1
|
Cahill AE, Meglécz E, Chenuil A. Scientific history, biogeography, and biological traits predict presence of cryptic or overlooked species. Biol Rev Camb Philos Soc 2024; 99:546-561. [PMID: 38049930 DOI: 10.1111/brv.13034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 11/13/2023] [Accepted: 11/15/2023] [Indexed: 12/06/2023]
Abstract
Genetic data show that many nominal species are composed of more than one biological species, and thus contain cryptic species in the broad sense (including overlooked species). When ignored, cryptic species generate confusion which, beyond biodiversity or vulnerability underestimation, blurs our understanding of ecological and evolutionary processes and may impact the soundness of decisions in conservation or medicine. However, very few hypotheses have been tested about factors that predispose a taxon to contain cryptic or overlooked species. To fill this gap, we surveyed the literature on free-living marine metazoans and built two data sets, one of 187,603 nominal species and another of 83 classes or phyla, to test several hypotheses, correcting for sequence data availability, taxon size and phylogenetic relatedness. We found a strong effect of scientific history: the probability of a taxon containing cryptic species was highest for the earliest described species and varied among time periods potentially consistently with an influence of prevailing scientific theories. The probability of cryptic species being present was also increased for species with large distribution ranges. They were more frequent in the north polar and south polar zones, contradicting previous predictions of more cryptic species in the tropics, and supporting the hypothesis that many cryptic species diverged recently. The number of cryptic species varied among classes, with an excess in hydrozoans and polychaetes, and a deficit in actinopterygians, for example, but precise class ranking was relatively sensitive to the statistical model used. For all models, biological traits, rather than phylum, appeared responsible for the variation among classes: there were fewer cryptic species than expected in classes with hard skeletons (perhaps because they provide good characters for taxonomy) and image-forming vision (in which selection against heterospecific mating may enhance morphological divergence), and more in classes with internal fertilisation. We estimate that among marine free-living metazoans, several thousand additional cryptic species complexes could be identified as more sequence data become available. The factors identified as important for marine animal cryptic species are likely important for other biomes and taxa and should aid many areas in biology that rely on accurate species identification.
Collapse
Affiliation(s)
- Abigail E Cahill
- Biology Department, Albion College, 611 East Porter St., Albion, MI, 49224, USA
| | - Emese Meglécz
- Aix Marseille Univ, Avignon Univ, CNRS, IRD, IMBE, Station Marine d'Endoume, Chemin de la Batterie des Lions, Marseille, 13007, France
| | - Anne Chenuil
- Aix Marseille Univ, Avignon Univ, CNRS, IRD, IMBE, Station Marine d'Endoume, Chemin de la Batterie des Lions, Marseille, 13007, France
| |
Collapse
|
2
|
Phillips JD, Griswold CK, Young RG, Hubert N, Hanner RH. A Measure of the DNA Barcode Gap for Applied and Basic Research. Methods Mol Biol 2024; 2744:375-390. [PMID: 38683332 DOI: 10.1007/978-1-0716-3581-0_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
DNA barcoding has largely established itself as a mainstay for rapid molecular taxonomic identification in both academic and applied research. The use of DNA barcoding as a molecular identification method depends on a "DNA barcode gap"-the separation between the maximum within-species difference and the minimum between-species difference. Previous work indicates the presence of a gap hinges on sampling effort for focal taxa and their close relatives. Furthermore, both theory and empirical work indicate a gap may not occur for related pairs of biological species. Here, we present a novel evaluation approach in the form of an easily calculated set of nonparametric metrics to quantify the extent of proportional overlap in inter- and intraspecific distributions of pairwise differences among target species and their conspecifics. The metrics are based on a simple count of the number of overlapping records for a species falling within the bounds of maximum intraspecific distance and minimum interspecific distance. Our approach takes advantage of the asymmetric directionality inherent in pairwise genetic distance distributions, which has not been previously done in the DNA barcoding literature. We apply the metrics to the predatory diving beetle genus Agabus as a case study because this group poses significant identification challenges due to its morphological uniformity despite both relative sampling ease and well-established taxonomy. Results herein show that target species and their nearest neighbor species were found to be tightly clustered and therefore difficult to distinguish. Such findings demonstrate that DNA barcoding can fail to fully resolve species in certain cases. Moving forward, we suggest the implementation of the proposed metrics be integrated into a common framework to be reported in any study that uses DNA barcoding for identification. In so doing, the importance of the DNA barcode gap and its components for the success of DNA-based identification using DNA barcodes can be better appreciated.
Collapse
Affiliation(s)
- Jarrett D Phillips
- School of Computer Science, University of Guelph, Guelph, ON, Canada.
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada.
| | - Cortland K Griswold
- School of Computer Science, University of Guelph, Guelph, ON, Canada
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | - Robert G Young
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | - Nicolas Hubert
- UMR ISEM (IRD, UM, CNRS), Université de Montpellier, Montpellier, France
| | - Robert H Hanner
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| |
Collapse
|
3
|
Bae S, Kim P, Yi CH. Biodiversity and spatial distribution of ascidian using environmental DNA metabarcoding. MARINE ENVIRONMENTAL RESEARCH 2023; 185:105893. [PMID: 36689844 DOI: 10.1016/j.marenvres.2023.105893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/16/2023] [Accepted: 01/17/2023] [Indexed: 06/17/2023]
Abstract
Monitoring studies are necessary to understand the biodiversity of marine ecosystems and are useful for identifying and managing rare or invasive species. Because monitoring has traditionally relied only on visual surveys (e.g., trapping, netting, electrofishing, and SCUBA diving) with limited time and physical resources, environmental DNA (eDNA) analysis is being applied as an efficient monitoring method. This study compared whether the eDNA metabarcoding technique can replace the traditional visual survey in an ascidian fauna study. We designed ascidian-specific primers and identified a clear gap (3.75%) by barcoding gap analysis. Then, we collected seawater samples for eDNA analysis during the summer (August-September) of 2021 at three sites (Mokpo, Yeosu, and Uljin) in South Korea. In the survey sites of this study, 25 species were observed through literature and visual survey, among which 9 species were detected by metabarcoding and 16 species were not detected. On the other hand, 10 species were detected only by metabarcoding, and one of them was identified as Pyura mirabilis, an unrecorded species in South Korea. This study succeeded in detecting cryptic or rare species with one seawater collection, which can be used to determine their unexplored habitat. Therefore, we conclude that monitoring using eDNA is more efficient than visual surveys for detecting rare or cryptic ascidian species. We also suggest that, when combined with traditional monitoring methods, it could be a tool to complement ascidian fauna studies.
Collapse
Affiliation(s)
- Seongjun Bae
- Department of Ecology and Conservation, National Marine Biodiversity Institute of Korea, Seocheon, 33662, Republic of Korea; Department of Ocean Environmental Sciences, College of Natural Science, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Philjae Kim
- Department of Biodiversity, National Marine Biodiversity Institute of Korea, Seocheon, 33662, Republic of Korea; Department of Marine Biotechnology, Kunsan National University, Kunsan, 54150, Republic of Korea
| | - Chang-Ho Yi
- Department of Ecology and Conservation, National Marine Biodiversity Institute of Korea, Seocheon, 33662, Republic of Korea.
| |
Collapse
|
4
|
Exploring Large-Scale Patterns of Genetic Variation in the COI Gene among Insecta: Implications for DNA Barcoding and Threshold-Based Species Delimitation Studies. INSECTS 2022; 13:insects13050425. [PMID: 35621761 PMCID: PMC9147995 DOI: 10.3390/insects13050425] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 04/26/2022] [Accepted: 04/29/2022] [Indexed: 12/04/2022]
Abstract
The genetic variation in the COI gene has had a great effect on the final results of species delimitation studies. However, little research has comprehensively investigated the genetic divergence in COI among Insecta. The fast-growing COI data in BOLD provide an opportunity for the comprehensive appraisal of the genetic variation in COI among Insecta. We calculated the K2P distance of 64,414 insect species downloaded from BOLD. The match ratios of the clustering analysis, based on different thresholds, were also compared among 4288 genera (35,068 species). The results indicate that approximately one-quarter of the species of Insecta showed high intraspecific genetic variation (>3%), and a conservative estimate of this proportion ranges from 12.05% to 22.58%. The application of empirical thresholds (e.g., 2% and 3%) in the clustering analysis may result in the overestimation of the species diversity. If the minimum interspecific genetic distance of the congeneric species is greater than or equal to 2%, it is possible to avoid overestimating the species diversity on the basis of the empirical thresholds. In comparison to the fixed thresholds, the “threshOpt” and “localMinima” algorithms are recommended for the provision of a reference threshold for threshold-based species delimitation studies.
Collapse
|
5
|
Phillips JD, Gillis DJ, Hanner RH. Lack of Statistical Rigor in DNA Barcoding Likely Invalidates the Presence of a True Species' Barcode Gap. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.859099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
DNA barcoding has been largely successful in satisfactorily exposing levels of standing genetic diversity for a wide range of taxonomic groups through the employment of only one or a few universal gene markers. However, sufficient coverage of geographically-broad intra-specific haplotype variation within genomic databases like the Barcode of Life Data Systems (BOLD) and GenBank remains relatively sparse. As reference sequence libraries continue to grow exponentially in size, there is now the need to identify novel ways of meaningfully analyzing vast amounts of available DNA barcode data. This is an important issue to address promptly for the routine tasks of specimen identification and species discovery, which have seen broad adoption in areas as diverse as regulatory forensics and resource conservation. Here, it is demonstrated that the interpretation of DNA barcoding data is lacking in statistical rigor. To highlight this, focus is set specifically on one key concept that has become a household name in the field: the DNA barcode gap. Arguments outlined herein specifically center on DNA barcoding in animal taxa and stem from three angles: (1) the improper allocation of specimen sampling effort necessary to capture adequate levels of within-species genetic variation, (2) failing to properly visualize intra-specific and interspecific genetic distances, and (3) the inconsistent, inappropriate use, or absence of statistical inferential procedures in DNA barcoding gap analyses. Furthermore, simple statistical solutions are outlined which can greatly propel the use of DNA barcoding as a tool to irrefutably match unknowns to knowns on the basis of the barcoding gap with a high degree of confidence. Proposed methods examined herein are illustrated through application to DNA barcode sequence data from Canadian Pacific fish species as a case study.
Collapse
|
6
|
DNA barcoding allows identification of undescribed crab megalopas from the open sea. Sci Rep 2021; 11:20573. [PMID: 34663862 PMCID: PMC8523566 DOI: 10.1038/s41598-021-99486-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 08/12/2021] [Indexed: 11/13/2022] Open
Abstract
Megalopas of 15 brachyuran crab species collected in the open sea plankton, and unknown until now, were identified using DNA barcodes (COI and 16S rRNA). Specimens belonging to the families Portunidae, Pseudorhombilidae and Xanthidae (Crustacea, Decapoda, Brachyura), and corresponding to the species Achelous floridanus, Arenaeus mexicanus, Callinectes amnicola, C. arcuatus, C. ornatus, C. toxones, Charybdis (Charybdis) hellerii, Portunus hastatus, Thalamita admete, Scopolius nuttingi, Etisus odhneri, Liomera cinctimanus, Neoliomera cerasinus, Pseudoliomera variolosa, and Williamstimpsonia stimpsoni, are described and illustrated, and compared with other congeneric species previously described. We also provide a new geographical record for N. cerasinus and the most remarkable features for each species.
Collapse
|
7
|
Collins RA, Trauzzi G, Maltby KM, Gibson TI, Ratcliffe FC, Hallam J, Rainbird S, Maclaine J, Henderson PA, Sims DW, Mariani S, Genner MJ. Meta-Fish-Lib: A generalised, dynamic DNA reference library pipeline for metabarcoding of fishes. JOURNAL OF FISH BIOLOGY 2021; 99:1446-1454. [PMID: 34269417 DOI: 10.1111/jfb.14852] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 07/06/2021] [Accepted: 07/12/2021] [Indexed: 06/13/2023]
Abstract
The accuracy and reliability of DNA metabarcoding analyses depend on the breadth and quality of the reference libraries that underpin them. However, there are limited options available to obtain and curate the huge volumes of sequence data that are available on public repositories such as NCBI and BOLD. Here, we provide a pipeline to download, clean and annotate mitochondrial DNA sequence data for a given list of fish species. Features of this pipeline include (a) support for multiple metabarcode markers; (b) searches on species synonyms and taxonomic name validation; (c) phylogeny assisted quality control for identification and removal of misannotated sequences; (d) automatically generated coverage reports for each new GenBank release update; and (e) citable, versioned DOIs. As an example we provide a ready-to-use curated reference library for the marine and freshwater fishes of the U.K. To augment this reference library for environmental DNA metabarcoding specifically, we generated 241 new MiFish-12S sequences for 88 U.K. marine species, and make available new primer sets useful for sequencing these. This brings the coverage of common U.K. species for the MiFish-12S fragment to 93%, opening new avenues for scaling up fish metabarcoding across wide spatial gradients. The Meta-Fish-Lib reference library and pipeline is hosted at https://github.com/genner-lab/meta-fish-lib.
Collapse
Affiliation(s)
- Rupert A Collins
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Giulia Trauzzi
- School of Biological Sciences, University of Bristol, Bristol, UK
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Katherine M Maltby
- Centre for Environment, Fisheries and Aquaculture Science, Lowestoft, UK
| | - Thomas I Gibson
- Molecular Ecology and Fisheries Genetics Laboratory, Bangor University School of Natural Sciences, Environment Centre Wales, Bangor, UK
| | | | - Jane Hallam
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Sophie Rainbird
- Marine Biological Association of the United Kingdom, Plymouth, UK
| | - James Maclaine
- Department of Life Sciences, The Natural History Museum, London, UK
| | | | - David W Sims
- Marine Biological Association of the United Kingdom, Plymouth, UK
- Ocean and Earth Science, University of Southampton, National Oceanography Centre Southampton, Southampton, UK
| | - Stefano Mariani
- Ecosystems & Environment Research Centre, School of Environment & Life Sciences, University of Salford, Salford, UK
- School of Biological & Environmental Sciences, Liverpool John Moores University, Liverpool, UK
| | - Martin J Genner
- School of Biological Sciences, University of Bristol, Bristol, UK
| |
Collapse
|
8
|
Rodrigues BL, Baton LA, Shimabukuro PHF. Single-locus DNA barcoding and species delimitation of the sandfly subgenus Evandromyia (Aldamyia). MEDICAL AND VETERINARY ENTOMOLOGY 2020; 34:420-431. [PMID: 32590879 DOI: 10.1111/mve.12458] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 05/05/2020] [Accepted: 05/27/2020] [Indexed: 06/11/2023]
Abstract
Sandfly specimens from the subgenus Evandromyia (Aldamyia) Galati, 2003 (Diptera: Psychodidae: Phlebotominae) were collected between 2012 and 2019 from nine localities in seven Brazilian states, morphologically-identified, and then DNA barcoded by sequencing the mitochondrial cytochrome c oxidase subunit I (coi) gene. Forty-four new barcode sequences generated from 10 morphospecies were combined with 49 previously published sequences from the same subgenus and analysed using sequence-similarity methods (best-match criteria) to assess their ability at specimen identification, while four different species delimitation methods (ABGD, GMYC, PTP and TCS) were used to infer molecular operational taxonomic units (MOTUs). Overall, seven of the 11 morphospecies analysed were congruent with both the well-supported clades identified by phylogenetic analysis and the MOTUs inferred by species delimitation, while the remaining four morphospecies - E. carmelinoi, E. evandroi, E. lenti and E. piperiformis - were merged into a single well-supported clade/MOTU. Although E. carmelinoi, E. evandroi and E. lenti were indistinguishable using coi DNA barcodes, E. piperiformis did form a distinct phylogenetic cluster and could be correctly identified using best-match criteria. Despite their apparent morphological differences, we propose on the basis of the molecular similarity of their DNA barcodes that these latter four morphospecies should be considered members of a recently-diverged species complex.
Collapse
Affiliation(s)
- B L Rodrigues
- Grupo de Estudos em Leishmanioses, Instituto René Rachou-Fiocruz Minas, Belo Horizonte, Minas Gerais, Brazil
| | - L A Baton
- 50 Rowntree Way Saffron Walden, Essex, CB11 4DL, U.K
| | - P H F Shimabukuro
- Grupo de Estudos em Leishmanioses, Instituto René Rachou-Fiocruz Minas, Belo Horizonte, Minas Gerais, Brazil
- Coleção de Flebotomíneos (FIOCRUZ/COLFLEB), Instituto René Rachou-Fiocruz Minas, Belo Horizonte, Minas Gerais, Brazil
| |
Collapse
|
9
|
Hao M, Jin Q, Meng G, Yang C, Yang S, Shi Z, Tang M, Liu S, Li Y, Li J, Zhang D, Su X, Shih C, Sun Y, Wilson JJ, Zhou X, Zhang A. Using full-length metabarcoding and DNA barcoding to infer community assembly for speciose taxonomic groups: a case study. Evol Ecol 2020. [DOI: 10.1007/s10682-020-10072-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
10
|
Limmon G, Delrieu-Trottin E, Patikawa J, Rijoly F, Dahruddin H, Busson F, Steinke D, Hubert N. Assessing species diversity of Coral Triangle artisanal fisheries: A DNA barcode reference library for the shore fishes retailed at Ambon harbor (Indonesia). Ecol Evol 2020; 10:3356-3366. [PMID: 32273993 PMCID: PMC7141007 DOI: 10.1002/ece3.6128] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 01/30/2020] [Accepted: 02/03/2020] [Indexed: 01/01/2023] Open
Abstract
The Coral Triangle (CT), a region spanning across Indonesia and Philippines, is home to about 4,350 marine fish species and is among the world's most emblematic regions in terms of conservation. Threatened by overfishing and oceans warming, the CT fisheries have faced drastic declines over the last decades. Usually monitored through a biomass-based approach, fisheries trends have rarely been characterized at the species level due to the high number of taxa involved and the difficulty to accurately and routinely identify individuals to the species level. Biomass, however, is a poor proxy of species richness, and automated methods of species identification are required to move beyond biomass-based approaches. Recent meta-analyses have demonstrated that species richness peaks at intermediary levels of biomass. Consequently, preserving biomass is not equal to preserving biodiversity. We present the results of a survey to estimate the shore fish diversity retailed at the harbor of Ambon Island, an island located at the center of the CT that display exceptionally high biomass despite high levels of threat, while building a DNA barcode reference library of CT shore fishes targeted by artisanal fisheries. We sampled 1,187 specimens and successfully barcoded 696 of the 760 selected specimens that represent 202 species. Our results show that DNA barcodes were effective in capturing species boundaries for 96% of the species examined, which opens new perspectives for the routine monitoring of the CT fisheries.
Collapse
Affiliation(s)
- Gino Limmon
- Pusat Kemaritiman dan Kelautan Universitas Pattimura (Maritime and Marine Science Center of Excellence) Ambon Indonesia
| | - Erwan Delrieu-Trottin
- Institut de Recherche pour le Développement UMR 226 ISEM (UM-CNRS-IRD-EPHE) Montpellier France
- Museum für Naturkunde Leibniz-Institut für Evolutions-und Biodiversitätsforschung an der Humboldt-Universität zu Berlin Berlin Germany
| | - Jesaya Patikawa
- Pusat Kemaritiman dan Kelautan Universitas Pattimura (Maritime and Marine Science Center of Excellence) Ambon Indonesia
| | - Frederik Rijoly
- Pusat Kemaritiman dan Kelautan Universitas Pattimura (Maritime and Marine Science Center of Excellence) Ambon Indonesia
| | - Hadi Dahruddin
- Division of Zoology Research Center for Biology Indonesian Institute of Sciences (LIPI) Cibinong Indonesia
| | - Frédéric Busson
- Institut de Recherche pour le Développement UMR 226 ISEM (UM-CNRS-IRD-EPHE) Montpellier France
- UMR 7208 BOREA (MNHN-CNRS-UPMC-IRD-UCBN) Muséum National d'Histoire Naturelle Paris France
| | - Dirk Steinke
- Department of Integrative Biology Centre for Biodiversity Genomics University of Guelph Guelph ON Canada
| | - Nicolas Hubert
- Institut de Recherche pour le Développement UMR 226 ISEM (UM-CNRS-IRD-EPHE) Montpellier France
| |
Collapse
|
11
|
Collins RA, Bakker J, Wangensteen OS, Soto AZ, Corrigan L, Sims DW, Genner MJ, Mariani S. Non‐specific amplification compromises environmental DNA metabarcoding with COI. Methods Ecol Evol 2019. [DOI: 10.1111/2041-210x.13276] [Citation(s) in RCA: 132] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
| | - Judith Bakker
- Department of Biological Sciences Florida International University Miami FL USA
- Ecosystems & Environment Research Centre, School of Environment & Life Sciences University of Salford Salford UK
| | - Owen S. Wangensteen
- Ecosystems & Environment Research Centre, School of Environment & Life Sciences University of Salford Salford UK
- Norwegian College of Fishery Science, UiT The Arctic University of Norway Tromsø Norway
| | - Ana Z. Soto
- Ecosystems & Environment Research Centre, School of Environment & Life Sciences University of Salford Salford UK
| | - Laura Corrigan
- Environment Agency Tyneside House Newcastle upon Tyne UK
| | - David W. Sims
- The Laboratory Marine Biological Association of the United Kingdom Plymouth UK
- Ocean and Earth Science, National Oceanography Centre Southampton University of Southampton Southampton UK
| | | | - Stefano Mariani
- Ecosystems & Environment Research Centre, School of Environment & Life Sciences University of Salford Salford UK
- School of Natural Sciences & Psychology Liverpool John Moores University Liverpool UK
| |
Collapse
|
12
|
Andersen JC, Oboyski P, Davies N, Charlat S, Ewing C, Meyer C, Krehenwinkel H, Lim JY, Noriyuki S, Ramage T, Gillespie RG, Roderick GK. Categorization of species as native or nonnative using DNA sequence signatures without a complete reference library. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2019; 29:e01914. [PMID: 31050090 PMCID: PMC7079013 DOI: 10.1002/eap.1914] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 03/18/2019] [Accepted: 04/01/2019] [Indexed: 05/26/2023]
Abstract
New genetic diagnostic approaches have greatly aided efforts to document global biodiversity and improve biosecurity. This is especially true for organismal groups in which species diversity has been underestimated historically due to difficulties associated with sampling, the lack of clear morphological characteristics, and/or limited availability of taxonomic expertise. Among these methods, DNA sequence barcoding (also known as "DNA barcoding") and by extension, meta-barcoding for biological communities, has emerged as one of the most frequently utilized methods for DNA-based species identifications. Unfortunately, the use of DNA barcoding is limited by the availability of complete reference libraries (i.e., a collection of DNA sequences from morphologically identified species), and by the fact that the vast majority of species do not have sequences present in reference databases. Such conditions are critical especially in tropical locations that are simultaneously biodiversity rich and suffer from a lack of exploration and DNA characterization by trained taxonomic specialists. To facilitate efforts to document biodiversity in regions lacking complete reference libraries, we developed a novel statistical approach that categorizes unidentified species as being either likely native or likely nonnative based solely on measures of nucleotide diversity. We demonstrate the utility of this approach by categorizing a large sample of specimens of terrestrial insects and spiders (collected as part of the Moorea BioCode project) using a generalized linear mixed model (GLMM). Using a training data set of known endemic (n = 45) and known introduced species (n = 102), we then estimated the likely native/nonnative status for 4,663 specimens representing an estimated 1,288 species (412 identified species), including both those specimens that were either unidentified or whose endemic/introduced status was uncertain. Using this approach, we were able to increase the number of categorized specimens by a factor of 4.4 (from 794 to 3,497), and the number of categorized species by a factor of 4.8 from (147 to 707) at a rate much greater than chance (77.6% accuracy). The study identifies phylogenetic signatures of both native and nonnative species and suggests several practical applications for this approach including monitoring biodiversity and facilitating biosecurity.
Collapse
Affiliation(s)
- Jeremy C. Andersen
- Department of Environmental Science Policy and ManagementUniversity of California Berkeley130 Mulford HallBerkeleyCalifornia94720‐3114USA
| | - Peter Oboyski
- Essig Museum of EntomologyUniversity of California BerkeleyBerkeleyCalifornia94720USA
| | - Neil Davies
- Gump South Pacific Research StationUniversity of California BerkeleyMaharepaMooreaFrench Polynesia
| | - Sylvain Charlat
- Biométrie et Biologie ÉvolutiveUMR CNRS69622VilleurbanneFrance
| | - Curtis Ewing
- Komohana Research and Extension CenterUniversity of Hawai'i at MānoaHiloHawaii96720USA
| | | | | | - Jun Ying Lim
- Department of Integrated BiologyUniversity of California Berkeley3040 Valley Life Sciences BuildingBerkeleyCalifornia94720USA
| | - Suzuki Noriyuki
- Faculty of Agriculture and Marine ScienceKochi UniversityKochiJapan
| | | | - Rosemary G. Gillespie
- Department of Environmental Science Policy and ManagementUniversity of California Berkeley130 Mulford HallBerkeleyCalifornia94720‐3114USA
| | - George K. Roderick
- Department of Environmental Science Policy and ManagementUniversity of California Berkeley130 Mulford HallBerkeleyCalifornia94720‐3114USA
| |
Collapse
|
13
|
Klimov PB, Skoracki M, Bochkov AV. Cox1 barcoding versus multilocus species delimitation: validation of two mite species with contrasting effective population sizes. Parasit Vectors 2019; 12:8. [PMID: 30611284 PMCID: PMC6321676 DOI: 10.1186/s13071-018-3242-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 11/28/2018] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The cox1-barcoding approach is currently extensively used for high-throughput species delimitation and discovery. However, this method has several limitations, particularly when organisms have large effective population sizes. Paradoxically, most common, abundant, and widely distributed species may be misclassified by this technique. RESULTS We conducted species delimitation analyses for two host-specific lineages of scab mites of the genus Caparinia, having small population sizes. Cox1 divergence between these lineages was high (7.4-7.8%) while that of nuclear genes was low (0.06-0.53%). This system was contrasted with the medically important American house dust mite, Dermatophagoides farinae, a globally distributed species with very large population size. This species has two distinct, sympatric cox1 lineages with 4.2% divergence. We tested several species delimitation algorithms PTP, GMYC, ABGD, BPP, STACEY and PHRAPL, which inferred different species boundaries for these entities. Notably, STACEY recovered the Caparinia lineages as two species and D. farinae as a single species. BPP agreed with these results when the prior on ancestral effective population sizes was set to expected values, although delimitation of Caparinia was still equivocal. No other cox1 species delimitation algorithms inferred D. farinae as a single species, despite the fact that the nuclear CPW2 gene shows some evidence for introgression between the cox1 groups. This indicates that the cox1-barcoding approach may result in excessive species splitting. CONCLUSIONS Our research highlights the importance of using nuclear genes and demographic characteristics to infer species boundaries rather than relying on a single-gene barcoding approach, particularly for putative species having large effective population sizes.
Collapse
Affiliation(s)
- Pavel B. Klimov
- Department of Ecology and Evolutionary Biology, Museum of Zoology, University of Michigan, 3600 Varsity Drive, Ann Arbor, Michigan 48108 USA
- Tyumen State University, 10 Semakova Str, 625003 Tyumen, Russia
| | - Maciej Skoracki
- Department of Animal Morphology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 60-614 Poznan, Poland
| | - Andre V. Bochkov
- Tyumen State University, 10 Semakova Str, 625003 Tyumen, Russia
- Zoological Institute, Russian Academy of Sciences, Universitetskaya emb. 1, 199034 St Petersburg, Russia
| |
Collapse
|
14
|
Mulcahy DG, Lee JL, Miller AH, Chand M, Thura MK, Zug GR. Filling the BINs of life: Report of an amphibian and reptile survey of the Tanintharyi (Tenasserim) Region of Myanmar, with DNA barcode data. Zookeys 2018:85-152. [PMID: 29780268 PMCID: PMC5958176 DOI: 10.3897/zookeys.757.24453] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 04/09/2018] [Indexed: 11/12/2022] Open
Abstract
Despite threats of species extinctions, taxonomic crises, and technological advances in genomics and natural history database informatics, we are still distant from cataloguing all of the species of life on earth. Amphibians and reptiles are no exceptions; in fact new species are described nearly every day and many species face possible extinction. The number of described species continues to climb as new areas of the world are explored and as species complexes are examined more thoroughly. The use of DNA barcoding provides a mechanism for rapidly estimating the number of species at a given site and has the potential to record all of the species of life on Earth. Though DNA barcoding has its caveats, it can be useful to estimate the number of species in a more systematic and efficient manner, to be followed in combination with more traditional, morphology-based identifications and species descriptions. Herein, we report the results of a voucher-based herpetological expedition to the Tanintharyi (Tenasserim) Region of Myanmar, enhanced with DNA barcode data. Our main surveys took place in the currently proposed Tanintharyi National Park. We combine our results with photographs and observational data from the Chaung-nauk-pyan forest reserve. Additionally, we provide the first checklist of amphibians and reptiles of the region, with species based on the literature and museum. Amphibians, anurans in particular, are one of the most poorly known groups of vertebrates in terms of taxonomy and the number of known species, particularly in Southeast Asia. Our rapid-assessment program combined with DNA barcoding and use of Barcode Index Numbers (BINs) of voucher specimens reveals the depth of taxonomic diversity in the southern Tanintharyi herpetofauna even though only a third of the potential amphibians and reptiles were seen. A total of 51 putative species (one caecilian, 25 frogs, 13 lizards, 10 snakes, and two turtles) were detected, several of which represent potentially undescribed species. Several of these species were detected by DNA barcode data alone. Furthermore, five species were recorded for the first time in Myanmar, two amphibians (Ichthyophis cf. kohtaoensis and Chalcorana eschatia) and three snakes (Ahaetulla mycterizans, Boiga dendrophila, and Boiga drapiezii).
Collapse
Affiliation(s)
- Daniel G Mulcahy
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, 10th & Constitution Ave., Washington, DC, 20013 USA
| | - Justin L Lee
- College of Computer, Mathematical and Natural Sciences, University of Maryland, College Park Maryland, 20742 USA
| | - Aryeh H Miller
- Department of Biology, University of North Carolina Asheville, Asheville, NC 28804 USA
| | - Mia Chand
- College of William & Mary, Williamsburg, Virginia, 23187 USA
| | - Myint Kyaw Thura
- Myanmar Environment Sustainable Conservation (MESC), Yangon, Myanmar
| | - George R Zug
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20013 USA
| |
Collapse
|
15
|
Mallo D, Posada D. Multilocus inference of species trees and DNA barcoding. Philos Trans R Soc Lond B Biol Sci 2017; 371:rstb.2015.0335. [PMID: 27481787 PMCID: PMC4971187 DOI: 10.1098/rstb.2015.0335] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/10/2016] [Indexed: 11/30/2022] Open
Abstract
The unprecedented amount of data resulting from next-generation sequencing has opened a new era in phylogenetic estimation. Although large datasets should, in theory, increase phylogenetic resolution, massive, multilocus datasets have uncovered a great deal of phylogenetic incongruence among different genomic regions, due both to stochastic error and to the action of different evolutionary process such as incomplete lineage sorting, gene duplication and loss and horizontal gene transfer. This incongruence violates one of the fundamental assumptions of the DNA barcoding approach, which assumes that gene history and species history are identical. In this review, we explain some of the most important challenges we will have to face to reconstruct the history of species, and the advantages and disadvantages of different strategies for the phylogenetic analysis of multilocus data. In particular, we describe the evolutionary events that can generate species tree—gene tree discordance, compare the most popular methods for species tree reconstruction, highlight the challenges we need to face when using them and discuss their potential utility in barcoding. Current barcoding methods sacrifice a great amount of statistical power by only considering one locus, and a transition to multilocus barcodes would not only improve current barcoding methods, but also facilitate an eventual transition to species-tree-based barcoding strategies, which could better accommodate scenarios where the barcode gap is too small or inexistent. This article is part of the themed issue ‘From DNA barcodes to biomes’.
Collapse
Affiliation(s)
- Diego Mallo
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo 36310, Spain
| | - David Posada
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo 36310, Spain
| |
Collapse
|
16
|
Liu J, Jiang J, Song S, Tornabene L, Chabarria R, Naylor GJP, Li C. Multilocus DNA barcoding - Species Identification with Multilocus Data. Sci Rep 2017; 7:16601. [PMID: 29192249 PMCID: PMC5709489 DOI: 10.1038/s41598-017-16920-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 11/20/2017] [Indexed: 02/07/2023] Open
Abstract
Species identification using DNA sequences, known as DNA barcoding has been widely used in many applied fields. Current barcoding methods are usually based on a single mitochondrial locus, such as cytochrome c oxidase subunit I (COI). This type of barcoding method does not always work when applied to species separated by short divergence times or that contain introgressed genes from closely related species. Herein we introduce a more effective multi-locus barcoding framework that is based on gene capture and "next-generation" sequencing. We selected 500 independent nuclear markers for ray-finned fishes and designed a three-step pipeline for multilocus DNA barcoding. We applied our method on two exemplar datasets each containing a pair of sister fish species: Siniperca chuatsi vs. Sini. kneri and Sicydium altum vs. Sicy. adelum, where the COI barcoding approach failed. Both of our empirical and simulated results demonstrated that under limited gene flow and enough separation time, we could correctly identify species using multilocus barcoding method. We anticipate that, as the cost of DNA sequencing continues to fall that our multilocus barcoding approach will eclipse existing single-locus DNA barcoding methods as a means to better understand the diversity of the living world.
Collapse
Affiliation(s)
- Junning Liu
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai, 201306, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, 201306, China
- National Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University), Shanghai, 201306, China
| | - Jiamei Jiang
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai, 201306, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, 201306, China
- National Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University), Shanghai, 201306, China
| | - Shuli Song
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai, 201306, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, 201306, China
- National Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University), Shanghai, 201306, China
| | - Luke Tornabene
- School of Aquatic and Fisheries Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Ryan Chabarria
- College of Science & Engineering, Texas A&M University - Corpus Christi, Corpus Christi, TX, 78412-5806, USA
| | | | - Chenhong Li
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai, 201306, China.
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, 201306, China.
- National Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University), Shanghai, 201306, China.
| |
Collapse
|
17
|
Conte-Grand C, Britz R, Dahanukar N, Raghavan R, Pethiyagoda R, Tan HH, Hadiaty RK, Yaakob NS, Rüber L. Barcoding snakeheads (Teleostei, Channidae) revisited: Discovering greater species diversity and resolving perpetuated taxonomic confusions. PLoS One 2017; 12:e0184017. [PMID: 28931084 PMCID: PMC5606936 DOI: 10.1371/journal.pone.0184017] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 08/16/2017] [Indexed: 11/19/2022] Open
Abstract
Snakehead fishes of the family Channidae are predatory freshwater teleosts from Africa and Asia comprising 38 valid species. Snakeheads are important food fishes (aquaculture, live food trade) and have been introduced widely with several species becoming highly invasive. A channid barcode library was recently assembled by Serrao and co-workers to better detect and identify potential and established invasive snakehead species outside their native range. Comparing our own recent phylogenetic results of this taxonomically confusing group with those previously reported revealed several inconsistencies that prompted us to expand and improve on previous studies. By generating 343 novel snakehead coxI sequences and combining them with an additional 434 coxI sequences from GenBank we highlight several problems with previous efforts towards the assembly of a snakehead reference barcode library. We found that 16.3% of the channid coxI sequences deposited in GenBank are based on misidentifications. With the inclusion of our own data we were, however, able to solve these cases of perpetuated taxonomic confusion. Different species delimitation approaches we employed (BIN, GMYC, and PTP) were congruent in suggesting a potentially much higher species diversity within snakeheads than currently recognized. In total, 90 BINs were recovered and within a total of 15 currently recognized species multiple BINs were identified. This higher species diversity is mostly due to either the incorporation of undescribed, narrow range, endemics from the Eastern Himalaya biodiversity hotspot or the incorporation of several widespread species characterized by deep genetic splits between geographically well-defined lineages. In the latter case, over-lumping in the past has deflated the actual species numbers. Further integrative approaches are clearly needed for providing a better taxonomic understanding of snakehead diversity, new species descriptions and taxonomic revisions of the group.
Collapse
Affiliation(s)
| | - Ralf Britz
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Neelesh Dahanukar
- Indian Institute of Science Education and Research, Pashan, Pune, Maharashtra, India.,Systematics, Ecology & Conservation Laboratory, Zoo Outreach Organization, Saravanampatti, Coimbatore, Tamil Nadu, India
| | - Rajeev Raghavan
- Department of Fisheries Resource Management, Kerala University of Fisheries and Ocean Studies, Kochi, Kerala, India
| | | | - Heok Hui Tan
- Lee Kong Chian Natural History Museum, National University of Singapore, Singapore, Singapore
| | - Renny K Hadiaty
- Museum Zoologicum Bogoriense, Research Center for Biology, Indonesian Institute of Sciences, Cibinong, Indonesia
| | - Norsham S Yaakob
- Forest Research Institute Malaysia, Kepong, Kuala Lumpur, Malaysia
| | - Lukas Rüber
- Naturhistorisches Museum der Burgergemeinde Bern, Bern, Switzerland.,Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| |
Collapse
|
18
|
Somervuo P, Yu DW, Xu CC, Ji Y, Hultman J, Wirta H, Ovaskainen O. Quantifying uncertainty of taxonomic placement in
DNA
barcoding and metabarcoding. Methods Ecol Evol 2017. [DOI: 10.1111/2041-210x.12721] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Panu Somervuo
- Department of Biosciences University of Helsinki P.O. Box 65 Helsinki FI‐00014 Finland
| | - Douglas W. Yu
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences 32 Jiaochang East Road Kunming Yunnan 650223 China
- School of Biological Sciences University of East Anglia Norwich Research Park Norwich Norfolk NR47TJ UK
| | - Charles C.Y. Xu
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences 32 Jiaochang East Road Kunming Yunnan 650223 China
- Groningen Institute for Evolutionary Life Sciences University of Groningen P.O. Box 11103 9700 CC Groningen The Netherlands
| | - Yinqiu Ji
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences 32 Jiaochang East Road Kunming Yunnan 650223 China
| | - Jenni Hultman
- Department of Food and Environmental Sciences University of Helsinki P.O. Box 56 Helsinki FI‐00014 Finland
| | - Helena Wirta
- Department of Agricultural Sciences University of Helsinki P.O. Box 27 Helsinki FI‐00014 Finland
| | - Otso Ovaskainen
- Department of Biosciences University of Helsinki P.O. Box 65 Helsinki FI‐00014 Finland
- Centre for Biodiversity Dynamics Department of Biology Norwegian University of Science and Technology N‐7491 Trondheim Norway
| |
Collapse
|
19
|
Yang Z, Rannala B. Bayesian species identification under the multispecies coalescent provides significant improvements to DNA barcoding analyses. Mol Ecol 2017; 26:3028-3036. [DOI: 10.1111/mec.14093] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 02/15/2017] [Accepted: 02/16/2017] [Indexed: 11/29/2022]
Affiliation(s)
- Ziheng Yang
- Department of Genetics, Evolution and Environment; University College London; Gower Street London WC1E 6BT UK
- College of Life Sciences; Beijing Normal University; Beijing 100875 China
| | - Bruce Rannala
- College of Life Sciences; Beijing Normal University; Beijing 100875 China
- Department of Evolution and Ecology; University of California at Davis; One Shields Avenue Davis CA 95616 USA
| |
Collapse
|
20
|
Young RG, Abbott CL, Therriault TW, Adamowicz SJ. Barcode-based species delimitation in the marine realm: a test using Hexanauplia (Multicrustacea: Thecostraca and Copepoda). Genome 2017; 60:169-182. [DOI: 10.1139/gen-2015-0209] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
DNA barcoding has been used successfully for identifying specimens belonging to marine planktonic groups. However, the ability to delineate species within taxonomically diverse and widely distributed marine groups, such as the Copepoda and Thecostraca, remains largely untested. We investigate whether a cytochrome c oxidase subunit I (COI-5P) global pairwise sequence divergence threshold exists between intraspecific and interspecific divergences in the copepods plus the thecostracans (barnacles and allies). Using publicly accessible sequence data, we applied a graphical method to determine an optimal threshold value. With these thresholds, and using a newly generated planktonic marine data set, we quantify the degree of concordance using a bidirectional analysis and discuss different analytical methods for sequence-based species delimitation (e.g., BIN, ABGD, jMOTU, UPARSE, Mothur, PTP, and GMYC). Our results support a COI-5P threshold between 2.1% and 2.6% p-distance across methods for these crustacean taxa, yielding molecular groupings largely concordant with traditional, morphologically defined species. The adoption of internal methods for clustering verification enables rapid biodiversity studies and the exploration of unknown faunas using DNA barcoding. The approaches taken here for concordance assessment also provide a more quantitative comparison of clustering results (as contrasted with “success/failure” of barcoding), and we recommend their further consideration for barcoding studies.
Collapse
Affiliation(s)
- Robert G. Young
- Biodiversity Institute of Ontario and Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
| | - Cathryn L. Abbott
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, BC V9T 6N7, Canada
| | - Thomas W. Therriault
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, BC V9T 6N7, Canada
| | - Sarah J. Adamowicz
- Biodiversity Institute of Ontario and Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
| |
Collapse
|
21
|
Geiger MF, Moriniere J, Hausmann A, Haszprunar G, Wägele W, Hebert PDN, Rulik B. Testing the Global Malaise Trap Program - How well does the current barcode reference library identify flying insects in Germany? Biodivers Data J 2016:e10671. [PMID: 27932930 PMCID: PMC5136679 DOI: 10.3897/bdj.4.e10671] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 11/29/2016] [Indexed: 11/25/2022] Open
Abstract
Background Biodiversity patterns are inherently complex and difficult to comprehensively assess. Yet, deciphering shifts in species composition through time and space are crucial for efficient and successful management of ecosystem services, as well as for predicting change. To better understand species diversity patterns, Germany participated in the Global Malaise Trap Program, a world-wide collection program for arthropods using this sampling method followed by their DNA barcode analysis. Traps were deployed at two localities: “Nationalpark Bayerischer Wald” in Bavaria, the largest terrestrial Natura 2000 area in Germany, and the nature conservation area Landskrone, an EU habitats directive site in the Rhine Valley. Arthropods were collected from May to September to track shifts in the taxonomic composition and temporal succession at these locations. New information In total, 37,274 specimens were sorted and DNA barcoded, resulting in 5,301 different genetic clusters (BINs, Barcode Index Numbers, proxy for species) with just 7.6% of their BINs shared. Accumulation curves for the BIN count versus the number of specimens analyzed suggest that about 63% of the potential diversity at these sites was recovered with this single season of sampling. Diversity at both sites rose from May (496 & 565 BINs) to July (1,236 & 1,522 BINs) before decreasing in September (572 & 504 BINs). Unambiguous species names were assigned to 35% of the BINs (1,868) which represented 12,640 specimens. Another 7% of the BINs (386) with 1,988 specimens were assigned to genus, while 26% (1,390) with 12,092 specimens were only placed to a family. These results illustrate how a comprehensive DNA barcode reference library can identify unknown specimens, but also reveal how this potential is constrained by gaps in the quantity and quality of records in BOLD, especially for Hymenoptera and Diptera. As voucher specimens are available for morphological study, we invite taxonomic experts to assist in the identification of unnamed BINs.
Collapse
Affiliation(s)
| | | | | | | | - Wolfgang Wägele
- Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - Paul D N Hebert
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Canada
| | - Björn Rulik
- Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| |
Collapse
|
22
|
Zhang XS, Liu GC, Zhang DX, Shi CM. Novel trophic interaction: the scuttle fly Megaselia scalaris (Diptera: Phoridae) is a facultative parasitoid of the desert scorpion Mesobuthus eupeus mongolicus (Scorpiones: Buthidae). J NAT HIST 2016. [DOI: 10.1080/00222933.2016.1236222] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Xue-Shu Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Guang-Chun Liu
- Liaoning Key Laboratory of Urban Integrated Pest Management and Ecological Security, Shenyang University, Shenyang, China
| | - De-Xing Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Cheng-Min Shi
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
23
|
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.
Collapse
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
| |
Collapse
|
24
|
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'.
Collapse
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
| |
Collapse
|
25
|
Choi SC. Methods for delimiting species via population genetics and phylogenetics using genotype data. Genes Genomics 2016. [DOI: 10.1007/s13258-016-0458-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
26
|
Wu HY, Wang YH, Xie Q, Ke YL, Bu WJ. Molecular classification based on apomorphic amino acids (Arthropoda, Hexapoda): Integrative taxonomy in the era of phylogenomics. Sci Rep 2016; 6:28308. [PMID: 27312960 PMCID: PMC4911608 DOI: 10.1038/srep28308] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 05/31/2016] [Indexed: 11/10/2022] Open
Abstract
With the great development of sequencing technologies and systematic methods, our understanding of evolutionary relationships at deeper levels within the tree of life has greatly improved over the last decade. However, the current taxonomic methodology is insufficient to describe the growing levels of diversity in both a standardised and general way due to the limitations of using only morphological traits to describe clades. Herein, we propose the idea of a molecular classification based on hierarchical and discrete amino acid characters. Clades are classified based on the results of phylogenetic analyses and described using amino acids with group specificity in phylograms. Practices based on the recently published phylogenomic datasets of insects together with 15 de novo sequenced transcriptomes in this study demonstrate that such a methodology can accommodate various higher ranks of taxonomy. Such an approach has the advantage of describing organisms in a standard and discrete way within a phylogenetic framework, thereby facilitating the recognition of clades from the view of the whole lineage, as indicated by PhyloCode. By combining identification keys and phylogenies, the molecular classification based on hierarchical and discrete characters may greatly boost the progress of integrative taxonomy.
Collapse
Affiliation(s)
- Hao-Yang Wu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Yan-Hui Wang
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China
- College of Computer and Control Engineering, Nankai University, 38 Tongyan Road, Haihe Education Park, Jinnan District, Tianjin 300350, China
| | - Qiang Xie
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Yun-Ling Ke
- Guangdong Entomological Institute, Guangzhou 510260, China
| | - Wen-Jun Bu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China
| |
Collapse
|
27
|
Eberle J, Warnock RCM, Ahrens D. Bayesian species delimitation in Pleophylla chafers (Coleoptera) - the importance of prior choice and morphology. BMC Evol Biol 2016; 16:94. [PMID: 27149864 PMCID: PMC4858874 DOI: 10.1186/s12862-016-0659-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 04/18/2016] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Defining species units can be challenging, especially during the earliest stages of speciation, when phylogenetic inference and delimitation methods may be compromised by incomplete lineage sorting (ILS) or secondary gene flow. Integrative approaches to taxonomy, which combine molecular and morphological evidence, have the potential to be valuable in such cases. In this study we investigated the South African scarab beetle genus Pleophylla using data collected from 110 individuals of eight putative morphospecies. The dataset included four molecular markers (cox1, 16S, rrnL, ITS1) and morphometric data based on male genital morphology. We applied a suite of molecular and morphological approaches to species delimitation, and implemented a novel Bayesian approach in the software iBPP, which enables continuous morphological trait and molecular data to be combined. RESULTS Traditional morphology-based species assignments were supported quantitatively by morphometric analyses of the male genitalia (eigenshape analysis, CVA, LDA). While the ITS1-based delineation was also broadly congruent with the morphospecies, the cox1 data resulted in over-splitting (GMYC modelling, haplotype networks, PTP, ABGD). In the most extreme case morphospecies shared identical haplotypes, which may be attributable to ILS based on statistical tests performed using the software JML. We found the strongest support for putative morphospecies based on phylogenetic evidence using the combined approach implemented in iBPP. However, support for putative species was sensitive to the use of alternative guide trees and alternative combinations of priors on the population size (θ) and rootage (τ 0 ) parameters, especially when the analysis was based on molecular or morphological data alone. CONCLUSIONS We demonstrate that continuous morphological trait data can be extremely valuable in assessing competing hypotheses to species delimitation. In particular, we show that the inclusion of morphological data in an integrative Bayesian framework can improve the resolution of inferred species units. However, we also demonstrate that this approach is extremely sensitive to guide tree and prior parameter choice. These parameters should be chosen with caution - if possible - based on independent empirical evidence, or careful sensitivity analyses should be performed to assess the robustness of results. Young species provide exemplars for investigating the mechanisms of speciation and for assessing the performance of tools used to delimit species on the basis of molecular and/or morphological evidence.
Collapse
Affiliation(s)
- Jonas Eberle
- Zoologisches Forschungsmuseum Alexander Koenig Bonn, Centre of Taxonomy and Evolutionary Research, Adenauerallee 160, 53113, Bonn, Germany
| | - Rachel C M Warnock
- Department of Entomology, Natural History Museum, London, SW7 5BD, UK
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, SL7 5PY, UK
- School of Earth Sciences, University of Bristol, Bristol, BS8 1RJ, UK
| | - Dirk Ahrens
- Zoologisches Forschungsmuseum Alexander Koenig Bonn, Centre of Taxonomy and Evolutionary Research, Adenauerallee 160, 53113, Bonn, Germany.
- Department of Entomology, Natural History Museum, London, SW7 5BD, UK.
| |
Collapse
|
28
|
Senderov V, Penev L. The Open Biodiversity Knowledge Management System in Scholarly Publishing. RESEARCH IDEAS AND OUTCOMES 2016. [DOI: 10.3897/rio.2.e7757] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
|
29
|
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.
Collapse
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
| |
Collapse
|
30
|
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.
Collapse
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
| |
Collapse
|
31
|
Hinsinger DD, Debruyne R, Thomas M, Denys GPJ, Mennesson M, Utage J, Dettai A. Fishing for barcodes in the Torrent: from COI to complete mitogenomes on NGS platforms. ACTA ACUST UNITED AC 2015. [DOI: 10.1515/dna-2015-0019] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractThe adoption of Next-Generation Sequencing (NGS) by the field of DNA barcoding of Metazoa has been hindered by the fit between the classical COI barcode and the Sanger-based sequencing method. Here we describe a framework for the sequencing and multiplexing of mitogenomes on NGS platforms that implements (I) a universal long-range PCR-based amplification technique, (II) a two-level multiplexing approach (i.e. divergence-based and specific tag indexing), and (III) a dedicated demultiplexing and assembling script from an Ion Torrent sequencing platform. We provide a case study of mitogenomes obtained for two vouchered individuals of daces Leuciscus burdigalensis and L. oxyrrhis and show that this workflow enables to recover over 100 mitogenomes per sequencing chip on a PGM sequencer, bringing the individual cost down below 7,50€ per mitogenome (as of current 2015 sequencing costs). The use of several kilobases for identification purposes, as involved in the improved DNA-barcode we propose, stress the need for data reliability, especially through metadata. Based on both scientific and economic considerations, this framework presents a relevant approach for multiplexing samples, adaptable on any desktop NGS platform. It enables to extend from the prevalent barcoding approach by shifting from the single COI to complete mitogenome sequencing
Collapse
|
32
|
Status and prospects of DNA barcoding in medically important parasites and vectors. Trends Parasitol 2014; 30:582-91. [PMID: 25447202 DOI: 10.1016/j.pt.2014.09.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 09/18/2014] [Accepted: 09/19/2014] [Indexed: 11/23/2022]
Abstract
For over 10 years, DNA barcoding has been used to identify specimens and discern species. Its potential benefits in parasitology were recognized early, but its utility and uptake remain unclear. Here we review studies using DNA barcoding in parasites and vectors affecting humans and find that the technique is accurate (accords with author identifications based on morphology or other markers) in 94-95% of cases, although aspects of DNA barcoding (vouchering, marker implicated) have often been misunderstood. In a newly compiled checklist of parasites, vectors, and hazards, barcodes are available for 43% of all 1403 species and for more than half of 429 species of greater medical importance. This is encouraging coverage that would improve with an active campaign targeting parasites and vectors.
Collapse
|