151
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Raschmanová N, Žurovcová M, Kováč Ľ, Paučulová L, Šustr V, Jarošová A, Chundelová D. The cold-adapted population ofFolsomia manolachei(Hexapoda, Collembola) from a glaciated karst doline of Central Europe: evidence for a cryptic species? J ZOOL SYST EVOL RES 2016. [DOI: 10.1111/jzs.12150] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Natália Raschmanová
- Institute of Biology and Ecology; Faculty of Science; P. J. Šafárik University; Košice Slovakia
| | - Martina Žurovcová
- Institute of Entomology; Biology Centre AS CR v. v. i.; České Budějovice Czech Republic
- Faculty of Science; University of South Bohemia; České Budějovice Czech Republic
| | - Ľubomír Kováč
- Institute of Biology and Ecology; Faculty of Science; P. J. Šafárik University; Košice Slovakia
| | - Lenka Paučulová
- Institute of Biology and Ecology; Faculty of Science; P. J. Šafárik University; Košice Slovakia
| | - Vladimír Šustr
- Institute of Soil Biology; Biology Centre AS CR v. v. i.; České Budějovice Czech Republic
| | - Andrea Jarošová
- Institute of Entomology; Biology Centre AS CR v. v. i.; České Budějovice Czech Republic
- Faculty of Science; University of South Bohemia; České Budějovice Czech Republic
| | - Daniela Chundelová
- Institute of Entomology; Biology Centre AS CR v. v. i.; České Budějovice Czech Republic
- Faculty of Science; University of South Bohemia; České Budějovice Czech Republic
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152
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Yang Z, Landry JF, Hebert PDN. A DNA Barcode Library for North American Pyraustinae (Lepidoptera: Pyraloidea: Crambidae). PLoS One 2016; 11:e0161449. [PMID: 27736878 PMCID: PMC5063472 DOI: 10.1371/journal.pone.0161449] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 08/06/2016] [Indexed: 11/24/2022] Open
Abstract
Although members of the crambid subfamily Pyraustinae are frequently important crop pests, their identification is often difficult because many species lack conspicuous diagnostic morphological characters. DNA barcoding employs sequence diversity in a short standardized gene region to facilitate specimen identifications and species discovery. This study provides a DNA barcode reference library for North American pyraustines based upon the analysis of 1589 sequences recovered from 137 nominal species, 87% of the fauna. Data from 125 species were barcode compliant (>500bp, <1% n), and 99 of these taxa formed a distinct cluster that was assigned to a single BIN. The other 26 species were assigned to 56 BINs, reflecting frequent cases of deep intraspecific sequence divergence and a few instances of barcode sharing, creating a total of 155 BINs. Two systems for OTU designation, ABGD and BIN, were examined to check the correspondence between current taxonomy and sequence clusters. The BIN system performed better than ABGD in delimiting closely related species, while OTU counts with ABGD were influenced by the value employed for relative gap width. Different species with low or no interspecific divergence may represent cases of unrecognized synonymy, whereas those with high intraspecific divergence require further taxonomic scrutiny as they may involve cryptic diversity. The barcode library developed in this study will also help to advance understanding of relationships among species of Pyraustinae.
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Affiliation(s)
- Zhaofu Yang
- Key laboratory of Plant Protection Resources and Pest Management, Ministry of Education, Northwest A&F University, Yangling, Shaanxi, China
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
- * E-mail:
| | - Jean-François Landry
- Agriculture and Agri-Food Canada, Ottawa Research & Development Centre, Ottawa, Ontario, Canada
| | - Paul D. N. Hebert
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
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153
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Sun S, Li Q, Kong L, Yu H, Zheng X, Yu R, Dai L, Sun Y, Chen J, Liu J, Ni L, Feng Y, Yu Z, Zou S, Lin J. DNA barcoding reveal patterns of species diversity among northwestern Pacific molluscs. Sci Rep 2016; 6:33367. [PMID: 27640675 PMCID: PMC5027561 DOI: 10.1038/srep33367] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 08/25/2016] [Indexed: 11/26/2022] Open
Abstract
This study represents the first comprehensive molecular assessment of northwestern Pacific molluscs. In total, 2801 DNA barcodes belonging to 569 species from China, Japan and Korea were analyzed. An overlap between intra- and interspecific genetic distances was present in 71 species. We tested the efficacy of this library by simulating a sequence-based specimen identification scenario using Best Match (BM), Best Close Match (BCM) and All Species Barcode (ASB) criteria with three threshold values. BM approach returned 89.15% true identifications (95.27% when excluding singletons). The highest success rate of congruent identifications was obtained with BCM at 0.053 threshold. The analysis of our barcode library together with public data resulted in 582 Barcode Index Numbers (BINs), 72.2% of which was found to be concordantly with morphology-based identifications. The discrepancies were divided in two groups: sequences from different species clustered in a single BIN and conspecific sequences divided in one more BINs. In Neighbour-Joining phenogram, 2,320 (83.0%) queries fromed 355 (62.4%) species-specific barcode clusters allowing their successful identification. 33 species showed paraphyletic and haplotype sharing. 62 cases are represented by deeply diverged lineages. This study suggest an increased species diversity in this region, highlighting taxonomic revision and conservation strategy for the cryptic complexes.
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Affiliation(s)
- Shao’e Sun
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Lingfeng Kong
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Hong Yu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Xiaodong Zheng
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Ruihai Yu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Lina Dai
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Yan Sun
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Jun Chen
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Jun Liu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Lehai Ni
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Yanwei Feng
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Zhenzhen Yu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Shanmei Zou
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Jiping Lin
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
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154
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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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155
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Zhou X, Frandsen PB, Holzenthal RW, Beet CR, Bennett KR, Blahnik RJ, Bonada N, Cartwright D, Chuluunbat S, Cocks GV, Collins GE, deWaard J, Dean J, Flint OS, Hausmann A, Hendrich L, Hess M, Hogg ID, Kondratieff BC, Malicky H, Milton MA, Morinière J, Morse JC, Mwangi FN, Pauls SU, Gonzalez MR, Rinne A, Robinson JL, Salokannel J, Shackleton M, Smith B, Stamatakis A, StClair R, Thomas JA, Zamora-Muñoz C, Ziesmann T, Kjer KM. The Trichoptera barcode initiative: a strategy for generating a species-level Tree of Life. Philos Trans R Soc Lond B Biol Sci 2016; 371:20160025. [PMID: 27481793 PMCID: PMC4971193 DOI: 10.1098/rstb.2016.0025] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/01/2016] [Indexed: 12/15/2022] Open
Abstract
DNA barcoding was intended as a means to provide species-level identifications through associating DNA sequences from unknown specimens to those from curated reference specimens. Although barcodes were not designed for phylogenetics, they can be beneficial to the completion of the Tree of Life. The barcode database for Trichoptera is relatively comprehensive, with data from every family, approximately two-thirds of the genera, and one-third of the described species. Most Trichoptera, as with most of life's species, have never been subjected to any formal phylogenetic analysis. Here, we present a phylogeny with over 16 000 unique haplotypes as a working hypothesis that can be updated as our estimates improve. We suggest a strategy of implementing constrained tree searches, which allow larger datasets to dictate the backbone phylogeny, while the barcode data fill out the tips of the tree. We also discuss how this phylogeny could be used to focus taxonomic attention on ambiguous species boundaries and hidden biodiversity. We suggest that systematists continue to differentiate between 'Barcode Index Numbers' (BINs) and 'species' that have been formally described. Each has utility, but they are not synonyms. We highlight examples of integrative taxonomy, using both barcodes and morphology for species description.This article is part of the themed issue 'From DNA barcodes to biomes'.
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Affiliation(s)
- Xin Zhou
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing 100193, People's Republic of China College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, People's Republic of China
| | - Paul B Frandsen
- Office of Research Information Services, Office of the Chief Information Officer, Smithsonian Institution, PO Box 37012, Washington, DC 20013-7012, USA
| | - Ralph W Holzenthal
- Department of Entomology, University of Minnesota, 1980 Folwell Avenue, St Paul, MN 55108, USA
| | - Clare R Beet
- School of Science, University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - Kristi R Bennett
- School of Science, University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - Roger J Blahnik
- Department of Entomology, University of Minnesota, 1980 Folwell Avenue, St Paul, MN 55108, USA
| | - Núria Bonada
- Grup de Recerca Freshwater Ecology and Management (FEM), Departament d'Ecologia, Facultat de Biologia, Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Diagonal, 643, 08028 Barcelona, Catalonia, Spain
| | | | - Suvdtsetseg Chuluunbat
- Department of Biology, Mongolian National University of Education, 3rd Palace, Beijing Street, Ulaanbaatar 14191, Mongolia
| | - Graeme V Cocks
- 44 Marks Street, Hermit Park, Queensland 4812, Australia
| | - Gemma E Collins
- School of Science, University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - Jeremy deWaard
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - John Dean
- Environment Protection Authority Victoria, Ernest Jones Drive, Macleod 3085, Australia
| | - Oliver S Flint
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013-7012, USA
| | - Axel Hausmann
- SNSB-Bavarian State Collection of Zoology, Münchhausenstr. 21, 81247 Munich, Germany
| | - Lars Hendrich
- SNSB-Bavarian State Collection of Zoology, Münchhausenstr. 21, 81247 Munich, Germany
| | - Monika Hess
- Büro H2-Ökologische Gutachten, Hess+Heckes GbR, Rumfordstraße 42, 80469 München, Germany
| | - Ian D Hogg
- School of Science, University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - Boris C Kondratieff
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, 1177 Campus Delivery, Fort Collins, CO 80523, USA
| | - Hans Malicky
- Biologische Station Lunz, Austrian Academy of Sciences, A-3293 Lunz am see, Austria
| | - Megan A Milton
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - Jérôme Morinière
- SNSB-Bavarian State Collection of Zoology, Münchhausenstr. 21, 81247 Munich, Germany
| | - John C Morse
- Department of Plant and Environmental Sciences, Clemson University, PO Box 340310, Clemson, SC 29634-0310, USA
| | | | - Steffen U Pauls
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - María Razo Gonzalez
- Unidad Multidisciplinaria de Docencia e Investigación, Universidad Nacional Autónoma de Mexcio, Facultad de Ciencias, Campus Juriquilla, Querétaro, 76230, México
| | - Aki Rinne
- Finnish Environment Institute, Merikasarminkatu 8 D, 00160 Helsinki, Finland
| | - Jason L Robinson
- Illinois Natural History Survey, Prairie Research Institute at the University of Illinois at Urbana-Champaign, 1816 S. Oak Street, MC 652, Champaign, IL 61820, USA
| | - Juha Salokannel
- Aquatic Insects Expert Group of Finland, Siikinkatu 13, 33710, Tampere, Finland
| | - Michael Shackleton
- Murray-Darling Freshwater Research Centre, La Trobe University, 133 McKoy Street, Wodonga, Victoria 3691, Australia
| | - Brian Smith
- National Institute of Water and Atmospheric Research, PO Box, 11115, Hamilton 3240, New Zealand
| | - Alexandros Stamatakis
- Scientific Computing Group, Heidelberg Institute for Theoretical Studies (HITS), 69118 Heidelberg, Germany Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, 35 D-69118 Heidelberg, Germany
| | - Ros StClair
- Environment Protection Authority Victoria, Ernest Jones Drive, Macleod 3085, Australia
| | - Jessica A Thomas
- BioArch, Environment Building, Department of Biology, University of York, York, YO10 5DD, UK
| | - Carmen Zamora-Muñoz
- Department of Zoology, Faculty of Sciences, University of Granada, C/Severo Ochoa s/n, 18071 Granada, Spain
| | - Tanja Ziesmann
- Zoologisches Forschungsmuseum Alexander Koenig (ZFMK)/Zentrum fu¨r Molekulare Biodiversitätsforschung (ZMB), Bonn 5 76131 Karlsruhe, Germany
| | - Karl M Kjer
- Department of Entomology and Nematology, University of California-Davis, 1282 Academic Surge, Davis, CA 95616, USA
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156
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Yahr R, Schoch CL, Dentinger BTM. Scaling up discovery of hidden diversity in fungi: impacts of barcoding approaches. Philos Trans R Soc Lond B Biol Sci 2016; 371:20150336. [PMID: 27481788 PMCID: PMC4971188 DOI: 10.1098/rstb.2015.0336] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/31/2016] [Indexed: 11/15/2022] Open
Abstract
The fungal kingdom is a hyperdiverse group of multicellular eukaryotes with profound impacts on human society and ecosystem function. The challenge of documenting and describing fungal diversity is exacerbated by their typically cryptic nature, their ability to produce seemingly unrelated morphologies from a single individual and their similarity in appearance to distantly related taxa. This multiplicity of hurdles resulted in the early adoption of DNA-based comparisons to study fungal diversity, including linking curated DNA sequence data to expertly identified voucher specimens. DNA-barcoding approaches in fungi were first applied in specimen-based studies for identification and discovery of taxonomic diversity, but are now widely deployed for community characterization based on sequencing of environmental samples. Collectively, fungal barcoding approaches have yielded important advances across biological scales and research applications, from taxonomic, ecological, industrial and health perspectives. A major outstanding issue is the growing problem of 'sequences without names' that are somewhat uncoupled from the traditional framework of fungal classification based on morphology and preserved specimens. This review summarizes some of the most significant impacts of fungal barcoding, its limitations, and progress towards the challenge of effective utilization of the exponentially growing volume of data gathered from high-throughput sequencing technologies.This article is part of the themed issue 'From DNA barcodes to biomes'.
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Affiliation(s)
- Rebecca Yahr
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, UK
| | - Conrad L Schoch
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Bryn T M Dentinger
- Royal Botanic Gardens Kew, Richmond, Surrey, UK Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Cledwyn Building, Penglais, Aberystwyth SY23 3DD, UK
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157
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Ashfaq M, Hebert PDN. DNA barcodes for bio-surveillance: regulated and economically important arthropod plant pests. Genome 2016; 59:933-945. [PMID: 27753511 DOI: 10.1139/gen-2016-0024] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Many of the arthropod species that are important pests of agriculture and forestry are impossible to discriminate morphologically throughout all of their life stages. Some cannot be differentiated at any life stage. Over the past decade, DNA barcoding has gained increasing adoption as a tool to both identify known species and to reveal cryptic taxa. Although there has not been a focused effort to develop a barcode library for them, reference sequences are now available for 77% of the 409 species of arthropods documented on major pest databases. Aside from developing the reference library needed to guide specimen identifications, past barcode studies have revealed that a significant fraction of arthropod pests are a complex of allied taxa. Because of their importance as pests and disease vectors impacting global agriculture and forestry, DNA barcode results on these arthropods have significant implications for quarantine detection, regulation, and management. The current review discusses these implications in light of the presence of cryptic species in plant pests exposed by DNA barcoding.
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Affiliation(s)
- Muhammad Ashfaq
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, ON N1G 2W1, Canada.,Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Paul D N Hebert
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, ON N1G 2W1, Canada.,Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, ON N1G 2W1, Canada
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158
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Zhang HG, Lv MH, Yi WB, Zhu WB, Bu WJ. Species diversity can be overestimated by a fixed empirical threshold: insights from DNA barcoding of the genus Cletus (Hemiptera: Coreidae) and the meta-analysis of COI data from previous phylogeographical studies. Mol Ecol Resour 2016; 17:314-323. [PMID: 27437861 DOI: 10.1111/1755-0998.12571] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 05/01/2016] [Accepted: 06/23/2016] [Indexed: 11/28/2022]
Abstract
The use of genetic distances to identify species within the framework of DNA barcoding has to some extent improved the development of biodiversity studies. However, using a fixed empirical threshold to delimit species may lead to overestimating species diversity. In this study, we use a new data set of COI sequences for 366 specimens within the genus of Cletus as well as conduct an analysis on the same genetic data for collected morphologically defined species from previous phylogeographical studies, to test whether high intraspecific genetic divergences are common with the premises of comprehensive sampling. The results indicate C. graminis Hsiao & Cheng , is the same species with C. punctiger (Dallas, 1852) and should be synonymized and that the distributional record of C. pugnator (Fabricius, 1787) in China is correct. High intraspecific genetic differentiations (0%-4.35%) were found in C. punctiger. Furthermore, as to the mined data, the maximum intraspecific K2P distances of 186 species (48.44% of 384) exceed 3%, and 101 species (26.30%) can be divided into two or more clusters with a threshold of 3% in cluster analysis. If genetic distance is used to delimit species boundaries, the minimum interspecific K2P distance of the congeneric species should be considered rather than only using the fixed empirical value; otherwise, the species richness may be overestimated in some cases.
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Affiliation(s)
- Hai-Guang Zhang
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Nankai District, Tianjin, 300071, China.,Shanghai Entomological Museum, Institute of Plant Physiology & Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Xuhui District, Shanghai, 200032, China
| | - Min-Hua Lv
- Center for Experimental Medicine, First Affiliated Hospital of Nanchang University, Nanchang, 330006, China
| | - Wen-Bo Yi
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Nankai District, Tianjin, 300071, China
| | - Wei-Bing Zhu
- Shanghai Entomological Museum, Institute of Plant Physiology & Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Xuhui District, Shanghai, 200032, China
| | - Wen-Jun Bu
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Nankai District, Tianjin, 300071, China
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159
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The probability of monophyly of a sample of gene lineages on a species tree. Proc Natl Acad Sci U S A 2016; 113:8002-9. [PMID: 27432988 DOI: 10.1073/pnas.1601074113] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Monophyletic groups-groups that consist of all of the descendants of a most recent common ancestor-arise naturally as a consequence of descent processes that result in meaningful distinctions between organisms. Aspects of monophyly are therefore central to fields that examine and use genealogical descent. In particular, studies in conservation genetics, phylogeography, population genetics, species delimitation, and systematics can all make use of mathematical predictions under evolutionary models about features of monophyly. One important calculation, the probability that a set of gene lineages is monophyletic under a two-species neutral coalescent model, has been used in many studies. Here, we extend this calculation for a species tree model that contains arbitrarily many species. We study the effects of species tree topology and branch lengths on the monophyly probability. These analyses reveal new behavior, including the maintenance of nontrivial monophyly probabilities for gene lineage samples that span multiple species and even for lineages that do not derive from a monophyletic species group. We illustrate the mathematical results using an example application to data from maize and teosinte.
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160
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Kocher A, Gantier JC, Gaborit P, Zinger L, Holota H, Valiere S, Dusfour I, Girod R, Bañuls AL, Murienne J. Vector soup: high-throughput identification of Neotropical phlebotomine sand flies using metabarcoding. Mol Ecol Resour 2016; 17:172-182. [PMID: 27292284 DOI: 10.1111/1755-0998.12556] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 05/31/2016] [Accepted: 05/31/2016] [Indexed: 11/26/2022]
Abstract
Phlebotomine sand flies are haematophagous dipterans of primary medical importance. They represent the only proven vectors of leishmaniasis worldwide and are involved in the transmission of various other pathogens. Studying the ecology of sand flies is crucial to understand the epidemiology of leishmaniasis and further control this disease. A major limitation in this regard is that traditional morphological-based methods for sand fly species identifications are time-consuming and require taxonomic expertise. DNA metabarcoding holds great promise in overcoming this issue by allowing the identification of multiple species from a single bulk sample. Here, we assessed the reliability of a short insect metabarcode located in the mitochondrial 16S rRNA for the identification of Neotropical sand flies, and constructed a reference database for 40 species found in French Guiana. Then, we conducted a metabarcoding experiment on sand flies mixtures of known content and showed that the method allows an accurate identification of specimens in pools. Finally, we applied metabarcoding to field samples caught in a 1-ha forest plot in French Guiana. Besides providing reliable molecular data for species-level assignations of phlebotomine sand flies, our study proves the efficiency of metabarcoding based on the mitochondrial 16S rRNA for studying sand fly diversity from bulk samples. The application of this high-throughput identification procedure to field samples can provide great opportunities for vector monitoring and eco-epidemiological studies.
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Affiliation(s)
- Arthur Kocher
- CNRS, Université Toulouse III Paul Sabatier, ENFA, UMR5174 EDB (Laboratoire Evolution et Diversité Biologique), Toulouse, France.,UMR MIVEGEC (IRD 224 - CNRS 5290 - Université de Montpellier), 911 Avenue Agropolis, F34394, Montpellier, France
| | - Jean-Charles Gantier
- Laboratoire des Identifications Fongiques et Entomo-parasitologiques, Mennecy, France
| | - Pascal Gaborit
- Medical Entomology Unit, Institut Pasteur de la Guyane, 23 Avenue Pasteur, BP 6010, 97306, Cayenne Cedex, French Guiana
| | - Lucie Zinger
- CNRS, Université Toulouse III Paul Sabatier, ENFA, UMR5174 EDB (Laboratoire Evolution et Diversité Biologique), Toulouse, France
| | - Helene Holota
- CNRS, Université Toulouse III Paul Sabatier, ENFA, UMR5174 EDB (Laboratoire Evolution et Diversité Biologique), Toulouse, France
| | - Sophie Valiere
- GeT-PlaGe, Genotoul, INRA Auzeville, 31326, Castanet-Tolosan, France
| | - Isabelle Dusfour
- Medical Entomology Unit, Institut Pasteur de la Guyane, 23 Avenue Pasteur, BP 6010, 97306, Cayenne Cedex, French Guiana
| | - Romain Girod
- Medical Entomology Unit, Institut Pasteur de la Guyane, 23 Avenue Pasteur, BP 6010, 97306, Cayenne Cedex, French Guiana
| | - Anne-Laure Bañuls
- UMR MIVEGEC (IRD 224 - CNRS 5290 - Université de Montpellier), 911 Avenue Agropolis, F34394, Montpellier, France
| | - Jerome Murienne
- CNRS, Université Toulouse III Paul Sabatier, ENFA, UMR5174 EDB (Laboratoire Evolution et Diversité Biologique), Toulouse, France
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161
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Pentinsaari M, Vos R, Mutanen M. Algorithmic single-locus species delimitation: effects of sampling effort, variation and nonmonophyly in four methods and 1870 species of beetles. Mol Ecol Resour 2016; 17:393-404. [DOI: 10.1111/1755-0998.12557] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 05/30/2016] [Accepted: 05/31/2016] [Indexed: 11/29/2022]
Affiliation(s)
- Mikko Pentinsaari
- Department of Genetics and Physiology; University of Oulu; PO Box 3000 Oulu FI-90014 Finland
| | - Rutger Vos
- Naturalis Biodiversity Center; Darwinweg 4 2333 CR Leiden the Netherlands
| | - Marko Mutanen
- Department of Genetics and Physiology; University of Oulu; PO Box 3000 Oulu FI-90014 Finland
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162
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Subtle Ecological Gradient in the Tropics Triggers High Species-Turnover in a Local Geographical Scale. PLoS One 2016; 11:e0156840. [PMID: 27276228 PMCID: PMC4898766 DOI: 10.1371/journal.pone.0156840] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 05/21/2016] [Indexed: 11/19/2022] Open
Abstract
Our perception of diversity, including both alpha- and beta-diversity components, depends on spatial scale. Studies of spatial variation of the latter are just starting, with a paucity of research on beta-diversity patterns at smaller scales. Understanding these patterns and the processes shaping the distribution of diversity is critical to describe this diversity, but it is paramount in conservation too. Here, we investigate the diversity and structure of a tropical community of herbivorous beetles at a reduced local scale of some 10 km2, evaluating the effect of a small, gradual ecological change on this structure. We sampled leaf beetles in the Núi Chúa National Park (S Vietnam), studying changes in alpha- and beta-diversity across an elevation gradient up to 500 m, encompassing the ecotone between critically endangered lowland dry deciduous forest and mixed evergreen forest at higher elevations. Leaf beetle diversity was assessed using several molecular tree-based species delimitation approaches (with mtDNA cox1 data), species richness using rarefaction and incidence-based diversity indexes, and beta-diversity was investigated decomposing the contribution of species turnover and nestedness. We documented 155 species in the area explored and species-richness estimates 1.5-2.0x higher. Species diversity was similar in both forest types and changes in alpha-diversity along the elevation gradient showed an expected local increase of diversity in the ecotone. Beta-diversity was high among forest paths (average Sørensen's dissimilarity = 0.694) and, tentatively fixing at 300 m the boundary between otherwise continuous biomes, demonstrated similarly high beta-diversity (Sørensen's dissimilarity = 0.581), with samples clustering according to biome/elevation. Highly relevant considering the local scale of the study, beta-diversity had a high contribution of species replacement among locales (54.8%) and between biomes (79.6%), suggesting environmental heterogeneity as the dominant force shaping diversity at such small scale, directly and indirectly on the plant communities. Protection actions in the Park, especially these addressed at the imperative conservation of dry forest, must ponder the small scale at which processes shape species diversity and community structure for inconspicuous, yet extraordinarily diverse organisms such as the leaf beetles.
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163
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Tsai CL, Yeh WB. Subspecific Differentiation Events of Montane Stag Beetles (Coleoptera, Lucanidae) Endemic to Formosa Island. PLoS One 2016; 11:e0156600. [PMID: 27257861 PMCID: PMC4892689 DOI: 10.1371/journal.pone.0156600] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 05/17/2016] [Indexed: 11/18/2022] Open
Abstract
Taxonomic debates have been carrying on for decades over Formosan stag beetles, which consist of a high proportion of endemic species and subspecies featuring morphological variations associated with local adaptation. With the influence of periodical Pleistocene glaciations and the presence of several mountain ranges, the genetic differentiation and taxonomic recognition, within this medium-size island, of two endemic subspecies for each of four montane stag beetles, i.e. Lucanus ogakii, L. kanoi, Prismognathus davidis, and Neolucanus doro, has been an appealing issue. Based on monophyletic lineages and population structure, possible divergent scenarios have been proposed to clarify the subspecific status for each of the above mentioned stag beetles. Phylogenetic inferences based on COI+16S rDNA+28S rDNA of 240 Formosan lucanids have confirmed most species are monophyletic groups; and the intraspecific (<2%) and interspecific (>2%) genetic distances of the two mitochondrial genes could be applied concordantly for taxonomic identification. On account of Bayesian-based species delimitation, geographic distribution, population structure, and sequence divergences, the subspecific status for L. ogakii, L. kanoi, and Pri. davidis are congruent with their geographic distribution in this island; and the calibration time based on the mitochondrial genes shows the subspecific split events occurred 0.7–1 million years ago. In addition, a more complicated scenario, i.e. genetic differentiation including introgression/hybridization events, might have occurred among L. ogakii, L. kanoi, and L. maculifemoratus. The geological effects of mountain hindrance accompanied by periodical glaciations could have been vital in leading to the geographical subspecific differentiation of these montane stag beetles.
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Affiliation(s)
- Cheng-Lung Tsai
- Department of Entomology, National Chung Hsing University, Taichung, Taiwan
| | - Wen-Bin Yeh
- Department of Entomology, National Chung Hsing University, Taichung, Taiwan
- * E-mail:
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164
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Raupach MJ, Hannig K, Morinière J, Hendrich L. A DNA barcode library for ground beetles (Insecta, Coleoptera, Carabidae) of Germany: The genus Bembidion Latreille, 1802 and allied taxa. Zookeys 2016; 592:121-41. [PMID: 27408547 PMCID: PMC4926639 DOI: 10.3897/zookeys.592.8316] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 04/23/2016] [Indexed: 12/23/2022] Open
Abstract
As molecular identification method, DNA barcoding based on partial cytochrome c oxidase subunit 1 (COI) sequences has been proven to be a useful tool for species determination in many insect taxa including ground beetles. In this study we tested the effectiveness of DNA barcodes to discriminate species of the ground beetle genus Bembidion and some closely related taxa of Germany. DNA barcodes were obtained from 819 individuals and 78 species, including sequences from previous studies as well as more than 300 new generated DNA barcodes. We found a 1:1 correspondence between BIN and traditionally recognized species for 69 species (89%). Low interspecific distances with maximum pairwise K2P values below 2.2% were found for three species pairs, including two species pairs with haplotype sharing (Bembidion atrocaeruleum/Bembidion varicolor and Bembidion guttula/Bembidion mannerheimii). In contrast to this, deep intraspecific sequence divergences with distinct lineages were revealed for two species (Bembidion geniculatum/Ocys harpaloides). Our study emphasizes the use of DNA barcodes for the identification of the analyzed ground beetles species and represents an important step in building-up a comprehensive barcode library for the Carabidae in Germany and Central Europe as well.
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Affiliation(s)
- Michael J. Raupach
- Molecular Taxonomy of Marine Organisms, German Centre of Marine Biodiversity Research (DZMB), Senckenberg am Meer, Südstrand 44, 26382 Wilhelmshaven, Germany
| | | | - Jérome Morinière
- Taxonomic coordinator – Barcoding Fauna Bavarica, Bavarian State Collection of Zoology (SNSB – ZSM), Münchhausenstraße 21, 81247 München, Germany
| | - Lars Hendrich
- Sektion Insecta varia, Bavarian State Collection of Zoology (SNSB – ZSM), Münchhausenstraße 21, 81247 München, Germany
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165
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Dahruddin H, Hutama A, Busson F, Sauri S, Hanner R, Keith P, Hadiaty R, Hubert N. Revisiting the ichthyodiversity of Java and Bali through DNA barcodes: taxonomic coverage, identification accuracy, cryptic diversity and identification of exotic species. Mol Ecol Resour 2016; 17:288-299. [DOI: 10.1111/1755-0998.12528] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Revised: 10/22/2015] [Accepted: 10/29/2015] [Indexed: 01/31/2023]
Affiliation(s)
- Hadi Dahruddin
- LIPI; Research Center for Biology; Zoology Division; MZB; Gedung Widyasatwaloka; Jl. Raya Jakarta Bogor Km. 46 Cibinong- Bogor 16911 Indonesia
| | - Aditya Hutama
- Faculty of Mathematics and Natural Science; Animal Bioscience; Bogor Agricultural University; Jl. Raya Darmaga Bogor 16680 Indonesia
| | - Frédéric Busson
- Muséum national d'Histoire naturelle; UMR 7208 (MNHN-CNRS-UPMC-IRD-UCBN); CP 026, 43, rue Cuvier Paris Cedex 05 F-75231 France
| | - Sopian Sauri
- LIPI; Research Center for Biology; Zoology Division; MZB; Gedung Widyasatwaloka; Jl. Raya Jakarta Bogor Km. 46 Cibinong- Bogor 16911 Indonesia
| | - Robert Hanner
- Biodiversity Institute of Ontario and Department of Integrative Biology; University of Guelph; Guelph ON Canada
| | - Philippe Keith
- Muséum national d'Histoire naturelle; UMR 7208 (MNHN-CNRS-UPMC-IRD-UCBN); CP 026, 43, rue Cuvier Paris Cedex 05 F-75231 France
| | - Renny Hadiaty
- LIPI; Research Center for Biology; Zoology Division; MZB; Gedung Widyasatwaloka; Jl. Raya Jakarta Bogor Km. 46 Cibinong- Bogor 16911 Indonesia
| | - Nicolas Hubert
- Institut de Recherche pour le Développement; UMR 226 ISEM (UM2-CNRS-IRD); Place Eugène Bataillon CC 065 F-34095 Montpellier cedex 05 France
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166
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Silveira L, Khattar G, Souto P, Mermudes JRM, Takiya DM, Monteiro RF. Integrative taxonomy of new firefly taxa from the Atlantic Rainforest. SYST BIODIVERS 2016. [DOI: 10.1080/14772000.2016.1153006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Luiz Silveira
- Laboratório de Entomologia, Departamento de Zoologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro, A1-107, Bloco A, Av. Carlos Chagas Filho, 373, Cidade Universitária, Ilha do Fundão, Rio de Janeiro, RJ, Brazil
- Programa de Pós-Graduação em Ecologia/UFRJ, Laboratório de Ecologia de Insetos, Departamento de Ecologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro, A0-113, Bloco A, Av. Carlos Chagas Filho, 373, Cidade Universitária, Ilha do Fundão, Rio de Janeiro, RJ, Brazil
| | - Gabriel Khattar
- Programa de Pós-Graduação em Ecologia/UFRJ, Laboratório de Ecologia de Insetos, Departamento de Ecologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro, A0-113, Bloco A, Av. Carlos Chagas Filho, 373, Cidade Universitária, Ilha do Fundão, Rio de Janeiro, RJ, Brazil
| | - Paula Souto
- Laboratório de Entomologia, Departamento de Zoologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro, A1-107, Bloco A, Av. Carlos Chagas Filho, 373, Cidade Universitária, Ilha do Fundão, Rio de Janeiro, RJ, Brazil
- Programa de Pós-Graduação em Ciências Biológicas (Biologia Animal), Universidade Federal do Espírito Santo, Vitória, ES, Brazil
| | - José Ricardo M. Mermudes
- Laboratório de Entomologia, Departamento de Zoologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro, A1-107, Bloco A, Av. Carlos Chagas Filho, 373, Cidade Universitária, Ilha do Fundão, Rio de Janeiro, RJ, Brazil
| | - Daniela M. Takiya
- Laboratório de Entomologia, Departamento de Zoologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro, A1-107, Bloco A, Av. Carlos Chagas Filho, 373, Cidade Universitária, Ilha do Fundão, Rio de Janeiro, RJ, Brazil
| | - Ricardo F. Monteiro
- Programa de Pós-Graduação em Ecologia/UFRJ, Laboratório de Ecologia de Insetos, Departamento de Ecologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro, A0-113, Bloco A, Av. Carlos Chagas Filho, 373, Cidade Universitária, Ilha do Fundão, Rio de Janeiro, RJ, Brazil
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167
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Sing KW, Dong H, Wang WZ, Wilson JJ. Can butterflies cope with city life? Butterfly diversity in a young megacity in southern China. Genome 2016; 59:751-61. [PMID: 27314400 DOI: 10.1139/gen-2015-0192] [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: 11/22/2022]
Abstract
During 30 years of unprecedented urbanization, plant diversity in Shenzhen, a young megacity in southern China, has increased dramatically. Although strongly associated with plant diversity, butterfly diversity generally declines with urbanization, but this has not been investigated in Shenzhen. Considering the speed of urbanization in Shenzhen and the large number of city parks, we investigated butterfly diversity in Shenzhen parks. We measured butterfly species richness in four microhabitats (groves, hedges, flowerbeds, and unmanaged areas) across 10 parks and examined the relationship with three park variables: park age, park size, and distance from the central business district. Butterflies were identified based on wing morphology and DNA barcoding. We collected 1933 butterflies belonging to 74 species from six families; 20% of the species were considered rare. Butterfly species richness showed weak negative correlations with park age and distance from the central business district, but the positive correlation with park size was statistically significant (p = 0.001). Among microhabitat types, highest species richness was recorded in unmanaged areas. Our findings are consistent with others in suggesting that to promote urban butterfly diversity it is necessary to make parks as large as possible and to set aside areas for limited management. In comparison to neighbouring cities, Shenzhen parks have high butterfly diversity.
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Affiliation(s)
- Kong-Wah Sing
- a Ecology and Biodiversity Program, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia.,b Museum of Zoology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia.,c Fairy Lake Botanical Garden, Shenzhen and Chinese Academy of Sciences, Shenzhen, Guangdong 518004, China
| | - Hui Dong
- c Fairy Lake Botanical Garden, Shenzhen and Chinese Academy of Sciences, Shenzhen, Guangdong 518004, China
| | - Wen-Zhi Wang
- d State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang Donglu, Kunming 650223, China
| | - John-James Wilson
- a Ecology and Biodiversity Program, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia.,b Museum of Zoology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia.,c Fairy Lake Botanical Garden, Shenzhen and Chinese Academy of Sciences, Shenzhen, Guangdong 518004, China
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168
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Ritchie AM, Lo N, Ho SYW. Examining the sensitivity of molecular species delimitations to the choice of mitochondrial marker. ORG DIVERS EVOL 2016. [DOI: 10.1007/s13127-016-0275-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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169
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Kuchta SR, Brown AD, Converse PE, Highton R. Multilocus Phylogeography and Species Delimitation in the Cumberland Plateau Salamander, Plethodon kentucki: Incongruence among Data Sets and Methods. PLoS One 2016; 11:e0150022. [PMID: 26974148 PMCID: PMC4790894 DOI: 10.1371/journal.pone.0150022] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Accepted: 02/08/2016] [Indexed: 11/29/2022] Open
Abstract
Species are a fundamental unit of biodiversity, yet can be challenging to delimit objectively. This is particularly true of species complexes characterized by high levels of population genetic structure, hybridization between genetic groups, isolation by distance, and limited phenotypic variation. Previous work on the Cumberland Plateau Salamander, Plethodon kentucki, suggested that it might constitute a species complex despite occupying a relatively small geographic range. To examine this hypothesis, we sampled 135 individuals from 43 populations, and used four mitochondrial loci and five nuclear loci (5693 base pairs) to quantify phylogeographic structure and probe for cryptic species diversity. Rates of evolution for each locus were inferred using the multidistribute package, and time calibrated gene trees and species trees were inferred using BEAST 2 and *BEAST 2, respectively. Because the parameter space relevant for species delimitation is large and complex, and all methods make simplifying assumptions that may lead them to fail, we conducted an array of analyses. Our assumption was that strongly supported species would be congruent across methods. Putative species were first delimited using a Bayesian implementation of the GMYC model (bGMYC), Geneland, and Brownie. We then validated these species using the genealogical sorting index and BPP. We found substantial phylogeographic diversity using mtDNA, including four divergent clades and an inferred common ancestor at 14.9 myr (95% HPD: 10.8-19.7 myr). By contrast, this diversity was not corroborated by nuclear sequence data, which exhibited low levels of variation and weak phylogeographic structure. Species trees estimated a far younger root than did the mtDNA data, closer to 1.0 myr old. Mutually exclusive putative species were identified by the different approaches. Possible causes of data set discordance, and the problem of species delimitation in complexes with high levels of population structure and introgressive hybridization, are discussed.
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Affiliation(s)
- Shawn R. Kuchta
- Department of Biological Sciences, Ohio Center for Ecology and Evolutionary Studies, Ohio University, Athens, Ohio, United States of America
| | - Ashley D. Brown
- Department of Biological Sciences, Ohio Center for Ecology and Evolutionary Studies, Ohio University, Athens, Ohio, United States of America
| | - Paul E. Converse
- Department of Biological Sciences, Ohio Center for Ecology and Evolutionary Studies, Ohio University, Athens, Ohio, United States of America
| | - Richard Highton
- Department of Biology, University of Maryland, College Park, Maryland, United States of America
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170
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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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171
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Vasconcelos R, Montero-Mendieta S, Simó-Riudalbas M, Sindaco R, Santos X, Fasola M, Llorente G, Razzetti E, Carranza S. Unexpectedly High Levels of Cryptic Diversity Uncovered by a Complete DNA Barcoding of Reptiles of the Socotra Archipelago. PLoS One 2016; 11:e0149985. [PMID: 26930572 PMCID: PMC4772999 DOI: 10.1371/journal.pone.0149985] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 01/28/2016] [Indexed: 11/19/2022] Open
Abstract
Few DNA barcoding studies of squamate reptiles have been conducted. Due to the significance of the Socotra Archipelago (a UNESCO Natural World Heritage site and a biodiversity hotspot) and the conservation interest of its reptile fauna (94% endemics), we performed the most comprehensive DNA barcoding study on an island group to date to test its applicability to specimen identification and species discovery. Reptiles constitute Socotra's most important vertebrate fauna, yet their taxonomy remains under-studied. We successfully DNA-barcoded 380 individuals of all 31 presently recognized species. The specimen identification success rate is moderate to high, and almost all species presented local barcoding gaps. The unexpected high levels of intra-specific variability found within some species suggest cryptic diversity. Species richness may be under-estimated by 13.8-54.4%. This has implications in the species' ranges and conservation status that should be considered for conservation planning. Other phylogenetic studies using mitochondrial and nuclear markers are congruent with our results. We conclude that, despite its reduced length (663 base pairs), cytochrome c oxidase 1, COI, is very useful for specimen identification and for detecting intra-specific diversity, and has a good phylogenetic signal. We recommend DNA barcoding to be applied to other biodiversity hotspots for quickly and cost-efficiently flagging species discovery, preferentially incorporated into an integrative taxonomic framework.
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Affiliation(s)
- Raquel Vasconcelos
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- Institute of Evolutionary Biology (CSIC-UPF, Consejo Superior de Investigaciones Científicas- Universitat Pompeu Fabra), Barcelona, Spain
| | - Santiago Montero-Mendieta
- Institute of Evolutionary Biology (CSIC-UPF, Consejo Superior de Investigaciones Científicas- Universitat Pompeu Fabra), Barcelona, Spain
| | - Marc Simó-Riudalbas
- Institute of Evolutionary Biology (CSIC-UPF, Consejo Superior de Investigaciones Científicas- Universitat Pompeu Fabra), Barcelona, Spain
| | | | - Xavier Santos
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
| | - Mauro Fasola
- Dipartimento Scienze della Terra e dell'Ambiente, Università degli studi di Pavia, Pavia, Italy
| | - Gustavo Llorente
- Departament de Biologia Animal, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| | - Edoardo Razzetti
- Museo di Storia Naturale, Università degli studi di Pavia, Pavia, Italy
| | - Salvador Carranza
- Institute of Evolutionary Biology (CSIC-UPF, Consejo Superior de Investigaciones Científicas- Universitat Pompeu Fabra), Barcelona, Spain
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172
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Drastic underestimation of amphipod biodiversity in the endangered Irano-Anatolian and Caucasus biodiversity hotspots. Sci Rep 2016; 6:22507. [PMID: 26928527 PMCID: PMC4772388 DOI: 10.1038/srep22507] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 02/16/2016] [Indexed: 11/17/2022] Open
Abstract
Biodiversity hotspots are centers of biological diversity and particularly threatened by anthropogenic activities. Their true magnitude of species diversity and endemism, however, is still largely unknown as species diversity is traditionally assessed using morphological descriptions only, thereby ignoring cryptic species. This directly limits evidence-based monitoring and management strategies. Here we used molecular species delimitation methods to quantify cryptic diversity of the montane amphipods in the Irano-Anatolian and Caucasus biodiversity hotspots. Amphipods are ecosystem engineers in rivers and lakes. Species diversity was assessed by analysing two genetic markers (mitochondrial COI and nuclear 28S rDNA), compared with morphological assignments. Our results unambiguously demonstrate that species diversity and endemism is dramatically underestimated, with 42 genetically identified freshwater species in only five reported morphospecies. Over 90% of the newly recovered species cluster inside Gammarus komareki and G. lacustris; 69% of the recovered species comprise narrow range endemics. Amphipod biodiversity is drastically underestimated for the studied regions. Thus, the risk of biodiversity loss is significantly greater than currently inferred as most endangered species remain unrecognized and/or are only found locally. Integrative application of genetic assessments in monitoring programs will help to understand the true magnitude of biodiversity and accurately evaluate its threat status.
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173
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Garnica S, Schön ME, Abarenkov K, Riess K, Liimatainen K, Niskanen T, Dima B, Soop K, Frøslev TG, Jeppesen TS, Peintner U, Kuhnert-Finkernagel R, Brandrud TE, Saar G, Oertel B, Ammirati JF. Determining threshold values for barcoding fungi: lessons from Cortinarius (Basidiomycota), a highly diverse and widespread ectomycorrhizal genus. FEMS Microbiol Ecol 2016; 92:fiw045. [PMID: 26929438 DOI: 10.1093/femsec/fiw045] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Indexed: 11/14/2022] Open
Abstract
Different distance-based threshold selection approaches were used to assess and compare use of the internal transcribed spacer (ITS) region to distinguish among 901 Cortinarius species represented by >3000 collections. Sources of error associated with genetic markers and selection approaches were explored and evaluated using MOTUs from genus and lineage based-alignments. Our study indicates that 1%-2% more species can be distinguished by using the full-length ITS barcode as compared to either the ITS1 or ITS2 regions alone. Optimal threshold values for different picking approaches and genetic marker lengths inferred from a subset of species containing major lineages ranged from 97.0% to 99.5% sequence similarity using clustering optimization and UNITE SH, and from 1% to 2% sequence dissimilarity with CROP. Errors for the optimal cutoff ranged from 0% to 70%, and these can be reduced to a maximum of 22% when excluding species lacking a barcode gap. A threshold value of 99% is suitable for distinguishing species in the majority of lineages in the genus using the entire ITS region but only 90% of the species could be identified using just the ITS1 or ITS2 region. Prior identification of species, lacking barcode gaps and their subsequent separate analyses, maximized the accuracy of threshold approaches.
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Affiliation(s)
- Sigisfredo Garnica
- Institute of Evolution and Ecology, Plant Evolutionary Ecology, University of Tübingen, Auf der Morgenstelle 5, D-72076 Tübingen, Germany
| | - Max Emil Schön
- Institute of Evolution and Ecology, Plant Evolutionary Ecology, University of Tübingen, Auf der Morgenstelle 5, D-72076 Tübingen, Germany
| | - Kessy Abarenkov
- Institute of Ecology and Earth Sciences, University of Tartu, 51005 Tartu, Estonia
| | - Kai Riess
- Institute of Evolution and Ecology, Plant Evolutionary Ecology, University of Tübingen, Auf der Morgenstelle 5, D-72076 Tübingen, Germany
| | - Kare Liimatainen
- Department of Biosciences, Plant Biology, University of Helsinki, PO Box 65, 00014 Lahti, Finland
| | - Tuula Niskanen
- Jodrell Laboratory, Royal Botanic Gardens, Kew, TW9 3DS, UK
| | - Bálint Dima
- Department of Biosciences, Plant Biology, University of Helsinki, PO Box 65, 00014 Lahti, Finland
| | - Karl Soop
- Honorary Research Associate, Swedish Museum of Natural History, Department of Cryptogamic Botany, Naturhistoriska riksmuseet, 104 05 Stockholm, Sweden
| | - Tobias Guldberg Frøslev
- Natural History Museum of Denmark, Center for Geogenetics, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark
| | - Thomas Stjernegaard Jeppesen
- Natural History Museum of Denmark, Collections, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen Ø, Denmark
| | - Ursula Peintner
- Institute of Microbiology, University Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
| | | | - Tor Erik Brandrud
- Department of Landscape Ecology (Oslo), Norwegian Institute for Nature Research, N-Oslo 5, Norway
| | | | - Bernhard Oertel
- INRES, University of Bonn, Auf dem Hügel 6, D-53121 Bonn, Germany
| | - Joseph F Ammirati
- Department of Biology, University of Washington, Seattle, Washington 98195, USA
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174
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Fossen EI, Ekrem T, Nilsson AN, Bergsten J. Species delimitation in northern European water scavenger beetles of the genus Hydrobius (Coleoptera, Hydrophilidae). Zookeys 2016; 564:71-120. [PMID: 27081333 PMCID: PMC4820092 DOI: 10.3897/zookeys.564.6558] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2015] [Accepted: 12/23/2015] [Indexed: 12/18/2022] Open
Abstract
The chiefly Holarctic Hydrobius species complex (Coleoptera, Hydrophilidae) currently consists of Hydrobius arcticus Kuwert, 1890, and three morphological variants of Hydrobius fuscipes (Linnaeus, 1758): var. fuscipes, var. rottenbergii and var. subrotundus in northern Europe. Here molecular and morphological data are used to test the species boundaries in this species complex. Three gene segments (COI, H3 and ITS2) were sequenced and analyzed with Bayesian methods to infer phylogenetic relationships. The Generalized Mixed Yule Coalescent (GMYC) model and two versions of the Bayesian species delimitation method BPP, with or without an a priori defined guide tree (v2.2 & v3.0), were used to evaluate species limits. External and male genital characters of primarily Fennoscandian specimens were measured and statistically analyzed to test for significant differences in quantitative morphological characters. The four morphotypes formed separate genetic clusters on gene trees and were delimited as separate species by GMYC and by both versions of BPP, despite specimens of Hydrobius fuscipes var. fuscipes and Hydrobius fuscipes var. subrotundus being sympatric. Hydrobius arcticus and Hydrobius fuscipes var. rottenbergii could only be separated genetically with ITS2, and were delimited statistically with GMYC on ITS2 and with BPP on the combined data. In addition, six or seven potentially cryptic species of the Hydrobius fuscipes complex from regions outside northern Europe were delimited genetically. Although some overlap was found, the mean values of six male genital characters were significantly different between the morphotypes (p < 0.001). Morphological characters previously presumed to be diagnostic were less reliable to separate Hydrobius fuscipes var. fuscipes from Hydrobius fuscipes var. subrotundus, but characters in the literature for Hydrobius arcticus and Hydrobius fuscipes var. rottenbergii were diagnostic. Overall, morphological and molecular evidence strongly suggest that Hydrobius arcticus and the three morphological variants of Hydrobius fuscipes are separate species and Hydrobius rottenbergii Gerhardt, 1872, stat. n. and Hydrobius subrotundus Stephens, 1829, stat. n. are elevated to valid species. An identification key to northern European species of Hydrobius is provided.
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Affiliation(s)
- Erlend I. Fossen
- Department of Biology, Centre for Biodiversity Dynamics, NTNU Norwegian University of Science and Technology, 7491 Trondheim, Norway
- Department of Natural History, NTNU University Museum, 7491 Trondheim, Norway
| | - Torbjørn Ekrem
- Department of Natural History, NTNU University Museum, 7491 Trondheim, Norway
| | - Anders N. Nilsson
- Department of Ecology and Environmental Science, University of Umeå, S-901 87 Umeå, Sweden
| | - Johannes Bergsten
- Department of Zoology, Swedish Museum of Natural History, Box 50007, SE-10405 Stockholm, Sweden
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175
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With a little help from DNA barcoding: investigating the diversity of Gastropoda from the Portuguese coast. Sci Rep 2016; 6:20226. [PMID: 26876495 PMCID: PMC4753432 DOI: 10.1038/srep20226] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 12/30/2015] [Indexed: 01/13/2023] Open
Abstract
The Gastropoda is one of the best studied classes of marine invertebrates. Yet, most species have been delimited based on morphology only. The application of DNA barcodes has shown to be greatly useful to help delimiting species. Therefore, sequences of the cytochrome c oxidase I gene from 108 specimens of 34 morpho-species were used to investigate the molecular diversity within the gastropods from the Portuguese coast. To the above dataset, we added available COI-5P sequences of taxonomically close species, in a total of 58 morpho-species examined. There was a good match between ours and sequences from independent studies, in public repositories. We found 32 concordant (91.4%) out of the 35 Barcode Index Numbers (BINs) generated from our sequences. The application of a ranking system to the barcodes yield over 70% with top taxonomic congruence, while 14.2% of the species barcodes had insufficient data. In the majority of the cases, there was a good concordance between morphological identification and DNA barcodes. Nonetheless, the discordance between morphological and molecular data is a reminder that even the comparatively well-known European marine gastropods can benefit from being probed using the DNA barcode approach. Discordant cases should be reviewed with more integrative studies.
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176
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Thormann B, Ahrens D, Marín Armijos D, Peters MK, Wagner T, Wägele JW. Exploring the Leaf Beetle Fauna (Coleoptera: Chrysomelidae) of an Ecuadorian Mountain Forest Using DNA Barcoding. PLoS One 2016; 11:e0148268. [PMID: 26849826 PMCID: PMC4744027 DOI: 10.1371/journal.pone.0148268] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 01/16/2016] [Indexed: 12/15/2022] Open
Abstract
Background Tropical mountain forests are hotspots of biodiversity hosting a huge but little known diversity of insects that is endangered by habitat destruction and climate change. Therefore, rapid assessment approaches of insect diversity are urgently needed to complement slower traditional taxonomic approaches. We empirically compare different DNA-based species delimitation approaches for a rapid biodiversity assessment of hyperdiverse leaf beetle assemblages along an elevational gradient in southern Ecuador and explore their effect on species richness estimates. Methodology/Principal Findings Based on a COI barcode data set of 674 leaf beetle specimens (Coleoptera: Chrysomelidae) of 266 morphospecies from three sample sites in the Podocarpus National Park, we employed statistical parsimony analysis, distance-based clustering, GMYC- and PTP-modelling to delimit species-like units and compared them to morphology-based (parataxonomic) species identifications. The four different approaches for DNA-based species delimitation revealed highly similar numbers of molecular operational taxonomic units (MOTUs) (n = 284–289). Estimated total species richness was considerably higher than the sampled amount, 414 for morphospecies (Chao2) and 469–481 for the different MOTU types. Assemblages at different elevational levels (1000 vs. 2000 m) had similar species numbers but a very distinct species composition for all delimitation methods. Most species were found only at one elevation while this turnover pattern was even more pronounced for DNA-based delimitation. Conclusions/Significance Given the high congruence of DNA-based delimitation results, probably due to the sampling structure, our study suggests that when applied to species communities on a regionally limited level with high amount of rare species (i.e. ~50% singletons), the choice of species delimitation method can be of minor relevance for assessing species numbers and turnover in tropical insect communities. Therefore, DNA-based species delimitation is confirmed as a valuable tool for evaluating biodiversity of hyperdiverse insect communities, especially when exact taxonomic identifications are missing.
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Affiliation(s)
- Birthe Thormann
- Zoological Research Museum Alexander Koenig, Bonn, Germany
- * E-mail:
| | - Dirk Ahrens
- Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Diego Marín Armijos
- Museo de Colecciones Biológicas MUTPL, Departamento de Ciencias Naturales, Universidad Técnica Particular de Loja, Loja, Ecuador
| | - Marcell K. Peters
- Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Thomas Wagner
- Abteilung Biologie, Institut für Integrierte Naturwissenschaften, Universität Koblenz–Landau, Koblenz, Germany
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177
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Failla AJ, Vasquez AA, Hudson P, Fujimoto M, Ram JL. Morphological identification and COI barcodes of adult flies help determine species identities of chironomid larvae (Diptera, Chironomidae). BULLETIN OF ENTOMOLOGICAL RESEARCH 2016; 106:34-46. [PMID: 26072670 DOI: 10.1017/s0007485315000486] [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] [Indexed: 06/04/2023]
Abstract
Establishing reliable methods for the identification of benthic chironomid communities is important due to their significant contribution to biomass, ecology and the aquatic food web. Immature larval specimens are more difficult to identify to species level by traditional morphological methods than their fully developed adult counterparts, and few keys are available to identify the larval species. In order to develop molecular criteria to identify species of chironomid larvae, larval and adult chironomids from Western Lake Erie were subjected to both molecular and morphological taxonomic analysis. Mitochondrial cytochrome c oxidase I (COI) barcode sequences of 33 adults that were identified to species level by morphological methods were grouped with COI sequences of 189 larvae in a neighbor-joining taxon-ID tree. Most of these larvae could be identified only to genus level by morphological taxonomy (only 22 of the 189 sequenced larvae could be identified to species level). The taxon-ID tree of larval sequences had 45 operational taxonomic units (OTUs, defined as clusters with >97% identity or individual sequences differing from nearest neighbors by >3%; supported by analysis of all larval pairwise differences), of which seven could be identified to species or 'species group' level by larval morphology. Reference sequences from the GenBank and BOLD databases assigned six larval OTUs with presumptive species level identifications and confirmed one previously assigned species level identification. Sequences from morphologically identified adults in the present study grouped with and further classified the identity of 13 larval OTUs. The use of morphological identification and subsequent DNA barcoding of adult chironomids proved to be beneficial in revealing possible species level identifications of larval specimens. Sequence data from this study also contribute to currently inadequate public databases relevant to the Great Lakes region, while the neighbor-joining analysis reported here describes the application and confirmation of a useful tool that can accelerate identification and bioassessment of chironomid communities.
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Affiliation(s)
- A J Failla
- Department of Physiology,Wayne State University School of Medicine,5374 Scott Hall,540 E. Canfield St.,Detroit,MI 48201
| | - A A Vasquez
- Department of Physiology,Wayne State University School of Medicine,5374 Scott Hall,540 E. Canfield St.,Detroit,MI 48201
| | - P Hudson
- Great Lakes Science Center,U.S. Geological Survey,1451 Green Road,Ann Arbor,MI 48105,USA
| | - M Fujimoto
- Department of Physiology,Wayne State University School of Medicine,5374 Scott Hall,540 E. Canfield St.,Detroit,MI 48201
| | - J L Ram
- Department of Physiology,Wayne State University School of Medicine,5374 Scott Hall,540 E. Canfield St.,Detroit,MI 48201
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178
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De Biase A, Colonnelli E, Belvedere S, La Marca A, Cristofaro M, Smith L. Genetic and morphological studies of Trichosirocalus species introduced to North America, Australia and New Zealand for the biological control of thistles. BULLETIN OF ENTOMOLOGICAL RESEARCH 2016; 106:99-113. [PMID: 26548721 DOI: 10.1017/s000748531500084x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Trichosirocalus horridus sensu lato has been used as a biological control agent of several invasive thistles (Carduus spp., Cirsium spp. and Onopordum spp.) since 1974. It has been recognized as a single species until 2002, when it was split into three species based on morphological characters: T. horridus, Trichosirocalus briesei and Trichosirocalus mortadelo, each purported to have different host plants. Because of this taxonomic change, uncertainty exists as to which species were released in various countries; furthermore, there appears to be some exceptions to the purported host plants of some of these species. To resolve these questions, we conducted an integrative taxonomic study of the T. horridus species complex using molecular genetic and morphological analyses of specimens from three continents. Both mitochondrial cytochrome c oxidase subunit I and nuclear elongation factor 1α markers clearly indicate that there are only two distinct species, T. horridus and T. briesei. Molecular evidence, morphological analysis and host plant associations support the synonymy of T. horridus (Panzer, 1801) and T. mortadelo Alonso-Zarazaga & Sánchez-Ruiz, 2002. We determine that T. horridus has been established in Canada, USA, New Zealand and Australia and that T. briesei is established in Australia. The former species was collected from Carduus, Cirsium and Onopordum spp. in the field, whereas the latter appears to be specific to Onopordum.
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Affiliation(s)
- A De Biase
- Dipartimento di Biologia e Biotecnologie 'Charles Darwin',Università di Roma La Sapienza,Viale dell'Università 32,00185 Rome,Italy
| | | | - S Belvedere
- Dipartimento di Biologia e Biotecnologie 'Charles Darwin',Università di Roma La Sapienza,Viale dell'Università 32,00185 Rome,Italy
| | - A La Marca
- BBCA-onlus,Via Angelo Signorelli 105,00123 Rome,Italy
| | - M Cristofaro
- ENEA C.R. Casaccia SSPT-BIOAG-PROBIO,Via Anguillarese 301,00123 S. Maria di Galeria (Rome),Italy
| | - L Smith
- USDA-ARS,810 Avenue du Campus Agropolis,34980 Montferrier-sur-Lez,France
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179
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Klopfstein S, Kropf C, Baur H. Wolbachiaendosymbionts distort DNA barcoding in the parasitoid wasp genusDiplazon(Hymenoptera: Ichneumonidae). Zool J Linn Soc 2016. [DOI: 10.1111/zoj.12380] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Seraina Klopfstein
- Department of Invertebrates; Naturhistorisches Museum der Burgergemeinde Bern; Bernastrasse 15 CH-3005 Bern Switzerland
- Division of Community Ecology; Institute of Ecology and Evolution; University of Bern; Baltzerstrasse 7 3012 Bern Switzerland
| | - Christian Kropf
- Department of Invertebrates; Naturhistorisches Museum der Burgergemeinde Bern; Bernastrasse 15 CH-3005 Bern Switzerland
- Division of Community Ecology; Institute of Ecology and Evolution; University of Bern; Baltzerstrasse 7 3012 Bern Switzerland
| | - Hannes Baur
- Department of Invertebrates; Naturhistorisches Museum der Burgergemeinde Bern; Bernastrasse 15 CH-3005 Bern Switzerland
- Division of Community Ecology; Institute of Ecology and Evolution; University of Bern; Baltzerstrasse 7 3012 Bern Switzerland
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180
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Mamos T, Wattier R, Burzyński A, Grabowski M. The legacy of a vanished sea: a high level of diversification within a European freshwater amphipod species complex driven by 15 My of Paratethys regression. Mol Ecol 2016; 25:795-810. [DOI: 10.1111/mec.13499] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Revised: 11/19/2015] [Accepted: 11/24/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Tomasz Mamos
- Department of Invertebrate Zoology and Hydrobiology; University of Lodz; Banacha 12/16, 90-237 Lodz Poland
| | - Remi Wattier
- Equipe Ecologie Evolutive; UMR CNRS 6282 Biogéosciences; Université de Bourgogne; 6 Boulevard Gabriel 21000 Dijon France
| | - Artur Burzyński
- Department of Genetics and Marine Biotechnology; Institute of Oceanology, Polish Academy of Sciences; Powstańców Warszawy 55 81-712 Sopot, Poland
| | - Michał Grabowski
- Department of Invertebrate Zoology and Hydrobiology; University of Lodz; Banacha 12/16, 90-237 Lodz Poland
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181
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Guarnizo CE, Werneck FP, Giugliano LG, Santos MG, Fenker J, Sousa L, D’Angiolella AB, dos Santos AR, Strüssmann C, Rodrigues MT, Dorado-Rodrigues TF, Gamble T, Colli GR. Cryptic lineages and diversification of an endemic anole lizard (Squamata, Dactyloidae) of the Cerrado hotspot. Mol Phylogenet Evol 2016; 94:279-89. [DOI: 10.1016/j.ympev.2015.09.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 08/06/2015] [Accepted: 09/08/2015] [Indexed: 01/17/2023]
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182
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Martinsson S, Rhodén C, Erséus C. Barcoding gap, but no support for cryptic speciation in the earthworm Aporrectodea longa (Clitellata: Lumbricidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 28:147-155. [PMID: 26709635 DOI: 10.3109/19401736.2015.1115487] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
DNA-barcoding, using the mitochondrial marker COI, has been found successful for the identification of specimens in many animal groups, but may not be suited for species discovery and delimitation if used alone. In this study, we investigate whether two observed COI haplogroups in the earthworm Aporrectodea longa correspond to two cryptic species or if the variation is intraspecific. This is done by complementing COI with two nuclear markers, ITS2 and Histone 3. The variation is studied using distance methods, parsimony networks and Bayesian coalescent trees, and the statistical distinctness of the groups is tested on gene trees using the genealogical sorting index, Rosenberg's PAB and Rodrigo et al.'s P(RD). We also applied multilocus species delimitation based on the multispecies coalescence model. The two haplogroups were found in COI, and all tests except P(RD) found them to be significantly distinct. However, in ITS2, the same groups were not recovered in any analyses or tests. H3 was invariable in A. longa, and was, therefore, included only in the multilocus analysis, which preferred a model treating A. longa as one species over a model splitting it into two. We also compared two measurements of size, body length, and no. of segments between the groups. No difference in body length was found, and although a significant difference in no. of segments was noted the haplogroup with the lower mean showed both the highest and the lowest value. When combined, these results led us to the conclusion that there is no support for the separation of A. longa into two cryptic species. This study again highlights the importance of complementing mitochondrial barcodes with more data when establishing species boundaries.
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Affiliation(s)
- Svante Martinsson
- a Division of Systematics and Biodiversity, Department of Biological and Environmental Sciences , University of Gothenburg , Göteborg , Sweden
| | - Caroline Rhodén
- a Division of Systematics and Biodiversity, Department of Biological and Environmental Sciences , University of Gothenburg , Göteborg , Sweden
| | - Christer Erséus
- a Division of Systematics and Biodiversity, Department of Biological and Environmental Sciences , University of Gothenburg , Göteborg , Sweden
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183
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Luo A, Lan H, Ling C, Zhang A, Shi L, Ho SYW, Zhu C. A simulation study of sample size for DNA barcoding. Ecol Evol 2015; 5:5869-79. [PMID: 26811761 PMCID: PMC4717336 DOI: 10.1002/ece3.1846] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 10/20/2015] [Accepted: 10/21/2015] [Indexed: 01/31/2023] Open
Abstract
For some groups of organisms, DNA barcoding can provide a useful tool in taxonomy, evolutionary biology, and biodiversity assessment. However, the efficacy of DNA barcoding depends on the degree of sampling per species, because a large enough sample size is needed to provide a reliable estimate of genetic polymorphism and for delimiting species. We used a simulation approach to examine the effects of sample size on four estimators of genetic polymorphism related to DNA barcoding: mismatch distribution, nucleotide diversity, the number of haplotypes, and maximum pairwise distance. Our results showed that mismatch distributions derived from subsamples of ≥20 individuals usually bore a close resemblance to that of the full dataset. Estimates of nucleotide diversity from subsamples of ≥20 individuals tended to be bell‐shaped around that of the full dataset, whereas estimates from smaller subsamples were not. As expected, greater sampling generally led to an increase in the number of haplotypes. We also found that subsamples of ≥20 individuals allowed a good estimate of the maximum pairwise distance of the full dataset, while smaller ones were associated with a high probability of underestimation. Overall, our study confirms the expectation that larger samples are beneficial for the efficacy of DNA barcoding and suggests that a minimum sample size of 20 individuals is needed in practice for each population.
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Affiliation(s)
- Arong Luo
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing 100101 China
| | - Haiqiang Lan
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing 100101 China; School of Statistics and Mathematics Yunnan University of Finance and Economics Kunming 650221 China
| | - Cheng Ling
- Department of Computer Science and Technology College of Information Science and Technology Beijing University of Chemical Technology Beijing 100029 China
| | - Aibing Zhang
- College of Life Sciences Capital Normal University Beijing 100048 China
| | - Lei Shi
- School of Statistics and Mathematics Yunnan University of Finance and Economics Kunming 650221 China
| | - Simon Y W Ho
- School of Biological Sciences University of Sydney Sydney New South Wales 2006 Australia
| | - Chaodong Zhu
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing 100101 China; College of Life Sciences University of Chinese Academy of Sciences Beijing 100049 China
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184
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Argüello Caro EB, Dumón AD, Mattio MF, Alemandri V, Truol G. A molecular framework for the identification of planthopper vectors (Hemiptera: Delphacidae) of central Argentina. BULLETIN OF ENTOMOLOGICAL RESEARCH 2015; 105:754-762. [PMID: 26353811 DOI: 10.1017/s0007485315000735] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Planthoppers are important worldwide crop pests as well as vectors of numerous diseases. Different species transmit Mal de Río Cuarto virus, which causes the most economically important corn disease in central Argentina. Epidemiological studies rely on the accurate identification of the species present in the field. Presently, morphological identification of planthoppers requires taxonomic expertise and there are no taxonomic keys for females and nymphs. Nevertheless, no molecular protocols are available for accurate species identification of most frequent delphacid species from central Argentina. In this context, the aim of this study was to evaluate the utility of the cytochrome oxidase I gene (COI) as a DNA barcode and its digestion with restriction enzymes (Restriction Fragment Length Polymorphism, RFLP) for the identification of the most common species of planthoppers in central Argentina. We amplified and sequenced a 843 bp fragment of the COI gene of taxonomically identified specimens and evaluated its use as a DNA barcode. Restriction enzymes were also selected for digesting the COI fragment via RFLP. The high interspecific variability (20.79%; ± 2.32%) and low intraspecific divergence (0.12%; ± 0.17%) observed in the studied species, demonstrate the effectiveness of the COI gene for species identification of major vector delphacids affecting corn crops in Argentina. Moreover, the digestion of this COI gene fragment with Bfa I and Apo I enzymes allows a fast and cost-effective species identification method when numerous specimens need to be processed. Both molecular techniques developed here, allow the accurate identification of planthopper species at regional scale. These new tools would assist traditional identification of these insects, especially for aiding non-experts in morphological taxonomy.
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Affiliation(s)
- E B Argüello Caro
- Instituto de Patología Vegetal - Centro de Investigaciones Agropecuarias - Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA).Av. 11 de Septiembre 4755,B° Cárcano,Ciudad de Córdoba. CP X5020ICA,Córdoba,Argentina
| | - A D Dumón
- Instituto de Patología Vegetal - Centro de Investigaciones Agropecuarias - Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA).Av. 11 de Septiembre 4755,B° Cárcano,Ciudad de Córdoba. CP X5020ICA,Córdoba,Argentina
| | - M F Mattio
- Instituto de Patología Vegetal - Centro de Investigaciones Agropecuarias - Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA).Av. 11 de Septiembre 4755,B° Cárcano,Ciudad de Córdoba. CP X5020ICA,Córdoba,Argentina
| | - V Alemandri
- Instituto de Patología Vegetal - Centro de Investigaciones Agropecuarias - Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA).Av. 11 de Septiembre 4755,B° Cárcano,Ciudad de Córdoba. CP X5020ICA,Córdoba,Argentina
| | - G Truol
- Instituto de Patología Vegetal - Centro de Investigaciones Agropecuarias - Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA).Av. 11 de Septiembre 4755,B° Cárcano,Ciudad de Córdoba. CP X5020ICA,Córdoba,Argentina
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185
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Drotz MK, Brodin T, Nilsson AN. Changing Names with Changed Address: Integrated Taxonomy and Species Delimitation in the Holarctic Colymbetes paykulli Group (Coleoptera: Dytiscidae). PLoS One 2015; 10:e0143577. [PMID: 26619278 PMCID: PMC4664258 DOI: 10.1371/journal.pone.0143577] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 11/08/2015] [Indexed: 11/29/2022] Open
Abstract
Species delimitation of geographically isolated forms is a long-standing problem in less studied insect groups. Often taxonomic decisions are based directly on morphologic variation, and lack a discussion regarding sample size and the efficiency of migration barriers or dispersal/migration capacity of the studied species. These problems are here exemplified in a water beetle complex from the Bering Sea region that separates North America from Eurasia. Only a few sampled specimens occur from this particular area and they are mostly found in museum and private collections. Here we utilize the theory of integrated taxonomy to discuss the speciation of the Holarctic Colymbetes paykulli water beetle complex, which historically has included up to five species of which today only two are recognized. Three delimitation methods are used; landmark based morphometry of body shape, variation in reticulation patterns of the pronotum exo-skeleton and sequence variation of the partial mitochondrial gene Cyt b. Our conclusion is that the Palearctic and Nearctic populations of C. paykulli are given the status of separate species, based on the fact that all methods showed significant separation between populations. As a consequence the name of the Palearctic species is C. paykulli Erichson and the Nearctic species should be known as C. longulus LeConte. There is no clear support for delineation between Palearctic and Nearctic populations of C. dahuricus based on mtDNA. However, significant difference in size and reticulation patterns from the two regions is shown. The combined conclusion is that the C. dahuricus complex needs a more thorough investigation to fully disentangle its taxonomic status. Therefore it is here still regarded as a Holarctic species. This study highlights the importance to study several diagnosable characters that has the potential to discriminate evolutionary lineage during speciation.
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Affiliation(s)
- Marcus K. Drotz
- Lake Vänern Museum of Natural and Cultural History, Lidköping, Västra Götaland, Sweden
| | - Tomas Brodin
- Department of Ecology and Environmental Science, Umeå University, Umeå, Västerbotten, Sweden
| | - Anders N. Nilsson
- Department of Ecology and Environmental Science, Umeå University, Umeå, Västerbotten, Sweden
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186
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Ryberg M. Molecular operational taxonomic units as approximations of species in the light of evolutionary models and empirical data from Fungi. Mol Ecol 2015; 24:5770-7. [DOI: 10.1111/mec.13444] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 10/23/2015] [Accepted: 10/27/2015] [Indexed: 11/27/2022]
Affiliation(s)
- Martin Ryberg
- Systematic Biology; Evolutionary Biology Centre; Uppsala University; Norbyvägen 18D 75236 Uppsala Sweden
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187
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Raupach MJ, Radulovici AE. Looking back on a decade of barcoding crustaceans. Zookeys 2015; 539:53-81. [PMID: 26798245 PMCID: PMC4714055 DOI: 10.3897/zookeys.539.6530] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 10/20/2015] [Indexed: 02/07/2023] Open
Abstract
Species identification represents a pivotal component for large-scale biodiversity studies and conservation planning but represents a challenge for many taxa when using morphological traits only. Consequently, alternative identification methods based on molecular markers have been proposed. In this context, DNA barcoding has become a popular and accepted method for the identification of unknown animals across all life stages by comparison to a reference library. In this review we examine the progress of barcoding studies for the Crustacea using the Web of Science data base from 2003 to 2014. All references were classified in terms of taxonomy covered, subject area (identification/library, genetic variability, species descriptions, phylogenetics, methods, pseudogenes/numts), habitat, geographical area, authors, journals, citations, and the use of the Barcode of Life Data Systems (BOLD). Our analysis revealed a total number of 164 barcoding studies for crustaceans with a preference for malacostracan crustaceans, in particular Decapoda, and for building reference libraries in order to identify organisms. So far, BOLD did not establish itself as a popular informatics platform among carcinologists although it offers many advantages for standardized data storage, analyses and publication.
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Affiliation(s)
- Michael J. Raupach
- Molecular Taxonomy of Marine Organisms, German Centre of Marine Biodiversity Research (DZMB), Senckenberg am Meer, Südstrand 44, 26382 Wilhelmshaven, Germany
| | - Adriana E. Radulovici
- Biodiversity Institute of Ontario (BIO), University of Guelph, 50 Stone Road E, Guelph (ON) N1G 2W1, Ontario, Canada
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188
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The Dual Challenges of Generality and Specificity When Developing Environmental DNA Markers for Species and Subspecies of Oncorhynchus. PLoS One 2015; 10:e0142008. [PMID: 26536367 PMCID: PMC4633235 DOI: 10.1371/journal.pone.0142008] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 10/15/2015] [Indexed: 11/29/2022] Open
Abstract
Environmental DNA (eDNA) sampling is a powerful tool for detecting invasive and native aquatic species. Often, species of conservation interest co-occur with other, closely related taxa. Here, we developed qPCR (quantitative PCR) markers which distinguish westslope cutthroat trout (Oncorhynchus clarkii lewsi), Yellowstone cutthroat trout (O. clarkii bouvieri), and rainbow trout (O. mykiss), which are of conservation interest both as native species and as invasive species across each other’s native ranges. We found that local polymorphisms within westslope cutthroat trout and rainbow trout posed a challenge to designing assays that are generally applicable across the range of these widely-distributed species. Further, poorly-resolved taxonomies of Yellowstone cutthroat trout and Bonneville cutthroat trout (O. c. utah) prevented design of an assay that distinguishes these recognized taxa. The issues of intraspecific polymorphism and unresolved taxonomy for eDNA assay design addressed in this study are likely to be general problems for closely-related taxa. Prior to field application, we recommend that future studies sample populations and test assays more broadly than has been typical of published eDNA assays to date.
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189
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Pinto IDS, Chagas BDD, Rodrigues AAF, Ferreira AL, Rezende HR, Bruno RV, Falqueto A, Andrade-Filho JD, Galati EAB, Shimabukuro PHF, Brazil RP, Peixoto AA. DNA Barcoding of Neotropical Sand Flies (Diptera, Psychodidae, Phlebotominae): Species Identification and Discovery within Brazil. PLoS One 2015; 10:e0140636. [PMID: 26506007 PMCID: PMC4624639 DOI: 10.1371/journal.pone.0140636] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 08/19/2015] [Indexed: 11/24/2022] Open
Abstract
DNA barcoding has been an effective tool for species identification in several animal groups. Here, we used DNA barcoding to discriminate between 47 morphologically distinct species of Brazilian sand flies. DNA barcodes correctly identified approximately 90% of the sampled taxa (42 morphologically distinct species) using clustering based on neighbor-joining distance, of which four species showed comparatively higher maximum values of divergence (range 4.23–19.04%), indicating cryptic diversity. The DNA barcodes also corroborated the resurrection of two species within the shannoni complex and provided an efficient tool to differentiate between morphologically indistinguishable females of closely related species. Taken together, our results validate the effectiveness of DNA barcoding for species identification and the discovery of cryptic diversity in sand flies from Brazil.
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Affiliation(s)
- Israel de Souza Pinto
- Lab. de Biologia Molecular de Insetos, Instituto Oswaldo Cruz, FIOCRUZ, Brasil Ave. 4365, 21040360, Rio de Janeiro, RJ, Brazil
- Unidade de Medicina Tropical, UFES, Marechal Campos Ave. 1468, 29043900, Vitória, Espírito Santo, Brazil
- * E-mail:
| | - Bruna Dias das Chagas
- Lab. de Biologia Molecular de Insetos, Instituto Oswaldo Cruz, FIOCRUZ, Brasil Ave. 4365, 21040360, Rio de Janeiro, RJ, Brazil
| | | | - Adelson Luiz Ferreira
- Unidade de Medicina Tropical, UFES, Marechal Campos Ave. 1468, 29043900, Vitória, Espírito Santo, Brazil
| | - Helder Ricas Rezende
- Unidade de Medicina Tropical, UFES, Marechal Campos Ave. 1468, 29043900, Vitória, Espírito Santo, Brazil
| | - Rafaela Vieira Bruno
- Lab. de Biologia Molecular de Insetos, Instituto Oswaldo Cruz, FIOCRUZ, Brasil Ave. 4365, 21040360, Rio de Janeiro, RJ, Brazil
- Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular – INCT-EM/CNPq, Rio de Janeiro, Brazil
| | - Aloisio Falqueto
- Unidade de Medicina Tropical, UFES, Marechal Campos Ave. 1468, 29043900, Vitória, Espírito Santo, Brazil
| | - José Dilermando Andrade-Filho
- Grupo de Estudos em Leishmanioses, Centro de Pesquisas René Rachou, FIOCRUZ, Augusto de Lima Ave. 1715, 30190002, Belo Horizonte, MG, Brazil
| | - Eunice Aparecida Bianchi Galati
- Departamento de Epidemiologia, Faculdade de Saúde Pública, USP, Dr. Arnaldo Cerqueira Cesar Ave. 715, 01246904, São Paulo, SP, Brazil
| | - Paloma Helena Fernandes Shimabukuro
- Grupo de Estudos em Leishmanioses, Centro de Pesquisas René Rachou, FIOCRUZ, Augusto de Lima Ave. 1715, 30190002, Belo Horizonte, MG, Brazil
| | - Reginaldo Peçanha Brazil
- Lab. de Doenças Parasitárias, Instituto Oswaldo Cruz, FIOCRUZ, Brasil Ave. 4365, 21040360, Rio de Janeiro, RJ, Brazil
| | - Alexandre Afranio Peixoto
- Lab. de Biologia Molecular de Insetos, Instituto Oswaldo Cruz, FIOCRUZ, Brasil Ave. 4365, 21040360, Rio de Janeiro, RJ, Brazil
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190
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Cardoni S, Tenchini R, Ficulle I, Piredda R, Simeone MC, Belfiore C. DNA barcode assessment of Mediterranean mayflies (Ephemeroptera), benchmark data for a regional reference library for rapid biomonitoring of freshwaters. BIOCHEM SYST ECOL 2015. [DOI: 10.1016/j.bse.2015.07.035] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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191
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Wang XB, Deng J, Zhang JT, Zhou QS, Zhang YZ, Wu SA. DNA barcoding of common soft scales (Hemiptera: Coccoidea: Coccidae) in China. BULLETIN OF ENTOMOLOGICAL RESEARCH 2015; 105:545-554. [PMID: 25989705 DOI: 10.1017/s0007485315000413] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The soft scales (Hemiptera: Coccoidea: Coccidae) are a group of sap-sucking plant parasites, many of which are notorious agricultural pests. The quarantine and economic importance of soft scales necessitates rapid and reliable identification of these taxa. Nucleotide sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene (barcoding region) and 28S rDNA were generated from 340 individuals of 36 common soft scales in China. Distance-based [(best match, Automated Barcode Gap Discovery (ABGD)], tree-based (neighbor-joining, Bayesian inference), Klee diagrams, and general mixed Yule coalescent (GMYC) models were used to evaluate barcoding success rates in the data set. Best match showed that COI and 28S sequences could provide 100 and 95.52% correct identification, respectively. The average interspecific divergences were 19.81% for COI data and 20.38% for 28S data, and mean intraspecific divergences were 0.56 and 0.07%, respectively. For COI data, multiple methods (ABGD, Klee, and tree-based methods) resulted in general congruence with morphological identifications. However, GMYC analysis tended to provide more molecular operational taxonomic units (MOTUs). Twelve MOTUs derived from five morphospecies (Rhodococcus sariuoni, Pulvinaria vitis, Pulvinaria aurantii, Parasaissetia nigra, and Ceroplastes rubens) were observed using the GMYC approach. In addition, tree-based methods showed that 28S sequences could be used for species-level identification (except for Ceroplastes ceriferus - Ceroplastes pseudoceriferus), even with low genetic variation (<1%). This report demonstrates the robustness of DNA barcoding for species discrimination of soft scales with two molecular markers (COI and 28S) and provides a reliable barcode library and rapid diagnostic tool for common soft scales in China.
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Affiliation(s)
- X-B Wang
- The Key Laboratory for Silviculture and Conservation of Ministry of Education,Beijing Forestry University,Beijing 100083,China
| | - J Deng
- The Key Laboratory for Silviculture and Conservation of Ministry of Education,Beijing Forestry University,Beijing 100083,China
| | - J-T Zhang
- The Key Laboratory for Silviculture and Conservation of Ministry of Education,Beijing Forestry University,Beijing 100083,China
| | - Q-S Zhou
- Key Laboratory of Zoological Systematics and Evolution,Institute of Zoology,Chinese Academy of Sciences,Beijing 100101,China
| | - Y-Z Zhang
- Key Laboratory of Zoological Systematics and Evolution,Institute of Zoology,Chinese Academy of Sciences,Beijing 100101,China
| | - S-A Wu
- The Key Laboratory for Silviculture and Conservation of Ministry of Education,Beijing Forestry University,Beijing 100083,China
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192
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Lin X, Stur E, Ekrem T. Exploring Genetic Divergence in a Species-Rich Insect Genus Using 2790 DNA Barcodes. PLoS One 2015; 10:e0138993. [PMID: 26406595 PMCID: PMC4583400 DOI: 10.1371/journal.pone.0138993] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 09/07/2015] [Indexed: 01/08/2023] Open
Abstract
DNA barcoding using a fragment of the mitochondrial cytochrome c oxidase subunit 1 gene (COI) has proven to be successful for species-level identification in many animal groups. However, most studies have been focused on relatively small datasets or on large datasets of taxonomically high-ranked groups. We explore the quality of DNA barcodes to delimit species in the diverse chironomid genus Tanytarsus (Diptera: Chironomidae) by using different analytical tools. The genus Tanytarsus is the most species-rich taxon of tribe Tanytarsini (Diptera: Chironomidae) with more than 400 species worldwide, some of which can be notoriously difficult to identify to species-level using morphology. Our dataset, based on sequences generated from own material and publicly available data in BOLD, consist of 2790 DNA barcodes with a fragment length of at least 500 base pairs. A neighbor joining tree of this dataset comprises 131 well separated clusters representing 121 morphological species of Tanytarsus: 77 named, 16 unnamed and 28 unidentified theoretical species. For our geographically widespread dataset, DNA barcodes unambiguously discriminate 94.6% of the Tanytarsus species recognized through prior morphological study. Deep intraspecific divergences exist in some species complexes, and need further taxonomic studies using appropriate nuclear markers as well as morphological and ecological data to be resolved. The DNA barcodes cluster into 120-242 molecular operational taxonomic units (OTUs) depending on whether Objective Clustering, Automatic Barcode Gap Discovery (ABGD), Generalized Mixed Yule Coalescent model (GMYC), Poisson Tree Process (PTP), subjective evaluation of the neighbor joining tree or Barcode Index Numbers (BINs) are used. We suggest that a 4-5% threshold is appropriate to delineate species of Tanytarsus non-biting midges.
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Affiliation(s)
- Xiaolong Lin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Elisabeth Stur
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Torbjørn Ekrem
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
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193
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Locke SA, Al-Nasiri FS, Caffara M, Drago F, Kalbe M, Lapierre AR, McLaughlin JD, Nie P, Overstreet RM, Souza GTR, Takemoto RM, Marcogliese DJ. Diversity, specificity and speciation in larval Diplostomidae (Platyhelminthes: Digenea) in the eyes of freshwater fish, as revealed by DNA barcodes. Int J Parasitol 2015; 45:841-55. [PMID: 26276524 DOI: 10.1016/j.ijpara.2015.07.001] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2015] [Revised: 06/23/2015] [Accepted: 07/08/2015] [Indexed: 11/19/2022]
Abstract
Larvae (metacercariae) in some species of Diplostomidae (Platyhelminthes: Digenea) inhabit fish eyes and are difficult to identify to species based on morphology. DNA barcoding has clarified the diversity and life cycles of diplostomids in North America, Europe and Africa, but has seldom been used in parasites sampled in large numbers or at large spatial scales. Here, distance-based analysis of cytochrome c oxidase 1 barcodes and, in some specimens, internal transcribed spacer (ITS-1, 5.8S, ITS-2) sequences was performed for over 2000 diplostomids from Africa, the Middle East, Europe, Asia and the Americas. Fifty-two species of Diplostomum, Tylodelphys and Austrodiplostomum (Digenea: Diplostomidae) were distinguished. The 52 species comprise 12 identified species, six species in two species complexes and 34 putative species, and 33/52 had been delineated in previous studies. Most (23/40) of the unidentified, putative species distinguished by cytochrome c oxidase 1 distances were supported by at least one additional line of evidence. As the intensity of sampling of the 52 species increased, variation in cytochrome c oxidase 1 decreased between and increased within species, while the spatial scale at which species were sampled had no effect. Nonetheless, variation between species always exceeded variation within species. New life-cycle linkages, geographic and host records, and genetic data were recorded in several species, including Tylodelphys jenynsiae, Tylodelphys immer and Diplostomum ardeae. Species of Diplostomum inhabiting the lens are less host-specific and less numerous than those infecting other tissues, suggesting that reduced immune activity in the lens has influenced rates of speciation.
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Affiliation(s)
- Sean A Locke
- Department of Biology, University of Puerto Rico at Mayagüez, Box 9000, Mayagüez, 00681-9000, Puerto Rico; Aquatic Biodiversity Section, Watershed Hydrology and Ecology Research Division, Water Science and Technology Directorate, Science and Technology Branch, St. Lawrence Centre, Environment Canada, 105 McGill, 7th floor, Montreal, Quebec H2Y 2E7, Canada.
| | - Fatima S Al-Nasiri
- Department of Biology, College of Science, University of Tikreet, Tikreet, Iraq
| | - Monica Caffara
- Department of Veterinary Medical Sciences, Alma Mater Studiorum Università di Bologna, Via Tolara di Sopra 50, 40064 Ozzano Emilia (BO), Italy
| | - Fabiana Drago
- Museo de La Plata, División Zoología Invertebrados, Paseo del Bosque S/N° (1900), La Plata, Buenos Aires, Argentina
| | - Martin Kalbe
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, August-Thienemann-Strasse 2, 24302 Plön, Germany
| | - Angela Rose Lapierre
- Biology Department, Concordia University, 7141 Sherbrooke Street West, Montreal, Quebec H4B 1R6, Canada
| | - J Daniel McLaughlin
- Biology Department, Concordia University, 7141 Sherbrooke Street West, Montreal, Quebec H4B 1R6, Canada
| | - Pin Nie
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province 430072, People's Republic of China
| | - Robin M Overstreet
- University of Southern Mississippi, Gulf Coast Research Laboratory, 703 East Beach Drive, Ocean Springs, MS 39564, USA
| | - Geza T R Souza
- Post-Doctor National Program Scholarship/CAPES, Post-Graduate Program in Health and Environment, Tiradentes University, Murilo Dantas Avenue, 300, Farolândia, Aracaju, Sergipe 49032-490, Brazil; State University of Maringá, Center of Biological Sciences, Nupelia - Icthyoparasitology Laboratory, Av Colombo, No. 5790, Block G90, room 11, villa 7, 87020-900 Maringá, PR, Brazil
| | - Ricardo M Takemoto
- State University of Maringá, Center of Biological Sciences, Nupelia - Icthyoparasitology Laboratory, Av Colombo, No. 5790, Block G90, room 11, villa 7, 87020-900 Maringá, PR, Brazil
| | - David J Marcogliese
- Aquatic Biodiversity Section, Watershed Hydrology and Ecology Research Division, Water Science and Technology Directorate, Science and Technology Branch, St. Lawrence Centre, Environment Canada, 105 McGill, 7th floor, Montreal, Quebec H2Y 2E7, Canada
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194
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Schwarzfeld MD, Sperling FAH. Comparison of five methods for delimitating species in Ophion Fabricius, a diverse genus of parasitoid wasps (Hymenoptera, Ichneumonidae). Mol Phylogenet Evol 2015; 93:234-48. [PMID: 26265257 DOI: 10.1016/j.ympev.2015.08.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Revised: 07/31/2015] [Accepted: 08/04/2015] [Indexed: 10/23/2022]
Abstract
DNA taxonomy has been proposed as a method to quickly assess diversity and species limits in highly diverse, understudied taxa. Here we use five methods for species delimitation and two genetic markers (COI and ITS2) to assess species diversity within the parasitoid genus, Ophion. We searched for compensatory base changes (CBC's) in ITS2, and determined that they are too rare to be of practical use in delimiting species in this genus. The other four methods used both COI and ITS2, and included distance-based (threshold analysis and ABGD) and tree-based (GMYC and PTP) models. We compared the results of these analyses to each other under various parameters and tested their performance with respect to 11 Nearctic species/morphospecies and 15 described Palearctic species. We also computed barcode accumulation curves of COI sequences to assess the completeness of sampling. The species count was highly variable depending on the method and parameters used, ranging from 47 to 168 species, with more conservative estimates of 89-121 species. Despite this range, many of the Nearctic test species were fairly robust with respect to method. We concluded that while there was often good congruence between methods, GMYC and PTP were less reliant on arbitrary parameters than the other two methods and more easily applied to genetic markers other than COI. However, PTP was less successful at delimiting test species than was GMYC. All methods, as well as the barcode accumulation curves, indicate that several Palearctic species remain undescribed and that we have scarcely begun to appreciate the Nearctic diversity within this genus.
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Affiliation(s)
- Marla D Schwarzfeld
- Department of Biological Sciences, CW 405 Biological Sciences Building, University of Alberta, Edmonton, Alberta T6G 2E9, Canada.
| | - Felix A H Sperling
- Department of Biological Sciences, CW 405 Biological Sciences Building, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
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195
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Rozo-Lopez P, Mengual X. Mosquito species (Diptera, Culicidae) in three ecosystems from the Colombian Andes: identification through DNA barcoding and adult morphology. Zookeys 2015; 513:39-64. [PMID: 26257568 PMCID: PMC4524277 DOI: 10.3897/zookeys.513.9561] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 06/01/2015] [Indexed: 01/09/2023] Open
Abstract
Colombia, one of the world's megadiverse countries, has a highly diverse mosquito fauna and a high prevalence of mosquito-borne diseases. In order to provide relevant information about the diversity and taxonomy of mosquito species in Colombia and to test the usefulness of DNA barcodes, mosquito species collected at different elevations in the departments of Antioquia and Caldas were identified combining adult morphology and barcode sequences. A total of 22 mosquito species from eight genera were identified using these combined techniques. We generated 77 barcode sequences with 16 species submitted as new country records for public databases. We examined the usefulness of DNA barcodes to discriminate mosquito species from the Neotropics by compiling 1,292 sequences from a total of 133 species and using the tree-based methods of neighbor-joining and maximum likelihood. Both methodologies provided similar results by resolving 105 species of mosquitoes separated into distinct clusters. This study shows the importance of combining classic morphological methodologies with molecular tools to accurately identify mosquitoes from Colombia.
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Affiliation(s)
- Paula Rozo-Lopez
- Rheinische Friedrich-Wilhelms-Universität Bonn. An der Immenburg 1, 53121 Bonn, Germany
| | - Ximo Mengual
- Zoologisches Forschungsmuseum Alexander Koenig. Adenauerallee 160, 53113 Bonn, Germany
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196
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Lang AS, Bocksberger G, Stech M. Phylogeny and species delimitations in European Dicranum (Dicranaceae, Bryophyta) inferred from nuclear and plastid DNA. Mol Phylogenet Evol 2015; 92:217-25. [PMID: 26149758 DOI: 10.1016/j.ympev.2015.06.019] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 06/24/2015] [Accepted: 06/29/2015] [Indexed: 11/26/2022]
Abstract
DNA sequences have been widely used for taxonomy, inferring phylogenetic relationships and identifying species boundaries. Several specific methods to define species delimitations based on molecular phylogenies have appeared recently, with the generalized mixed Yule coalescent (GMYC) method being most popular. However, only few studies on land plants have been published so far and GMYC analyses of bryophytes are missing. Dicranum is a large genus of mosses whose (morpho-)species are partly ill-defined and frequently confused. To infer molecular species delimitations, we reconstructed phylogenetic trees based on five chloroplast markers and nuclear ribosomal ITS sequences from 27 out of 30 species occurring in Europe. We applied the species delimitation methods GMYC and Poisson tree processes (PTP) in order to compare their discriminatory power with species boundaries inferred from the molecular phylogenetic reconstructions and with the morphological species concept. Phylogenetic circumscriptions were congruent with the morphological concept for 19 species, while eight species were molecularly not well delimited, mostly forming closely related species pairs. The automated species delimitation methods achieved similar results but tended to overestimate the number of potential species and exposed several incongruences between the morphological concept and inference from molecular phylogenetic reconstructions. It is concluded that GMYC and PTP methods potentially provide a useful and objective way of delimiting bryophyte species, but studies on further bryophyte data sets are necessary to infer whether incongruences might ensue from evolutionary processes and to test the suitability of these approaches.
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Affiliation(s)
- Annick S Lang
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands; Leiden University, Leiden, The Netherlands.
| | - Gaëlle Bocksberger
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Michael Stech
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands; Leiden University, Leiden, The Netherlands
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197
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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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198
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Wesener T, Voigtländer K, Decker P, Oeyen JP, Spelda J, Lindner N. First results of the German Barcode of Life (GBOL) - Myriapoda project: Cryptic lineages in German Stenotaenialinearis (Koch, 1835) (Chilopoda, Geophilomorpha). Zookeys 2015; 510:15-29. [PMID: 26257532 PMCID: PMC4523762 DOI: 10.3897/zookeys.510.8852] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 05/15/2015] [Indexed: 02/08/2023] Open
Abstract
As part of the German Barcode of Life (GBOL) Myriapoda program, which aims to sequence the COI barcoding fragment for 2000 specimens of Germany's 200 myriapod species in the near future, 44 sequences of the centipede order Geophilomorpha are analyzed. The analyses are limited to the genera Geophilus Leach, 1814 and Stenotaenia Koch, 1847 and include a total of six species. A special focus is Stenotaenia, of which 19 specimens from southern, western and eastern Germany could be successfully sequenced. The Stenotaenia data shows the presence of three to four vastly different (13.7-16.7% p-distance) lineages of the genus in Germany. At least two of the three lineages show a wide distribution across Germany, only the lineage including topotypes of Stenotaenialinearis shows a more restricted distribution in southern Germany. In a maximum likelihood phylogenetic analysis the Italian species Stenotaenia 'sorrentina' (Attems, 1903) groups with the different German Stenotaenialinearis clades. The strongly different Stenotaenialinearis lineages within Germany, independent of geography, are a strong hint for the presence of additional, cryptic Stenotaenia species in Germany.
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Affiliation(s)
- Thomas Wesener
- Zoologisches Forschungsmuseum Alexander Koenig, Leibniz Institute for Animal Biodiversity, Center for Taxonomy and Evolutionary Research (Section Myriapoda), Adenauerallee 160, 53113 Bonn, Germany
| | - Karin Voigtländer
- Senckenberg Museum of Natural History Görlitz, Am Museum 1, 02826 Görlitz, Germany
| | - Peter Decker
- Senckenberg Museum of Natural History Görlitz, Am Museum 1, 02826 Görlitz, Germany
| | - Jan Philip Oeyen
- Zoologisches Forschungsmuseum Alexander Koenig, Leibniz Institute for Animal Biodiversity, Center for Taxonomy and Evolutionary Research (Section Myriapoda), Adenauerallee 160, 53113 Bonn, Germany
| | - Jörg Spelda
- Bavarian State Collection of Zoology, Münchhausenstraße 21, 81247 Munich, Germany
| | - Norman Lindner
- Bavarian State Collection of Zoology, Münchhausenstraße 21, 81247 Munich, Germany
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Boyle EE, Adamowicz SJ. Community Phylogenetics: Assessing Tree Reconstruction Methods and the Utility of DNA Barcodes. PLoS One 2015; 10:e0126662. [PMID: 26110886 PMCID: PMC4481530 DOI: 10.1371/journal.pone.0126662] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 04/04/2015] [Indexed: 12/02/2022] Open
Abstract
Studies examining phylogenetic community structure have become increasingly prevalent, yet little attention has been given to the influence of the input phylogeny on metrics that describe phylogenetic patterns of co-occurrence. Here, we examine the influence of branch length, tree reconstruction method, and amount of sequence data on measures of phylogenetic community structure, as well as the phylogenetic signal (Pagel’s λ) in morphological traits, using Trichoptera larval communities from Churchill, Manitoba, Canada. We find that model-based tree reconstruction methods and the use of a backbone family-level phylogeny improve estimations of phylogenetic community structure. In addition, trees built using the barcode region of cytochrome c oxidase subunit I (COI) alone accurately predict metrics of phylogenetic community structure obtained from a multi-gene phylogeny. Input tree did not alter overall conclusions drawn for phylogenetic signal, as significant phylogenetic structure was detected in two body size traits across input trees. As the discipline of community phylogenetics continues to expand, it is important to investigate the best approaches to accurately estimate patterns. Our results suggest that emerging large datasets of DNA barcode sequences provide a vast resource for studying the structure of biological communities.
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Affiliation(s)
- Elizabeth E. Boyle
- Biodiversity Institute of Ontario & Department of Integrative Biology, University of Guelph, 50 Stone Rd. E., Guelph, Ontario, N1G 2W1, Canada
| | - Sarah J. Adamowicz
- Biodiversity Institute of Ontario & Department of Integrative Biology, University of Guelph, 50 Stone Rd. E., Guelph, Ontario, N1G 2W1, Canada
- * E-mail:
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Wu S, Xiong J, Yu Y. Taxonomic resolutions based on 18S rRNA genes: a case study of subclass copepoda. PLoS One 2015; 10:e0131498. [PMID: 26107258 PMCID: PMC4479608 DOI: 10.1371/journal.pone.0131498] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Accepted: 06/01/2015] [Indexed: 01/20/2023] Open
Abstract
Biodiversity studies are commonly conducted using 18S rRNA genes. In this study, we compared the inter-species divergence of variable regions (V1-9) within the copepod 18S rRNA gene, and tested their taxonomic resolutions at different taxonomic levels. Our results indicate that the 18S rRNA gene is a good molecular marker for the study of copepod biodiversity, and our conclusions are as follows: 1) 18S rRNA genes are highly conserved intra-species (intra-species similarities are close to 100%); and could aid in species-level analyses, but with some limitations; 2) nearly-whole-length sequences and some partial regions (around V2, V4, and V9) of the 18S rRNA gene can be used to discriminate between samples at both the family and order levels (with a success rate of about 80%); 3) compared with other regions, V9 has a higher resolution at the genus level (with an identification success rate of about 80%); and 4) V7 is most divergent in length, and would be a good candidate marker for the phylogenetic study of Acartia species. This study also evaluated the correlation between similarity thresholds and the accuracy of using nuclear 18S rRNA genes for the classification of organisms in the subclass Copepoda. We suggest that sample identification accuracy should be considered when a molecular sequence divergence threshold is used for taxonomic identification, and that the lowest similarity threshold should be determined based on a pre-designated level of acceptable accuracy.
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Affiliation(s)
- Shu Wu
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jie Xiong
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Yuhe Yu
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- * E-mail:
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