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Marcionetti A, Bertrand JAM, Cortesi F, Donati GFA, Heim S, Huyghe F, Kochzius M, Pellissier L, Salamin N. Recurrent gene flow events occurred during the diversification of clownfishes of the skunk complex. Mol Ecol 2024; 33:e17347. [PMID: 38624248 DOI: 10.1111/mec.17347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 03/15/2024] [Accepted: 03/26/2024] [Indexed: 04/17/2024]
Abstract
Clownfish (subfamily Amphiprioninae) are an iconic group of coral reef fish that evolved a mutualistic interaction with sea anemones, which triggered the adaptive radiation of the clade. Within clownfishes, the "skunk complex" is particularly interesting. Besides ecological speciation, interspecific gene flow and hybrid speciation are thought to have shaped the evolution of the group. We investigated the mechanisms characterizing the diversification of this complex. By taking advantage of their disjunct geographical distribution, we obtained whole-genome data of sympatric and allopatric populations of the three main species of the complex (Amphiprion akallopisos, A. perideraion and A. sandaracinos). We examined population structure, genomic divergence and introgression signals and performed demographic modelling to identify the most realistic diversification scenario. We excluded scenarios of strict isolation or hybrid origin of A. sandaracinos. We discovered moderate gene flow from A. perideraion to the ancestor of A. akallopisos + A. sandaracinos and weak gene flow between the species in the Indo-Australian Archipelago throughout the diversification of the group. We identified introgressed regions in A. sandaracinos and detected in A. perideraion two large regions of high divergence from the two other species. While we found that gene flow has occurred throughout the species' diversification, we also observed that recent admixture was less pervasive than initially thought, suggesting a role of host repartition or behavioural barriers in maintaining the genetic identity of the species in sympatry.
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Affiliation(s)
- Anna Marcionetti
- Department of Computational Biology, Génopode, University of Lausanne, Lausanne, Switzerland
| | - Joris A M Bertrand
- Department of Computational Biology, Génopode, University of Lausanne, Lausanne, Switzerland
- Laboratoire Génome et Développement Des Plantes (UMR 5096 UPVD/CNRS), University of Perpignan via Domitia, Perpignan, France
| | - Fabio Cortesi
- School of the Environment and Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Giulia F A Donati
- EAWAG Swiss Federal Institute of Aquatic Science & Technology, Dübendorf, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Sara Heim
- Department of Computational Biology, Génopode, University of Lausanne, Lausanne, Switzerland
| | - Filip Huyghe
- Marine Biology - Ecology, Evolution and Genetics, Vrije Universiteit Brussel (VUB), Pleinlaan 2, Brussels, Belgium
| | - Marc Kochzius
- Marine Biology - Ecology, Evolution and Genetics, Vrije Universiteit Brussel (VUB), Pleinlaan 2, Brussels, Belgium
| | - Loïc Pellissier
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
- Ecosystems and Landscape Evolution, Department of Environmental System Science, Institute of Terrestrial Ecosystems, ETH Zürich, Zurich, Switzerland
| | - Nicolas Salamin
- Department of Computational Biology, Génopode, University of Lausanne, Lausanne, Switzerland
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Boehm JT, Bovee E, Harris SE, Eddins K, Akahoho I, Foster M, Pell SK, Hickerson MJ, Amato G, DeSalle R, Waldman J. The United States dried seahorse trade: A comparison of traditional Chinese medicine and ecommerce-curio markets using molecular identification. PLoS One 2023; 18:e0291874. [PMID: 37788253 PMCID: PMC10547177 DOI: 10.1371/journal.pone.0291874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 09/07/2023] [Indexed: 10/05/2023] Open
Abstract
Tens of millions of dried seahorses (genus Hippocampus) are traded annually, and the pressure from this trade along with their life history traits (involved parental care and small migration distances and home ranges) has led to near global population declines. This and other forms of overexploitation have led to all seahorse species being listed in Appendix II under the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). The signatory nations of CITES recommended a 10-cm size limit of seahorses to ensure harvested individuals have reached reproductive maturity, and have thus had the chance to produce offspring, to maintain a more sustainable global seahorse fishery. We assessed adherence to CITES recommendations using DNA barcoding and size measurements to compare two prominent U.S. dried seahorse markets: (1) traditional Chinese medicine (TCM), and (2) non-medicinal ecommerce and coastal curio (ECC). We also estimated U.S. import abundance from CITES records. Of the nine species identified among all samples (n = 532), eight were found in the TCM trade (n = 168); composed mostly (75%) of the Indo-Pacific species Hippocampus trimaculatus, and Hippocampus spinosissimus, and the Latin American Hippocampus ingens. In contrast, ECC samples (n = 344) included 5 species, primarily juvenile Indo-Pacific Hippocampus kuda (51.5%) and the western Atlantic Hippocampus zosterae (40.7). The majority of TCM samples (85.7%) met the CITES size recommendation, in contrast to 4.8% of ECC samples. These results suggest non-size discriminatory bycatch is the most likely source of imported ECC specimens. In addition, CITES records indicate that approximately 602,275 dried specimens were imported into the U.S. from 2004-2020, but the exact species composition remains unknown as many U.S. imports records list one species or Hippocampus spp. from confiscated shipments due to difficulties in morphological identification and large numbers of individuals per shipment. Molecular identification was used to identify the species composition of confiscated shipment imports containing undesignated species, and similar to TCM, found H. trimaculatus and H. spinosissimus the most abundant. By combining DNA barcoding, size comparisons, and CITES database records, these results provide an important glimpse into the two primary dried U.S. seahorse end-markets, and may further inform the conservation status of several Hippocampus species.
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Affiliation(s)
- J T Boehm
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, United States of America
- Department of Biology, City College of New York, New York, New York, United States of America
- Subprogram in Ecology, Evolution Biology and Behavior, The Graduate Center of the City University of New York, New York, New York, United States of America
| | - Eric Bovee
- School of Forest, Fisheries, and Geomatics Sciences, University of Florida, Gainesville, Florida, United States of America
| | - Stephen E Harris
- Subprogram in Ecology, Evolution Biology and Behavior, The Graduate Center of the City University of New York, New York, New York, United States of America
- School of Natural and Social Science, SUNY Purchase College, Purchase, New York, United States of America
| | - Kathryn Eddins
- The New School, New York, New York, United States of America
| | - Ishmael Akahoho
- Brooklyn Academy of Science and the Environment High School, Brooklyn, New York, United States of America
| | - Marcia Foster
- Brooklyn Academy of Science and the Environment High School, Brooklyn, New York, United States of America
| | - Susan K Pell
- Brooklyn Botanic Garden, Brooklyn, New York, United States of America
| | - Michael J Hickerson
- Department of Biology, City College of New York, New York, New York, United States of America
- Subprogram in Ecology, Evolution Biology and Behavior, The Graduate Center of the City University of New York, New York, New York, United States of America
- Division of Invertebrate Zoology, American Museum of Natural History, New York, New York, United States of America
| | - George Amato
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, United States of America
| | - Rob DeSalle
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, United States of America
- Division of Invertebrate Zoology, American Museum of Natural History, New York, New York, United States of America
| | - John Waldman
- Subprogram in Ecology, Evolution Biology and Behavior, The Graduate Center of the City University of New York, New York, New York, United States of America
- Biology Department, Queens College, City University of New York, New York, United States of America
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Stiller J, Wilson NG, Rouse GW. Range-wide population genomics of common seadragons shows secondary contact over a former barrier and insights on illegal capture. BMC Biol 2023; 21:129. [PMID: 37248474 DOI: 10.1186/s12915-023-01628-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 05/16/2023] [Indexed: 05/31/2023] Open
Abstract
BACKGROUND Common seadragons (Phyllopteryx taeniolatus, Syngnathidae) are an emblem of the diverse endemic fauna of Australia's southern rocky reefs, the newly recognized "Great Southern Reef." A lack of assessments spanning this global biodiversity hotspot in its entirety is currently hampering an understanding of the factors that have contributed to its diversity. The common seadragon has a wide range across Australia's entire temperate south and includes a geogenetic break over a former land bridge, which has called its status as a single species into question. As a popular aquarium display that sells for high prices, common seadragons are also vulnerable to illegal capture. RESULTS Here, we provide range-wide nuclear sequences (986 variable Ultraconserved Elements) for 198 individuals and mitochondrial genomes for 140 individuals to assess species status, identify genetic units and their diversity, and trace the source of two poached individuals. Using published data of the other two seadragon species, we found that lineages of common seadragons have diverged relatively recently (< 0.63 Ma). Within common seadragons, we found pronounced genetic structure, falling into three major groups in the western, central, and eastern parts of the range. While populations across the Bassian Isthmus were divergent, there is also evidence for secondary contact since the passage opened. We found a strong cline of genetic diversity from the range center tapering symmetrically towards the range peripheries. Based on their genetic similarities, the poached individuals were inferred to have originated from around Albany in southwestern Australia. CONCLUSIONS We conclude that common seadragons constitute a single species with strong geographic structure but coherence through gene flow. The low genetic diversity on the east and west coasts is concerning given that these areas are projected to face fast climate change. Our results suggest that in addition to their life history, geological events and demographic expansions have all played a role in shaping populations in the temperate south. These insights are an important step towards understanding the historical determinants of the diversity of species endemic to the Great Southern Reef.
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Affiliation(s)
- Josefin Stiller
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, 92093 , USA.
- Centre for Biodiversity Genomics, University of Copenhagen, 2100, Copenhagen, Denmark.
| | - Nerida G Wilson
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, 92093 , USA
- Research & Collections, Western Australian Museum, Perth, Western Australia, 6106, Australia
- School of Biological Sciences, University of Western Australia, Perth, Western Australia, 6009, Australia
| | - Greg W Rouse
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, 92093 , USA.
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Couëdel M, Dettai A, Guillaume MMM, Bruggemann F, Bureau S, Frattini B, Verde Ferreira A, Azie J, Bruggemann JH. New insights into the diversity of cryptobenthic Cirripectes blennies in the Mascarene Archipelago sampled using Autonomous Reef Monitoring Structures (ARMS). Ecol Evol 2023; 13:e9850. [PMID: 36937067 PMCID: PMC10019914 DOI: 10.1002/ece3.9850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 01/25/2023] [Accepted: 01/30/2023] [Indexed: 03/18/2023] Open
Abstract
Autonomous Reef Monitoring Structures (ARMS) are artificial mini-reefs designed for standardized sampling of sessile and small motile cryptobenthic organisms. ARMS are also effective for collecting small cryptobenthic fishes, such as the combtooth blennies of the genus Cirripectes. Recent studies discovered several Cirripectes species endemic to islands or archipelagos, in spite of the generally broad distributions of tropical and subtropical blennies. Thus, to evaluate the diversity and distribution of Cirripectes species in the Mascarene Archipelago, a little-studied region but an important biodiversity hotspot, complete mitochondrial genomes, and nuclear rhodopsin genes were sequenced for 39 specimens collected with ARMS deployed on outer reef slopes at Reunion and Rodrigues islands. Mitochondrial COI sequences were analyzed to integrate these specimens within the largest dataset of publicly available sequences. Three species were found in the Mascarene Archipelago, Cirripectes castaneus, Cirripectes randalli, and Cirripectes stigmaticus. C. castaneus and C. stigmaticus both have an Indo-Pacific distribution with several haplotypes shared among distant localities. In agreement with the literature, C. randalli shows a small-range endemism restricted to the Mascarenes. We confirmed the presence of C. castaneus, C. randalli, and C. stigmaticus in Rodrigues, and the presence of C. stigmaticus in Reunion. This study contributes to filling the gaps in taxonomic and molecular knowledge of the reef cryptobiome in the South-West Indian Ocean, and provides the first complete mitogenomes for the genus, a crucial step for future molecular-based inventories (e.g., eDNA).
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Affiliation(s)
- Marion Couëdel
- Université de La Réunion, UMR 9220 ENTROPIE (Université de La Réunion, IRD, IFREMER, Université de Nouvelle‐Calédonie, CNRS)La RéunionSaint‐DenisFrance
| | - Agnes Dettai
- Muséum national d'Histoire naturelle (MNHN), UMR 7205 ISYEB (MNHN, CNRS, Sorbonne Université, EPHE, Université des Antilles)ParisFrance
| | - Mireille M. M. Guillaume
- Muséum national d'Histoire naturelle (MNHN)UMR 8067 BOrEA (MNHN, CNRS 2030, Sorbonne Université, IRD 207, Uni Caen‐Normandie, Université des Antilles)ParisFrance
- LabEx CORAILUniversité de PerpignanPerpignanFrance
| | - Fleur Bruggemann
- Université de La Réunion, UMR 9220 ENTROPIE (Université de La Réunion, IRD, IFREMER, Université de Nouvelle‐Calédonie, CNRS)La RéunionSaint‐DenisFrance
| | - Sophie Bureau
- Université de La Réunion, UMR 9220 ENTROPIE (Université de La Réunion, IRD, IFREMER, Université de Nouvelle‐Calédonie, CNRS)La RéunionSaint‐DenisFrance
| | - Baptiste Frattini
- Université de La Réunion, UMR 9220 ENTROPIE (Université de La Réunion, IRD, IFREMER, Université de Nouvelle‐Calédonie, CNRS)La RéunionSaint‐DenisFrance
- Muséum national d'Histoire naturelle (MNHN)UMR 8067 BOrEA (MNHN, CNRS 2030, Sorbonne Université, IRD 207, Uni Caen‐Normandie, Université des Antilles)ParisFrance
| | - Amélie Verde Ferreira
- Muséum national d'Histoire naturelle (MNHN), UMR 7205 ISYEB (MNHN, CNRS, Sorbonne Université, EPHE, Université des Antilles)ParisFrance
| | | | - J. Henrich Bruggemann
- Université de La Réunion, UMR 9220 ENTROPIE (Université de La Réunion, IRD, IFREMER, Université de Nouvelle‐Calédonie, CNRS)La RéunionSaint‐DenisFrance
- LabEx CORAILUniversité de PerpignanPerpignanFrance
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Pragmatic applications of DNA barcoding markers in identification of fish species – a review. ANNALS OF ANIMAL SCIENCE 2023. [DOI: 10.2478/aoas-2022-0073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Abstract
DNA barcoding and mini barcoding involve Cytochrome Oxidase Subunit I (COI) gene in mitochondrial genome and is used for accurate identification of species and biodiversity. The basic goal of the current study is to develop a complete reference database of fishes. It also evaluates the applicability of COI gene to identify fish at the species level with other aspects i.e., as Kimura 2 parameter (K2P) distance. The mean observed length of the sequence was ranging between 500 to 700 base pairs for fish species in DNA barcoding and 80 to 650 base pairs for DNA mini barcoding. This method describes the status of known to unknown samples but it also facilitates the detection of previously un-sampled species at distinct level. So, mini-barcoding is a method focuses on the analysis of short-length DNA markers has been demonstrated to be effective for species identification of processed food containing degraded DNA. While DNA meta-barcoding refers to the automated identification of multiple species from a single bulk sample. The may contain entire organisms or a single environmental sample containing degraded DNA. Despite DNA barcoding, mini barcoding and meta-barcoding are efficient methods for species identification which are helpful in conservation and proper management of biodiversity. It aids researchers to take an account of genetic as well as evolutionary relationships by collecting their morphological, distributional and molecular data. Overall, this paper discusses DNA barcoding technology and how it has been used to various fish species, as well as its universality, adaptability, and novel approach to DNA-based species identification.
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Nascimento BM, de Paula TS, Brito PMM. DNA barcode of tilapia fish fillet from the Brazilian market and a standardized COI haplotyping for molecular identification of Oreochromis spp. (Actinopterygii, Cichlidae). FORENSIC SCIENCE INTERNATIONAL: ANIMALS AND ENVIRONMENTS 2022. [DOI: 10.1016/j.fsiae.2022.100059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Unwanted Guest Continues its Northern Journey in the Aegean Sea: Pterois miles (Bennett, 1828). TRANSYLVANIAN REVIEW OF SYSTEMATICAL AND ECOLOGICAL RESEARCH 2022. [DOI: 10.2478/trser-2022-0020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023] Open
Abstract
Abstract
Pterois miles (Bennett, 1828), one of the most destructive marine invaders, was reported from the Mediterranean in 1991. It has invaded most parts of the Mediterranean from 2013, when it was reported for the second time, until today. On 7th October 2020, a single specimen of P. miles was collected by the bottom trawl from the Edremit Bay (Northern Aegean Sea). COI barcode region was used for the molecular identification of the specimen. DNA barcode data suggest that the specimen used in the present study is P. miles with a 99.69% probability. The current study is presented by providing the northernmost occurrence of the P. miles from the Aegean Sea with molecular confirmation.
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Yuanawati D, Farizky HS, Santanumurti MB, Jamal MT, Iqbal Sani LM, Madduppa H, Sari PDW. The newest COI molecular detection of Asian redtail catfish Hemibagrus nemurus (Valenciennes, 1840) in Progo River, Magelang, Central Java, Indonesia. J Adv Vet Anim Res 2022; 9:591-600. [PMID: 36714512 PMCID: PMC9868792 DOI: 10.5455/javar.2022.i628] [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: 08/05/2022] [Revised: 09/19/2022] [Accepted: 09/26/2022] [Indexed: 01/13/2023] Open
Abstract
Objective This study describes the newest deoxyribonucleic acid (DNA) barcoding Asian redtail catfish (Hemibagrus nemurus) in the Progo River, Magelang, Central Java, Indonesia. Materials and Methods Ten fish were caught in the Progo River, Magelang, Central Java, Indonesia. The polymerase chain reaction was the molecular diagnosis to detect the sequences of DNA of Cytochrome Oxidase I compared to National Center for Biotechnology Information data (GenBank). Results The results showed that the percent identity was not 100% with H. nemurus data from other locations (GenBank), including Indonesia. The closest percent identity was H. nemurus from Java Island (Accession ID: MK312566.1) with 97.6% similarity. The genetic mutation that happened might be due to environmental change (pollution) in the Progo River recently. Conclusions This study showed a genetic mutation in H. nemurus from Progo River may be caused by environmental change. Low pollution exposure levels may not be detrimental (lethal) to fish. However, it can affect fish fertility, which leads to population degradation (gene variation). Attention must be increased for fish survival in the future.
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Affiliation(s)
- Desyiamililia Yuanawati
- Program Study of Aquaculture, Faculty of Fisheries and Marine, Universitas Airlangga, Surabaya, Indonesia
| | - Hutama Satriana Farizky
- Program Study of Aquaculture, Faculty of Fisheries and Marine, Universitas Airlangga, Surabaya, Indonesia
| | - Muhammad Browijoyo Santanumurti
- Department of Aquaculture, Faculty of Fisheries and Marine, Universitas Airlangga, Surabaya, Indonesia,Department of Marine Biology, Faculty of Marine Sciences, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Mamdoh T. Jamal
- Department of Marine Biology, Faculty of Marine Sciences, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Lalu M. Iqbal Sani
- Oceanogen Environmental Biotechnology Laboklinikum, Cilendek Timur, Bogor, Indonesia
| | - Hawis Madduppa
- Oceanogen Environmental Biotechnology Laboklinikum, Cilendek Timur, Bogor, Indonesia
| | - Putri Desi Wulan Sari
- Department of Aquaculture, Faculty of Fisheries and Marine, Universitas Airlangga, Surabaya, Indonesia
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Laskar BA, Adimalla H, Kundu S, Jaiswal D, Chandra K. DNA barcoding of a lesser-known catfish, Clupisoma bastari (Actinopterygii: Ailiidae) from Deccan Peninsula, India. JOURNAL OF THREATENED TAXA 2022. [DOI: 10.11609/jott.6900.14.8.21605-21611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
DNA barcoding substantiates species identification, and simultaneously indicates the misnomer taxa. Based on the morphological descriptions, we identified a lesser-known catfish, Clupisoma bastari, from Godavari River basin, and contributed novel DNA barcode data to the GenBank. The Kimura 2 parameter genetic divergence between species, and the neighbour-joining phylogeny clearly depicted a distinct clade of C. bastari in the studied dataset. Clupisoma bastari maintained sufficient K2P genetic divergence (8.3% to 11.2%) with other congeners, and branched as a sister-species of C. garua. The present study highlights possible existence of a few misnomer taxa in the GenBank. We encourage further extensive sampling of different congeners of Clupisoma from a wide range of habitats to explore the species diversity and phylogenetic relationship.
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Phylogeography and evolutionary history of the Panamic Clingfish Gobiesox adustus in the Tropical Eastern Pacific. Mol Phylogenet Evol 2022; 173:107496. [PMID: 35569809 DOI: 10.1016/j.ympev.2022.107496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 02/26/2022] [Accepted: 04/18/2022] [Indexed: 11/20/2022]
Abstract
The Panamic Clingfish Gobiesox adustus is widely distributed in the Tropical Eastern Pacific (TEP), from the central Gulf of California, Mexico to Ecuador, including the oceanic Revillagigedo Archipelago, and Isla del Coco. This cryptobenthic species is restricted to very shallow rocky-reef habitats. Here, we used one mitochondrial and three nuclear DNA markers from 155 individuals collected across the distribution range of the species in order to evaluate if geographically structured populations exist and to elucidate its evolutionary history. Phylogenetic analyses recovered a monophyletic group, with four well-supported, allopatric subgroups. Each subgroup corresponded to one of the following well-known biogeographic regions/provinces: 1) the Revillagigedo Archipelago, 2) the Cortez + Mexican provinces (Mexico), 3) the Panamic province (from El Salvador to Ecuador), and 4) Isla del Coco. A molecular-clock analysis showed a mean date for the divergence between clade I (the Revillagigedos and Cortez + Mexican provinces) and clade II (Panamic province and Isla del Coco) in the Pliocene, at ca. 5.33 Mya. Within clade I, the segregation between the Revillagigedos and Cortez + Mexican province populations was dated at ca. 1.18 Mya, during the Pleistocene. Within clade II, the segregation between samples of Isla del Coco and the Panamic province samples was dated at ca. 0.77 Mya, during the Pleistocene. The species tree, Bayesian species delimitation tests (BPP and STACEY), the ΦST, AMOVA, and the substantial genetic distances that exist between those four subgroups, indicate that they are independent evolutionary units. These cladogenetic events seem to be related to habitat discontinuities, and oceanographic and geological processes that produce barriers to gene flow for G. adustus, effects of which are enhanced by the intrinsic ecological characteristics of this species.
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Phillips JD, Gillis DJ, Hanner RH. Lack of Statistical Rigor in DNA Barcoding Likely Invalidates the Presence of a True Species' Barcode Gap. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.859099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
DNA barcoding has been largely successful in satisfactorily exposing levels of standing genetic diversity for a wide range of taxonomic groups through the employment of only one or a few universal gene markers. However, sufficient coverage of geographically-broad intra-specific haplotype variation within genomic databases like the Barcode of Life Data Systems (BOLD) and GenBank remains relatively sparse. As reference sequence libraries continue to grow exponentially in size, there is now the need to identify novel ways of meaningfully analyzing vast amounts of available DNA barcode data. This is an important issue to address promptly for the routine tasks of specimen identification and species discovery, which have seen broad adoption in areas as diverse as regulatory forensics and resource conservation. Here, it is demonstrated that the interpretation of DNA barcoding data is lacking in statistical rigor. To highlight this, focus is set specifically on one key concept that has become a household name in the field: the DNA barcode gap. Arguments outlined herein specifically center on DNA barcoding in animal taxa and stem from three angles: (1) the improper allocation of specimen sampling effort necessary to capture adequate levels of within-species genetic variation, (2) failing to properly visualize intra-specific and interspecific genetic distances, and (3) the inconsistent, inappropriate use, or absence of statistical inferential procedures in DNA barcoding gap analyses. Furthermore, simple statistical solutions are outlined which can greatly propel the use of DNA barcoding as a tool to irrefutably match unknowns to knowns on the basis of the barcoding gap with a high degree of confidence. Proposed methods examined herein are illustrated through application to DNA barcode sequence data from Canadian Pacific fish species as a case study.
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Abstract
Since their inception, DNA barcodes have become a powerful tool for understanding the biodiversity and biology of aquatic species, with multiple applications in diverse fields such as food security, fisheries, environmental DNA, conservation, and exotic species detection. Nevertheless, most aquatic ecosystems, from marine to freshwater, are understudied, with many species disappearing due to environmental stress, mostly caused by human activities. Here we highlight the progress that has been made in studying aquatic organisms with DNA barcodes, and encourage its further development in assisting sustainable use of aquatic resources and conservation.
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Tang KL, Stiassny MLJ, Mayden RL, DeSalle R. Systematics of Damselfishes. ICHTHYOLOGY & HERPETOLOGY 2021. [DOI: 10.1643/i2020105] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Kevin L. Tang
- University of Michigan–Flint, Department of Biology, 303 East Kearsley St., Flint, Michigan 48502; . Send reprint requests to this address
| | - Melanie L. J. Stiassny
- American Museum of Natural History, Department of Ichthyology, Central Park West at 79th St., New York, New York 10024;
| | - Richard L. Mayden
- Saint Louis University, Department of Biology, 3507 Laclede Ave., St. Louis, Missouri 63103;
| | - Robert DeSalle
- American Museum of Natural History, Division of Invertebrate Zoology, Central Park West at 79th St., New York, New York 10024;
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14
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Diversity of Seahorse Species (Hippocampus spp.) in the International Aquarium Trade. DIVERSITY 2021. [DOI: 10.3390/d13050187] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Seahorses (Hippocampus spp.) are threatened as a result of habitat degradation and overfishing. They have commercial value as traditional medicine, curio objects, and pets in the aquarium industry. There are 48 valid species, 27 of which are represented in the international aquarium trade. Most species in the aquarium industry are relatively large and were described early in the history of seahorse taxonomy. In 2002, seahorses became the first marine fishes for which the international trade became regulated by CITES (Convention for the International Trade in Endangered Species of Wild Fauna and Flora), with implementation in 2004. Since then, aquaculture has been developed to improve the sustainability of the seahorse trade. This review provides analyses of the roles of wild-caught and cultured individuals in the international aquarium trade of various Hippocampus species for the period 1997–2018. For all species, trade numbers declined after 2011. The proportion of cultured seahorses in the aquarium trade increased rapidly after their listing in CITES, although the industry is still struggling to produce large numbers of young in a cost-effective way, and its economic viability is technically challenging in terms of diet and disease. Whether seahorse aquaculture can benefit wild populations will largely depend on its capacity to provide an alternative livelihood for subsistence fishers in the source countries. For most species, CITES trade records of live animals in the aquarium industry started a few years earlier than those of dead bodies in the traditional medicine trade, despite the latter being 15 times higher in number. The use of DNA analysis in the species identification of seahorses has predominantly been applied to animals in the traditional medicine market, but not to the aquarium trade. Genetic tools have already been used in the description of new species and will also help to discover new species and in various other kinds of applications.
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Gunnels T, Creswell M, McFerrin J, Whittall JB. The ITS region provides a reliable DNA barcode for identifying reishi/lingzhi (Ganoderma) from herbal supplements. PLoS One 2020; 15:e0236774. [PMID: 33180770 PMCID: PMC7660467 DOI: 10.1371/journal.pone.0236774] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 10/28/2020] [Indexed: 11/18/2022] Open
Abstract
The dietary supplement industry is rapidly growing yet, a recent study revealed that up to 60% of supplements may have substituted ingredients, some of which can be harmful contaminants or additives. When ingredients cannot be verified morphologically or biochemically, DNA barcoding complemented with a molecular phylogenetic analysis can be a powerful method for species authentication. We employed a molecular phylogenetic analysis for species authentication of the commonly used fungal supplement, reishi (Ganoderma lingzhi), by amplifying and sequencing the nuclear ribosomal internal transcribed spacer regions (ITS) with genus-specific primers. PCR of six powdered samples and one dried sample all sold as G. lucidum representing independent suppliers produced single, strong amplification products in the expected size-range for Ganoderma. Both best-hit BLAST and molecular phylogenetic analyses clearly identified the presence of G. lingzhi DNA in all seven herbal supplements. We detected variation in the ITS sequences among our samples, but all herbal supplement samples fall within a large clade of G. lingzhi ITS sequences. ITS-based phylogenetic analysis is a successful and cost-effective method for DNA-based species authentication that could be used in the herbal supplement industry for this and other fungal and plant species that are otherwise difficult to identify.
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Affiliation(s)
- Tess Gunnels
- Department of Biology, Santa Clara University, Santa Clara, California, United States of America
- Oregon’s Wild Harvest, Redmond, Oregon, United States of America
| | - Matthew Creswell
- Oregon’s Wild Harvest, Redmond, Oregon, United States of America
| | - Janis McFerrin
- Oregon’s Wild Harvest, Redmond, Oregon, United States of America
| | - Justen B. Whittall
- Department of Biology, Santa Clara University, Santa Clara, California, United States of America
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Shivambu TC, Shivambu N, Lyle R, Jacobs A, Kumschick S, Foord SH, Robertson MP. Tarantulas (Araneae: Theraphosidae) in the pet trade in South Africa. AFRICAN ZOOLOGY 2020. [DOI: 10.1080/15627020.2020.1823879] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Tinyiko C Shivambu
- Centre for Invasion Biology, School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
- Centre for Invasion Biology, Zoology and Entomology, University of Pretoria, Pretoria, South Africa
| | - Ndivhuwo Shivambu
- Centre for Invasion Biology, School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
- Centre for Invasion Biology, Zoology and Entomology, University of Pretoria, Pretoria, South Africa
| | - Robin Lyle
- Biosystematics Division, Agriculture Research Council-Plant Protection Health and Protection, Pretoria, South Africa
| | - Adriaana Jacobs
- Biosystematics Division, Agriculture Research Council-Plant Protection Health and Protection, Pretoria, South Africa
| | - Sabrina Kumschick
- Centre for Invasion Biology, Department of Botany and Zoology, Stellenbosch University, Stellenbosch, South Africa
- South African National Biodiversity Institute, Kirstenbosch Research Centre, Cape Town, South Africa
| | - Stefan H Foord
- Department of Zoology and Centre for Invasion Biology, University of Venda, Thohoyandou, South Africa
| | - Mark P Robertson
- Centre for Invasion Biology, Zoology and Entomology, University of Pretoria, Pretoria, South Africa
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Ali FS, Ismail M, Aly W. DNA barcoding to characterize biodiversity of freshwater fishes of Egypt. Mol Biol Rep 2020; 47:5865-5877. [PMID: 32661870 DOI: 10.1007/s11033-020-05657-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 07/08/2020] [Indexed: 12/16/2022]
Abstract
The current study represents the first molecular characterization of freshwater fish species in Egypt from two major fish resources; the River Nile and Lake Nasser. A total of 160 DNA barcodes using a 655-bp-long fragment of the mitochondrial cytochrome oxidase subunit I (COI) gene were generated from 37 species belonging to 32 genera that represent 15 families from nine orders. The studied species were identified using different molecular-based identification approaches, in addition to the morphological identification, including neighbor-joining (NJ) trees, Barcode Index Number, and Automatic Barcode Gap Discovery (ABGD). The average genetic divergence based on the Kimura two-parameter model (K2P) within orders, families, genera, and species were 0.175, 0.067, 0.02, and 0.008, respectively. The minimum and maximum K2P distance-based genetic divergences were 0.0 and 0.154, respectively. Nucleotide diversity (π) varied among families and ranged between 0.0% for families Malapteruridae, Auchenoglanididae, Schilbeidae, Anguillidae, Centropomidae and Tetraodontidae and 17% for family Cyprinidae. The current study cautions against the lack of species coverage at public databases which limits the accurate identification of newly surveyed species and recommends that multiple methods are encouraged for accurate species identification. The findings of the current study also support that COI barcode enabled effective fish species identification in River Nile and Lake Nasser. Moreover, the results of the current study will establish a comprehensive DNA barcode library for freshwater fishes along the River Nile in Egypt. Egyptian freshwater fish DNA barcodes will contribute substantially to future efforts in monitoring, conservation, and management of fisheries in Egypt.
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Affiliation(s)
- Fawzia S Ali
- Genetics Laboratory, Aquaculture Division, National Institute of Oceanography and Fisheries (NIOF), Cairo, Egypt.
| | - Mohamed Ismail
- Genetics Department, Faculty of Agriculture, Menoufia University, Shibin El-Kom, Egypt
| | - Walid Aly
- Fisheries Division, National Institute of Oceanography and Fisheries (NIOF), Cairo, Egypt
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18
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DNA barcoding for identification of fish species from freshwater in Enugu and Anambra States of Nigeria. CONSERV GENET RESOUR 2020. [DOI: 10.1007/s12686-020-01155-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
AbstractWithin Enugu and Anambra States, Nigeria, identification of fishes has been based on morphological traits and do not account for existing biodiversity. For DNA barcoding, assessment of biodiversity, conservation and fishery management, 44 fish sampled from Enugu and Anambra States were isolated, amplified and sequenced with mitochondrial cytochrome oxidase subunit I (COI). Twenty groups clustering at 100% bootstrap value including monophyletic ones were identified. The phylogenetic diversity (PD) ranged from 0.0397 (Synodontis obesus) to 0.2147 (Parachanna obscura). The highest percentage of genetic distance based on Kimura 2-parameter was 37.00 ± 0.0400. Intergeneric distances ranged from 15.8000 to 37.0000%. Congeneric distances were 6.9000 ± 0.0140–28.1000 ± 0.0380, with Synodontis as the existing synonymous genus. Confamilial distances in percentage were 16.0000 ± 0.0140 and 25.7000 ± 0.0300. Forty-two haplotypes and haplotype diversity of 0.9990 ± 0.0003 were detected. Nucleotide diversity was 0.7372, while Fu and Li’s D* test statistic was 2.1743 (P < 0.02). Tajima’s D was 0.2424 (P > 0.10) and nucleotide frequencies were C (17.70%), T (29.40%), A (24.82%), G (18.04%) and A + T (54.22%). Transitional mutations were more than transversions. Twenty species (99–100%) were identified with the e-value, maximum coverage and bit-score of 1e−43, 99–100 and 185–1194, respectively. Seventeen genera and 12 families were found and Clariidae (n = 14) was the most dominant among other families. The fish species resolution, diversity assessment and phylogenetic relationships were successfully obtained with the COI marker. Clariidae had the highest number of genera and families. Phylogenetic diversity analysis identified Parachanna obscura as the most evolutionarily divergent one. This study will contribute to fishery management, and conservation of freshwater fishes in Enugu and Anambra States, Nigeria.
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Yang CQ, Lv Q, Zhang AB. Sixteen Years of DNA Barcoding in China: What Has Been Done? What Can Be Done? Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00057] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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20
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Limmon G, Delrieu-Trottin E, Patikawa J, Rijoly F, Dahruddin H, Busson F, Steinke D, Hubert N. Assessing species diversity of Coral Triangle artisanal fisheries: A DNA barcode reference library for the shore fishes retailed at Ambon harbor (Indonesia). Ecol Evol 2020; 10:3356-3366. [PMID: 32273993 PMCID: PMC7141007 DOI: 10.1002/ece3.6128] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 01/30/2020] [Accepted: 02/03/2020] [Indexed: 01/01/2023] Open
Abstract
The Coral Triangle (CT), a region spanning across Indonesia and Philippines, is home to about 4,350 marine fish species and is among the world's most emblematic regions in terms of conservation. Threatened by overfishing and oceans warming, the CT fisheries have faced drastic declines over the last decades. Usually monitored through a biomass-based approach, fisheries trends have rarely been characterized at the species level due to the high number of taxa involved and the difficulty to accurately and routinely identify individuals to the species level. Biomass, however, is a poor proxy of species richness, and automated methods of species identification are required to move beyond biomass-based approaches. Recent meta-analyses have demonstrated that species richness peaks at intermediary levels of biomass. Consequently, preserving biomass is not equal to preserving biodiversity. We present the results of a survey to estimate the shore fish diversity retailed at the harbor of Ambon Island, an island located at the center of the CT that display exceptionally high biomass despite high levels of threat, while building a DNA barcode reference library of CT shore fishes targeted by artisanal fisheries. We sampled 1,187 specimens and successfully barcoded 696 of the 760 selected specimens that represent 202 species. Our results show that DNA barcodes were effective in capturing species boundaries for 96% of the species examined, which opens new perspectives for the routine monitoring of the CT fisheries.
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Affiliation(s)
- Gino Limmon
- Pusat Kemaritiman dan Kelautan Universitas Pattimura (Maritime and Marine Science Center of Excellence) Ambon Indonesia
| | - Erwan Delrieu-Trottin
- Institut de Recherche pour le Développement UMR 226 ISEM (UM-CNRS-IRD-EPHE) Montpellier France
- Museum für Naturkunde Leibniz-Institut für Evolutions-und Biodiversitätsforschung an der Humboldt-Universität zu Berlin Berlin Germany
| | - Jesaya Patikawa
- Pusat Kemaritiman dan Kelautan Universitas Pattimura (Maritime and Marine Science Center of Excellence) Ambon Indonesia
| | - Frederik Rijoly
- Pusat Kemaritiman dan Kelautan Universitas Pattimura (Maritime and Marine Science Center of Excellence) Ambon Indonesia
| | - Hadi Dahruddin
- Division of Zoology Research Center for Biology Indonesian Institute of Sciences (LIPI) Cibinong Indonesia
| | - Frédéric Busson
- Institut de Recherche pour le Développement UMR 226 ISEM (UM-CNRS-IRD-EPHE) Montpellier France
- UMR 7208 BOREA (MNHN-CNRS-UPMC-IRD-UCBN) Muséum National d'Histoire Naturelle Paris France
| | - Dirk Steinke
- Department of Integrative Biology Centre for Biodiversity Genomics University of Guelph Guelph ON Canada
| | - Nicolas Hubert
- Institut de Recherche pour le Développement UMR 226 ISEM (UM-CNRS-IRD-EPHE) Montpellier France
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Toomes A, García-Díaz P, Wittmann TA, Virtue J, Cassey P. New aliens in Australia: 18 years of vertebrate interceptions. WILDLIFE RESEARCH 2020. [DOI: 10.1071/wr18185] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Abstract
ContextAustralia has a high diversity of endemic vertebrate fauna. Yet, transnational human activities continue to increase the rate of transportation, introduction and establishment of new alien vertebrates in Australia, to the detriment of environmental and socioeconomic services. Eradication of invasive vertebrates is often costly and without guarantee of success; therefore, methods for detecting, intercepting and preventing the transport of alien species earlier in the invasion pathway provide substantial benefit.
AimTo anticipate emergent threats to Australian biosecurity posed by the transport and introduction of new alien vertebrates over time.
MethodsWe collated vertebrate interception data from various mainland Australian State, Territory and Commonwealth government reporting agencies, including data from a previously published study, at both pre-border and post-border stages from 1999 to 2016. Using generalised linear and generalised additive modelling, we predicted trends in interception frequency using predictors such as vertebrate taxa, detection category and alien status.
Key resultsInterception frequency increased over time for all vertebrate classes, for pre-border stowaways and for post-border captive and at-large interceptions, with no saturation in the accumulation of new species over time. Five species were responsible for almost half of all incidents, of which red-eared sliders (Trachemys scripta elegans), boa constrictors (Boa constrictor) and corn snakes (Pantherophis guttatus) are prominent in Australia’s illegal alien pet trade. Rose-ringed parakeets (Psittacula krameri) are prominent in the legal alien cage-bird trade, which remains poorly regulated. Asian common toads (Duttaphrynus melanostictus) were frequently detected as stowaways, and most stowaway incidents originated from Southeast Asia, particularly Indonesia, via shipping. Data deficiency for pre-border incidents increased rapidly in 2015 and 2016.
ConclusionsAustralia is subject to a persistent and increasing risk of alien vertebrate introductions and incursions over time, owing partly to emergent trends in the alien pet trade as well as increased global trade and tourism.
ImplicationsThe future of Australia’s biosecurity remains dependent on stringent border security to prevent the arrival of novel species, but our findings also highlight the importance of ongoing management and control of high-risk species already present, often illegally, within Australia.
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Ip YCA, Tay YC, Gan SX, Ang HP, Tun K, Chou LM, Huang D, Meier R. From marine park to future genomic observatory? Enhancing marine biodiversity assessments using a biocode approach. Biodivers Data J 2019; 7:e46833. [PMID: 31866739 PMCID: PMC6917626 DOI: 10.3897/bdj.7.e46833] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 11/21/2019] [Indexed: 12/27/2022] Open
Abstract
Few tropical marine sites have been thoroughly characterised for their animal species, even though they constitute the largest proportion of multicellular diversity. A number of focused biodiversity sampling programmes have amassed immense collections to address this shortfall, but obstacles remain due to the lack of identification tools and large proportion of undescribed species globally. These problems can be partially addressed with DNA barcodes ("biocodes"), which have the potential to facilitate the estimation of species diversity and identify animals to named species via barcode databases. Here, we present the first results of what is intended to be a sustained, systematic study of the marine fauna of Singapore's first marine park, reporting more than 365 animal species, determined based on DNA barcodes and/or morphology represented by 931 specimens (367 zooplankton, 564 macrofauna including 36 fish). Due to the lack of morphological and molecular identification tools, only a small proportion could be identified to species solely based on either morphology (24.5%) or barcodes (24.6%). Estimation of species numbers for some taxa was difficult because of the lack of sufficiently clear barcoding gaps. The specimens were imaged and added to "Biodiversity of Singapore" (http://singapore.biodiversity.online), which now contains images for > 13,000 species occurring in the country.
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Affiliation(s)
- Yin Cheong Aden Ip
- Department of Biological Sciences, National University of Singapore, Singapore, SingaporeDepartment of Biological Sciences, National University of SingaporeSingaporeSingapore
| | - Ywee Chieh Tay
- National University of Singapore, Singapore, SingaporeNational University of SingaporeSingaporeSingapore
- Temasek Life Sciences Laboratory, Singapore, SingaporeTemasek Life Sciences LaboratorySingaporeSingapore
| | - Su Xuan Gan
- Department of Biological Sciences, National University of Singapore, Singapore, SingaporeDepartment of Biological Sciences, National University of SingaporeSingaporeSingapore
| | - Hui Ping Ang
- National Parks Board, Singapore, SingaporeNational Parks BoardSingaporeSingapore
| | - Karenne Tun
- National Parks Board, Singapore, SingaporeNational Parks BoardSingaporeSingapore
| | - Loke Ming Chou
- Department of Biological Sciences, National University of Singapore, Singapore, SingaporeDepartment of Biological Sciences, National University of SingaporeSingaporeSingapore
- Tropical Marine Science Institute, National University of Singapore, Singapore, SingaporeTropical Marine Science Institute, National University of SingaporeSingaporeSingapore
| | - Danwei Huang
- Department of Biological Sciences, National University of Singapore, Singapore, SingaporeDepartment of Biological Sciences, National University of SingaporeSingaporeSingapore
- Tropical Marine Science Institute, National University of Singapore, Singapore, SingaporeTropical Marine Science Institute, National University of SingaporeSingaporeSingapore
| | - Rudolf Meier
- Department of Biological Sciences, National University of Singapore, Singapore, SingaporeDepartment of Biological Sciences, National University of SingaporeSingaporeSingapore
- Tropical Marine Science Institute, National University of Singapore, Singapore, SingaporeTropical Marine Science Institute, National University of SingaporeSingaporeSingapore
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Ferrito V, Raffa A, Rossitto L, Federico C, Saccone S, Pappalardo AM. Swordfish or Shark Slice? A Rapid Response by COIBar-RFLP. Foods 2019; 8:foods8110537. [PMID: 31683903 PMCID: PMC6915651 DOI: 10.3390/foods8110537] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 10/21/2019] [Accepted: 10/28/2019] [Indexed: 11/19/2022] Open
Abstract
Market transparency is in strong demand by consumers, and the authentication of species is an important step for seafood traceability. In this study, a simple molecular strategy, COIBar–RFLP (cytochrome oxidase I barcode–restriction fragment length polymorphism), is proposed to unveil commercial fraud based on the practice of species substitution in the swordfish trade. In particular, COI barcoding allowed the identification of the species Prionace glauca, Mustelus mustelus, and Oxynotus centrina in slices labeled as Xiphias gladius. Furthermore, the enzymatic digestion of COI amplicons using the MboI restriction endonuclease allowed the simultaneous discrimination of the four species. Interestingly, an intraspecific differential MboI pattern was obtained for the swordfish samples. This pattern was useful to differentiate the two different clades revealed in this species by phylogenetic analyses using several molecular markers. These results indicate the need to strengthen regulations and define molecular tools for combating the occurrence of fraud along the seafood supply chain and show that COIBar–RFLP could become a standardized molecular tool to assess seafood authenticity.
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Affiliation(s)
- Venera Ferrito
- Department of Biological, Geological and Environmental Sciences, Section of Animal Biology "M. La Greca", University of Catania, Via Androne 81, 95124 Catania, Italy.
| | - Alessandra Raffa
- Department of Biological, Geological and Environmental Sciences, Section of Animal Biology "M. La Greca", University of Catania, Via Androne 81, 95124 Catania, Italy.
| | - Luana Rossitto
- Department of Biological, Geological and Environmental Sciences, Section of Animal Biology "M. La Greca", University of Catania, Via Androne 81, 95124 Catania, Italy.
| | - Concetta Federico
- Department of Biological, Geological and Environmental Sciences, Section of Animal Biology "M. La Greca", University of Catania, Via Androne 81, 95124 Catania, Italy.
| | - Salvatore Saccone
- Department of Biological, Geological and Environmental Sciences, Section of Animal Biology "M. La Greca", University of Catania, Via Androne 81, 95124 Catania, Italy.
| | - Anna Maria Pappalardo
- Department of Biological, Geological and Environmental Sciences, Section of Animal Biology "M. La Greca", University of Catania, Via Androne 81, 95124 Catania, Italy.
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Baraf LM, Pratchett MS, Cowman PF. Ancestral biogeography and ecology of marine angelfishes (F: Pomacanthidae). Mol Phylogenet Evol 2019; 140:106596. [DOI: 10.1016/j.ympev.2019.106596] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 08/13/2019] [Accepted: 08/13/2019] [Indexed: 12/27/2022]
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Tea Y, Van Der Wal C, Ludt WB, Gill AC, Lo N, Ho SYW. Boomeranging around Australia: Historical biogeography and population genomics of the anti‐equatorial fish
Microcanthus strigatus
(Teleostei: Microcanthidae). Mol Ecol 2019; 28:3771-3785. [DOI: 10.1111/mec.15172] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 06/13/2019] [Accepted: 06/17/2019] [Indexed: 12/15/2022]
Affiliation(s)
- Yi‐Kai Tea
- School of Life and Environmental Sciences University of Sydney Sydney NSW Australia
- Australian Museum Research Institute, Australian Museum Sydney NSW Australia
| | - Cara Van Der Wal
- School of Life and Environmental Sciences University of Sydney Sydney NSW Australia
- Australian Museum Research Institute, Australian Museum Sydney NSW Australia
| | - William B. Ludt
- National Museum of Natural History, Smithsonian Institution Washington DC USA
- Natural History Museum of Los Angeles County Los Angeles CA USA
| | - Anthony C. Gill
- School of Life and Environmental Sciences University of Sydney Sydney NSW Australia
- Australian Museum Research Institute, Australian Museum Sydney NSW Australia
- Macleay Museum University of Sydney Sydney NSW Australia
| | - Nathan Lo
- School of Life and Environmental Sciences University of Sydney Sydney NSW Australia
| | - Simon Y. W. Ho
- School of Life and Environmental Sciences University of Sydney Sydney NSW Australia
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Kundu S, Chandra K, Tyagi K, Pakrashi A, Kumar V. DNA barcoding of freshwater fishes from Brahmaputra River in Eastern Himalaya biodiversity hotspot. MITOCHONDRIAL DNA PART B-RESOURCES 2019; 4:2411-2419. [PMID: 33365567 PMCID: PMC7710314 DOI: 10.1080/23802359.2019.1637290] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The genetic diversity of freshwater fishes is still anonymous in several drainage systems in northeast India. Moreover, the comparative genetic analysis is largely sporadic to judge their actual diversity and true status. We generated 89 DNA barcodes of 40 morphologically identified fishes collected from two major tributaries of Brahmaputra River. The comparative study revealed that most of the species were clearly discriminated by their estimated genetic distances and monophyletic clustering in Bayesian (BA) tree. Considering the genetic divergence (2%) for species discrimination boundary, the high genetic diversity (2.36–10.73%) was detected in 11 species (Macrognathus pancalus, Channa punctata, Puntius terio, Bangana ariza, Garra arupi, Badis badis, Mystus vittatus, Rita rita, Gagata cenia, Mastacembelus armatus, and Danio dangila), which signified the occurrence of concealed genetic diversity in this ecozone. However, the insignificant genetic distances were also noticed in few reportedly valid species: Channa stiktos and C. ornatipinnis (1.43%); Mystus ngasep, M. rufescens, and M. carcio (0.4%); Glyptothorax trilineatus, G. churamanii, and G. verrucosus (0.4%); Botia almorhae, B. histrionica, B. lohachata, and B. rostrata (0–0.4%); Barilius barilia and B. vagra (0.4%); Batasio merianiensis and B. tengana (1.2%); Puntius chola and P. fraseri (0%), Schistura beavani and S. paucireticulata (0%); hence to validate this species, generation of more barcode data was required from their types or topotypes. The present study would help to develop conservation schemes for the native species and collegiate ecosystem, which associated with the livelihoods of millions of ethnic communities in this region.
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Affiliation(s)
- Shantanu Kundu
- 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
| | - Kaomud Tyagi
- 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
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Frable BW, Tea YK. A New Species of Damselfish (Teleostei: Pomacentridae: Pomacentrus) from Nosy Faho, Madagascar. COPEIA 2019. [DOI: 10.1643/ci-19-221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Benjamin W. Frable
- Marine Vertebrate Collection, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California;
| | - Yi-Kai Tea
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia; . Send reprint requests to this address
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Kundu S, Rath S, Laishram K, Pakrashi A, Das U, Tyagi K, Kumar V, Chandra K. DNA barcoding identified selected ornamental fishes in Murti river of East India. MITOCHONDRIAL DNA PART B-RESOURCES 2019. [DOI: 10.1080/23802359.2018.1561220] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Shantanu Kundu
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Shibananda Rath
- Freshwater Fish Section, FPS Building, Zoological Survey of India, Kolkata, India
| | - Kosygin Laishram
- Freshwater Fish Section, FPS Building, Zoological Survey of India, Kolkata, India
| | - Avas Pakrashi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Ujjal Das
- Freshwater Fish Section, FPS Building, Zoological Survey of India, Kolkata, India
| | - Kaomud Tyagi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Vikas Kumar
- Freshwater Fish Section, FPS Building, Zoological Survey of India, Kolkata, India
| | - Kailash Chandra
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
- Freshwater Fish Section, FPS Building, Zoological Survey of India, Kolkata, India
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Bernardi G, Nelson P, Paddack M, Rulmal J, Crane N. Genomic islands of divergence in the Yellow Tang and the Brushtail Tang Surgeonfishes. Ecol Evol 2018; 8:8676-8685. [PMID: 30271536 PMCID: PMC6157655 DOI: 10.1002/ece3.4417] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 05/14/2018] [Accepted: 05/29/2018] [Indexed: 12/15/2022] Open
Abstract
The current ease of obtaining thousands of molecular markers challenges the notion that full phylogenetic concordance, as proposed by phylogenetic species concepts, is a requirement for defining species delimitations. Indeed, the presence of genomic islands of divergence, which may be the cause, or in some cases the consequence, of speciation, precludes concordance. Here, we explore this issue using thousands of RAD markers on two sister species of surgeonfishes (Teleostei: Acanthuridae), Zebrasoma flavescens and Z. scopas, and several populations within each species. Species are readily distinguished based on their colors (solid yellow and solid brown, respectively), yet populations and species are neither distinguishable using mitochondrial markers (cytochrome c oxidase 1), nor using 5193 SNPs (pairwise Φst = 0.034). In contrast, when using outlier loci, some of them presumably under selection, species delimitations, and strong population structure follow recognized taxonomic positions (pairwise Φst = 0.326). Species and population delimitation differences based on neutral and selected markers are likely due to local adaptation, thus being consistent with the idea that these genomic islands of divergence arose as a consequence of isolation. These findings, which are not unique, raise the question of a potentially important pathway of divergence based on local adaptation that is only evident when looking at thousands of loci.
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Affiliation(s)
- Giacomo Bernardi
- Department of Ecology and Evolutionary BiologyUniversity of California Santa CruzSanta CruzCalifornia
| | | | | | - John Rulmal
- Ulithi Falalop Community Action ProgramYapFederated States of Micronesia
| | - Nicole Crane
- Department of BiologyCabrillo CollegeAptosCalifornia
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30
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Iyiola OA, Nneji LM, Mustapha MK, Nzeh CG, Oladipo SO, Nneji IC, Okeyoyin AO, Nwani CD, Ugwumba OA, Ugwumba AAA, Faturoti EO, Wang Y, Chen J, Wang W, Adeola AC. DNA barcoding of economically important freshwater fish species from north-central Nigeria uncovers cryptic diversity. Ecol Evol 2018; 8:6932-6951. [PMID: 30073057 PMCID: PMC6065348 DOI: 10.1002/ece3.4210] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 04/17/2018] [Accepted: 04/22/2018] [Indexed: 11/25/2022] Open
Abstract
This study examines the utility of morphology and DNA barcoding in species identification of freshwater fishes from north-central Nigeria. We compared molecular data (mitochondrial cytochrome c oxidase subunit I (COI) sequences) of 136 de novo samples from 53 morphologically identified species alongside others in GenBank and BOLD databases. Using DNA sequence similarity-based (≥97% cutoff) identification technique, 50 (94.30%) and 24 (45.30%) species were identified to species level using GenBank and BOLD databases, respectively. Furthermore, we identified cases of taxonomic problems in 26 (49.00%) morphologically identified species. There were also four (7.10%) cases of mismatch in DNA barcoding in which our query sequence in GenBank and BOLD showed a sequence match with different species names. Using DNA barcode reference data, we also identified four unknown fish samples collected from fishermen to species level. Our Neighbor-joining (NJ) tree analysis recovers several intraspecific species clusters with strong bootstrap support (≥95%). Analysis uncovers two well-supported lineages within Schilbe intermedius. The Bayesian phylogenetic analyses of Nigerian S. intermedius with others from GenBank recover four lineages. Evidence of genetic structuring is consistent with geographic regions of sub-Saharan Africa. Thus, cryptic lineage diversity may illustrate species' adaptive responses to local environmental conditions. Finally, our study underscores the importance of incorporating morphology and DNA barcoding in species identification. Although developing a complete DNA barcode reference library for Nigerian ichthyofauna will facilitate species identification and diversity studies, taxonomic revisions of DNA sequences submitted in databases alongside voucher specimens are necessary for a reliable taxonomic and diversity inventory.
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Affiliation(s)
- Oluyinka A. Iyiola
- Department of ZoologyFaculty of Life SciencesUniversity of IlorinIlorinKwara StateNigeria
| | - Lotanna M. Nneji
- Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
- Sino‐Africa Joint Research CenterChinese Academy of SciencesKunmingChina
- Kunming College of Life ScienceUniversity of Chinese Academy of SciencesKunmingChina
| | - Moshood K. Mustapha
- Department of ZoologyFaculty of Life SciencesUniversity of IlorinIlorinKwara StateNigeria
| | - Chioma G. Nzeh
- Department of ZoologyFaculty of Life SciencesUniversity of IlorinIlorinKwara StateNigeria
| | - Segun O. Oladipo
- Department of Biosciences and BiotechnologyKwara State UniversityMaleteKwara StateNigeria
| | | | - Agboola O. Okeyoyin
- Nigerian National Park Service HeadquartersFederal Capital TerritoryAbujaNigeria
| | - Christopher D. Nwani
- Department of Zoology and Environmental BiologyUniversity of NigeriaNsukkaNigeria
| | - Obih A. Ugwumba
- Department of ZoologyUniversity of IbadanIbadanOyo StateNigeria
| | | | - Emmanuel O. Faturoti
- Department of Aquaculture and Fisheries ManagementUniversity of IbadanIbadanOyo StateNigeria
| | - Yun‐yu Wang
- Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
| | | | - Wen‐Zhi Wang
- Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
- Sino‐Africa Joint Research CenterChinese Academy of SciencesKunmingChina
- Wild Forensic CenterKunmingChina
| | - Adeniyi C. Adeola
- Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
- Sino‐Africa Joint Research CenterChinese Academy of SciencesKunmingChina
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31
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Bingpeng X, Heshan L, Zhilan Z, Chunguang W, Yanguo W, Jianjun W. DNA barcoding for identification of fish species in the Taiwan Strait. PLoS One 2018; 13:e0198109. [PMID: 29856794 PMCID: PMC5983523 DOI: 10.1371/journal.pone.0198109] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 05/14/2018] [Indexed: 11/30/2022] Open
Abstract
DNA barcoding based on a fragment of the cytochrome c oxidase subunit I (COI) gene in the mitochondrial genome is widely applied in species identification and biodiversity studies. The aim of this study was to establish a comprehensive barcoding reference database of fishes in the Taiwan Strait and evaluate the applicability of using the COI gene for the identification of fish at the species level. A total of 284 mitochondrial COI barcode sequences were obtained from 85 genera, 38 families and 12 orders of fishes. The mean length of the sequences was 655 base pairs. The average Kimura two parameter (K2P) distances within species, genera, families, orders and classes were 0.21%, 6.50%, 23.70% and 25.60%, respectively. The mean interspecific distance was 31-fold higher than the mean intraspecific distance. The K2P neighbor-joining trees based on the sequence generally clustered species in accordance with their taxonomic classifications. High efficiency of species identification was demonstrated in the present study by DNA barcoding, and we conclude that COI sequencing can be used to identify fish species.
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Affiliation(s)
- Xing Bingpeng
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography State Oceanic Administration, Xiamen, Fujian, China
| | - Lin Heshan
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography State Oceanic Administration, Xiamen, Fujian, China
| | - Zhang Zhilan
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography State Oceanic Administration, Xiamen, Fujian, China
| | - Wang Chunguang
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography State Oceanic Administration, Xiamen, Fujian, China
| | - Wang Yanguo
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography State Oceanic Administration, Xiamen, Fujian, China
| | - Wang Jianjun
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography State Oceanic Administration, Xiamen, Fujian, China
- * E-mail:
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32
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Oruç AÇ, Engin S. The taxonomic status of the Black Sea and Marmara Sea populations of the Broadnosed Pipefish Syngnathus cf. argentatus Pallas (Teleostei: Syngnathidae) based on morphological and molecular characters. ZOOLOGY IN THE MIDDLE EAST 2018. [DOI: 10.1080/09397140.2018.1444569] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
| | - Semih Engin
- Faculty of Fisheries, İzmir Katip Çelebi University, İzmir, Turkey
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Marcionetti A, Rossier V, Bertrand JAM, Litsios G, Salamin N. First draft genome of an iconic clownfish species (Amphiprion frenatus). Mol Ecol Resour 2018; 18:1092-1101. [PMID: 29455459 DOI: 10.1111/1755-0998.12772] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Revised: 01/29/2018] [Accepted: 02/06/2018] [Indexed: 11/30/2022]
Abstract
Clownfishes (or anemonefishes) form an iconic group of coral reef fishes, principally known for their mutualistic interaction with sea anemones. They are characterized by particular life history traits, such as a complex social structure and mating system involving sequential hermaphroditism, coupled with an exceptionally long lifespan. Additionally, clownfishes are considered to be one of the rare groups to have experienced an adaptive radiation in the marine environment. Here, we assembled and annotated the first genome of a clownfish species, the tomato clownfish (Amphiprion frenatus). We obtained 17,801 assembled scaffolds, containing a total of 26,917 genes. The completeness of the assembly and annotation was satisfying, with 96.5% of the Actinopterygii Benchmarking Universal Single-Copy Orthologs (BUSCOs) being retrieved in A. frenatus assembly. The quality of the resulting assembly is comparable to other bony fish assemblies. This resource is valuable for advancing studies of the particular life history traits of clownfishes, as well as being useful for population genetic studies and the development of new phylogenetic markers. It will also open the way to comparative genomics. Indeed, future genomic comparison among closely related fishes may provide means to identify genes related to the unique adaptations to different sea anemone hosts, as well as better characterize the genomic signatures of an adaptive radiation.
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Affiliation(s)
- Anna Marcionetti
- Department of Computational Biology, Biophore, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Victor Rossier
- Department of Computational Biology, Biophore, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Joris A M Bertrand
- Department of Computational Biology, Biophore, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Glenn Litsios
- Department of Computational Biology, Biophore, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Nicolas Salamin
- Department of Computational Biology, Biophore, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
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34
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Getlekha N, Cioffi MDB, Maneechot N, Bertollo LAC, Supiwong W, Tanomtong A, Molina WF. Contrasting Evolutionary Paths Among Indo-Pacific Pomacentrus Species Promoted by Extensive Pericentric Inversions and Genome Organization of Repetitive Sequences. Zebrafish 2017; 15:45-54. [PMID: 29023226 DOI: 10.1089/zeb.2017.1484] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Pomacentrus (damselfishes) is one of the most characteristic groups of fishes in the Indo-Pacific coral reef. Its 77 described species exhibit a complex taxonomy with cryptic lineages across their extensive distribution. Periods of evolutionary divergences between them are very variable, and the cytogenetic events that followed their evolutionary diversification are largely unknown. In this respect, analyses of chromosomal divergence, within a phylogenetic perspective, are particularly informative regarding karyoevolutionary trends. As such, we conducted conventional cytogenetic and cytogenomic analyses in four Pomacentrus species (Pomacentrus similis, Pomacentrus auriventris, Pomacentrus moluccensis, and Pomacentrus cuneatus), through the mapping of repetitive DNA classes and transposable elements, including 18S rDNA, 5S rDNA, (CA)15, (GA)15, (CAA)10, Rex6, and U2 snDNA as markers. P. auriventris and P. similis, belonging to the Pomacentrus coelestis complex, have indistinguishable karyotypes (2n = 48; NF = 48), with a peculiar syntenic organization of ribosomal genes. On the other hand, P. moluccensis and P. cuneatus, belonging to another clade, exhibit very different karyotypes (2n = 48, NF = 86 and 92, respectively), with a large number of bi-armed chromosomes, where multiple pericentric inversions played a significant role in their karyotype organization. In this sense, different chromosomal pathways followed the phyletic diversification in the Pomacentrus genus, making possible the characterization of two well-contrasting species groups regarding their karyotype features. Despite this, pericentric inversions act as an effective postzygotic barrier in many organisms, which appear to be also the case for P. moluccensis and P. cuneatus; the extensive chromosomal similarities in the two species of P. coelestis complex suggest minor participation of chromosomal postzygotic barriers in the phyletic diversification of these species.
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Affiliation(s)
- Nuntaporn Getlekha
- 1 Department of Biology, Faculty of Science, Khon Kaen University , Khon Kaen, Thailand
| | - Marcelo de Bello Cioffi
- 2 Departamento de Genética e Evolução, Universidade Federal de São Carlos , São Paulo, Brazil
| | - Nuntiya Maneechot
- 1 Department of Biology, Faculty of Science, Khon Kaen University , Khon Kaen, Thailand
| | | | - Weerayuth Supiwong
- 3 Department of Fisheries, Faculty of Applied Science and Engineering, Khon Kaen University , Khon Kaen, Thailand
| | - Alongklod Tanomtong
- 1 Department of Biology, Faculty of Science, Khon Kaen University , Khon Kaen, Thailand .,4 Toxic Substances in Livestock and Aquatic Animals Research Group, KhonKaen University , Khon Kaen, Thailand
| | - Wagner Franco Molina
- 5 Departamento de Biologia Celular e Genética, Centro de Biociências, Universidade Federal do Rio Grande do Norte , Natal, Brazil
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35
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Hutama A, Dahruddin H, Busson F, Sauri S, Keith P, Hadiaty RK, Hanner R, Suryobroto B, Hubert N. Identifying spatially concordant evolutionary significant units across multiple species through DNA barcodes: Application to the conservation genetics of the freshwater fishes of Java and Bali. Glob Ecol Conserv 2017. [DOI: 10.1016/j.gecco.2017.11.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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36
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Development of environmental DNA (eDNA) methods for detecting high-risk freshwater fishes in live trade in Canada. Biol Invasions 2017. [DOI: 10.1007/s10530-017-1532-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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37
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Barcoding utility in a mega-diverse, cross-continental genus: keeping pace with Cyrtodactylus geckos. Sci Rep 2017; 7:5592. [PMID: 28717207 PMCID: PMC5514027 DOI: 10.1038/s41598-017-05261-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 05/25/2017] [Indexed: 11/09/2022] Open
Abstract
Over the past decade, DNA barcoding has become a staple of low-cost molecular systematic investigations. The availability of universal primers and subsidized sequencing projects (PolarBOL, SharkBOL, SpongeBOL) have driven this popularity, often without appropriate investigation into the utility of barcoding data for the taxonomic group of interest. Here, our primary aim is to determine the phylogenetic value of DNA barcoding (mitochondrial locus COI) within the gecko genus Cyrtodactylus. With >40 new species described since last systematic investigation, Cyrtodactylus represents one of the most diverse extant squamate genera, and their contemporary distribution spans the Indian subcontinent, eastward through Indochina, and into AustraloPapua. The complex biogeographic history of this group, and morphology-only designation of many species have complicated our phylogenetic understanding of Cyrtodactylus. To highlight the need for continued inclusive molecular assessment, we use Vietnamese Cyrtodactylus as a case study showing the geopolitically paraphyletic nature of their history. We compare COI to the legacy marker ND2, and discuss the value of COI as an interspecific marker, as well as its shortcomings at deeper evolutionary scales. We draw attention back to the Cold Code as a subsidized method for incorporating molecular methods into species descriptions in the effort to maintain accurate phylogenies.
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38
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Dhar B, Ghosh SK. Mini-DNA barcode in identification of the ornamental fish: A case study from Northeast India. Gene 2017; 627:248-254. [PMID: 28652184 DOI: 10.1016/j.gene.2017.06.043] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 05/28/2017] [Accepted: 06/22/2017] [Indexed: 11/30/2022]
Abstract
The ornamental fishes were exported under the trade names or generic names, thus creating problems in species identification. In this regard, DNA barcoding could effectively elucidate the actual species status. However, the problem arises if the specimen is having taxonomic disputes, falsified by trade/generic names, etc., On the other hand, barcoding the archival museum specimens would be of greater benefit to address such issues as it would create firm, error-free reference database for rapid identification of any species. This can be achieved only by generating short sequences as DNA from chemically preserved are mostly degraded. Here we aimed to identify a short stretch of informative sites within the full-length barcode segment, capable of delineating diverse group of ornamental fish species, commonly traded from NE India. We analyzed 287 full-length barcode sequences from the major fish orders and compared the interspecific K2P distance with nucleotide substitutions patterns and found a strong correlation of interspecies distance with transversions (0.95, p<0.001). We, therefore, proposed a short stretch of 171bp (transversion rich) segment as mini-barcode. The proposed segment was compared with the full-length barcodes and found to delineate the species effectively. Successful PCR amplification and sequencing of the 171bp segment using designed primers for different orders validated it as mini-barcodes for ornamental fishes. Thus, our findings would be helpful in strengthening the global database with the sequence of archived fish species as well as an effective identification tool of the traded ornamental fish species, as a less time consuming, cost effective field-based application.
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Affiliation(s)
- Bishal Dhar
- Department of Biotechnology, Assam University, Silchar 788011, Assam, India
| | - Sankar Kumar Ghosh
- Department of Biotechnology, Assam University, Silchar 788011, Assam, India; University of Kalyani, Kalyani 741235, West Bengal, India.
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39
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Steinke D, deWaard JR, Gomon MF, Johnson JW, Larson HK, Lucanus O, Moore GI, Reader S, Ward RD. DNA barcoding the fishes of Lizard Island (Great Barrier Reef). Biodivers Data J 2017:e12409. [PMID: 28765727 PMCID: PMC5515069 DOI: 10.3897/bdj.5.e12409] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 04/12/2017] [Indexed: 11/12/2022] Open
Affiliation(s)
- Dirk Steinke
- Centre for Biodiversity Genomics - University of Guelph, Guelph, Canada.,Department of Integrative Biology - University of Guelph, Guelph, Canada
| | - Jeremy R deWaard
- Centre for Biodiversity Genomics - University of Guelph, Guelph, Canada
| | | | - Jeffrey W Johnson
- Queensland Museum, PO Box 3300, South Brisbane QLD 4101, Australia, Brisbane, Australia
| | - Helen K Larson
- Museum and Art Gallery of the Northern Territory, Darwin, Australia
| | | | | | | | - Robert D Ward
- CSIRO Marine and Atmospheric Research, Hobart, Australia
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40
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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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41
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Singh AK, Kumar R, Mishra AK, Singh M, Baisvar VS, Chauhan UK, Kushwaha B, Nagpure NS. Authentication of five Barilius species from Indian waters using DNA barcoding. RUSS J GENET+ 2016. [DOI: 10.1134/s1022795416060119] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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42
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Ng TH, Tan SK, Wong WH, Meier R, Chan SY, Tan HH, Yeo DCJ. Molluscs for Sale: Assessment of Freshwater Gastropods and Bivalves in the Ornamental Pet Trade. PLoS One 2016; 11:e0161130. [PMID: 27525660 PMCID: PMC4985174 DOI: 10.1371/journal.pone.0161130] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 07/29/2016] [Indexed: 01/24/2023] Open
Abstract
The ornamental pet trade is often considered a key culprit for conservation problems such as the introduction of invasive species (including infectious diseases) and overharvesting of rare species. Here, we present the first assessment of the biodiversity of freshwater molluscs in the ornamental pet trade in Singapore, one of the most important global hubs of the ornamental aquarium trade, and discuss associated conservation concerns. We recorded freshwater molluscs from ornamental pet shops and major exporters including non-ornamental species (e.g., hitchhikers, molluscs sold as fish feed). We recorded an unexpectedly high diversity-59 species-of freshwater bivalves and gastropods, with the majority (38 species or 64%) being from the Oriental region. In addition to morphological examination, we sequenced the DNA barcode region of mitochondrial CO1 and 16S genes to provide molecular data for the confirmation of the identification and for future re-identification. DNA barcodes were obtained for 50 species, and all but four were separated by > 3% uncorrected pairwise distances. The trade has been considered a main introduction pathway for non-native species to Singapore, and we found that out of 15 species in the trade as well as in the wild in Singapore, 12 are either introduced or of unknown origin, representing almost half of the known non-native freshwater molluscs in Singapore. Particularly prevalent are non-ornamental species: six hitchhikers on aquarium plants and six species sold as fish feed. We found that a quarter of the trade species have a history of introduction, which includes 11 known or potentially invasive species. We conclude that potential overharvesting is difficult to assess because only half of the trade species have been treated by IUCN. Of these, 21 species are of Least Concern and three are Data Deficient. Our checklist, with accompanying DNA barcodes, images, and museum vouchers, provides an important reference library for future monitoring, and constitutes a step toward creating a more sustainable ornamental pet trade.
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Affiliation(s)
- Ting Hui Ng
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Siong Kiat Tan
- Lee Kong Chian Natural History Museum, National University of Singapore, Singapore
| | - Wing Hing Wong
- The Division of Biology and Biomedical Sciences, Washington University in St. Louis, United States of America
| | - Rudolf Meier
- Department of Biological Sciences, National University of Singapore, Singapore
- Lee Kong Chian Natural History Museum, National University of Singapore, Singapore
| | | | - Heok Hui Tan
- Lee Kong Chian Natural History Museum, National University of Singapore, Singapore
| | - Darren C. J. Yeo
- Department of Biological Sciences, National University of Singapore, Singapore
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43
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Amin Laskar B, Kumar V, Darshan A, Kundu S, Narayan Das D. DNA barcoding of Amblyceps congeners (Siluriformes: Amblycipitidae) from Brahmaputra drainage in northeast India. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 28:698-702. [DOI: 10.3109/24701394.2016.1174223] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Boni Amin Laskar
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, West Bengal, India
| | - Vikas Kumar
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, West Bengal, India
| | - Achom Darshan
- Center with Potential for Excellence in Biodiversity, Rajiv Gandhi University, Doimukh, Arunachal Pradesh, India
| | - Shantanu Kundu
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, West Bengal, India
| | - Debangshu Narayan Das
- Center with Potential for Excellence in Biodiversity, Rajiv Gandhi University, Doimukh, Arunachal Pradesh, India
- Fishery and Aquatic Ecology Laboratory, Department of Zoology, Rajiv Gandhi University, Doimukh, Arunachal Pradesh, India
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44
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Shen Y, Guan L, Wang D, Gan X. DNA barcoding and evaluation of genetic diversity in Cyprinidae fish in the midstream of the Yangtze River. Ecol Evol 2016; 6:2702-13. [PMID: 27066250 PMCID: PMC4798831 DOI: 10.1002/ece3.2060] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 01/31/2016] [Accepted: 02/02/2016] [Indexed: 11/29/2022] Open
Abstract
The Yangtze River is the longest river in China and is divided into upstream and mid-downstream regions by the Three Gorges (the natural barriers of the Yangtze River), resulting in a complex distribution of fish. Dramatic changes to habitat environments may ultimately threaten fish survival; thus, it is necessary to evaluate the genetic diversity and propose protective measures. Species identification is the most significant task in many fields of biological research and in conservation efforts. DNA barcoding, which constitutes the analysis of a short fragment of the mitochondrial cytochrome c oxidase subunit I (COI) sequence, has been widely used for species identification. In this study, we collected 561 COI barcode sequences from 35 fish from the midstream of the Yangtze River. The intraspecific distances of all species were below 2% (with the exception of Acheilognathus macropterus and Hemibarbus maculatus). Nevertheless, all species could be unambiguously identified from the trees, barcoding gaps and taxonomic resolution ratio values. Furthermore, the COI barcode diversity was found to be low (≤0.5%), with the exception of H. maculatus (0.87%), A. macropterus (2.02%) and Saurogobio dabryi (0.82%). No or few shared haplotypes were detected between the upstream and downstream populations for ten species with overall nucleotide diversities greater than 0.00%, which indicated the likelihood of significant population genetic structuring. Our analyses indicated that DNA barcoding is an effective tool for the identification of cyprinidae fish in the midstream of the Yangtze River. It is vital that some protective measures be taken immediately because of the low COI barcode diversity.
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Affiliation(s)
- Yanjun Shen
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of SciencesInstitute of HydrobiologyChinese Academy of SciencesWuhan430072HubeiChina
- University of Chinese Academy of SciencesBeijing100039China
| | - Lihong Guan
- College of Life Science and TechnologyXinxiang Medical UniversityHe'nan Xinxiang453003China
| | - Dengqiang Wang
- The Key Laboratory of Freshwater Biodiversity ConservationMinistry of AgricultureYangtze River Fisheries Research InstituteChinese Academy of Fishery SciencesWuhanChina
| | - Xiaoni Gan
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of SciencesInstitute of HydrobiologyChinese Academy of SciencesWuhan430072HubeiChina
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45
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Chambers EA, Hebert PDN. Assessing DNA Barcodes for Species Identification in North American Reptiles and Amphibians in Natural History Collections. PLoS One 2016; 11:e0154363. [PMID: 27116180 PMCID: PMC4846166 DOI: 10.1371/journal.pone.0154363] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 04/12/2016] [Indexed: 11/19/2022] Open
Abstract
Background High rates of species discovery and loss have led to the urgent need for more rapid assessment of species diversity in the herpetofauna. DNA barcoding allows for the preliminary identification of species based on sequence divergence. Prior DNA barcoding work on reptiles and amphibians has revealed higher biodiversity counts than previously estimated due to cases of cryptic and undiscovered species. Past studies have provided DNA barcodes for just 14% of the North American herpetofauna, revealing the need for expanded coverage. Methodology/Principal Findings This study extends the DNA barcode reference library for North American herpetofauna, assesses the utility of this approach in aiding species delimitation, and examines the correspondence between current species boundaries and sequence clusters designated by the BIN system. Sequences were obtained from 730 specimens, representing 274 species (43%) from the North American herpetofauna. Mean intraspecific divergences were 1% and 3%, while average congeneric sequence divergences were 16% and 14% in amphibians and reptiles, respectively. BIN assignments corresponded with current species boundaries in 79% of amphibians, 100% of turtles, and 60% of squamates. Deep divergences (>2%) were noted in 35% of squamate and 16% of amphibian species, and low divergences (<2%) occurred in 12% of reptiles and 23% of amphibians, patterns reflected in BIN assignments. Sequence recovery declined with specimen age, and variation in recovery success was noted among collections. Within collections, barcodes effectively flagged seven mislabeled tissues, and barcode fragments were recovered from five formalin-fixed specimens. Conclusions/Significance This study demonstrates that DNA barcodes can effectively flag errors in museum collections, while BIN splits and merges reveal taxa belonging to deeply diverged or hybridizing lineages. This study is the first effort to compile a reference library of DNA barcodes for herpetofauna on a continental scale.
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Affiliation(s)
- E. Anne Chambers
- Department of Integrative Biology, University of Texas, Austin, Texas, United States of America
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
- * E-mail:
| | - Paul D. N. Hebert
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
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Steinke D, Connell AD, Hebert PDN. Linking adults and immatures of South African marine fishes. Genome 2016; 59:959-967. [PMID: 27653340 DOI: 10.1139/gen-2015-0212] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The early life-history stages of fishes are poorly known, impeding acquisition of the identifications needed to monitor larval recruitment and year-class strength. A comprehensive database of COI sequences, linked to authoritatively identified voucher specimens, promises to change this situation, representing a significant advance for fisheries science. Barcode records were obtained from 2526 early larvae and pelagic eggs of fishes collected on the inshore shelf within 5 km of the KwaZulu-Natal coast, about 50 km south of Durban, South Africa. Barcodes were also obtained from 3215 adults, representing 946 South African fish species. Using the COI reference library on BOLD based on adults, 89% of the immature fishes could be identified to a species level; they represented 450 species. Most of the uncertain sequences could be assigned to a genus, family, or order; only 92 specimens (4%) were unassigned. Accumulation curves based on inference of phylogenetic diversity indicate near-completeness of the collecting effort. The entire set of adult and larval fishes included 1006 species, representing 43% of all fish species known from South African waters. However, this total included 189 species not previously recorded from this region. The fact that almost 90% of the immatures gained a species identification demonstrates the power and completeness of the DNA barcode reference library for fishes generated during the 10 years of FishBOL.
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Affiliation(s)
- Dirk Steinke
- a Canadian Centre for DNA Barcoding, Biodiversity Institute of Ontario, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Allan D Connell
- b South African Institute of Aquatic Biodiversity, Private Bag 1015, Grahamstown, South Africa 6140
| | - Paul D N Hebert
- a Canadian Centre for DNA Barcoding, Biodiversity Institute of Ontario, University of Guelph, Guelph, ON N1G 2W1, Canada
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Breman FC, Loix S, Jordaens K, Snoeks J, Van Steenberge M. Testing the potential of DNA barcoding in vertebrate radiations: the case of the littoral cichlids (Pisces, Perciformes, Cichlidae) from Lake Tanganyika. Mol Ecol Resour 2016; 16:1455-1464. [DOI: 10.1111/1755-0998.12523] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 02/26/2016] [Accepted: 02/26/2016] [Indexed: 11/28/2022]
Affiliation(s)
- Floris C. Breman
- Biology Department; Royal Museum for Central Africa; Leuvensesteenweg 13 B-3080 Tervuren Belgium
| | - Sara Loix
- Laboratory of Biodiversity and Evolutionary Genomics; KU Leuven; Charles Debériotstraat 32 B-3000 Leuven Belgium
| | - Kurt Jordaens
- Biology Department; Royal Museum for Central Africa; Leuvensesteenweg 13 B-3080 Tervuren Belgium
| | - Jos Snoeks
- Biology Department; Royal Museum for Central Africa; Leuvensesteenweg 13 B-3080 Tervuren Belgium
- Laboratory of Biodiversity and Evolutionary Genomics; KU Leuven; Charles Debériotstraat 32 B-3000 Leuven Belgium
| | - Maarten Van Steenberge
- Biology Department; Royal Museum for Central Africa; Leuvensesteenweg 13 B-3080 Tervuren Belgium
- Laboratory of Biodiversity and Evolutionary Genomics; KU Leuven; Charles Debériotstraat 32 B-3000 Leuven Belgium
- Institute of Zoology; University of Graz; Universitätsplatz 2 8010 Graz Austria
- Operational Directorate Taxonomy and Phylogeny; Royal Belgian Institute of Natural Sciences; Vautierstraat 29 1000 Brussels Belgium
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48
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DNA barcoding for the identification of common economic aquatic products in Central China and its application for the supervision of the market trade. Food Control 2016. [DOI: 10.1016/j.foodcont.2015.08.038] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Trivedi S, Aloufi AA, Ansari AA, Ghosh SK. Role of DNA barcoding in marine biodiversity assessment and conservation: An update. Saudi J Biol Sci 2016; 23:161-71. [PMID: 26980996 PMCID: PMC4778524 DOI: 10.1016/j.sjbs.2015.01.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 12/09/2014] [Accepted: 01/05/2015] [Indexed: 12/18/2022] Open
Abstract
More than two third area of our planet is covered by oceans and assessment of marine biodiversity is a challenging task. With the increasing global population, there is a tendency to exploit marine resources for food, energy and other requirements. This puts pressure on the fragile marine environment and necessitates sustainable conservation efforts. Marine species identification using traditional taxonomical methods is often burdened with taxonomic controversies. Here we discuss the comparatively new concept of DNA barcoding and its significance in marine perspective. This molecular technique can be useful in the assessment of cryptic species which is widespread in marine environment and linking the different life cycle stages to the adult which is difficult to accomplish in the marine ecosystem. Other advantages of DNA barcoding include authentication and safety assessment of seafood, wildlife forensics, conservation genetics and detection of invasive alien species (IAS). Global DNA barcoding efforts in the marine habitat include MarBOL, CeDAMar, CMarZ, SHARK-BOL, etc. An overview on DNA barcoding of different marine groups ranging from the microbes to mammals is revealed. In conjugation with newer and faster techniques like high-throughput sequencing, DNA barcoding can serve as an effective modern tool in marine biodiversity assessment and conservation.
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Affiliation(s)
- Subrata Trivedi
- Department of Biology, Faculty of Science, University of Tabuk, Tabuk 71491, Saudi Arabia
| | - Abdulhadi A. Aloufi
- Department of Biology, Faculty of Science, University of Tabuk, Tabuk 71491, Saudi Arabia
| | - Abid A. Ansari
- Department of Biology, Faculty of Science, University of Tabuk, Tabuk 71491, Saudi Arabia
| | - Sankar K. Ghosh
- Department of Biotechnology, Assam University, Silchar 788011, Assam, India
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50
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Cleaners among wrasses: Phylogenetics and evolutionary patterns of cleaning behavior within Labridae. Mol Phylogenet Evol 2016; 94:424-35. [DOI: 10.1016/j.ympev.2015.09.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Revised: 09/05/2015] [Accepted: 09/08/2015] [Indexed: 11/15/2022]
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