutral processes varies among taxa, along environmental gradients, and across scales. Towards that goal, we suggest a set of traits that probably confer increasing community neutrality and regionality and review the influences of stress, disturbance and scale on the importance of niche assembly. We advocate increasing the complexity of experiments in order to assess the relative importance of multiple processes. As an example, we provide evidence that dispersal, niche processes and trait interdependencies have about equal influence on trait-based assembly in an experimental grassland.
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Affiliation(s)
- Evan Weiher
- Department of Biology, University of Wisconsin-Eau Claire, PO Box 4004, Eau Claire, WI, USA.
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