201
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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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202
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Pohjoismäki JLO, Kahanpää J, Mutanen M. DNA Barcodes for the Northern European Tachinid Flies (Diptera: Tachinidae). PLoS One 2016; 11:e0164933. [PMID: 27814365 PMCID: PMC5096672 DOI: 10.1371/journal.pone.0164933] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 10/04/2016] [Indexed: 11/18/2022] Open
Abstract
This data release provides COI barcodes for 366 species of parasitic flies (Diptera: Tachinidae), enabling the DNA based identification of the majority of northern European species and a large proportion of Palearctic genera, regardless of the developmental stage. The data will provide a tool for taxonomists and ecologists studying this ecologically important but challenging parasitoid family. A comparison of minimum distances between the nearest neighbors revealed the mean divergence of 5.52% that is approximately the same as observed earlier with comparable sampling in Lepidoptera, but clearly less than in Coleoptera. Full barcode-sharing was observed between 13 species pairs or triplets, equaling to 7.36% of all species. Delimitation based on Barcode Index Number (BIN) system was compared with traditional classification of species and interesting cases of possible species oversplits and cryptic diversity are discussed. Overall, DNA barcodes are effective in separating tachinid species and provide novel insight into the taxonomy of several genera.
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Affiliation(s)
- Jaakko L. O. Pohjoismäki
- University of Eastern Finland, Department of Environmental and Biological Sciences, P.O.Box 111, 80101, Joensuu, Finland
| | - Jere Kahanpää
- University of Helsinki, Finnish Museum of Natural History, Helsinki, Finland
| | - Marko Mutanen
- Department of Genetics and Physiology, PO. Box 3000, 90014 University of Oulu, Oulu, Finland
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203
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Littlefair JE, Clare EL. Barcoding the food chain: from Sanger to high-throughput sequencing. Genome 2016; 59:946-958. [DOI: 10.1139/gen-2016-0028] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Society faces the complex challenge of supporting biodiversity and ecosystem functioning, while ensuring food security by providing safe traceable food through an ever-more-complex global food chain. The increase in human mobility brings the added threat of pests, parasites, and invaders that further complicate our agro-industrial efforts. DNA barcoding technologies allow researchers to identify both individual species, and, when combined with universal primers and high-throughput sequencing techniques, the diversity within mixed samples (metabarcoding). These tools are already being employed to detect market substitutions, trace pests through the forensic evaluation of trace “environmental DNA”, and to track parasitic infections in livestock. The potential of DNA barcoding to contribute to increased security of the food chain is clear, but challenges remain in regulation and the need for validation of experimental analysis. Here, we present an overview of the current uses and challenges of applied DNA barcoding in agriculture, from agro-ecosystems within farmland to the kitchen table.
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Affiliation(s)
- Joanne E. Littlefair
- School of Biological and Chemical Sciences, Queen Mary University of London. Mile End Rd., London, E1 4NS, UK
- School of Biological and Chemical Sciences, Queen Mary University of London. Mile End Rd., London, E1 4NS, UK
| | - Elizabeth L. Clare
- School of Biological and Chemical Sciences, Queen Mary University of London. Mile End Rd., London, E1 4NS, UK
- School of Biological and Chemical Sciences, Queen Mary University of London. Mile End Rd., London, E1 4NS, UK
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204
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Hodgetts J, Ostojá-Starzewski JC, Prior T, Lawson R, Hall J, Boonham N. DNA barcoding for biosecurity: case studies from the UK plant protection program. Genome 2016; 59:1033-1048. [PMID: 27792411 DOI: 10.1139/gen-2016-0010] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Since its conception, DNA barcoding has seen a rapid uptake within the research community. Nevertheless, as with many new scientific tools, progression towards the point of routine deployment within diagnostic laboratories has been slow. In this paper, we discuss the application of DNA barcoding in the Defra plant health diagnostic laboratories, where DNA barcoding is used primarily for the identification of invertebrate pests. We present a series of case studies that demonstrate the successful application of DNA barcoding but also reveal some potential limitations to expanded use. The regulated plant pest, Bursephalenchus xylophilus, and one of its vectors, Monochamus alternatus, were found in dining chairs. Some traded wood products are potentially high risk, allowing the movement of longhorn beetles; Trichoferus campestris, Leptura quadrifasciata, and Trichoferus holosericeus were found in a wooden cutlery tray, a railway sleeper, and a dining chair, respectively. An outbreak of Meloidogyne fallax was identified in Allium ampeloprasum and in three weed species. Reference sequences for UK native psyllids were generated to enable the development of rapid diagnostics to be used for monitoring following the release of Aphalara itadori as a biological control agent for Fallopia japonica.
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Affiliation(s)
- Jennifer Hodgetts
- Fera, The National Agri-Food Innovation Campus, Sand Hutton, York, YO41 1LZ, United Kingdom.,Fera, The National Agri-Food Innovation Campus, Sand Hutton, York, YO41 1LZ, United Kingdom
| | - Jozef C Ostojá-Starzewski
- Fera, The National Agri-Food Innovation Campus, Sand Hutton, York, YO41 1LZ, United Kingdom.,Fera, The National Agri-Food Innovation Campus, Sand Hutton, York, YO41 1LZ, United Kingdom
| | - Thomas Prior
- Fera, The National Agri-Food Innovation Campus, Sand Hutton, York, YO41 1LZ, United Kingdom.,Fera, The National Agri-Food Innovation Campus, Sand Hutton, York, YO41 1LZ, United Kingdom
| | - Rebecca Lawson
- Fera, The National Agri-Food Innovation Campus, Sand Hutton, York, YO41 1LZ, United Kingdom.,Fera, The National Agri-Food Innovation Campus, Sand Hutton, York, YO41 1LZ, United Kingdom
| | - Jayne Hall
- Fera, The National Agri-Food Innovation Campus, Sand Hutton, York, YO41 1LZ, United Kingdom.,Fera, The National Agri-Food Innovation Campus, Sand Hutton, York, YO41 1LZ, United Kingdom
| | - Neil Boonham
- Fera, The National Agri-Food Innovation Campus, Sand Hutton, York, YO41 1LZ, United Kingdom.,Fera, The National Agri-Food Innovation Campus, Sand Hutton, York, YO41 1LZ, United Kingdom
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205
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Wilson JJ, Sing KW, Lee PS, Wee AKS. Application of DNA barcodes in wildlife conservation in Tropical East Asia. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2016; 30:982-9. [PMID: 27341687 DOI: 10.1111/cobi.12787] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 02/12/2016] [Indexed: 05/24/2023]
Abstract
Over the past 50 years, Tropical East Asia has lost more biodiversity than any tropical region. Tropical East Asia is a megadiverse region with an acute taxonomic impediment. DNA barcodes are short standardized DNA sequences used for taxonomic purposes and have the potential to lessen the challenges of biodiversity inventory and assessments in regions where they are most needed. We reviewed DNA barcoding efforts in Tropical East Asia relative to other tropical regions. We suggest DNA barcodes (or metabarcodes from next-generation sequencers) may be especially useful for characterizing and connecting species-level biodiversity units in inventories encompassing taxa lacking formal description (particularly arthropods) and in large-scale, minimal-impact approaches to vertebrate monitoring and population assessments through secondary sources of DNA (invertebrate derived DNA and environmental DNA). We suggest interest and capacity for DNA barcoding are slowly growing in Tropical East Asia, particularly among the younger generation of researchers who can connect with the barcoding analogy and understand the need for new approaches to the conservation challenges being faced.
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Affiliation(s)
- John-James Wilson
- Ecology and Biodiversity Program, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia.
- Museum of Zoology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Kong-Wah Sing
- Ecology and Biodiversity Program, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
- Museum of Zoology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Ping-Shin Lee
- Ecology and Biodiversity Program, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
- Museum of Zoology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Alison K S Wee
- Centre for Integrative Conservation, Xisshangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun Township, Mengla County, Yunnan Province, 666303, China
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206
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Krehenwinkel H, Kennedy S, Pekár S, Gillespie RG. A cost‐efficient and simple protocol to enrich prey
DNA
from extractions of predatory arthropods for large‐scale gut content analysis by Illumina sequencing. Methods Ecol Evol 2016. [DOI: 10.1111/2041-210x.12647] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Henrik Krehenwinkel
- Department of Environmental Science, Policy and Management University of California Berkeley 130 Mulford Hall #3114 Berkeley CA 94720 USA
| | - Susan Kennedy
- Department of Environmental Science, Policy and Management University of California Berkeley 130 Mulford Hall #3114 Berkeley CA 94720 USA
| | - Stano Pekár
- Department of Botany and Zoology Faculty of Science Masaryk University Kotlářská 2 Brno 61137 Czech Republic
| | - Rosemary G. Gillespie
- Department of Environmental Science, Policy and Management University of California Berkeley 130 Mulford Hall #3114 Berkeley CA 94720 USA
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207
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Haarsma A, Siepel H, Gravendeel B. Added value of metabarcoding combined with microscopy for evolutionary studies of mammals. ZOOL SCR 2016. [DOI: 10.1111/zsc.12214] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Anne‐Jifke Haarsma
- Radboud University Animal Ecology and Physiology department Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
- Naturalis Biodiversity Center Endless Forms group Darwinweg 2 2333 CR Leiden The Netherlands
| | - Henk Siepel
- Radboud University Animal Ecology and Physiology department Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
- Wageningen University Plant Ecology and Nature Conservation group Droevendaalsesteeg 3 6708 AA Wageningen The Netherlands
| | - Barbara Gravendeel
- Naturalis Biodiversity Center Endless Forms group Darwinweg 2 2333 CR Leiden The Netherlands
- University of Applied Sciences Leiden Life Sciences cluster Zernikedreef 11 2333 CK Leiden The Netherlands
- Leiden University Institute Biology Leiden Sylviusweg 72 2333 BE Leiden The Netherlands
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208
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Walker FM, Williamson CHD, Sanchez DE, Sobek CJ, Chambers CL. Species From Feces: Order-Wide Identification of Chiroptera From Guano and Other Non-Invasive Genetic Samples. PLoS One 2016; 11:e0162342. [PMID: 27654850 PMCID: PMC5031397 DOI: 10.1371/journal.pone.0162342] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 08/22/2016] [Indexed: 11/25/2022] Open
Abstract
Bat guano is a relatively untapped reservoir of information, having great utility as a DNA source because it is often available at roosts even when bats are not and is an easy type of sample to collect from a difficult-to-study mammalian order. Recent advances from microbial community studies in primer design, sequencing, and analysis enable fast, accurate, and cost-effective species identification. Here, we borrow from this discipline to develop an order-wide DNA mini-barcode assay (Species from Feces) based on a segment of the mitochondrial gene cytochrome c oxidase I (COI). The assay works effectively with fecal DNA and is conveniently transferable to low-cost, high-throughput Illumina MiSeq technology that also allows simultaneous pairing with other markers. Our PCR primers target a region of COI that is highly discriminatory among Chiroptera (92% species-level identification of barcoded species), and are sufficiently degenerate to allow hybridization across diverse bat taxa. We successfully validated our system with 54 bat species across both suborders. Despite abundant arthropod prey DNA in guano, our primers were highly specific to bats; no arthropod DNA was detected in thousands of feces run on Sanger and Illumina platforms. The assay is extendable to fecal pellets of unknown age as well as individual and pooled guano, to allow for individual (using singular fecal pellets) and community (using combined pellets collected from across long-term roost sites) analyses. We developed a searchable database (http://nau.edu/CEFNS/Forestry/Research/Bats/Search-Tool/) that allows users to determine the discriminatory capability of our markers for bat species of interest. Our assay has applications worldwide for examining disease impacts on vulnerable species, determining species assemblages within roosts, and assessing the presence of bat species that are vulnerable or facing extinction. The development and analytical pathways are rapid, reliable, and inexpensive, and can be applied to ecology and conservation studies of other taxa.
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Affiliation(s)
- Faith M. Walker
- Bat Ecology & Genetics Laboratory, School of Forestry, Northern Arizona University, Flagstaff, Arizona, United States of America
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Charles H. D. Williamson
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Daniel E. Sanchez
- Bat Ecology & Genetics Laboratory, School of Forestry, Northern Arizona University, Flagstaff, Arizona, United States of America
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Colin J. Sobek
- Bat Ecology & Genetics Laboratory, School of Forestry, Northern Arizona University, Flagstaff, Arizona, United States of America
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Carol L. Chambers
- Bat Ecology & Genetics Laboratory, School of Forestry, Northern Arizona University, Flagstaff, Arizona, United States of America
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209
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Applying DNA Barcodes to Identify Closely Related Species of Ferns: A Case Study of the Chinese Adiantum (Pteridaceae). PLoS One 2016; 11:e0160611. [PMID: 27603700 PMCID: PMC5014338 DOI: 10.1371/journal.pone.0160611] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 07/21/2016] [Indexed: 11/19/2022] Open
Abstract
DNA barcoding is a fast-developing technique to identify species by using short and standard DNA sequences. Universal selection of DNA barcodes in ferns remains unresolved. In this study, five plastid regions (rbcL, matK, trnH-psbA, trnL-F and rps4-trnS) and eight nuclear regions (ITS, pgiC, gapC, LEAFY, ITS2, IBR3_2, DET1, and SQD1_1) were screened and evaluated in the fern genus Adiantum from China and neighboring areas. Due to low primer universality (matK) and/or the existence of multiple copies (ITS), the commonly used barcodes matK and ITS were not appropriate for Adiantum. The PCR amplification rate was extremely low in all nuclear genes except for IBR3_2. rbcL had the highest PCR amplification rate (94.33%) and sequencing success rate (90.78%), while trnH-psbA had the highest species identification rate (75%). With the consideration of discriminatory power, cost-efficiency and effort, the two-barcode combination of rbcL+ trnH-psbA seems to be the best choice for barcoding Adiantum, and perhaps basal polypod ferns in general. The nuclear IBR3_2 showed 100% PCR amplification success rate in Adiantum, however, it seemed that only diploid species could acquire clean sequences without cloning. With cloning, IBR3_2 can successfully distinguish cryptic species and hybrid species from their related species. Because hybridization and allopolyploidy are common in ferns, we argue for including a selected group of nuclear loci as barcodes, especially via the next-generation sequencing, as it is much more efficient to obtain single-copy nuclear loci without the cloning procedure.
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210
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Hebert PDN, Hollingsworth PM, Hajibabaei M. From writing to reading the encyclopedia of life. Philos Trans R Soc Lond B Biol Sci 2016; 371:20150321. [PMID: 27481778 PMCID: PMC4971178 DOI: 10.1098/rstb.2015.0321] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2016] [Indexed: 11/12/2022] Open
Abstract
Prologue 'As the study of natural science advances, the language of scientific description may be greatly simplified and abridged. This has already been done by Linneaus and may be carried still further by other invention. The descriptions of natural orders and genera may be reduced to short definitions, and employment of signs, somewhat in the manner of algebra, instead of long descriptions. It is more easy to conceive this, than it is to conceive with what facility, and in how short a time, a knowledge of all the objects of natural history may ultimately be acquired; and that which is now considered learning and science, and confined to a few specially devoted to it, may at length be universally possessed in every civilized country and in every rank of life'. J. C. Louden 1829. Magazine of natural history, vol. 1: This article is part of the themed issue 'From DNA barcodes to biomes'.
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Affiliation(s)
- Paul D N Hebert
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | | | - Mehrdad Hajibabaei
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada N1G 2W1
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211
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The Labile Limits of Forbidden Interactions. Trends Ecol Evol 2016; 31:700-710. [DOI: 10.1016/j.tree.2016.06.009] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 06/23/2016] [Accepted: 06/26/2016] [Indexed: 11/23/2022]
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212
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Hill GE. Mitonuclear coevolution as the genesis of speciation and the mitochondrial DNA barcode gap. Ecol Evol 2016; 6:5831-42. [PMID: 27547358 PMCID: PMC4983595 DOI: 10.1002/ece3.2338] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 06/27/2016] [Accepted: 06/30/2016] [Indexed: 12/12/2022] Open
Abstract
Mitochondrial genes are widely used in taxonomy and systematics because high mutation rates lead to rapid sequence divergence and because such changes have long been assumed to be neutral with respect to function. In particular, the nucleotide sequence of the mitochondrial gene cytochrome c oxidase subunit 1 has been established as a highly effective DNA barcode for diagnosing the species boundaries of animals. Rarely considered in discussions of mitochondrial evolution in the context of systematics, speciation, or DNA barcodes, however, is the genomic architecture of the eukaryotes: Mitochondrial and nuclear genes must function in tight coordination to produce the complexes of the electron transport chain and enable cellular respiration. Coadaptation of these interacting gene products is essential for organism function. I extend the hypothesis that mitonuclear interactions are integral to the process of speciation. To maintain mitonuclear coadaptation, nuclear genes, which code for proteins in mitochondria that cofunction with the products of mitochondrial genes, must coevolve with rapidly changing mitochondrial genes. Mitonuclear coevolution in isolated populations leads to speciation because population-specific mitonuclear coadaptations create between-population mitonuclear incompatibilities and hence barriers to gene flow between populations. In addition, selection for adaptive divergence of products of mitochondrial genes, particularly in response to climate or altitude, can lead to rapid fixation of novel mitochondrial genotypes between populations and consequently to disruption in gene flow between populations as the initiating step in animal speciation. By this model, the defining characteristic of a metazoan species is a coadapted mitonuclear genotype that is incompatible with the coadapted mitochondrial and nuclear genotype of any other population.
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Affiliation(s)
- Geoffrey E. Hill
- Department Biological ScienceAuburn University331 Funchess HallAuburnAlabama36849‐5414
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213
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Galimberti A, Spinelli S, Bruno A, Mezzasalma V, De Mattia F, Cortis P, Labra M. Evaluating the efficacy of restoration plantings through DNA barcoding of frugivorous bird diets. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2016; 30:763-773. [PMID: 26864475 DOI: 10.1111/cobi.12687] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 01/16/2016] [Accepted: 02/06/2016] [Indexed: 06/05/2023]
Abstract
Frugivores are critical components of restoration programs because they are seed dispersers. Thus, knowledge about bird-plant trophic relationships is essential in the evaluation of the efficacy of restoration processes. Traditionally, the diet of frugivores is characterized by microscopically identifying plant residues in droppings, which is time-consuming, requires botanical knowledge, and cannot be used for fragments lacking detectable morphological characteristics (e.g., fragmented seeds and skins). We examined whether DNA barcoding can be used as a universal tool to rapidly characterize the diet of a frugivorous bird, Eurasian blackcap (Sylvia atricapilla). We used the DNA barcoding results to assess restoration efforts and monitor the diversity of potentially dispersed plants in a protected area in northern Italy. We collected 642 Eurasian Blackcap droppings at the restored site during the autumn migration over 3 years. Intact seeds and fragmented plant material were analyzed at 2 plastidial barcode loci (rbcL and trnH-psbA), and the resulting plant identifications were validated by comparison with a reference molecular data set of local flora. At least 17 plant species, including 7 of the 11 newly transplanted taxa, were found. Our results demonstrate the potential for DNA barcoding to be used to monitor the effectiveness of restoration plantings and to obtain information about fruit consumption and dispersal of invasive or unexpected plant species. Such an approach provides valuable information that could be used to study local plant biodiversity and to survey its evolution over time.
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Affiliation(s)
- A Galimberti
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.za Della Scienza 2, 20126, Milan, Italy
| | - S Spinelli
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.za Della Scienza 2, 20126, Milan, Italy
| | - A Bruno
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.za Della Scienza 2, 20126, Milan, Italy
| | - V Mezzasalma
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.za Della Scienza 2, 20126, Milan, Italy
| | - F De Mattia
- FEM2-Ambiente s.r.l, P.za Della Scienza 2, 20126, Milan, Italy
| | - P Cortis
- Department of Life and Environmental Sciences, Macrosection of Botany and Botanic Garden, University of Cagliari, Viale S. Ignazio 13, 09123, Cagliari, Italy
| | - M Labra
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.za Della Scienza 2, 20126, Milan, Italy
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214
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Lu Z, Xu S, Song N, Gao T, Tian J, Han J. Analysis of the diet of finless porpoise (Neophocaena asiaeorientalis sunameri) based on prey morphological characters and DNA barcoding. CONSERV GENET RESOUR 2016. [DOI: 10.1007/s12686-016-0575-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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215
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Klinth MJ, Martinsson S, Erséus C. Phylogeny and species delimitation of North EuropeanLumbricillus(Clitellata, Enchytraeidae). ZOOL SCR 2016. [DOI: 10.1111/zsc.12187] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mårten J. Klinth
- Department of Biological & Environmental Sciences; University of Gothenburg; P.O. Box 463 SE-405 30 Gothenburg Sweden
| | - Svante Martinsson
- Department of Biological & Environmental Sciences; University of Gothenburg; P.O. Box 463 SE-405 30 Gothenburg Sweden
| | - Christer Erséus
- Department of Biological & Environmental Sciences; University of Gothenburg; P.O. Box 463 SE-405 30 Gothenburg Sweden
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216
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A Return to Linnaeus’s Focus on Diagnosis, Not Description: The Use of DNA Characters in the Formal Naming of Species. Syst Biol 2016; 65:1085-1095. [DOI: 10.1093/sysbio/syw032] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Accepted: 04/05/2016] [Indexed: 11/14/2022] Open
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217
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Roslin T, Majaneva S. The use of DNA barcodes in food web construction-terrestrial and aquatic ecologists unite! Genome 2016; 59:603-28. [PMID: 27484156 DOI: 10.1139/gen-2015-0229] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
By depicting who eats whom, food webs offer descriptions of how groupings in nature (typically species or populations) are linked to each other. For asking questions on how food webs are built and work, we need descriptions of food webs at different levels of resolution. DNA techniques provide opportunities for highly resolved webs. In this paper, we offer an exposé of how DNA-based techniques, and DNA barcodes in particular, have recently been used to construct food web structure in both terrestrial and aquatic systems. We highlight how such techniques can be applied to simultaneously improve the taxonomic resolution of the nodes of the web (i.e., the species), and the links between them (i.e., who eats whom). We end by proposing how DNA barcodes and DNA information may allow new approaches to the construction of larger interaction webs, and overcome some hurdles to achieving adequate sample size. Most importantly, we propose that the joint adoption and development of these techniques may serve to unite approaches to food web studies in aquatic and terrestrial systems-revealing the extent to which food webs in these environments are structured similarly to or differently from each other, and how they are linked by dispersal.
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Affiliation(s)
- Tomas Roslin
- a Department of Ecology, Swedish University of Agricultural Sciences, Box 7044, 750 07 Uppsala, Sweden.,b Spatial Foodweb Ecology Group, Department of Agricultural Sciences, PO Box 27, (Latokartanonkaari 5), FI-00014 University of Helsinki, Finland
| | - Sanna Majaneva
- c Centre for Ecology and Evolution in Microbial model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, 39182 Kalmar, Sweden
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218
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Xiong M, Shao X, Long Y, Bu H, Zhang D, Wang D, Li S, Wang R, Yao M. Molecular analysis of vertebrates and plants in scats of leopard cats (Prionailurus bengalensis) in southwest China. J Mammal 2016. [DOI: 10.1093/jmammal/gyw061] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Understanding the diets of carnivores is essential for resolving food web interactions and the population dynamics of both prey and predators and for designing effective strategies for species and ecosystem conservation. As effective predators, wild felids play important roles in various ecosystems, but relatively little is known about the dietary habits of many species, primarily owing to their elusive behavior. We used a DNA-based method to analyze the vertebrates and plants constituting the diet of leopard cats (Prionailurus bengalensis) in the temperate forests of the mountains of southwest China, a global biodiversity hotspot. DNA extracted from leopard cat scats was amplified with primers targeting either the vertebrate mitochondrial 12S rRNA gene (N = 25 scats) or the psbCL region of the chloroplast genome of vascular plants (N = 42 scats). The polymerase chain reaction products were sequenced and prey taxa were assigned based on sequence similarity. We identified a total of 16 taxa of vertebrate prey, with pikas (in 76% of the scats) and rodents (40%) predominating. Plant material belonging to 12 taxa was found in 76% of the samples, and the genus Solanum and subfamily Rosoideae were the most frequently detected plant taxa. The frequency of occurrence of identified plant taxa differed between the spring–summer and fall–winter months. Thus, the leopard cats in our study area have a diversified diet and are highly flexible in adapting their foraging behavior to the locally available prey. Our data suggest that preserving their natural prey base dominated by pikas and rodents may be vital for the subsistence of local populations. The high species resolution and detection sensitivity of the DNA-based method we used in this study make it a powerful and efficient tool for fine-scale analysis of complex diets.
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Affiliation(s)
- Mengyin Xiong
- School of Life Sciences, Peking University, R. 640, Beijing 100871, China
| | - Xinning Shao
- School of Life Sciences, Peking University, R. 640, Beijing 100871, China
| | - Ying Long
- School of Life Sciences, Peking University, R. 640, Beijing 100871, China
| | - Hongliang Bu
- School of Life Sciences, Peking University, R. 640, Beijing 100871, China
| | - Dan Zhang
- School of Life Sciences, Peking University, R. 640, Beijing 100871, China
| | - Dajun Wang
- School of Life Sciences, Peking University, R. 640, Beijing 100871, China
| | - Sheng Li
- School of Life Sciences, Peking University, R. 640, Beijing 100871, China
| | - Rongjiang Wang
- School of Life Sciences, Peking University, R. 640, Beijing 100871, China
| | - Meng Yao
- School of Life Sciences, Peking University, R. 640, Beijing 100871, China
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219
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Castro-romero R, Montes MM, Martorelli SR, Sepulveda D, Tapia S, Martínez-aquino A. Integrative taxonomy of Peniculus, Metapeniculus, and Trifur (Siphonostomatoida: Pennellidae), copepod parasites of marine fishes from Chile: species delimitation analyses using DNA barcoding and morphological evidence. SYST BIODIVERS 2016. [DOI: 10.1080/14772000.2016.1158213] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Raúl Castro-romero
- Universidad de Antofagasta, Facultad Ciencias del Mar, Depto. Ciencias Acuáticas y Ambientales, Antofagasta, Chile
| | - Martín M. Montes
- CEPAVE, Universidad Nacional de La Plata, Buenos Aires, Argentina
| | | | - Diego Sepulveda
- Universidad de Antofagasta, Depto. Biomédico, Antofagasta, Chile
| | - Silvia Tapia
- Universidad de Antofagasta, Facultad Ciencias del Mar, Depto. Ciencias Acuáticas y Ambientales, Antofagasta, Chile
- Universidad de Antofagasta, Depto. Biomédico, Antofagasta, Chile
| | - Andrés Martínez-aquino
- División Zoología Invertebrados, Museo de La Plata, FCNyM, UNLP, Paseo del Bosque s/n, 1900 La Plata, Argentina
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220
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Janjua S, Fakhar-I-Abbas, William K, Malik IU, Mehr J. DNA Mini-barcoding for wildlife trade control: a case study on identification of highly processed animal materials. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 28:544-546. [PMID: 27159715 DOI: 10.3109/24701394.2016.1155051] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Although DNA barcoding is an efficient tool for species identification, however, its efficiency is uncertain for samples having degraded DNA and incomplete isolation/amplification of COI gene fragment (>500 bp). DNA mini-barcoding is a solution to this problem because small DNA fragment of COI genes is used for species identification. Twelve highly processed, chemically treated and finished animal skin (coats, tanned skins) and fur (mufflers) samples, received from the Sindh Wildlife Department, Pakistan, were subjected to DNA mini-barcoding. Eight mufflers belonged to Vulpes vulpes, one coat to Ursus thibetanus, one tanned skin to Lutra sumatrana, and one muffler to Vulpes sp. Origin of only one coat sample remained unidentified, success rate of 92% indicative of the fact that the mini barcoding technique can be used as a substitute of conventional barcoding where full length barcode (∼650 bp Folmer region) cannot be generated.
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Affiliation(s)
- Safia Janjua
- a Bioresource Research Centre (BRC) , Islamabad , Pakistan.,b Institute of Natural and Management Sciences (INAM) , Rawalpindi , Pakistan
| | - Fakhar-I-Abbas
- a Bioresource Research Centre (BRC) , Islamabad , Pakistan.,b Institute of Natural and Management Sciences (INAM) , Rawalpindi , Pakistan
| | - Kainaat William
- a Bioresource Research Centre (BRC) , Islamabad , Pakistan.,b Institute of Natural and Management Sciences (INAM) , Rawalpindi , Pakistan
| | - Inayat Ullah Malik
- c Department of Zoology , Government College University , Faisalabad , Pakistan
| | - Javed Mehr
- d Sindh Wildlife Department , Karachi, Sindh , Pakistan
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221
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da Silva JM, Willows-Munro S. A review of over a decade of DNA barcoding in South Africa: a faunal perspective. AFRICAN ZOOLOGY 2016. [DOI: 10.1080/15627020.2016.1151377] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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222
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Phylogenetic Structure of Foliar Spectral Traits in Tropical Forest Canopies. REMOTE SENSING 2016. [DOI: 10.3390/rs8030196] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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223
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Limited tolerance by insects to high temperatures across tropical elevational gradients and the implications of global warming for extinction. Proc Natl Acad Sci U S A 2016; 113:680-5. [PMID: 26729867 DOI: 10.1073/pnas.1507681113] [Citation(s) in RCA: 146] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The critical thermal maximum (CTmax), the temperature at which motor control is lost in animals, has the potential to determine if species will tolerate global warming. For insects, tolerance to high temperatures decreases with latitude, suggesting that similar patterns may exist along elevational gradients as well. This study explored how CTmax varies among species and populations of a group of diverse tropical insect herbivores, the rolled-leaf beetles, across both broad and narrow elevational gradients. Data from 6,948 field observations and 8,700 museum specimens were used to map the elevational distributions of rolled-leaf beetles on two mountains in Costa Rica. CTmax was determined for 1,252 individual beetles representing all populations across the gradients. Initial morphological identifications suggested a total of 26 species with populations at different elevations displaying contrasting upper thermal limits. However, compared with morphological identifications, DNA barcodes (cytochrome oxidase I) revealed significant cryptic species diversity. DNA barcodes identified 42 species and haplotypes across 11 species complexes. These 42 species displayed much narrower elevational distributions and values of CTmax than the 26 morphologically defined species. In general, species found at middle elevations and on mountaintops are less tolerant to high temperatures than species restricted to lowland habitats. Species with broad elevational distributions display high CTmax throughout their ranges. We found no significant phylogenetic signal in CTmax, geography, or elevational range. The narrow variance in CTmax values for most rolled-leaf beetles, especially high-elevation species, suggests that the risk of extinction of insects may be substantial under some projected rates of global warming.
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224
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Bandow C, Ng EL, Schmelz RM, Sousa JP, Römbke J. A TME study with the fungicide pyrimethanil combined with different moisture regimes: effects on enchytraeids. ECOTOXICOLOGY (LONDON, ENGLAND) 2016; 25:213-224. [PMID: 26547875 DOI: 10.1007/s10646-015-1581-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/30/2015] [Indexed: 06/05/2023]
Abstract
Today's ecosystems are influenced by different factors that could evolve into stressors. Effects of pesticides, especially in agricultural areas, may interact with environmental factors, such as soil moisture fluctuation caused by global climate change. In this contribution, two semi-field studies conducted in Germany and Portugal with terrestrial model ecosystems are presented. Their aim was to assess the effects of the fungicide pyrimethanil under different soil moisture levels on Enchytraeidae. In Portugal a no observed effect concentration design was chosen, using two concentration levels: the maximum application rate (MAR) according to the safe use registration within the European Union and five times the MAR (1.82 and 9.09 mg/kg dry soil, respectively). Both concentrations did neither affect the total enchytraeid abundance nor single populations. In Germany an ECx design (effect concentration) was conducted, using 11 concentrations. In general, 14 EC50 values for different combinations of single species, moisture level and sampling date were determined. The strongest effects were found in dry soil, particularly for Fridericia connata (EC50: 3.48 mg/kg dry soil after 8 weeks of exposure). The advantages and challenges of these test designs are discussed with regard to the registration process of pesticides in the European Union. In any case, enchytraeids are suitable test organisms in such higher tier studies for the combined evaluation of chemical and climatic stressors due to their usually high diversity and abundances and their close contact with the soil solution.
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Affiliation(s)
- Cornelia Bandow
- LOEWE Biodiversity and Climate Research Centre BiK-F, Senckenberganlage 25, 60325, Frankfurt, Germany.
- ECT Oekotoxikologie GmbH, Böttgerstrasse 2-14, 65439, Flörsheim, Germany.
- Department Aquatic Ecotoxicology, Goethe University Frankfurt, Max-von-Laue-Str. 13, 60438, Frankfurt, Germany.
| | - Ee Ling Ng
- Future Soils Laboratory, Melbourne, VIC, Australia
| | - Rüdiger M Schmelz
- ECT Oekotoxikologie GmbH, Böttgerstrasse 2-14, 65439, Flörsheim, Germany
- Department of Animal Biology, Plant Biology and Ecology, Science Faculty, University of A Coruña, Coruña, Spain
| | - José Paulo Sousa
- CFE-Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Jörg Römbke
- LOEWE Biodiversity and Climate Research Centre BiK-F, Senckenberganlage 25, 60325, Frankfurt, Germany
- ECT Oekotoxikologie GmbH, Böttgerstrasse 2-14, 65439, Flörsheim, Germany
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225
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Hortal J, de Bello F, Diniz-Filho JAF, Lewinsohn TM, Lobo JM, Ladle RJ. Seven Shortfalls that Beset Large-Scale Knowledge of Biodiversity. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2015. [DOI: 10.1146/annurev-ecolsys-112414-054400] [Citation(s) in RCA: 544] [Impact Index Per Article: 60.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Joaquín Hortal
- Department of Biogeography and Global Change, Museo Nacional de Ciencias Naturales (MNCN-CSIC), 28006 Madrid, Spain; ,
- Department of Ecology, Instituto de Ciências Biologicas, Universidade Federal de Goiás, 74001-970 Goiânia, Brazil;
- Center for Ecology, Evolution, and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Francesco de Bello
- Institute of Botany, Czech Academy of Sciences, CZ-379 82 Třeboň, Czech Republic;
- Department of Botany, Faculty of Sciences, University of South Bohemia, 370 05 Budějovice, Czech Republic
| | | | - Thomas M. Lewinsohn
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas, 13083-862 Campinas, Brazil;
| | - Jorge M. Lobo
- Department of Biogeography and Global Change, Museo Nacional de Ciencias Naturales (MNCN-CSIC), 28006 Madrid, Spain; ,
| | - Richard J. Ladle
- Instituto de Ciências Biológicas e da Saúde (ICBS), Universidade Federal de Alagoas, 57072-900 Maceió, Brazil
- School of Geography and the Environment, University of Oxford, OX1 3QY Oxford, United Kingdom;
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226
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Brandon-Mong GJ, Gan HM, Sing KW, Lee PS, Lim PE, Wilson JJ. DNA metabarcoding of insects and allies: an evaluation of primers and pipelines. BULLETIN OF ENTOMOLOGICAL RESEARCH 2015; 105:717-27. [PMID: 26344799 DOI: 10.1017/s0007485315000681] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Metabarcoding, the coupling of DNA-based species identification and high-throughput sequencing, offers enormous promise for arthropod biodiversity studies but factors such as cost, speed and ease-of-use of bioinformatic pipelines, crucial for making the leapt from demonstration studies to a real-world application, have not yet been adequately addressed. Here, four published and one newly designed primer sets were tested across a diverse set of 80 arthropod species, representing 11 orders, to establish optimal protocols for Illumina-based metabarcoding of tropical Malaise trap samples. Two primer sets which showed the highest amplification success with individual specimen polymerase chain reaction (PCR, 98%) were used for bulk PCR and Illumina MiSeq sequencing. The sequencing outputs were subjected to both manual and simple metagenomics quality control and filtering pipelines. We obtained acceptable detection rates after bulk PCR and high-throughput sequencing (80-90% of input species) but analyses were complicated by putative heteroplasmic sequences and contamination. The manual pipeline produced similar or better outputs to the simple metagenomics pipeline (1.4 compared with 0.5 expected:unexpected Operational Taxonomic Units). Our study suggests that metabarcoding is slowly becoming as cheap, fast and easy as conventional DNA barcoding, and that Malaise trap metabarcoding may soon fulfill its potential, providing a thermometer for biodiversity.
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Affiliation(s)
- G-J Brandon-Mong
- Museum of Zoology,Institute of Biological Sciences,Faculty of Science,University of Malaya,50603 Kuala Lumpur,Malaysia
| | - H-M Gan
- School of Science,Monash University Malaysia,Jalan Lagoon Selatan,Bandar Sunway,47500 Petaling Jaya,Selangor,Malaysia
| | - K-W Sing
- Museum of Zoology,Institute of Biological Sciences,Faculty of Science,University of Malaya,50603 Kuala Lumpur,Malaysia
| | - P-S Lee
- Museum of Zoology,Institute of Biological Sciences,Faculty of Science,University of Malaya,50603 Kuala Lumpur,Malaysia
| | - P-E Lim
- Institute of Ocean and Earth Sciences (IOES),University of Malaya,50603 Kuala Lumpur,Malaysia
| | - J-J Wilson
- Museum of Zoology,Institute of Biological Sciences,Faculty of Science,University of Malaya,50603 Kuala Lumpur,Malaysia
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227
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Bello A, Daru BH, Stirton CH, Chimphango SBM, van der Bank M, Maurin O, Muasya AM. DNA barcodes reveal microevolutionary signals in fire response trait in two legume genera. AOB PLANTS 2015; 7:plv124. [PMID: 26507570 PMCID: PMC4670488 DOI: 10.1093/aobpla/plv124] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 10/19/2015] [Indexed: 06/05/2023]
Abstract
Large-scale DNA barcoding provides a new technique for species identification and evaluation of relationships across various levels (populations and species) and may reveal fundamental processes in recently diverged species. Here, we analysed DNA sequence variation in the recently diverged legumes from the Psoraleeae (Fabaceae) occurring in the Cape Floristic Region (CFR) of southern Africa to test the utility of DNA barcodes in species identification and discrimination. We further explored the phylogenetic signal on fire response trait (reseeding and resprouting) at species and generic levels. We showed that Psoraleoid legumes of the CFR exhibit a barcoding gap yielding the combination of matK and rbcLa (matK + rbcLa) data set as a better barcode than single regions. We found a high score (100 %) of correct identification of individuals to their respective genera but a very low score (<50 %) in identifying them to species. We found a considerable match (54 %) between genetic species and morphologically delimited species. We also found that different lineages showed a weak but significant phylogenetic conservatism in their response to fire as reseeders or resprouters, with more clustering of resprouters than would be expected by chance. These novel microevolutionary patterns might be acting continuously over time to produce multi-scale regularities of biodiversity. This study provides the first insight into the DNA barcoding campaign of land plants in species identification and detection of the phylogenetic signal in recently diverged lineages of the CFR.
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Affiliation(s)
- Abubakar Bello
- Bolus Herbarium, Biological Sciences Department, University of Cape Town, Private Bag X3, Rondebosch 7700, South Africa
| | - Barnabas H Daru
- Department of Plant Science, University of Pretoria, Private Bag X20, Hatfield 0028, Pretoria, South Africa
| | - Charles H Stirton
- Bolus Herbarium, Biological Sciences Department, University of Cape Town, Private Bag X3, Rondebosch 7700, South Africa
| | - Samson B M Chimphango
- Bolus Herbarium, Biological Sciences Department, University of Cape Town, Private Bag X3, Rondebosch 7700, South Africa
| | - Michelle van der Bank
- African Centre for DNA Barcoding, Department of Botany and Plant Biotechnology, University of Johannesburg, PO Box 524, Auckland Park 2006, Johannesburg, South Africa
| | - Olivier Maurin
- African Centre for DNA Barcoding, Department of Botany and Plant Biotechnology, University of Johannesburg, PO Box 524, Auckland Park 2006, Johannesburg, South Africa
| | - A Muthama Muasya
- Bolus Herbarium, Biological Sciences Department, University of Cape Town, Private Bag X3, Rondebosch 7700, South Africa
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228
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Telfer AC, Young MR, Quinn J, Perez K, Sobel CN, Sones JE, Levesque-Beaudin V, Derbyshire R, Fernandez-Triana J, Rougerie R, Thevanayagam A, Boskovic A, Borisenko AV, Cadel A, Brown A, Pages A, Castillo AH, Nicolai A, Glenn Mockford BM, Bukowski B, Wilson B, Trojahn B, Lacroix CA, Brimblecombe C, Hay C, Ho C, Steinke C, Warne CP, Garrido Cortes C, Engelking D, Wright D, Lijtmaer DA, Gascoigne D, Hernandez Martich D, Morningstar D, Neumann D, Steinke D, Marco DeBruin DD, Dobias D, Sears E, Richard E, Damstra E, Zakharov EV, Laberge F, Collins GE, Blagoev GA, Grainge G, Ansell G, Meredith G, Hogg I, McKeown J, Topan J, Bracey J, Guenther J, Sills-Gilligan J, Addesi J, Persi J, Layton KKS, D'Souza K, Dorji K, Grundy K, Nghidinwa K, Ronnenberg K, Lee KM, Xie L, Lu L, Penev L, Gonzalez M, Rosati ME, Kekkonen M, Kuzmina M, Iskandar M, Mutanen M, Fatahi M, Pentinsaari M, Bauman M, Nikolova N, Ivanova NV, Jones N, Weerasuriya N, Monkhouse N, Lavinia PD, Jannetta P, Hanisch PE, McMullin RT, Ojeda Flores R, Mouttet R, Vender R, Labbee RN, Forsyth R, Lauder R, Dickson R, Kroft R, Miller SE, MacDonald S, Panthi S, Pedersen S, Sobek-Swant S, Naik S, Lipinskaya T, Eagalle T, Decaëns T, Kosuth T, Braukmann T, Woodcock T, Roslin T, Zammit T, Campbell V, Dinca V, Peneva V, Hebert PDN, deWaard JR. Biodiversity inventories in high gear: DNA barcoding facilitates a rapid biotic survey of a temperate nature reserve. Biodivers Data J 2015; 3:e6313. [PMID: 26379469 PMCID: PMC4568406 DOI: 10.3897/bdj.3.e6313] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 08/24/2015] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Comprehensive biotic surveys, or 'all taxon biodiversity inventories' (ATBI), have traditionally been limited in scale or scope due to the complications surrounding specimen sorting and species identification. To circumvent these issues, several ATBI projects have successfully integrated DNA barcoding into their identification procedures and witnessed acceleration in their surveys and subsequent increase in project scope and scale. The Biodiversity Institute of Ontario partnered with the rare Charitable Research Reserve and delegates of the 6th International Barcode of Life Conference to complete its own rapid, barcode-assisted ATBI of an established land trust in Cambridge, Ontario, Canada. NEW INFORMATION The existing species inventory for the rare Charitable Research Reserve was rapidly expanded by integrating a DNA barcoding workflow with two surveying strategies - a comprehensive sampling scheme over four months, followed by a one-day bioblitz involving international taxonomic experts. The two surveys resulted in 25,287 and 3,502 specimens barcoded, respectively, as well as 127 human observations. This barcoded material, all vouchered at the Biodiversity Institute of Ontario collection, covers 14 phyla, 29 classes, 117 orders, and 531 families of animals, plants, fungi, and lichens. Overall, the ATBI documented 1,102 new species records for the nature reserve, expanding the existing long-term inventory by 49%. In addition, 2,793 distinct Barcode Index Numbers (BINs) were assigned to genus or higher level taxonomy, and represent additional species that will be added once their taxonomy is resolved. For the 3,502 specimens, the collection, sequence analysis, taxonomic assignment, data release and manuscript submission by 100+ co-authors all occurred in less than one week. This demonstrates the speed at which barcode-assisted inventories can be completed and the utility that barcoding provides in minimizing and guiding valuable taxonomic specialist time. The final product is more than a comprehensive biotic inventory - it is also a rich dataset of fine-scale occurrence and sequence data, all archived and cross-linked in the major biodiversity data repositories. This model of rapid generation and dissemination of essential biodiversity data could be followed to conduct regional assessments of biodiversity status and change, and potentially be employed for evaluating progress towards the Aichi Targets of the Strategic Plan for Biodiversity 2011-2020.
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Affiliation(s)
| | | | - Jenna Quinn
- rare Charitable Research Reserve, Cambridge, Canada
| | - Kate Perez
- Biodiversity Institute of Ontario, Guelph, Canada
| | | | | | | | | | | | | | | | | | | | - Alex Cadel
- University of Waterloo, Waterloo, Canada
| | | | - Anais Pages
- Université de Montpellier, Montpellier, France
| | | | | | | | - Belén Bukowski
- Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" (MACN-CONICET), Buenos Aires, Argentina
| | - Bill Wilson
- rare Charitable Research Reserve (Affiliate of), Cambridge, Canada
| | | | | | | | | | - Christmas Ho
- Biodiversity Institute of Ontario, Guelph, Canada
| | | | | | | | | | | | - Dario A Lijtmaer
- Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" (MACN-CONICET), Buenos Aires, Argentina
| | - David Gascoigne
- rare Charitable Research Reserve (Affiliate of), Cambridge, Canada
| | | | | | - Dirk Neumann
- SNSB, Zoologische Staatssammlung Muenchen, Munich, Germany
| | - Dirk Steinke
- Biodiversity Institute of Ontario, Guelph, Canada
| | | | | | | | | | - Emily Damstra
- rare Charitable Research Reserve (Affiliate of), Cambridge, Canada
| | | | | | | | | | - Gerrie Grainge
- rare Charitable Research Reserve (Affiliate of), Cambridge, Canada
| | | | | | - Ian Hogg
- University of Waikato, Hamilton, New Zealand
| | | | - Janet Topan
- Biodiversity Institute of Ontario, Guelph, Canada
| | - Jason Bracey
- rare Charitable Research Reserve (Affiliate of), Cambridge, Canada
| | - Jerry Guenther
- rare Charitable Research Reserve (Affiliate of), Cambridge, Canada
| | | | | | - Joshua Persi
- Biodiversity Institute of Ontario, Guelph, Canada
| | | | | | | | - Kevin Grundy
- rare Charitable Research Reserve (Affiliate of), Cambridge, Canada
| | - Kirsti Nghidinwa
- Ministry of Environment and Tourism in Namibia, Windhoek, Namibia
| | | | | | - Linxi Xie
- The University of Western Ontario, London, Canada
| | - Liuqiong Lu
- Biodiversity Institute of Ontario, Guelph, Canada
| | | | - Mailyn Gonzalez
- Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Bogotá, Colombia
| | - Margaret E Rosati
- Smithsonian National Museum of Natural History, Washington, United States of America
| | | | | | | | | | | | | | - Miriam Bauman
- rare Charitable Research Reserve (Affiliate of), Cambridge, Canada
| | | | | | | | | | | | - Pablo D Lavinia
- Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" (MACN-CONICET), Buenos Aires, Argentina
| | | | - Priscila E Hanisch
- Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" (MACN-CONICET), Buenos Aires, Argentina
| | | | | | - Raphaëlle Mouttet
- ANSES, Laboratoire de la Santé des Végétaux, Montferrier sur Lez, France
| | - Reid Vender
- Biodiversity Institute of Ontario, Guelph, Canada
| | | | | | | | - Ross Dickson
- rare Charitable Research Reserve (Affiliate of), Cambridge, Canada
| | - Ruth Kroft
- rare Charitable Research Reserve (Affiliate of), Cambridge, Canada
| | - Scott E Miller
- Smithsonian National Museum of Natural History, Washington, United States of America
| | | | - Sishir Panthi
- Ministry of Forests and Soil Conservation, Kathmandu, Nepal
| | | | | | - Suresh Naik
- Biodiversity Institute of Ontario, Guelph, Canada
| | - Tatsiana Lipinskaya
- Scientific and Practical Center for Bioresources, National Academy of Sciences of Belarus, Minsk, Belarus
| | | | - Thibaud Decaëns
- Université de Montpellier Centre d'Ecologie Fonctionnelle et Evolutive, Montpellier, France
| | | | | | - Tom Woodcock
- rare Charitable Research Reserve, Cambridge, Canada
| | - Tomas Roslin
- University of Helsinki, Helsinki, Finland
- Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Tony Zammit
- Grand River Conservation Authority, Cambridge, Canada
| | | | - Vlad Dinca
- Biodiversity Institute of Ontario, Guelph, Canada
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229
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Kissling WD, Hardisty A, García EA, Santamaria M, De Leo F, Pesole G, Freyhof J, Manset D, Wissel S, Konijn J, Los W. Towards global interoperability for supporting biodiversity research on essential biodiversity variables (EBVs). ACTA ACUST UNITED AC 2015. [DOI: 10.1080/14888386.2015.1068709] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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230
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Barco A, Raupach MJ, Laakmann S, Neumann H, Knebelsberger T. Identification of North Sea molluscs with DNA barcoding. Mol Ecol Resour 2015; 16:288-97. [DOI: 10.1111/1755-0998.12440] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 06/09/2015] [Accepted: 06/17/2015] [Indexed: 12/18/2022]
Affiliation(s)
- Andrea Barco
- GEOMAR-Helmholtz Centre for Ocean Research Kiel; Düsternbrooker Weg 20 24105 Kiel Germany
- German Centre for Marine Biodiversity Research (DZMB); Senckenberg am Meer; Südstrand 44 26382 Wilhelmshaven Germany
| | - Michael J. Raupach
- German Centre for Marine Biodiversity Research (DZMB); Senckenberg am Meer; Südstrand 44 26382 Wilhelmshaven Germany
| | - Silke Laakmann
- German Centre for Marine Biodiversity Research (DZMB); Senckenberg am Meer; Südstrand 44 26382 Wilhelmshaven Germany
| | - Hermann Neumann
- German Centre for Marine Biodiversity Research (DZMB); Senckenberg am Meer; Südstrand 44 26382 Wilhelmshaven Germany
| | - Thomas Knebelsberger
- German Centre for Marine Biodiversity Research (DZMB); Senckenberg am Meer; Südstrand 44 26382 Wilhelmshaven Germany
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