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Ottati S, Eberle J, Rulik B, Köhler F, Ahrens D. From DNA barcodes to ecology: Meta-analysis of central European beetles reveal link with species ecology but also to data pattern and gaps. Ecol Evol 2022; 12:e9650. [PMID: 36568864 PMCID: PMC9771709 DOI: 10.1002/ece3.9650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 11/23/2022] [Accepted: 12/02/2022] [Indexed: 12/24/2022] Open
Abstract
DNA barcoding has been used worldwide to identify biological specimens and to delimit species. It represents a cost-effective, fast, and efficient way to assess biodiversity with help of the public Barcode of Life Database (BOLD) accounting for more than 236,000 animal species and more than 10 million barcode sequences. Here, we performed a meta-analysis of available barcode data of central European Coleoptera to detect intraspecific genetic patterns among ecological groups in relation to geographic distance with the aim to investigate a possible link between infraspecific variation and species ecology. We collected information regarding feeding style, body size, as well as habitat and biotope preferences. Mantel tests and two variants of Procrustes analysis, both involving the Principal Coordinates Neighborhood Matrices (PCNM) approach, were applied on genetic and geographic distance matrices. However, significance levels were too low to further use the outcome for further trait investigation: these were in mean for all ecological guilds only 7.5, 9.4, or 15.6% for PCNM + PCA, NMDS + PCA, and Mantel test, respectively, or at best 28% for a single guild. Our study confirmed that certain ecological traits were associated with higher species diversity and foster stronger genetic differentiation. Results suggest that increased numbers of species, sampling localities, and specimens for a chosen area of interest may give new insights to explore barcode data and species ecology for the scope of conservation on a larger scale. We performed a meta-analysis of available barcode data of central European beetles to detect intraspecific genetic patterns among ecological groups in relation to geographic distance, regarding feeding style, body size, as well as habitat and biotope preferences. Our study confirmed that certain ecological traits were associated with higher species diversity and foster stronger genetic differentiation. However, significance levels were too low to further use the outcome for further trait investigation.
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Affiliation(s)
- Sara Ottati
- Zoologisches Forschungsmuseum A. Koenig (LIB)BonnGermany
- Department of Agricultural, Forest and Food Sciences (DISAFA)University of TorinoTurinItaly
| | - Jonas Eberle
- Zoologisches Forschungsmuseum A. Koenig (LIB)BonnGermany
- Department of Environment & BiodiversityUniversity of SalzburgSalzburgAustria
| | - Björn Rulik
- Department of Agricultural, Forest and Food Sciences (DISAFA)University of TorinoTurinItaly
| | - Frank Köhler
- Coleopterological Research OfficeBornheimGermany
| | - Dirk Ahrens
- Zoologisches Forschungsmuseum A. Koenig (LIB)BonnGermany
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2
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Cryptic diversity and population genetic structure of the mantis shrimp Oratosquilla oratoria in South Korea. Genes Genomics 2022; 44:1343-1352. [DOI: 10.1007/s13258-022-01303-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 08/07/2022] [Indexed: 11/04/2022]
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3
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Ranasinghe UGSL, Eberle J, Thormann J, Bohacz C, Benjamin SP, Ahrens D. Multiple species delimitation approaches with
COI
barcodes poorly fit each other and morphospecies – An integrative taxonomy case of Sri Lankan Sericini chafers (Coleoptera: Scarabaeidae). Ecol Evol 2022; 12:e8942. [PMID: 35600695 PMCID: PMC9120212 DOI: 10.1002/ece3.8942] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 04/14/2022] [Accepted: 05/04/2022] [Indexed: 11/07/2022] Open
Abstract
DNA taxonomy including barcoding and metabarcoding is widely used to explore the diversity in biodiversity hotspots. In most of these hotspot areas, chafers are represented by a multitude of species, which are well defined by the complex shape of male genitalia. Here, we explore how well COI barcode data reflect morphological species entities and thus their usability for accelerated species inventorization. We conducted dedicated field surveys in Sri Lanka to collect the species‐rich and highly endemic Sericini chafers (Coleoptera: Scarabaeidae). Congruence among results of a series of protocols for de novo species delimitation and with morphology‐based species identifications was investigated. Different delimitation methods, such as the Poisson tree processes (PTP) model, Statistical Parsimony Analysis (TCS), Automatic Barcode Gap Discovery (ABGD), Assemble Species by Automatic Partitioning (ASAP), and Barcode Index Number (BIN) assignments, resulted in different numbers of molecular operational taxonomic units (MOTUs). All methods showed both over‐splitting and lumping of morphologically identified species. Only 18 of the observed 45 morphospecies perfectly matched MOTUs from all methods. The congruence of delimitation between MOTUs and morphospecies expressed by the match ratio was low, ranging from 0.57 to 0.67. TCS and multirate PTP (mPTP) showed the highest match ratio, while (BIN) assignment resulted in the lowest match ratio and most splitting events. mPTP lumped more species than any other method. Principal coordinate analysis (PCoA) on a match ratio‐based distance matrix revealed incongruent outcomes of multiple DNA delimitation methods, although applied to the same data. Our results confirm that COI barcode data alone are unlikely to correctly delimit all species, in particular, when using only a single delimitation approach. We encourage the integration of various approaches and data, particularly morphology, to validate species boundaries.
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Affiliation(s)
| | - Jonas Eberle
- Zoological Research Museum A. Koenig Leibniz Institute for the Analysis of Biodiversity Change (LIB) Bonn Germany
- University of Salzburg Salzburg Austria
| | - Jana Thormann
- Zoological Research Museum A. Koenig Leibniz Institute for the Analysis of Biodiversity Change (LIB) Bonn Germany
| | - Claudia Bohacz
- Zoological Research Museum A. Koenig Leibniz Institute for the Analysis of Biodiversity Change (LIB) Bonn Germany
| | - Suresh P. Benjamin
- Zoological Research Museum A. Koenig Leibniz Institute for the Analysis of Biodiversity Change (LIB) Bonn Germany
- National Institute of Fundamental Studies Kandy Sri Lanka
| | - Dirk Ahrens
- Zoological Research Museum A. Koenig Leibniz Institute for the Analysis of Biodiversity Change (LIB) Bonn Germany
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Maslakova S, Ellison CI, Hiebert TC, Conable F, Heaphy MC, Venera-Pontón DE, Norenburg JL, Schwartz ML, Moss ND, Boyle MJ, Driskell AC, Macdonald KS, Zattara EE, Collin R. Sampling multiple life stages significantly increases estimates of marine biodiversity. Biol Lett 2022; 18:20210596. [PMID: 35414224 PMCID: PMC9039783 DOI: 10.1098/rsbl.2021.0596] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Biodiversity assessments are critical for setting conservation priorities, understanding ecosystem function and establishing a baseline to monitor change. Surveys of marine biodiversity that rely almost entirely on sampling adult organisms underestimate diversity because they tend to be limited to habitat types and individuals that can be easily surveyed. Many marine animals have planktonic larvae that can be sampled from the water column at shallow depths. This life stage often is overlooked in surveys but can be used to relatively rapidly document diversity, especially for the many species that are rare or live cryptically as adults. Using DNA barcode data from samples of nemertean worms collected in three biogeographical regions—Northeastern Pacific, the Caribbean Sea and Eastern Tropical Pacific—we found that most species were collected as either benthic adults or planktonic larvae but seldom in both stages. Randomization tests show that this deficit of operational taxonomic units collected as both adults and larvae is extremely unlikely if larvae and adults were drawn from the same pool of species. This effect persists even in well-studied faunas. These results suggest that sampling planktonic larvae offers access to a different subset of species and thus significantly increases estimates of biodiversity compared to sampling adults alone. Spanish abstract is available in the electronic supplementary material.
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Affiliation(s)
- Svetlana Maslakova
- Oregon Institute of Marine Biology, 63466 Boat Basin Road, Charleston, OR 97420, USA
| | - Christina I Ellison
- Oregon Institute of Marine Biology, 63466 Boat Basin Road, Charleston, OR 97420, USA
| | - Terra C Hiebert
- Oregon Institute of Marine Biology, 63466 Boat Basin Road, Charleston, OR 97420, USA
| | - Frances Conable
- Oregon Institute of Marine Biology, 63466 Boat Basin Road, Charleston, OR 97420, USA
| | - Maureen C Heaphy
- Oregon Institute of Marine Biology, 63466 Boat Basin Road, Charleston, OR 97420, USA
| | | | - Jon L Norenburg
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Megan L Schwartz
- University of Washington, 1900 Commerce Avenue, Tacoma, WA 98420, USA
| | - Nicole D Moss
- Oregon Institute of Marine Biology, 63466 Boat Basin Road, Charleston, OR 97420, USA
| | - Michael J Boyle
- Smithsonian Tropical Research Institute, Apartado Postal 0843-03092, Balboa Ancon, Panama
| | - Amy C Driskell
- Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Kenneth S Macdonald
- Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Eduardo E Zattara
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA.,INIBIOMA, Universidad Nacional del Comahue-CONICET, Bariloche, Río Negro, 8400, Argentina
| | - Rachel Collin
- Smithsonian Tropical Research Institute, Apartado Postal 0843-03092, Balboa Ancon, Panama
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Gold Z, Curd EE, Goodwin KD, Choi ES, Frable BW, Thompson AR, Walker HJ, Burton RS, Kacev D, Martz LD, Barber PH. Improving metabarcoding taxonomic assignment: A case study of fishes in a large marine ecosystem. Mol Ecol Resour 2021; 21:2546-2564. [PMID: 34235858 DOI: 10.1111/1755-0998.13450] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 05/25/2021] [Accepted: 06/03/2021] [Indexed: 01/08/2023]
Abstract
DNA metabarcoding is an important tool for molecular ecology. However, its effectiveness hinges on the quality of reference sequence databases and classification parameters employed. Here we evaluate the performance of MiFish 12S taxonomic assignments using a case study of California Current Large Marine Ecosystem fishes to determine best practices for metabarcoding. Specifically, we use a taxonomy cross-validation by identity framework to compare classification performance between a global database comprised of all available sequences and a curated database that only includes sequences of fishes from the California Current Large Marine Ecosystem. We demonstrate that the regional database provides higher assignment accuracy than the comprehensive global database. We also document a tradeoff between accuracy and misclassification across a range of taxonomic cutoff scores, highlighting the importance of parameter selection for taxonomic classification. Furthermore, we compared assignment accuracy with and without the inclusion of additionally generated reference sequences. To this end, we sequenced tissue from 597 species using the MiFish 12S primers, adding 252 species to GenBank's existing 550 California Current Large Marine Ecosystem fish sequences. We then compared species and reads identified from seawater environmental DNA samples using global databases with and without our generated references, and the regional database. The addition of new references allowed for the identification of 16 additional native taxa representing 17.0% of total reads from eDNA samples, including species with vast ecological and economic value. Together these results demonstrate the importance of comprehensive and curated reference databases for effective metabarcoding and the need for locus-specific validation efforts.
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Affiliation(s)
- Zachary Gold
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, California, USA
| | - Emily E Curd
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, California, USA
| | - Kelly D Goodwin
- Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Stationed at Southwest Fisheries Science Center, La Jolla, California, USA
| | - Emma S Choi
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Benjamin W Frable
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Andrew R Thompson
- Southwest Fisheries Science Center, National Oceanic and Atmospheric Administration, La Jolla, California, USA
| | - Harold J Walker
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Ronald S Burton
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Dovi Kacev
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Lucas D Martz
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Paul H Barber
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, California, USA
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6
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The development of species-specific AFLP-derived SCAR and SSCP markers to identify mantis shrimp species. Mol Biol Rep 2020; 47:6807-6816. [PMID: 32862353 DOI: 10.1007/s11033-020-05738-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 08/25/2020] [Indexed: 10/23/2022]
Abstract
Mantis shrimp has become commercially valuable in many countries, while the commercially aquaculture still unsuccessful. The stable supply of the species-specific markers for precise identification can play a key role of foods authentication as well as restoring/enhancing mantis shrimp stocks in future. The aim of this research was to identify species-specific markers for Squillid and Harpiosquillid mantis shrimp taxa using Amplified fragment length polymorphism-Single strand conformation polymorphism (AFLP-SSCP) approaches. Selective amplification would be substituted as a total of 40 primer combinations was performed using either three-base (i.e., EcoRI+3 and MseI+3 in 20 primer combinations) or two-base (i.e., EcoRI+2 and MseI+2 in 20 primer combinations) selective primers. These had been size-fractionated via 6% denaturing polyacrylamide gel electrophoresis, ten AFLP fragments exhibiting species or genus-specific characteristics were cloned, sequenced, and GenBank interrogated. A primer pair was designed and their specificity was tested versus the genomic DNA of various species. Results show that the primer E+2-13/M+2-13Hr158 generated PCR products for just H. harpax, while E+3-14/M+3-2HhHr151 and E+2-13/M+2-13Hh150 generated PCR products for both H. harpax and H. raphidea and not others (i.e., M. nepa, O. oratoria, and E. woodmasoni). SSCP was then applied in order to differentiate between H. harpax and H. raphidea. These SSCP results indicate that species can be differentiated based on polymorphic fragment nucleotides. Indeed, primers E+2-13/M+2-13Hr158, E+3-14/M+3-2HhHr151, and E+2-13/M+2-13Hh150 were all successfully confirmed as present in processed mantis shrimp samples (i.e., saline-preserved and heat-dried). These results provide new species-specific markers for mantis shrimp identification.
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7
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Palecanda S, Feller KD, Porter ML. Using larval barcoding to estimate stomatopod species richness at Lizard Island, Australia for conservation monitoring. Sci Rep 2020; 10:10990. [PMID: 32620832 PMCID: PMC7335096 DOI: 10.1038/s41598-020-67696-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 06/12/2020] [Indexed: 11/08/2022] Open
Abstract
Stomatopods (Crustacea, Stomatopoda) are well studied for their aggressive behavior and unique visual system as well as their commercial importance in Asian and European countries. Like many crustaceans, stomatopods undergo indirect development, passing though several larval stages before reaching maturity. Adult stomatopods can be difficult to catch due to their inaccessible habitats and cryptic coloration. By sampling larvae from the planktonic community, less effort is required to obtain accurate measures of species richness within a region. Stomatopod larvae were collected between 2006 and 2015 from the waters around the Lizard Island reef platform in Eastern Australia. Cytochrome oxidase I (COI) mitochondrial DNA sequences were generated from each larval sample and compared to a database of COI sequences tied to adult specimens. Of the 20 species collected from Lizard Island as adults which have COI data available, 18 species were identified from larval sampling. One additional species identified from larval samples, Busquilla plantei, was previously unknown from Lizard Island. Nine larval OTUs were found not to match any published adult sequences. Sampling larval stomatopod populations provides a comparable picture of the adult population to benthic sampling methods and may include species richness beyond what is measurable by sampling adult populations.
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Affiliation(s)
- Sitara Palecanda
- Department of Biology, University of Hawai'i at Mānoa, Honolulu, HI, USA.
| | - Kathryn D Feller
- Department of Biological Sciences, University of Bristol, Bristol, UK
- Department of Biological Sciences, Union College, Schenectady, NY, USA
| | - Megan L Porter
- Department of Biology, University of Hawai'i at Mānoa, Honolulu, HI, USA
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8
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Simmonds SE, Fritts‐Penniman AL, Cheng SH, Mahardika GN, Barber PH. Genomic signatures of host-associated divergence and adaptation in a coral-eating snail, Coralliophila violacea (Kiener, 1836). Ecol Evol 2020; 10:1817-1837. [PMID: 32128119 PMCID: PMC7042750 DOI: 10.1002/ece3.5977] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 11/25/2019] [Accepted: 12/06/2019] [Indexed: 12/31/2022] Open
Abstract
The fluid nature of the ocean, combined with planktonic dispersal of marine larvae, lowers physical barriers to gene flow. However, divergence can still occur despite gene flow if strong selection acts on populations occupying different ecological niches. Here, we examined the population genomics of an ectoparasitic snail, Coralliophila violacea (Kiener 1836), that specializes on Porites corals in the Indo-Pacific. Previous genetic analyses revealed two sympatric lineages associated with different coral hosts. In this study, we examined the mechanisms promoting and maintaining the snails' adaptation to their coral hosts. Genome-wide single nucleotide polymorphism (SNP) data from type II restriction site-associated DNA (2b-RAD) sequencing revealed two differentiated clusters of C. violacea that were largely concordant with coral host, consistent with previous genetic results. However, the presence of some admixed genotypes indicates gene flow from one lineage to the other. Combined, these results suggest that differentiation between host-associated lineages of C. violacea is occurring in the face of ongoing gene flow, requiring strong selection. Indeed, 2.7% of all SNP loci were outlier loci (73/2,718), indicative of divergence with gene flow, driven by adaptation of each C. violacea lineage to their specific coral hosts.
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Affiliation(s)
- Sara E. Simmonds
- Department of Ecology and Evolutionary BiologyUniversity of California Los AngelesLos AngelesCAUSA
| | | | - Samantha H. Cheng
- Department of Ecology and Evolutionary BiologyUniversity of California Los AngelesLos AngelesCAUSA
- Center for Biodiversity and ConservationAmerican Museum of Natural HistoryNew YorkNYUSA
| | - Gusti Ngurah Mahardika
- Animal Biomedical and Molecular Biology LaboratoryFaculty of Veterinary MedicineUdayana University BaliDenpasarIndonesia
| | - Paul H. Barber
- Department of Ecology and Evolutionary BiologyUniversity of California Los AngelesLos AngelesCAUSA
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9
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Cryptic ecological and geographic diversification in coral-associated nudibranchs. Mol Phylogenet Evol 2019; 144:106698. [PMID: 31812568 DOI: 10.1016/j.ympev.2019.106698] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 11/03/2019] [Accepted: 11/30/2019] [Indexed: 12/18/2022]
Abstract
Coral reefs are among the most biologically diverse ecosystems of the world, yet little is known about the processes creating and maintaining their diversity. Ecologically, corallivory in nudibranchs resembles phytophagy in insects- a process that for decades has served as a model for ecological speciation via host shifting. This study uses extensive field collections, DNA sequencing, and phylogenetic analyses to reconstruct the evolutionary history of coral-associated nudibranchs and assess the relative roles that host shifting and geography may have played in their diversification. We find that the number of species is three times higher than the number previously known to science, with evidence for both allopatric and ecological divergence through host shifting and host specialization. Results contribute to growing support for the importance of ecological diversification in marine environments and provide evidence for new species in the genus Tenellia.
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Amandita FY, Rembold K, Vornam B, Rahayu S, Siregar IZ, Kreft H, Finkeldey R. DNA barcoding of flowering plants in Sumatra, Indonesia. Ecol Evol 2019; 9:1858-1868. [PMID: 30847077 PMCID: PMC6392390 DOI: 10.1002/ece3.4875] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 11/28/2018] [Accepted: 12/04/2018] [Indexed: 12/02/2022] Open
Abstract
The rapid conversion of Southeast Asian lowland rainforests into monocultures calls for the development of rapid methods for species identification to support ecological research and sustainable land-use management. Here, we investigated the utilization of DNA barcodes for identifying flowering plants from Sumatra, Indonesia. A total of 1,207 matK barcodes (441 species) and 2,376 rbcL barcodes (750 species) were successfully generated. The barcode effectiveness is assessed using four approaches: (a) comparison between morphological and molecular identification results, (b) best-close match analysis with TaxonDNA, (c) barcoding gap analysis, and (d) formation of monophyletic groups. Results show that rbcL has a much higher level of sequence recoverability than matK (95% and 66%). The comparison between morphological and molecular identifications revealed that matK and rbcL worked best assigning a plant specimen to the genus level. Estimates of identification success using best-close match analysis showed that >70% of the investigated species were correctly identified when using single barcode. The use of two-loci barcodes was able to increase the identification success up to 80%. The barcoding gap analysis revealed that neither matK nor rbcL succeeded to create a clear gap between the intraspecific and interspecific divergences. However, these two barcodes were able to discriminate at least 70% of the species from each other. Fifteen genera and twenty-one species were found to be nonmonophyletic with both markers. The two-loci barcodes were sufficient to reconstruct evolutionary relationships among the plant taxa in the study area that are congruent with the broadly accepted APG III phylogeny.
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Affiliation(s)
- Fitri Y. Amandita
- Department of Forest Genetics and Forest Tree BreedingGeorg‐August UniversityGöttingenGermany
- Research and Development Center for Environmental Quality and Laboratory
| | - Katja Rembold
- Biodiversity, Macroecology, and Biogeography Research GroupGeorg‐August UniversityGöttingenGermany
- Botanical Garden of the University of BernBernSwitzerland
| | - Barbara Vornam
- Department of Forest Genetics and Forest Tree BreedingGeorg‐August UniversityGöttingenGermany
| | - Sri Rahayu
- Bogor Botanical GardenLembaga Ilmu Pengetahuan IndonesiaBogorIndonesia
| | | | - Holger Kreft
- Biodiversity, Macroecology, and Biogeography Research GroupGeorg‐August UniversityGöttingenGermany
| | - Reiner Finkeldey
- Department of Forest Genetics and Forest Tree BreedingGeorg‐August UniversityGöttingenGermany
- University of KasselKasselGermany
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11
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Rathipriya A, Karal Marx K, Jeyashakila R. Molecular identification and phylogenetic relationship of flying fishes of Tamil Nadu coast for fishery management purposes. Mitochondrial DNA A DNA Mapp Seq Anal 2019; 30:500-510. [PMID: 30691341 DOI: 10.1080/24701394.2018.1558220] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The partial sequences of cytochrome c oxidase subunit I (COI) mitochondrial gene were analysed for developing species specific molecular signatures and phylogenetic relationship among the commercially important flying fishes (Cheilopogon cyanopterus, Cheilopogon furcatus and Hirundichthys coromandelensis) distributed in Tamil Nadu coast. Accurate identification of these species is important for fishery management as its morphological characters are very similar. Since the morphological features are very similar, accurate identification using molecular tools is essential for sustainable utilization and management of these species across their distributional range. The estimated transition/transversion bias (R) is 3.45. The average nucleotide sequences calculated were A = 30.00%, T/U = 26.40%, C = 17.00% and G = 26.60%. Using COI data analysis, the intraspecies genetic distance ranged from 0.00 to 0.05, while it varied from 0.06 to 0.08 for interspecies. Partial sequences of the genes provided sufficient phylogenetic information to distinguish the three flying fishes indicating the usefulness of mtDNA-based approach in species identification.
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Affiliation(s)
- A Rathipriya
- a Tamil Nadu Dr. J. Jayalalithaa Fisheries University , Nagapattinam , India
| | - K Karal Marx
- b Institute of Postgraduate Studies, OMR Campus , Chennai , India
| | - R Jeyashakila
- c Fisheries College and Research Institute , Thoothukudi , India
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Abstract
Lingulids and discinids are the only brachiopods that exhibit life histories that include a feeding planktonic stage usually referred to as a “larva”. We collected planktotrophic brachiopod larvae from the Pacific and Caribbean coasts of Panama and took a DNA barcoding approach with mitochondrial cytochrome c oxidase subunit I (COI), mitochondrial ribosomal 16S, and nuclear ribosomal 18S genes to identify those larvae and to estimate their diversity in the region. We observed specimens from both coasts with distinct morphologies typical of lingulid and discinid larvae. COI and 16S were sequenced successfully for the lingulid larvae but failed consistently for all discinid larvae. 18S was sequenced successfully for larvae from both families. Sequence data from each gene revealed one lingulid operational taxonomic unit (OTU) from Bocas del Toro on the Caribbean coast, and one lingulid OTU from the Bay of Panama on the Pacific coast. These OTUs differed by >20% for COI, >10% for 16S and ~0.5% for 18S. Both OTUs clustered with GenBank sequences of Glottidia species, the only genus of lingulids in the Americas, but were distinct from G. pyramidata the only species reported for the Caribbean. Analysis of 18S sequence data for discinid larvae recovered 2 OTUs, one exclusively from the Pacific and one with a mixture of Pacific and Caribbean larvae. The 18S marker does not provide enough resolution to distinguish between species, and comparisons with GenBank sequences suggest that one OTU includes Pelagodiscus species, while the other may include Discradisca species. When compared with other marine invertebrates, our surveys of brachiopod larvae through DNA barcoding show relatively low levels of diversity for Panama.
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13
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Kundu S, Rath S, Tyagi K, Chakraborty R, Pakrashi A, Kumar V, Chandra K. DNA barcoding of Cloridopsis immaculata: genetic distance and phylogeny of stomatopods. Mitochondrial DNA B Resour 2018; 3:955-958. [PMID: 33474378 PMCID: PMC7800632 DOI: 10.1080/23802359.2018.1507632] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 07/29/2018] [Indexed: 11/05/2022] Open
Abstract
The changes of coastal topography might have genetically altered the extant species diversity in Chilika Lake. The genetic assessment of stomatopods has never been attempted from this ecosystem. The study generate the first genetic information (mtCOI) of Cloridopsis immaculata. DNA sequences of C. immaculata shows 12.9% genetic divergence with Harpiosquilla harpax and clade as sister species in NJ tree. Alima, Harpiosquilla, and Oratosquilla shows high congeneric/conspecific genetic divergence (20.9%, 15.7%, and 7.2%) and cladded separately in the phylogeny; correlate to their diverse populations. We recommend more extensive survey of stomatopods and generation of molecular data to resolve the taxonomic uncertainty.
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Affiliation(s)
- Shantanu Kundu
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Shibananda Rath
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Kaomud Tyagi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Rajasree Chakraborty
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Avas Pakrashi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Vikas Kumar
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Kailash Chandra
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
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Collet A, Durand JD, Desmarais E, Cerqueira F, Cantinelli T, Valade P, Ponton D. DNA barcoding post-larvae can improve the knowledge about fish biodiversity: an example from La Reunion, SW Indian Ocean. Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:905-918. [PMID: 28984152 DOI: 10.1080/24701394.2017.1383406] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The aim of this study was to demonstrate that fish larvae identified using their COI sequences offer a unique opportunity for improving the knowledge of local fish richness. Fish larvae were sampled at the end of their pelagic phase using light-traps set off the West Coast of La Reunion Island, southwestern Indian Ocean, once per month from October 2014 to March 2015. Among the 5174 larvae caught, 214 morphologically different specimens were selected, 196 successfully barcoded, giving a total of 101 different Barcode Index Numbers (BINs). Among these BINs, 55 had never been recorded in La Reunion exclusive economic zone (EEZ), and 13 were new for the BOLD database. Even if the sampling effort for collecting fish post-larvae during this study was relatively low, it allowed adding at least nine new species to an updated checklist of fishes of La Reunion EEZ.
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Affiliation(s)
| | - Jean-Dominique Durand
- b UMR 9190 MARBEC, IRD-CNRS-IFREMER-UM, Department of Ecology , Evolutionary Biology University of Science, VNUHCM , Ho Chi Minh City , Vietnam
| | - Eric Desmarais
- c ISEM, CNRS , University of Montpellier, IRD, EPHE , Montpellier , France
| | | | - Thomas Cantinelli
- c ISEM, CNRS , University of Montpellier, IRD, EPHE , Montpellier , France
| | | | - Dominique Ponton
- d ENTROPIE, IRD , Université de La Réunion, CNRS, Laboratoire d'Excellence CORAIL , La Réunion , France
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15
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Cheng J, Sha ZL. Cryptic diversity in the Japanese mantis shrimp Oratosquilla oratoria (Crustacea: Squillidae): Allopatric diversification, secondary contact and hybridization. Sci Rep 2017; 7:1972. [PMID: 28512346 PMCID: PMC5434036 DOI: 10.1038/s41598-017-02059-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 04/04/2017] [Indexed: 11/20/2022] Open
Abstract
Mounting evidence of cryptic species in the marine realm emphasizes the necessity to thoroughly revise our current perceptions of marine biodiversity and species distributions. Here, we used mitochondrial cytochrome oxidase subunit I (mtDNA COI) and nuclear ribosomal internal transcribed spacer (nrDNA ITS) to investigate cryptic diversity and potential hybridization in the Japanese mantis shrimp Oratosquilla oratoria in the Northwestern (NW) Pacific. Both mitochondrial and nuclear gene genealogies revealed two cryptic species in this morphotaxon, which was further confirmed by extensive population-level analyses. One cryptic species is restricted to cold waters with a distribution range corresponding to temperate affinities, while the other dwelled warm waters influenced by the Kuroshio Current. Their divergence was postulated to be attributable to the vicariant event which resulted from the isolation of the Sea of Japan during the middle Pliocene (c. 3.85 Mya, 95% HPD 2.23–6.07 Mya). Allopatric speciation was maintained by limited genetic exchange due to their habitat preferences. Furthermore, the observation of recombinant nrDNA ITS sequence and intra-individual ITS polymorphism suggested recent hybridization event of the two cryptic species occurred in sympatric areas. Our study also illustrated that the Changjiang River outflow might act as an oceanic barrier to gene flow and promoted allopatric diversification in O. oratoria species complex.
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Affiliation(s)
- Jiao Cheng
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Zhong-Li Sha
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
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16
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Palero F, Robainas-Barcia A, Corbari L, Macpherson E. Phylogeny and evolution of shallow-water squat lobsters (Decapoda, Galatheoidea) from the Indo-Pacific. ZOOL SCR 2016. [DOI: 10.1111/zsc.12230] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ferran Palero
- INRA, University of Nice Sophia Antipolis; CNRS, UMR 1355-7254, Institut Sophia Agrobiotech; Sophia Antipolis 06900 France
- Centre d'Estudis Avançats de Blanes (CEAB-CSIC); Carrer d'Accés a la Cala Sant Francesc 14 17300 Blanes Spain
| | - Aymee Robainas-Barcia
- Departament de Genètica; Facultat de Biologia; Universitat de Barcelona; Av. Diagonal 645 08028 Barcelona Spain
| | - Laure Corbari
- UMR 7205; Institut de Systématique; Evolution et Biodiversité; département Systématique et Evolution; Muséum national d'Histoire naturelle; 55 rue Buffon CP51 75005 Paris France
| | - Enrique Macpherson
- Centre d'Estudis Avançats de Blanes (CEAB-CSIC); Carrer d'Accés a la Cala Sant Francesc 14 17300 Blanes Spain
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Layton KKS, Corstorphine EA, Hebert PDN. Exploring Canadian Echinoderm Diversity through DNA Barcodes. PLoS One 2016; 11:e0166118. [PMID: 27870868 PMCID: PMC5117606 DOI: 10.1371/journal.pone.0166118] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 10/24/2016] [Indexed: 11/19/2022] Open
Abstract
DNA barcoding has proven an effective tool for species identification in varied groups of marine invertebrates including crustaceans, molluscs, polychaetes and echinoderms. In this study, we further validate its utility by analyzing almost half of the 300 species of Echinodermata known from Canadian waters. COI sequences from 999 specimens were assigned to 145 BINs. In most cases, species discrimination was straightforward due to the large difference (25-fold) between mean intra- (0.48%) and inter- (12.0%) specific divergence. Six species were flagged for further taxonomic investigation because specimens assigned to them fell into two or three discrete sequence clusters. The potential influence of larval dispersal capacity and glacial events on patterns of genetic diversity is discussed for 19 trans-oceanic species. Although additional research is needed to clarify biogeographic patterns and resolve taxonomic questions, this study represents an important step in the assembly of a DNA barcode library for all Canadian echinoderms, a valuable resource for future biosurveillance programs.
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Affiliation(s)
- Kara K. S. Layton
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, ON, N1G 2W1, Canada
- * E-mail:
| | - Erin A. Corstorphine
- 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
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Roslin T, Majaneva S. The use of DNA barcodes in food web construction-terrestrial and aquatic ecologists unite! Genome 2016; 59:603-28. [PMID: 27484156 DOI: 10.1139/gen-2015-0229] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
By depicting who eats whom, food webs offer descriptions of how groupings in nature (typically species or populations) are linked to each other. For asking questions on how food webs are built and work, we need descriptions of food webs at different levels of resolution. DNA techniques provide opportunities for highly resolved webs. In this paper, we offer an exposé of how DNA-based techniques, and DNA barcodes in particular, have recently been used to construct food web structure in both terrestrial and aquatic systems. We highlight how such techniques can be applied to simultaneously improve the taxonomic resolution of the nodes of the web (i.e., the species), and the links between them (i.e., who eats whom). We end by proposing how DNA barcodes and DNA information may allow new approaches to the construction of larger interaction webs, and overcome some hurdles to achieving adequate sample size. Most importantly, we propose that the joint adoption and development of these techniques may serve to unite approaches to food web studies in aquatic and terrestrial systems-revealing the extent to which food webs in these environments are structured similarly to or differently from each other, and how they are linked by dispersal.
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Affiliation(s)
- Tomas Roslin
- a Department of Ecology, Swedish University of Agricultural Sciences, Box 7044, 750 07 Uppsala, Sweden.,b Spatial Foodweb Ecology Group, Department of Agricultural Sciences, PO Box 27, (Latokartanonkaari 5), FI-00014 University of Helsinki, Finland
| | - Sanna Majaneva
- c Centre for Ecology and Evolution in Microbial model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, 39182 Kalmar, Sweden
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Feller KD, Cronin TW. Spectral absorption of visual pigments in stomatopod larval photoreceptors. J Comp Physiol A Neuroethol Sens Neural Behav Physiol 2016; 202:215-23. [PMID: 26767658 PMCID: PMC4759216 DOI: 10.1007/s00359-015-1063-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 12/08/2015] [Accepted: 12/13/2015] [Indexed: 11/30/2022]
Abstract
Larval stomatopod eyes appear to be much simpler versions of adult compound eyes, lacking most of the visual pigment diversity and photoreceptor specializations. Our understanding of the visual pigment diversity of larval stomatopods, however, is based on four species, which severely limits our understanding of stomatopod eye ontogeny. To investigate several poorly understood aspects of stomatopod larval eye function, we tested two hypotheses surrounding the spectral absorption of larval visual pigments. First, we examined a broad range of species to determine if stomatopod larvae generally express a single, spectral class of photoreceptor. Using microspectrophotometry (MSP) on larvae captured in the field, we found data which further support this long-standing hypothesis. MSP was also used to test whether larval species from the same geographical region express visual pigments with similar absorption spectra. Interestingly, despite occupation of the same geographical location, we did not find evidence to support our second hypothesis. Rather, there was significant variation in visual pigment absorption spectra among sympatric species. These data are important to further our understanding of larval photoreceptor spectral diversity, which is beneficial to ongoing investigations into the ontogeny, physiology, and molecular evolution of stomatopod eyes.
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Affiliation(s)
- Kathryn D Feller
- University of Bristol, Life Sciences Building Tyndall Avenue, Bristol, BS8 1TQ, UK.
| | - Thomas W Cronin
- University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA
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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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Raupach MJ, Barco A, Steinke D, Beermann J, Laakmann S, Mohrbeck I, Neumann H, Kihara TC, Pointner K, Radulovici A, Segelken-Voigt A, Wesse C, Knebelsberger T. The Application of DNA Barcodes for the Identification of Marine Crustaceans from the North Sea and Adjacent Regions. PLoS One 2015; 10:e0139421. [PMID: 26417993 PMCID: PMC4587929 DOI: 10.1371/journal.pone.0139421] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 09/14/2015] [Indexed: 12/02/2022] Open
Abstract
During the last years DNA barcoding has become a popular method of choice for molecular specimen identification. Here we present a comprehensive DNA barcode library of various crustacean taxa found in the North Sea, one of the most extensively studied marine regions of the world. Our data set includes 1,332 barcodes covering 205 species, including taxa of the Amphipoda, Copepoda, Decapoda, Isopoda, Thecostraca, and others. This dataset represents the most extensive DNA barcode library of the Crustacea in terms of species number to date. By using the Barcode of Life Data Systems (BOLD), unique BINs were identified for 198 (96.6%) of the analyzed species. Six species were characterized by two BINs (2.9%), and three BINs were found for the amphipod species Gammarus salinus Spooner, 1947 (0.4%). Intraspecific distances with values higher than 2.2% were revealed for 13 species (6.3%). Exceptionally high distances of up to 14.87% between two distinct but monophyletic clusters were found for the parasitic copepod Caligus elongatus Nordmann, 1832, supporting the results of previous studies that indicated the existence of an overlooked sea louse species. In contrast to these high distances, haplotype-sharing was observed for two decapod spider crab species, Macropodia parva Van Noort & Adema, 1985 and Macropodia rostrata (Linnaeus, 1761), underlining the need for a taxonomic revision of both species. Summarizing the results, our study confirms the application of DNA barcodes as highly effective identification system for the analyzed marine crustaceans of the North Sea and represents an important milestone for modern biodiversity assessment studies using barcode sequences.
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Affiliation(s)
- Michael J. Raupach
- German Center of Marine Biodiversity (DZMB), Senckenberg am Meer, Wilhelmshaven, Niedersachsen, Germany
- * E-mail:
| | - Andrea Barco
- German Center of Marine Biodiversity (DZMB), Senckenberg am Meer, Wilhelmshaven, Niedersachsen, Germany
| | - Dirk Steinke
- Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Jan Beermann
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Biologische Anstalt Helgoland, Helgoland, Schleswig-Holstein, Germany
| | - Silke Laakmann
- German Center of Marine Biodiversity (DZMB), Senckenberg am Meer, Wilhelmshaven, Niedersachsen, Germany
| | - Inga Mohrbeck
- German Center of Marine Biodiversity (DZMB), Senckenberg am Meer, Wilhelmshaven, Niedersachsen, Germany
| | - Hermann Neumann
- Department for Marine Research, Senckenberg am Meer, Wilhelmshaven, Niedersachsen, Germany
| | - Terue C. Kihara
- German Center of Marine Biodiversity (DZMB), Senckenberg am Meer, Wilhelmshaven, Niedersachsen, Germany
| | - Karin Pointner
- German Center of Marine Biodiversity (DZMB), Senckenberg am Meer, Wilhelmshaven, Niedersachsen, Germany
| | - Adriana Radulovici
- Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Alexandra Segelken-Voigt
- Animal Biodiversity and Evolutionary Biology, Institute for Biology and Environmental Sciences, V. School of Mathematics and Science, Carl von Ossietzky University Oldenburg, Oldenburg, Niedersachsen, Germany
| | - Christina Wesse
- German Center of Marine Biodiversity (DZMB), Senckenberg am Meer, Wilhelmshaven, Niedersachsen, Germany
| | - Thomas Knebelsberger
- German Center of Marine Biodiversity (DZMB), Senckenberg am Meer, Wilhelmshaven, Niedersachsen, Germany
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Grosjean S, Ohler A, Chuaynkern Y, Cruaud C, Hassanin A. Improving biodiversity assessment of anuran amphibians using DNA barcoding of tadpoles. Case studies from Southeast Asia. C R Biol 2015; 338:351-61. [DOI: 10.1016/j.crvi.2015.03.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Revised: 03/19/2015] [Accepted: 03/25/2015] [Indexed: 10/23/2022]
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Cowart DA, Pinheiro M, Mouchel O, Maguer M, Grall J, Miné J, Arnaud-Haond S. Metabarcoding is powerful yet still blind: a comparative analysis of morphological and molecular surveys of seagrass communities. PLoS One 2015; 10:e0117562. [PMID: 25668035 PMCID: PMC4323199 DOI: 10.1371/journal.pone.0117562] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 12/27/2014] [Indexed: 11/26/2022] Open
Abstract
In the context of the sixth wave of extinction, reliable surveys of biodiversity are increasingly needed to infer the cause and consequences of species and community declines, identify early warning indicators of tipping points, and provide reliable impact assessments before engaging in activities with potential environmental hazards. DNA metabarcoding has emerged as having potential to provide speedy assessment of community structure from environmental samples. Here we tested the reliability of metabarcoding by comparing morphological and molecular inventories of invertebrate communities associated with seagrasses through estimates of alpha and beta diversity, as well as the identification of the most abundant taxa. Sediment samples were collected from six Zostera marina seagrass meadows across Brittany, France. Metabarcoding surveys were performed using both mitochondrial (Cytochrome Oxidase I) and nuclear (small subunit 18S ribosomal RNA) markers, and compared to morphological inventories compiled by a long-term benthic monitoring network. A sampling strategy was defined to enhance performance and accuracy of results by preventing the dominance of larger animals, boosting statistical support through replicates, and using two genes to compensate for taxonomic biases. Molecular barcodes proved powerful by revealing a remarkable level of diversity that vastly exceeded the morphological survey, while both surveys identified congruent differentiation of the meadows. However, despite the addition of individual barcodes of common species into taxonomic reference databases, the retrieval of only 36% of these species suggest that the remaining were either not present in the molecular samples or not detected by the molecular screening. This finding exemplifies the necessity of comprehensive and well-curated taxonomic reference libraries and multi-gene surveys. Overall, results offer methodological guidelines and support for metabarcoding as a powerful and repeatable method of characterizing communities, while also presenting suggestions for improvement, including implementation of pilot studies prior to performing full "blind" metabarcoding assessments to optimize sampling and amplification protocols.
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Affiliation(s)
- Dominique A. Cowart
- IFREMER (Institut Français de Recherche pour l’Exploitation de la MER), Unité Environnement Profond, Département des Ressources physiques et Ecosystèmes de Fond de mer (REM), B.P. 70, 29280, Plouzané, France
| | - Miguel Pinheiro
- University of St. Andrews, Medical and Biological Sciences Building, North Haugh, St. Andrews, Fife, KY16 9TF, United Kingdom
| | - Olivier Mouchel
- IFREMER (Institut Français de Recherche pour l’Exploitation de la MER), Unité Environnement Profond, Département des Ressources physiques et Ecosystèmes de Fond de mer (REM), B.P. 70, 29280, Plouzané, France
| | - Marion Maguer
- Institut Universitaire Européen de la Mer (IUEM), Technopôle Brest-Iroiserue Dumont d’Urville, 29280, Plouzané, France
| | - Jacques Grall
- Institut Universitaire Européen de la Mer (IUEM), Technopôle Brest-Iroiserue Dumont d’Urville, 29280, Plouzané, France
| | - Jacques Miné
- Total Exploration & Production, Direction HSE, 2 Place Jean Millier, 92078, Paris la Défense, France
| | - Sophie Arnaud-Haond
- IFREMER (Institut Français de Recherche pour l’Exploitation de la MER), Unité Environnement Profond, Département des Ressources physiques et Ecosystèmes de Fond de mer (REM), B.P. 70, 29280, Plouzané, France
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Phylogenetic relationships within the snapping shrimp genus Synalpheus (Decapoda: Alpheidae). Mol Phylogenet Evol 2014; 77:116-25. [DOI: 10.1016/j.ympev.2014.03.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2013] [Revised: 03/09/2014] [Accepted: 03/11/2014] [Indexed: 11/20/2022]
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25
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Radulovici AE, Sainte-Marie B, Dufresne F. DNA barcoding of marine crustaceans from the Estuary and Gulf of St Lawrence: a regional-scale approach. Mol Ecol Resour 2013; 9 Suppl s1:181-7. [PMID: 21564977 DOI: 10.1111/j.1755-0998.2009.02643.x] [Citation(s) in RCA: 110] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Marine crustaceans are known as a group with a high level of morphological and ecological diversity but are difficult to identify by traditional approaches and usually require the help of highly trained taxonomists. A faster identification method, DNA barcoding, was found to be an effective tool for species identification in many metazoan groups including some crustaceans. Here we expand the DNA barcode database with a case study involving 80 malacostracan species from the Estuary and Gulf of St Lawrence. DNA sequences for 460 specimens grouped into clusters corresponding to known morphological species in 95% of cases. Genetic distances between species were on average 25 times higher than within species. Intraspecific divergence was high (3.78-13.6%) in specimens belonging to four morphological species, suggesting the occurrence of cryptic species. Moreover, we detected the presence of an invasive amphipod species in the St Lawrence Estuary. This study reconfirms the usefulness of DNA barcoding for the identification of marine crustaceans.
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Affiliation(s)
- Adriana E Radulovici
- Département de biologie, Université du Québec à Rimouski, 300 allée des Ursulines, Rimouski, Québec, Canada G5 L 3A1, Direction des sciences halieutiques et de l'aquaculture, Institut Maurice-Lamontagne, Pêches et Océans Canada, 850 route de la Mer, CP 1000, Mont-Joli, Québec, Canada G5H 3Z4
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Novo M, Fernández R, Marchán DF, Mónica Gutiérrez, Cosín DJD. Compilation of morphological and molecular data, a necessity for taxonomy: The case of Hormogaster abbatissae sp. n. (Annelida, Clitellata, Hormogastridae). Zookeys 2013:1-16. [PMID: 23378793 PMCID: PMC3560842 DOI: 10.3897/zookeys.242.3996] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Accepted: 10/31/2012] [Indexed: 12/05/2022] Open
Abstract
Conflict among data sources can be frequent in evolutionary biology, especially in cases where one character set poses limitations to resolution. Earthworm taxonomy, for example, remains a challenge because of the limited number of morphological characters taxonomically valuable. An explanation to this may be morphological convergence due to adaptation to a homogeneous habitat, resulting in high degrees of homoplasy. This sometimes impedes clear morphological diagnosis of species. Combination of morphology with molecular techniques has recently aided taxonomy in many groups difficult to delimit morphologically. Here we apply an integrative approach by combining morphological and molecular data, including also some ecological features, to describe a new earthworm species in the family Hormogastridae, Hormogaster abbatissaesp. n., collected in Sant Joan de les Abadesses (Girona, Spain). Its anatomical and morphological characters are discussed in relation to the most similar Hormogastridae species, which are not the closest species in a phylogenetic analysis of molecular data. Species delimitation using the GMYC method and genetic divergences with the closest species are also considered. The information supplied by the morphological and molecular sources is contradictory, and thus we discuss issues with species delimitation in other similar situations. Decisions should be based on a profound knowledge of the morphology of the studied group but results from molecular analyses should also be considered.
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Affiliation(s)
- Marta Novo
- Departamento de Zoología y Antropología Física, Facultad de Biología, Universidad Complutense de Madrid, C/ José Antonio Nováis 2, 28040, Madrid, Spain ; Cardiff School of Biosciences, Cardiff University, BIOSI 1, Museum Avenue, Cardiff CF10 3TL, UK
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Chen HN, Høeg JT, Chan BKK. Morphometric and molecular identification of individual barnacle cyprids from wild plankton: an approach to detecting fouling and invasive barnacle species. BIOFOULING 2013; 29:133-145. [PMID: 23327366 DOI: 10.1080/08927014.2012.753061] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The present study used DNA barcodes to identify individual cyprids to species. This enables accurate quantification of larvae of potential fouling species in the plankton. In addition, it explains the settlement patterns of barnacles and serves as an early warning system of unwanted immigrant species. Sequences from a total of 540 individual cypris larvae from Taiwanese waters formed 36 monophyletic clades (species) in a phylogenetic tree. Of these clades, 26 were identified to species, but 10 unknown monophyletic clades represented non-native species. Cyprids of the invasive barnacle, Megabalanus cocopoma, were identified. Multivariate analysis of antennular morphometric characters revealed three significant clusters in a nMDS plot, viz. a bell-shaped attachment organ (most species), a shoe-shaped attachment organ (some species), and a spear-shaped attachment organ (coral barnacles only). These differences in attachment organ structure indicate that antennular structures interact directly with the diverse substrata involved in cirripede settlement.
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Affiliation(s)
- Hsi-Nien Chen
- Institute of Ecology and Evolutionary Biology, National Taiwan University, No 1, Sec 4, Roosevelt Road, Taipei 106, Taipei, Taiwan
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Haye PA, Segovia NI, Vera R, Gallardo MDLÁ, Gallardo-Escárate C. Authentication of commercialized crab-meat in Chile using DNA Barcoding. Food Control 2012. [DOI: 10.1016/j.foodcont.2011.10.034] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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Taylor HR, Harris WE. An emergent science on the brink of irrelevance: a review of the past 8 years of DNA barcoding. Mol Ecol Resour 2012; 12:377-88. [PMID: 22356472 DOI: 10.1111/j.1755-0998.2012.03119.x] [Citation(s) in RCA: 149] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
DNA barcoding has become a well-funded, global enterprise since its proposition as a technique for species identification, delimitation and discovery in 2003. However, the rapid development of next generation sequencing (NGS) has the potential to render DNA barcoding irrelevant because of the speed with which it generates large volumes of genomic data. To avoid obsolescence, the DNA barcoding movement must adapt to use this new technology. This review examines the DNA barcoding enterprise, its continued resistance to improvement and the implications of this on the future of the discipline. We present the consistent failure of DNA barcoding to recognize its limitations and evolve its methodologies, reducing the usefulness of the data produced by the movement and throwing into doubt its ability to embrace NGS.
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Affiliation(s)
- H R Taylor
- Allan Wilson Centre for Molecular Ecology and Evolution, School of Biological Sciences, Victoria University of Wellington, Kelburn Parade, Kelburn, PO Box 600 Wellington, New Zealand.
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Abstract
It is a risky task to attempt to predict the direction that DNA barcoding and its applications may take in the future. In a very short time, the endeavor of DNA barcoding has gone from being a tool to facilitate taxonomy in difficult to identify species, to an ambitious, global initiative that seeks to tackle such pertinent and challenging issues as quantifying global biodiversity, revolutionizing the forensic identifications of species, advancing the study of interactions among species, and promoting the reconstruction of evolutionary relationships within communities. The core element of DNA barcoding will always remain the same: the generation of a set of well-identified samples collected and genotyped at one or more genetic barcode markers and assembled into a properly curated database. But the application of this body of data will depend on the creativity and need of the research community in using a "gold standard" of annotated DNA sequence data at the species level. We foresee several areas where the application of DNA barcode data is likely to yield important evolutionary, ecological, and societal insights, and while far from exclusive, provide examples of how DNA barcode data will continue to empower scientists to address hypothesis-driven research. Three areas of immediate and obvious concern are (1) biodiversity inventories, (2) phylogenetic applications, and (3) species interactions.
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Affiliation(s)
- David L Erickson
- Department of Botany, Smithsonian Institution, National Museum of Natural History, Washington, DC, USA.
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Sutou M, Kato T, Ito M. Recent discoveries of armyworms in Japan and their species identification using DNA barcoding. Mol Ecol Resour 2011; 11:992-1001. [PMID: 21693000 DOI: 10.1111/j.1755-0998.2011.03040.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Long columns of migrating larval sciarid armyworms were discovered in central and northern Japan, specifically Kanagawa, Gunma, Miyagi and Akita prefectures, as well as Hokkaido. This is the first examination of armyworms in East Asia. In Europe, armyworms have been identified as Sciara militaris, belonging to the family Sciaridae (sciarid flies or black fungus gnats), by rearing them to adulthood. In Japan, we were unable to obtain live samples for rearing; therefore, DNA barcodes were obtained from the samples of armyworms collected in the Gunma and Miyagi prefectures. The DNA barcodes were compared with those obtained from the following samples: pupae of S. militaris from UK, adults of Sciara kitakamiensis, Sciara humeralis, Sciara hemerobioides, Sciara thoracica, Sciara helvola and Sciara melanostyla from Japan, and adults of one undescribed Sciara species from Malaysia. Neighbour-joining, maximum parsimony, and maximum likelihood analyses revealed that the armyworms discovered in Japan are S. kitakamiensis. Although adults of this species have been recorded in several locations in Japan, this is the first report of migrating larval armyworms. DNA barcodes were effectively used to link different life stages of this species. The average intraspecific and interspecific pairwise genetic distances of the genus Sciara were 0.3% and 12.6%, respectively. The present study illustrates that DNA barcodes are an effective means of identifying sciarid flies in Japan.
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Affiliation(s)
- M Sutou
- Department of General Systems Studies, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan.
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Greenstone MH, Vandenberg NJ, Hu JH. Barcode haplotype variation in north American agroecosystem lady beetles (Coleoptera: Coccinellidae). Mol Ecol Resour 2011; 11:629-37. [PMID: 21457477 DOI: 10.1111/j.1755-0998.2011.03007.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA barcodes have proven invaluable in identifying and distinguishing insect pests, most notably for determining the provenance of exotic invasives, but relatively few insect natural enemies have been barcoded. We used Folmer et al.'s (1994) universal invertebrate primers and Hebert et al.'s (2004) for Lepidoptera, to amplify 658 bp at the 5' end of the mitochondrial cytochrome oxidase c subunit I (COI) gene in five species of lady beetles from crop fields in six states in the US Mid-Atlantic, Plains and Midwest: three native species, Hippodamia convergens Guérin-Méneville, H. parenthesis (Say) and Coleomegilla maculata (De Geer); and two exotic species, Harmonia axyridis (Pallas) and Coccinella septempunctata Linnaeus. Sequence divergences within species were low, never exceeding 0.9% (Kimura 2-parameter distances). Sequence divergences between the two Hippodamia species ranged from 14.7 to 16.4%, mirroring the relationships found for other arthropod taxa. Among the exotic species, C. septempunctata sequences were as variable as those of the three native species, while H. axyridis populations comprised a single haplotype. Limited data on two Coleomegilla subspecies, C. m. lengi Timberlake and C. m. fuscilabris (Mulsant), are consistent with their belonging to the same species, although morphological and reproductive data indicate that they represent separate species. Our results support the general utility of COI barcodes for distinguishing and diagnosing coccinellid species, but point to possible limitations in the use of barcodes to resolve species assignments in recently divergent sibling species.
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Affiliation(s)
- Matthew H Greenstone
- United States Department of Agriculture, Agricultural Research Service, Invasive Insect Biocontrol and Behavior Laboratory, Beltsville, MD 20705, USA.
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Asgharian H, Sahafi HH, Ardalan AA, Shekarriz S, Elahi E. Cytochrome c oxidase subunit 1 barcode data of fish of the Nayband National Park in the Persian Gulf and analysis using meta-data flag several cryptic species. Mol Ecol Resour 2011; 11:461-72. [PMID: 21481204 DOI: 10.1111/j.1755-0998.2011.02989.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We provide cytochrome c oxidase subunit 1 (COI) barcode sequences of fishes of the Nayband National Park, Persian Gulf, Iran. Industrial activities, ecological considerations and goals of The Fish Barcode of Life campaign make it crucial that fish species residing in the park be identified. To the best of our knowledge, this is the first report of barcoding data on fishes of the Persian Gulf. We examined 187 individuals representing 76 species, 56 genera and 32 families. The data flagged potentially cryptic species of Gerres filamentosus and Plectorhinchus schotaf. 16S rDNA data on these species are provided. Exclusion of these two potential cryptic species resulted in a mean COI intraspecific distance of 0.18%, and a mean inter- to intraspecific divergence ratio of 66.7. There was no overlap between maximum Kimura 2-parameter distances among conspecifics (1.66%) and minimum distance among congeneric species (6.19%). Barcodes shared among species were not observed. Neighbour-joining analysis showed that most species formed cohesive sequence units with little variation. Finally, the comparison of 16 selected species from this study with meta-data of conspecifics from Australia, India, China and South Africa revealed high interregion divergences and potential existence of six cryptic species. Pairwise interregional comparisons were more informative than global divergence assessments with regard to detection of cryptic variation. Our analysis exemplifies optimal use of the expanding barcode data now becoming available.
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Affiliation(s)
- Hosseinali Asgharian
- Department Biotechnology, College of Science, University of Tehran, No 13, Shafiie Alley, Qods St., Enghelab St., 14155-6455, Tehran, Iran
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Abstract
More than 230,000 known species representing 31 metazoan phyla populate the world's oceans. Perhaps another 1,000,000 or more species remain to be discovered. There is reason for concern that species extinctions may out-pace discovery, especially in diverse and endangered marine habitats such as coral reefs. DNA barcodes (i.e., short DNA sequences for species recognition and discrimination) are useful tools to accelerate species-level analysis of marine biodiversity and to facilitate conservation efforts. This review focuses on the usual barcode region for metazoans: a approximately 648 base-pair region of the mitochondrial cytochrome c oxidase subunit I (COI) gene. Barcodes have also been used for population genetic and phylogeographic analysis, identification of prey in gut contents, detection of invasive species, forensics, and seafood safety. More controversially, barcodes have been used to delimit species boundaries, reveal cryptic species, and discover new species. Emerging frontiers are the use of barcodes for rapid and increasingly automated biodiversity assessment by high-throughput sequencing, including environmental barcoding and the use of barcodes to detect species for which formal identification or scientific naming may never be possible.
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Affiliation(s)
- Ann Bucklin
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut 06340, USA.
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Using DNA barcoding and phylogenetics to identify Antarctic invertebrate larvae: Lessons from a large scale study. Mar Genomics 2010; 3:165-77. [DOI: 10.1016/j.margen.2010.09.004] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2010] [Revised: 09/05/2010] [Accepted: 09/05/2010] [Indexed: 11/21/2022]
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Dinca V, Zakharov EV, Hebert PDN, Vila R. Complete DNA barcode reference library for a country's butterfly fauna reveals high performance for temperate Europe. Proc Biol Sci 2010; 278:347-55. [PMID: 20702462 DOI: 10.1098/rspb.2010.1089] [Citation(s) in RCA: 118] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
DNA barcoding aims to accelerate species identification and discovery, but performance tests have shown marked differences in identification success. As a consequence, there remains a great need for comprehensive studies which objectively test the method in groups with a solid taxonomic framework. This study focuses on the 180 species of butterflies in Romania, accounting for about one third of the European butterfly fauna. This country includes five eco-regions, the highest of any in the European Union, and is a good representative for temperate areas. Morphology and DNA barcodes of more than 1300 specimens were carefully studied and compared. Our results indicate that 90 per cent of the species form barcode clusters allowing their reliable identification. The remaining cases involve nine closely related species pairs, some whose taxonomic status is controversial or that hybridize regularly. Interestingly, DNA barcoding was found to be the most effective identification tool, outperforming external morphology, and being slightly better than male genitalia. Romania is now the first country to have a comprehensive DNA barcode reference database for butterflies. Similar barcoding efforts based on comprehensive sampling of specific geographical regions can act as functional modules that will foster the early application of DNA barcoding while a global system is under development.
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Affiliation(s)
- Vlad Dinca
- Institute of Evolutionary Biology (UPF-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Spain
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Bärlocher F, Charette N, Letourneau A, Nikolcheva LG, Sridhar KR. Sequencing DNA extracted from single conidia of aquatic hyphomycetes. FUNGAL ECOL 2010. [DOI: 10.1016/j.funeco.2009.08.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Ficetola GF, Coissac E, Zundel S, Riaz T, Shehzad W, Bessière J, Taberlet P, Pompanon F. An in silico approach for the evaluation of DNA barcodes. BMC Genomics 2010; 11:434. [PMID: 20637073 PMCID: PMC3091633 DOI: 10.1186/1471-2164-11-434] [Citation(s) in RCA: 227] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2009] [Accepted: 07/16/2010] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND DNA barcoding is a key tool for assessing biodiversity in both taxonomic and environmental studies. Essential features of barcodes include their applicability to a wide spectrum of taxa and their ability to identify even closely related species. Several DNA regions have been proposed as barcodes and the region selected strongly influences the output of a study. However, formal comparisons between barcodes remained limited until now. Here we present a standard method for evaluating barcode quality, based on the use of a new bioinformatic tool that performs in silico PCR over large databases. We illustrate this approach by comparing the taxonomic coverage and the resolution of several DNA regions already proposed for the barcoding of vertebrates. To assess the relationship between in silico and in vitro PCR, we also developed specific primers amplifying different species of Felidae, and we tested them using both kinds of PCR RESULTS: Tests on specific primers confirmed the correspondence between in silico and in vitro PCR. Nevertheless, results of in silico and in vitro PCRs can be somehow different, also because tuning PCR conditions can increase the performance of primers with limited taxonomic coverage. The in silico evaluation of DNA barcodes showed a strong variation of taxonomic coverage (i.e., universality): barcodes based on highly degenerated primers and those corresponding to the conserved region of the Cyt-b showed the highest coverage. As expected, longer barcodes had a better resolution than shorter ones, which are however more convenient for ecological studies analysing environmental samples. CONCLUSIONS In silico PCR could be used to improve the performance of a study, by allowing the preliminary comparison of several DNA regions in order to identify the most appropriate barcode depending on the study aims.
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Affiliation(s)
- Gentile Francesco Ficetola
- Laboratoire d'Ecologie Alpine, CNRS UMR 5553, Université Joseph Fourier, BP 53, F-38041 Grenoble Cedex 9, France
- Dipartimento di Biologia, Università degli Studi di Milano. Via Celoria 26, 20133 Milano Italy
- Dipartimento di Scienze dell'Ambiente e del Territorio, Università degli Studi di Milano Bicocca. Piazza della Scienza 1, 20126 Milano Italy
| | - Eric Coissac
- Laboratoire d'Ecologie Alpine, CNRS UMR 5553, Université Joseph Fourier, BP 53, F-38041 Grenoble Cedex 9, France
| | - Stéphanie Zundel
- Laboratoire d'Ecologie Alpine, CNRS UMR 5553, Université Joseph Fourier, BP 53, F-38041 Grenoble Cedex 9, France
| | - Tiayyba Riaz
- Laboratoire d'Ecologie Alpine, CNRS UMR 5553, Université Joseph Fourier, BP 53, F-38041 Grenoble Cedex 9, France
| | - Wasim Shehzad
- Laboratoire d'Ecologie Alpine, CNRS UMR 5553, Université Joseph Fourier, BP 53, F-38041 Grenoble Cedex 9, France
| | - Julien Bessière
- Laboratoire d'Ecologie Alpine, CNRS UMR 5553, Université Joseph Fourier, BP 53, F-38041 Grenoble Cedex 9, France
| | - Pierre Taberlet
- Laboratoire d'Ecologie Alpine, CNRS UMR 5553, Université Joseph Fourier, BP 53, F-38041 Grenoble Cedex 9, France
| | - François Pompanon
- Laboratoire d'Ecologie Alpine, CNRS UMR 5553, Université Joseph Fourier, BP 53, F-38041 Grenoble Cedex 9, France
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Magnacca KN, Brown MJF. Mitochondrial heteroplasmy and DNA barcoding in Hawaiian Hylaeus (Nesoprosopis) bees (Hymenoptera: Colletidae). BMC Evol Biol 2010; 10:174. [PMID: 20540728 PMCID: PMC2891727 DOI: 10.1186/1471-2148-10-174] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2009] [Accepted: 06/11/2010] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND The past several years have seen a flurry of papers seeking to clarify the utility and limits of DNA barcoding, particularly in areas such as species discovery and paralogy due to nuclear pseudogenes. Heteroplasmy, the coexistence of multiple mitochondrial haplotypes in a single organism, has been cited as a potentially serious problem for DNA barcoding but its effect on identification accuracy has not been tested. In addition, few studies of barcoding have tested a large group of closely-related species with a well-established morphological taxonomy. In this study we examine both of these issues, by densely sampling the Hawaiian Hylaeus bee radiation. RESULTS Individuals from 21 of the 49 a priori morphologically-defined species exhibited coding sequence heteroplasmy at levels of 1-6% or more. All homoplasmic species were successfully identified by COI using standard methods of analysis, but only 71% of heteroplasmic species. The success rate in identifying heteroplasmic species was increased to 86% by treating polymorphisms as character states rather than ambiguities. Nuclear pseudogenes (numts) were also present in four species, and were distinguishable from heteroplasmic sequences by patterns of nucleotide and amino acid change. CONCLUSIONS Heteroplasmy significantly decreased the reliability of species identification. In addition, the practical issue of dealing with large numbers of polymorphisms- and resulting increased time and labor required - makes the development of DNA barcode databases considerably more complex than has previously been suggested. The impact of heteroplasmy on the utility of DNA barcoding as a bulk specimen identification tool will depend upon its frequency across populations, which remains unknown. However, DNA barcoding is still likely to remain an important identification tool for those species that are difficult or impossible to identify through morphology, as is the case for the ecologically important solitary bee fauna.
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Affiliation(s)
- Karl N Magnacca
- Department of Zoology, School of Natural Sciences, Trinity College Dublin, Dublin 2, Ireland
- Current address: Department of Biology, University of Hawai'i, 200 W. Kawili St., Hilo HI 96720, USA
| | - Mark JF Brown
- Department of Zoology, School of Natural Sciences, Trinity College Dublin, Dublin 2, Ireland
- School of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK
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TANG RICKYWK, YAU CYNTHIA, NG WAI. Identification of stomatopod larvae (Crustacea: Stomatopoda) from Hong Kong waters using DNA barcodes. Mol Ecol Resour 2010; 10:439-48. [DOI: 10.1111/j.1755-0998.2009.02794.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- RICKY W. K. TANG
- The Swire Institute of Marine Science, Faculty of Science, The University of Hong Kong, Cape d’Aguilar Road, Shek O; and Division of Ecology & Biodiversity, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong
| | - CYNTHIA YAU
- The Swire Institute of Marine Science, Faculty of Science, The University of Hong Kong, Cape d’Aguilar Road, Shek O; and Division of Ecology & Biodiversity, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong
| | - WAI‐CHUEN NG
- The Swire Institute of Marine Science, Faculty of Science, The University of Hong Kong, Cape d’Aguilar Road, Shek O; and Division of Ecology & Biodiversity, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong
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LARA ARIAGNA, PONCE de LEÓN JOSÉLUIS, RODRÍGUEZ RODET, CASANE DIDIER, CÔTÉ GUILLAUME, BERNATCHEZ LOUIS, GARCÍA‐MACHADO ERIK. DNA barcoding of Cuban freshwater fishes: evidence for cryptic species and taxonomic conflicts. Mol Ecol Resour 2010; 10:421-30. [DOI: 10.1111/j.1755-0998.2009.02785.x] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- ARIAGNA LARA
- Centro de Investigaciones Marinas, Universidad de La Habana, Calle 16, No. 114 Entre 1ra y 3ra, Miramar, Playa, Ciudad Habana 11300, Cuba
| | - JOSÉ LUIS PONCE de LEÓN
- Facultad de Biología, Universidad de La Habana, Calle 25, No. 455 Entre J e I, Vedado, Ciudad Habana 10400, Cuba
| | - RODET RODRÍGUEZ
- Facultad de Biología, Universidad de La Habana, Calle 25, No. 455 Entre J e I, Vedado, Ciudad Habana 10400, Cuba
| | - DIDIER CASANE
- Laboratoire Evolution Génomes et Spéciation (UPR9034), CNRS, 91198 Gif‐sur‐Yvette Cedex, France
| | - GUILLAUME CÔTÉ
- Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles‐Eugène Marchand, Université Laval, Quebec, QC, Canada G1V 0A6
| | - LOUIS BERNATCHEZ
- Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles‐Eugène Marchand, Université Laval, Quebec, QC, Canada G1V 0A6
| | - ERIK GARCÍA‐MACHADO
- Centro de Investigaciones Marinas, Universidad de La Habana, Calle 16, No. 114 Entre 1ra y 3ra, Miramar, Playa, Ciudad Habana 11300, Cuba
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PUILLANDRE N, STRONG EE, BOUCHET P, BOISSELIER M, COULOUX A, SAMADI S. Identifying gastropod spawn from DNA barcodes: possible but not yet practicable. Mol Ecol Resour 2009; 9:1311-21. [DOI: 10.1111/j.1755-0998.2009.02576.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- N PUILLANDRE
- UMR 7138, Systématique, adaptation, évolution (UPMC/IRD/MNHN/CNRS), Université Pierre et Marie Curie (UPMC), CP26, 57 rue Cuvier, 75231 Paris cedex 05, France
| | - E. E. STRONG
- Department of Invertebrate Zoology, Smithsonian Institution, National Museum of Natural History, MRC 163, PO Box 37012, Washington, DC 20013‐7012, USA
| | - P. BOUCHET
- Muséum National d’Histoire Naturelle, 57 rue Cuvier, 75231 Paris cedex 05, France
| | - M.‐C. BOISSELIER
- UMR 7138, Systématique, adaptation, évolution (UPMC/IRD/MNHN/CNRS), Université Pierre et Marie Curie (UPMC), CP26, 57 rue Cuvier, 75231 Paris cedex 05, France
| | - A. COULOUX
- GENOSCOPE, Centre National de Séquençage, 91000 Evry, France
| | - S SAMADI
- UMR 7138, Systématique, adaptation, évolution (UPMC/IRD/MNHN/CNRS), Université Pierre et Marie Curie (UPMC), CP26, 57 rue Cuvier, 75231 Paris cedex 05, France
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Perkins SL, Austin CC. Four new species of Plasmodium from New Guinea lizards: integrating morphology and molecules. J Parasitol 2009; 95:424-33. [PMID: 18823150 DOI: 10.1645/ge-1750.1] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2008] [Accepted: 09/18/2008] [Indexed: 11/10/2022] Open
Abstract
New Guinea is one of the most biodiverse regions of the world, particularly in terms of the herpetofauna present, yet surprisingly little is known about the parasites that infect these organisms. A survey of diverse scinid and agamid lizard hosts from this country showed a diversity of malaria parasites infecting these hosts. We combined morphological and morphometric observations of the parasites (primarily gametocytes) along with DNA sequence data from the mitochondrial cytochrome b and cytochrome oxidase I genes and here describe 4 new species of Plasmodium, i.e. Plasmodium minuoviride n. sp., Plasmodium koreafense n. sp., Plasmodium megalotrypa n. sp., and Plasmodium gemini n. sp. A fifth species, Plasmodium lacertiliae Thompson and Hart 1946, is redescribed based on new observations of hosts and localities and additional molecular data. This combined morphological and molecular approach is advised for all future descriptions of new malaria parasite species, particularly in light of situations where every life-history stage is not available.
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Affiliation(s)
- Susan L Perkins
- Sackler Institute for Comparative Genomics & Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th St., New York, New York 10024, USA.
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Magnacca KN, Brown MJF. Tissue segregation of mitochondrial haplotypes in heteroplasmic Hawaiian bees: implications for DNA barcoding. Mol Ecol Resour 2009; 10:60-8. [PMID: 21564991 DOI: 10.1111/j.1755-0998.2009.02724.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The issue of mitochondrial heteroplasmy has been cited as a theoretical problem for DNA barcoding but is only beginning to be examined in natural systems. We sequenced multiple DNA extractions from 20 individuals of four Hawaiian Hylaeus bee species known to be heteroplasmic. All species showed strong differences at polymorphic sites between abdominal and muscle tissue in most individuals, and only two individuals had no obvious segregation. Two specimens produced completely clean sequences from abdominal DNA. The fact that these differences are clearly visible by direct sequencing indicates that substantial intra-individual mtDNA diversity may be overlooked when DNA is taken from small tissue fragments. At the same time, differences in haplotype distribution among individuals may result in incorrect recognition of cryptic species. Because DNA barcoding studies typically use only a small fragment of an organism, they are particularly vulnerable to sequencing bias where heteroplasmy and haplotype segregation are present. It is important to anticipate this possibility prior to undertaking large-scale barcoding projects to reduce the likelihood of haplotype segregation confounding the results.
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Affiliation(s)
- Karl N Magnacca
- Department of Zoology, School of Natural Sciences, Trinity College Dublin, Dublin 2, Ireland School of Biological Sciences, Royal Holloway University of London, Egham, Surrey TW20 0EX, UK
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DeBoer TS, Subia MD, Erdmann MV, Kovitvongsa K, Barber PH. Phylogeography and limited genetic connectivity in the endangered boring giant clam across the Coral Triangle. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2008; 22:1255-66. [PMID: 18637905 DOI: 10.1111/j.1523-1739.2008.00983.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The Coral Triangle is the global center of marine biodiversity; however, its coral reefs are critically threatened. Because of the bipartite life history of many marine species with sedentary adults and dispersive pelagic larvae, designing effective marine protected areas requires an understanding of patterns of larval dispersal and connectivity among geographically discrete populations. We used mtDNA sequence data to examine patterns of genetic connectivity in the boring giant clam (Tridacna crocea) in an effort to guide conservation efforts within the Coral Triangle. We collected an approximately 485 base pair fragment of mtDNA cytochrome c oxidase 1 (CO1) from 414 individuals at 26 sites across Indonesia. Genetic structure was strong between regions (phi(ST)=0.549, p < 0.00001) with 3 strongly supported clades: one restricted to western Sumatra, another distributed across central Indonesia, and a third limited to eastern Indonesia and Papua. Even within the single largest clade, small but significant genetic structure was documented (phi(ST)=0.069, p < 0.00001), which indicates limited gene flow within and among phylogeographic regions. Significant patterns of isolation by distance indicated an average dispersal distance of only 25-50 km, which is far below dispersal predictions of 406-708 km derived from estimates of passive dispersal over 10 days via surface currents. The strong regional genetic structure we found indicates potent limits to genetic and demographic connectivity for this species throughout the Coral Triangle and provides a regional context for conservation planning. The recovery of 3 distinct evolutionarily significant units within a well-studied taxonomic group suggests that biodiversity in this region may be significantly underestimated and that Tridacna taxa may be more endangered than currently recognized.
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Affiliation(s)
- Timery S DeBoer
- Boston University, Biology Department, 5 Cummington Street, Boston, MA 02215, USA.
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Drew J, Allen GR, Kaufman L, Barber PH. Endemism and regional color and genetic differences in five putatively cosmopolitan reef fishes. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2008; 22:965-975. [PMID: 18786099 DOI: 10.1111/j.1523-1739.2008.01011.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Endemism is thought to be relatively rare in marine systems due to the lack of allopatric barriers and the potential for long-distance colonization via pelagic larval dispersal. Although many species of coral reef fishes exhibit regionally restricted color variants that are suggestive of regional endemism, such variation is typically ascribed to intraspecific variation. We examined the genetic structure in 5 putatively monospecific fishes from the Indo-West Pacific (Amphiprion melanopus, Chrysiptera talboti, and Pomacentrus moluccensis [Pomacentridae] and Cirrhilabrus punctatus, and Labroides dimidiatus [Labridae]) that express regional color variation unique to this area. Mitochondrial-control-region sequence analysis showed shallow to deep genetic divergence in all 5 species (sequence divergence 2-17%), with clades concordant with regional color variation. These results were partially supported by nuclear RAG2 data. An analysis of molecular variation (AMOVA) mirrored the phylogenetic results; Phi(ST) values ranged from 0.91 to 0.7, indicating high levels of geographic partitioning of genetic variation. Concordance of genetics and phenotype demonstrate the genetic uniqueness of southwestern Pacific color variants, indicating that these populations are at a minimum distinct evolutionarily significant units and perhaps distinct regionally endemic species. Our results indicate that the alpha biodiversity of the southwestern Pacific is likely underestimated even in well-studied groups, such as reef fishes, and that regional endemism may be more common in tropical marine systems than previously thought.
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Affiliation(s)
- Joshua Drew
- Boston University Marine Program, Boston University, 5 Cummington Street, Boston, MA 02215, USA.
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Hubert N, Hanner R, Holm E, Mandrak NE, Taylor E, Burridge M, Watkinson D, Dumont P, Curry A, Bentzen P, Zhang J, April J, Bernatchez L. Identifying Canadian freshwater fishes through DNA barcodes. PLoS One 2008; 3:e2490. [PMID: 22423312 PMCID: PMC3278308 DOI: 10.1371/journal.pone.0002490] [Citation(s) in RCA: 333] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2007] [Accepted: 05/19/2008] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND DNA barcoding aims to provide an efficient method for species-level identifications using an array of species specific molecular tags derived from the 5' region of the mitochondrial cytochrome c oxidase I (COI) gene. The efficiency of the method hinges on the degree of sequence divergence among species and species-level identifications are relatively straightforward when the average genetic distance among individuals within a species does not exceed the average genetic distance between sister species. Fishes constitute a highly diverse group of vertebrates that exhibit deep phenotypic changes during development. In this context, the identification of fish species is challenging and DNA barcoding provide new perspectives in ecology and systematics of fishes. Here we examined the degree to which DNA barcoding discriminate freshwater fish species from the well-known Canadian fauna, which currently encompasses nearly 200 species, some which are of high economic value like salmons and sturgeons. METHODOLOGY/PRINCIPAL FINDINGS We bi-directionally sequenced the standard 652 bp "barcode" region of COI for 1360 individuals belonging to 190 of the 203 Canadian freshwater fish species (95%). Most species were represented by multiple individuals (7.6 on average), the majority of which were retained as voucher specimens. The average genetic distance was 27 fold higher between species than within species, as K2P distance estimates averaged 8.3% among congeners and only 0.3% among concpecifics. However, shared polymorphism between sister-species was detected in 15 species (8% of the cases). The distribution of K2P distance between individuals and species overlapped and identifications were only possible to species group using DNA barcodes in these cases. Conversely, deep hidden genetic divergence was revealed within two species, suggesting the presence of cryptic species. CONCLUSIONS/SIGNIFICANCE The present study evidenced that freshwater fish species can be efficiently identified through the use of DNA barcoding, especially the species complex of small-sized species, and that the present COI library can be used for subsequent applications in ecology and systematics.
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Affiliation(s)
- Nicolas Hubert
- Département de biologie, Pavillon Charles-Eugène-Marchand, Université Laval, Sainte-Foy, Québec, Canada
| | - Robert Hanner
- Canadian Barcode of Life Network, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Erling Holm
- Department of Natural History, Royal Ontario Museum, Toronto, Ontario, Canada
| | - Nicholas E. Mandrak
- Great Lakes Laboratory for Fisheries and Aquatic Sciences, Fisheries and Oceans Canada, Burlington, Ontario, Canada
| | - Eric Taylor
- Department of Zoology, Vancouver, British Columbia, Canada
| | - Mary Burridge
- Department of Natural History, Royal Ontario Museum, Toronto, Ontario, Canada
| | - Douglas Watkinson
- Fisheries and Oceans Canada, Central & Arctic Region, Freshwater Institute, Winnipeg, Manitoba, Canada
| | - Pierre Dumont
- Ministère des Ressources naturelles et de la faune du Québec, Direction de l'aménagement de la faune de Montréal, de Laval et de la Montérégie, Longueuil, Québec, Canada
| | - Allen Curry
- Fish and Wildlife Research Unit, University of New Brunswick, Fredericton, New Brunswick, Canada
| | - Paul Bentzen
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Junbin Zhang
- Canadian Barcode of Life Network, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Julien April
- Département de biologie, Pavillon Charles-Eugène-Marchand, Université Laval, Sainte-Foy, Québec, Canada
| | - Louis Bernatchez
- Département de biologie, Pavillon Charles-Eugène-Marchand, Université Laval, Sainte-Foy, Québec, Canada
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Kochzius M, Nölte M, Weber H, Silkenbeumer N, Hjörleifsdottir S, Hreggvidsson GO, Marteinsson V, Kappel K, Planes S, Tinti F, Magoulas A, Garcia Vazquez E, Turan C, Hervet C, Campo Falgueras D, Antoniou A, Landi M, Blohm D. DNA microarrays for identifying fishes. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2008; 10:207-217. [PMID: 18270778 PMCID: PMC2263118 DOI: 10.1007/s10126-007-9068-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2007] [Revised: 11/05/2007] [Accepted: 11/07/2007] [Indexed: 05/25/2023]
Abstract
In many cases marine organisms and especially their diverse developmental stages are difficult to identify by morphological characters. DNA-based identification methods offer an analytically powerful addition or even an alternative. In this study, a DNA microarray has been developed to be able to investigate its potential as a tool for the identification of fish species from European seas based on mitochondrial 16S rDNA sequences. Eleven commercially important fish species were selected for a first prototype. Oligonucleotide probes were designed based on the 16S rDNA sequences obtained from 230 individuals of 27 fish species. In addition, more than 1200 sequences of 380 species served as sequence background against which the specificity of the probes was tested in silico. Single target hybridisations with Cy5-labelled, PCR-amplified 16S rDNA fragments from each of the 11 species on microarrays containing the complete set of probes confirmed their suitability. True-positive, fluorescence signals obtained were at least one order of magnitude stronger than false-positive cross-hybridisations. Single nontarget hybridisations resulted in cross-hybridisation signals at approximately 27% of the cases tested, but all of them were at least one order of magnitude lower than true-positive signals. This study demonstrates that the 16S rDNA gene is suitable for designing oligonucleotide probes, which can be used to differentiate 11 fish species. These data are a solid basis for the second step to create a "Fish Chip" for approximately 50 fish species relevant in marine environmental and fisheries research, as well as control of fisheries products.
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Affiliation(s)
- M Kochzius
- Centre for Applied Gene Sensor Technology (CAG), University of Bremen, Bremen, Germany.
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50
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Pfenninger M, Nowak C, Kley C, Steinke D, Streit B. Utility of DNA taxonomy and barcoding for the inference of larval community structure in morphologically cryptic Chironomus (Diptera) species. Mol Ecol 2007; 16:1957-68. [PMID: 17444904 DOI: 10.1111/j.1365-294x.2006.03136.x] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Biodiversity studies require species level analyses for the accurate assessment of community structures. However, while specialized taxonomic knowledge is only rarely available for routine identifications, DNA taxonomy and DNA barcoding could provide the taxonomic basis for ecological inferences. In this study, we assessed the community structure of sediment dwelling, morphologically cryptic Chironomus larvae in the Rhine-valley plain/Germany, comparing larval type classification, cytotaxonomy, DNA taxonomy and barcoding. While larval type classification performed poorly, cytotaxonomy and DNA-based methods yielded comparable results: detrended correspondence analysis and permutation analyses indicated that the assemblages are not randomly but competitively structured. However, DNA taxonomy identified an additional species that could not be resolved by the traditional method. We argue that DNA-based identification methods such as DNA barcoding can be a valuable tool to increase accuracy, objectivity and comparability of the taxonomic assessment in biodiversity and community ecology studies.
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Affiliation(s)
- Markus Pfenninger
- Abteilung Okologie & Evolution, J.W. Goethe-Universität, Frankfurt, Main, Germany.
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