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Lam TTH, Dinh QM, Truong VTB, Truong NT, Tran NS, Nguyen THD. The use of mtCOI gene sequences in identifying Butis species in the Southwest of Vietnam. Heliyon 2023; 9:e20139. [PMID: 37809956 PMCID: PMC10559908 DOI: 10.1016/j.heliyon.2023.e20139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 09/06/2023] [Accepted: 09/12/2023] [Indexed: 10/10/2023] Open
Abstract
Butis genus is characterised by their small body size and morphological variability, allowing them to adapt to different habitats. This paper analyses the mitochondrial cytochrome C oxidase subunit I gene sequences and morphology of Butis for identification purposes and to understand genetic relationships. The morphological characteristics of Butis koilomatodon differed obviously from Butis humeralis and Butis butis. After classification based on morphology, the total deoxyribonucleic acid of fish samples was isolated, and the mitochondrial cytochrome C oxidase subunit I genes were successfully amplified using the polymerase chain reaction method. At approximately 617bp, the obtained mitochondrial cytochrome C oxidase subunit I gene sequences were highly similar to the reference sequences on Genbank (85.90-100%). The phylogenetic graphic was divided into five distinct groups, where B. koilomatodon was grouped in one group; and B. humeralis and B. butis were grouped together. The results suggest that B. humeralis was an entirely different species from B. butis, with a mean genetic divergence of up to 14%. However, further studies using a combination of other types of deoxyribonucleic acid barcoding together with morphological features should be undertaken to confirm these findings.
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Affiliation(s)
- Tran Thi Huyen Lam
- Institute of Food and Biotechnology, Can Tho University, Xuan Khanh Ward, Ninh Kieu District, Can Tho, 900000, Viet Nam
- Institute of High Quality Biotechnology - Food Technology, Cuu Long University, National Road 1A, Phu Quoi Ward, Long Ho District, Vinh Long, 850000, Viet Nam
| | - Quang Minh Dinh
- Department of Biology, School of Education, Can Tho University, Xuan Khanh Ward, Ninh Kieu District, Can Tho, 900000, Viet Nam
| | - Van Thi Bich Truong
- Institute of Food and Biotechnology, Can Tho University, Xuan Khanh Ward, Ninh Kieu District, Can Tho, 900000, Viet Nam
| | - Ngon Trong Truong
- Institute of Food and Biotechnology, Can Tho University, Xuan Khanh Ward, Ninh Kieu District, Can Tho, 900000, Viet Nam
| | - Nam Sy Tran
- Department of Environmental Sciences, College of Environment and Natural Resources, Can Tho University, Can Tho, 900000, Viet Nam
| | - Ton Huu Duc Nguyen
- Department of Biology, School of Education, Can Tho University, Xuan Khanh Ward, Ninh Kieu District, Can Tho, 900000, Viet Nam
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Damadi E, Yazdani Moghaddam F, Ghanbarifardi M. Species delimitation, molecular phylogeny and historical biogeography of the sweetlips fish (Perciformes, Haemulidae). ZOOSYST EVOL 2023. [DOI: 10.3897/zse.99.96386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
The subfamily Plectorhinchinae (sweetlips) is composed of poorly-known species with high commercially and ecologically values that exhibit phenotypic plasticity and various morphologies. Few studies have assessed the validity of sweetlips, intergeneric relationships and evolutionary survey in this subfamily, which have not yet been resolved. This study investigated the DNA sequences of (1) the mitochondrial COI gene to delimit species, and (2) two mitochondrial (COI and Cyt b), and one nuclear (RAG1) markers to infer phylogenetic relationships and evolutionary and biogeographic history. The molecular results could differentiate Diagramma punctatum from the other species, but failed to distinguish D. labiosum as a distinct species with considerably lower genetic distances for the COI (0.53%) and Cyt b (0.51%) markers. However, additional taxonomic investigations are required to shed light on this issue. All previously described nominal species of sweetlips in the northwest Indian Ocean were found to be well supported. The monophyly of Plectorhinchus is not supported and Diagramma pictum and D. punctatum should be assigned to the genus Plectorhinchus. The biogeographic history of Plectorhinchinae likely originated in the Indo-Pacific ca. 34 Ma (30–39 Ma; late Eocene/ middle Oligocene) and subsequently colonised the Western Indian Ocean and the Central Indo-Pacific. Maximum diversification within the subfamily occurred from the middle Miocene to Pliocene, coinciding with dispersal and vicariance events. Diversification was probably driven by both biological and geographical factors.
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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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Neves JMM, Nolen ZJ, Fabré NN, Mott T, Pereira RJ. Genomic methods reveal independent demographic histories despite strong morphological conservatism in fish species. Heredity (Edinb) 2021; 127:323-333. [PMID: 34226671 PMCID: PMC8405619 DOI: 10.1038/s41437-021-00455-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 06/18/2021] [Accepted: 06/18/2021] [Indexed: 02/06/2023] Open
Abstract
Human overexploitation of natural resources has placed conservation and management as one of the most pressing challenges in modern societies, especially in regards to highly vulnerable marine ecosystems. In this context, cryptic species are particularly challenging to conserve because they are hard to distinguish based on morphology alone, and thus it is often unclear how many species coexist in sympatry, what are their phylogenetic relationships and their demographic history. We answer these questions using morphologically similar species of the genus Mugil that are sympatric in the largest coastal Marine Protected Area in the Tropical Southwestern Atlantic marine province. Using a sub-representation of the genome, we show that individuals are assigned to five highly differentiated genetic clusters that are coincident with five mitochondrial lineages, but discordant with morphological information, supporting the existence of five species with conserved morphology in this region. A lack of admixed individuals is consistent with strong genetic isolation between sympatric species, but the most likely species tree suggests that in one case speciation has occurred in the presence of interspecific gene flow. Patterns of genetic diversity within species suggest that effective population sizes differ up to two-fold, probably reflecting differences in the magnitude of population expansions since species formation. Together, our results show that strong morphologic conservatism in marine environments can lead to species that are difficult to distinguish morphologically but that are characterized by an independent evolutionary history, and thus that deserve species-specific management strategies.
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Affiliation(s)
- Jessika M M Neves
- Instituto de Ciências Biológicas e da Saúde, Universidade Federal de Alagoas, Maceió, Alagoas, Brazil.
| | - Zachary J Nolen
- Division of Evolutionary Biology, Faculty of Biology II, Ludwig-Maximilians-Universität München, Grosshaderner Strasse 2, Planegg-Martinsried, Germany
- Department of Biology, Lund University, Lund, Sweden
| | - Nidia N Fabré
- Instituto de Ciências Biológicas e da Saúde, Universidade Federal de Alagoas, Maceió, Alagoas, Brazil
| | - Tamí Mott
- Instituto de Ciências Biológicas e da Saúde, Universidade Federal de Alagoas, Maceió, Alagoas, Brazil
| | - Ricardo J Pereira
- Division of Evolutionary Biology, Faculty of Biology II, Ludwig-Maximilians-Universität München, Grosshaderner Strasse 2, Planegg-Martinsried, Germany.
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Damadi E, Moghaddam FY, Ghassemzadeh F, Ghanbarifardi M. Plectorhinchus makranensis (Teleostei, Haemulidae), a new species of sweetlips from the Persian Gulf and the Gulf of Oman. Zookeys 2020; 980:141-154. [PMID: 33192142 PMCID: PMC7642193 DOI: 10.3897/zookeys.980.50934] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 08/28/2020] [Indexed: 01/23/2023] Open
Abstract
Plectorhinchus makranensis sp. nov. is described on the basis of 16 specimens from the Persian Gulf and Gulf of Oman, in the Northwest Indian Ocean. The new species can be distinguished from congeners by a combination of dorsal fin rays XII, 18-20, pectoral-fin rays 16-17, tubed lateral-line scales 55-57, gill rakers count (10-12 on the upper limb and 16-17 on the lower limb), 17-18 scales between the lateral line and the first anal-fin spine, 30-31 circumpeduncular scale rows and color pattern. Plectorhinchus makranensis sp. nov. is distinguished from P. schotaf by having the posterior margin of the opercular membrane grey (vs. red in P. schotaf), fewer circumpeduncular scale rows, and a shorter base of the soft portion of the dorsal fin, 27.6-29.4% of standard length (SL) (vs. 31-32.3% of SL in P. schotaf). The new species resembles P. sordidus but is differentiated from it by having more gill rakers, a smaller orbit diameter 27.5-32.1% of head length (HL) (vs. 35.5-37.2% of HL in P. sordidus), a longer caudal peduncle 19.2-21.3% of SL (vs. 17.1-17.9% of SL in P. sordidus), and the first to third pectoral-fin rays light gray (vs. dark gray in P. sordidus). The new species can also be distinguished from the other species, including P. schotaf and P. sordidus, based on COI and Cyt b molecular markers. The phylogenetic position of this new species indicates that it is a sister taxon of P. schotaf.
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Affiliation(s)
- Ehsan Damadi
- Department of Biology, Faculty of Sciences, University of Ferdowsi, Mashhad, Iran University of Ferdowsi Mashhad Iran
| | - Faezeh Yazdani Moghaddam
- Department of Biology, Faculty of Sciences, University of Ferdowsi, Mashhad, Iran University of Ferdowsi Mashhad Iran.,Zoological Innovations Research Department, Institute of Applied Zoology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran Ferdowsi University of Mashhad Mashhad Iran
| | - Fereshteh Ghassemzadeh
- Department of Biology, Faculty of Sciences, University of Ferdowsi, Mashhad, Iran University of Ferdowsi Mashhad Iran.,Zoological Innovations Research Department, Institute of Applied Zoology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran Ferdowsi University of Mashhad Mashhad Iran
| | - Mehdi Ghanbarifardi
- Department of Biology, Faculty of Science, University of Sistan and Baluchestan, Zahedan, Iran University of Sistan and Baluchestan Zahedan Iran
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Purushothaman P, Chakraborty RD, Kuberan G, Maheswarudu G. Integrative taxonomy of commercially important deep water penaeoid shrimps from India. J Genet 2019. [DOI: 10.1007/s12041-018-1052-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Wang L, Wu Z, Liu M, Liu W, Zhao W, Liu H, You F. DNA barcoding of marine fish species from Rongcheng Bay, China. PeerJ 2018; 6:e5013. [PMID: 29967722 PMCID: PMC6022726 DOI: 10.7717/peerj.5013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 05/29/2018] [Indexed: 11/20/2022] Open
Abstract
Rongcheng Bay is a coastal bay of the Northern Yellow Sea, China. To investigate and monitor the fish resources in Rongcheng Bay, 187 specimens from 41 different species belonging to 28 families in nine orders were DNA-barcoded using the mitochondrial cytochrome c oxidase subunit I gene (COI). Most of the fish species could be discriminated using this COI sequence with the exception of Cynoglossus joyneri and Cynoglossus lighti. The average GC% content of the 41 fish species was 47.3%. The average Kimura 2-parameter genetic distances within the species, genera, families, and orders were 0.21%, 5.28%, 21.30%, and 23.63%, respectively. Our results confirmed that the use of combined morphological and DNA barcoding identification methods facilitated fish species identification in Rongcheng Bay, and also established a reliable DNA barcode reference library for these fish. DNA barcodes will contribute to future efforts to achieve better monitoring, conservation, and management of fisheries in this area.
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Affiliation(s)
- Lijuan Wang
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, Shandong, China
| | - Zhihao Wu
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, Shandong, China
| | - Mengxia Liu
- Marine Biology Institute of Shandong Province, Qingdao, Shandong, China
| | - Wei Liu
- Marine Biology Institute of Shandong Province, Qingdao, Shandong, China
| | - Wenxi Zhao
- Marine Biology Institute of Shandong Province, Qingdao, Shandong, China
| | - Hongjun Liu
- Marine Biology Institute of Shandong Province, Qingdao, Shandong, China
| | - Feng You
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, Shandong, China
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Collet A, Durand JD, Desmarais E, Cerqueira F, Cantinelli T, Valade P, Ponton D. DNA barcoding post-larvae can improve the knowledge about fish biodiversity: an example from La Reunion, SW Indian Ocean. Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:905-918. [PMID: 28984152 DOI: 10.1080/24701394.2017.1383406] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The aim of this study was to demonstrate that fish larvae identified using their COI sequences offer a unique opportunity for improving the knowledge of local fish richness. Fish larvae were sampled at the end of their pelagic phase using light-traps set off the West Coast of La Reunion Island, southwestern Indian Ocean, once per month from October 2014 to March 2015. Among the 5174 larvae caught, 214 morphologically different specimens were selected, 196 successfully barcoded, giving a total of 101 different Barcode Index Numbers (BINs). Among these BINs, 55 had never been recorded in La Reunion exclusive economic zone (EEZ), and 13 were new for the BOLD database. Even if the sampling effort for collecting fish post-larvae during this study was relatively low, it allowed adding at least nine new species to an updated checklist of fishes of La Reunion EEZ.
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Affiliation(s)
| | - Jean-Dominique Durand
- b UMR 9190 MARBEC, IRD-CNRS-IFREMER-UM, Department of Ecology , Evolutionary Biology University of Science, VNUHCM , Ho Chi Minh City , Vietnam
| | - Eric Desmarais
- c ISEM, CNRS , University of Montpellier, IRD, EPHE , Montpellier , France
| | | | - Thomas Cantinelli
- c ISEM, CNRS , University of Montpellier, IRD, EPHE , Montpellier , France
| | | | - Dominique Ponton
- d ENTROPIE, IRD , Université de La Réunion, CNRS, Laboratoire d'Excellence CORAIL , La Réunion , France
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Li J, Wang Y, Jin H, Li W, Yan C, Yan P, Zhang X, He S, Song Z. Identification of Triplophysa species from the Qinghai-Tibetan Plateau (QTP) and its adjacent regions through DNA barcodes. Gene 2016; 605:12-19. [PMID: 28104086 DOI: 10.1016/j.gene.2016.11.045] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 10/21/2016] [Accepted: 11/30/2016] [Indexed: 11/16/2022]
Abstract
The genus Triplophysa is the largest and most difficult to identity morphologically fish group of superfamily Cobitoidea with 140 currently valid species, and is mainly distributed in the Qinghai-Tibetan Plateau (QTP) and adjacent regions. Most species within this genus possess highly similar morphological characteristics for adaption to the highland environment and are very difficult to be identified only based on morphology. The traditional species identification, mainly based on external morphological diagnostic characters, leads to inconsistent results in many cases. Herein, we provided a molecular method based on mitochondrial cytochrome c subunit I (COI) for the identification of Triplophysa fishes. Thirty-three Triplophysa species, 244 individuals, were used to determine whether barcoding was effective in discriminating species for this genus. The mean intraspecific and interspecific K2P distances ranged from 0 to 14.9% (mean, 2.9%) and 0 to 23.4% (mean, 9.7%), respectively. The tree-based analysis displayed most of species formed discrete clusters with strong bootstrap support values (>90%). The results showed that most of Triplophysa species could be identified by DNA barcode and indicated DNA barcode could be used as a molecular marker for these species.
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Affiliation(s)
- Jiuxuan Li
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610065, PR China
| | - Ying Wang
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610065, PR China; Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China; School of Life Sciences, Jianghan University, Wuhan 430056, PR China
| | - Huifang Jin
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610065, PR China
| | - Wujiao Li
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610065, PR China
| | - Chaochao Yan
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610065, PR China
| | - Pengfei Yan
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610065, PR China
| | - Xiuyue Zhang
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610065, PR China
| | - Shunping He
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China
| | - Zhaobin Song
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610065, PR China; Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, PR China.
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Pugedo ML, de Andrade Neto FR, Pessali TC, Birindelli JLO, Carvalho DC. Integrative taxonomy supports new candidate fish species in a poorly studied neotropical region: the Jequitinhonha River Basin. Genetica 2016; 144:341-9. [PMID: 27170425 DOI: 10.1007/s10709-016-9903-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 05/04/2016] [Indexed: 10/21/2022]
Abstract
Molecular identification through DNA barcoding has been proposed as a way to standardize a global biodiversity identification system using a partial sequence of the mitochondrial COI gene. We applied an integrative approach using DNA barcoding and traditional morphology-based bioassessment to identify fish from a neotropical region possessing low taxonomic knowledge: the Jequitinhonha River Basin (Southeastern Brazil). The Jequitinhonha River Basin (JRB) has a high rate of endemism and is considered an area of high priority for fish conservation, with estimates indicating the presence of around 110 native and non-indigenous species. DNA barcodes were obtained from 260 individuals belonging to 52 species distributed among 35 genera, 21 families and 6 orders, including threatened and rare species such as Rhamdia jequitinhonha and Steindachneridion amblyurum. The mean Kimura two-parameter genetic distances within species, genera and families were: 0.44, 12.16 and 20.58 %, respectively. Mean intraspecific genetic variation ranged from 0 to 11.43 %, and high values (>2 %) were recovered for five species. Species with a deep intraspecific distance, possibly flagging overlooked taxa, were detected within the genus Pimelodella. Fifteen species, only identified to the genus level, had unique BINs, with a nearest neighbor distance over 2 % and therefore, potential new candidate species supported by DNA barcoding. The integrative taxonomy approach using DNA barcoding and traditional taxonomy may be a remedy to taxonomy impediment, accelerating species identification by flagging potential new candidate species and to adequately conserve the megadiverse neotropical ichthyofauna.
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Affiliation(s)
- Marina Lages Pugedo
- Programa de Pós-graduação em Zoologia de Vertebrados, Laboratório de Genética da Conservação, PUC Minas, Rua Dom José Gaspar, 500, 30535-901, Belo Horizonte, Minas Gerais, Brazil
| | | | - Tiago Casarim Pessali
- Laboratório de Ictiologia, Museu de Ciências Naturais, PUC Minas, Belo Horizonte, Minas Gerais, Brazil
| | | | - Daniel Cardoso Carvalho
- Programa de Pós-graduação em Zoologia de Vertebrados, Laboratório de Genética da Conservação, PUC Minas, Rua Dom José Gaspar, 500, 30535-901, Belo Horizonte, Minas Gerais, Brazil.
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Comparative phylogeography of the western Indian Ocean reef fauna. ACTA OECOLOGICA-INTERNATIONAL JOURNAL OF ECOLOGY 2016. [DOI: 10.1016/j.actao.2015.10.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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12
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Henderson AC, Reeve AJ, Jabado RW, Naylor GJP. Taxonomic assessment of sharks, rays and guitarfishes (Chondrichthyes: Elasmobranchii) from south-eastern Arabia, using the NADH dehydrogenase subunit 2 (NADH2) gene. Zool J Linn Soc 2015. [DOI: 10.1111/zoj.12309] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Aaron C. Henderson
- Department of Marine Science & Fisheries; College of Agricultural & Marine Sciences; Sultan Qaboos University; PO Box 34 Al-Khod Oman
| | - Alan J. Reeve
- Department of Marine Science & Fisheries; College of Agricultural & Marine Sciences; Sultan Qaboos University; PO Box 34 Al-Khod Oman
| | - Rima W. Jabado
- Gulf Elasmo Project; PO Box 29588 Dubai United Arab Emirates
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13
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Castro Paz FP, Batista JDS, Porto JIR. DNA barcodes of Rosy Tetras and allied species (Characiformes: Characidae: Hyphessobrycon) from the Brazilian Amazon basin. PLoS One 2014; 9:e98603. [PMID: 24878569 PMCID: PMC4039478 DOI: 10.1371/journal.pone.0098603] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 05/05/2014] [Indexed: 11/18/2022] Open
Abstract
DNA barcoding can be an effective tool for fast and accurate species-level identification based on sequencing of the mitochondrial cytochrome c oxidase subunit (COI) gene. The diversity of this fragment can be used to estimate the richness of the respective species. In this study, we explored the use of DNA barcoding in a group of ornamental freshwater fish of the genus Hyphessobrycon. We sequenced the COI from 10 species of Hyphessobrycon belonging to the "Rosy Tetra Clade" collected from the Amazon and Negro River basins and combined our results with published data. The average conspecific and congeneric Kimura 2-parameter distances were 2.3% and 19.3%, respectively. Six of the 10 species were easily distinguishable by DNA barcoding (H. bentosi, H. copelandi, H. eques, H. epicharis, H. pulchrippinis, and H. sweglesi), whereas the remaining species (H. erythrostigma, H. pyrrhonotus, H. rosaceus and H. socolofi) lacked reciprocal monophyly. Although the COI gene was not fully diagnostic, the discovery of distinct evolutionary units in certain Hyphessobrycon species under the same specific epithet as well as haplotype sharing between different species suggest that DNA barcoding is useful for species identification in this speciose genus.
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Affiliation(s)
| | - Jacqueline da Silva Batista
- Laboratorio Temático de Biologia Molecular, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus-AM, Brazil
| | - Jorge Ivan Rebelo Porto
- Laboratório de Genética Animal, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus-AM, Brazil
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Sparks JS, Schelly RC, Smith WL, Davis MP, Tchernov D, Pieribone VA, Gruber DF. The covert world of fish biofluorescence: a phylogenetically widespread and phenotypically variable phenomenon. PLoS One 2014; 9:e83259. [PMID: 24421880 PMCID: PMC3885428 DOI: 10.1371/journal.pone.0083259] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2013] [Accepted: 10/31/2013] [Indexed: 12/30/2022] Open
Abstract
The discovery of fluorescent proteins has revolutionized experimental biology. Whereas the majority of fluorescent proteins have been identified from cnidarians, recently several fluorescent proteins have been isolated across the animal tree of life. Here we show that biofluorescence is not only phylogenetically widespread, but is also phenotypically variable across both cartilaginous and bony fishes, highlighting its evolutionary history and the possibility for discovery of numerous novel fluorescent proteins. Fish biofluorescence is especially common and morphologically variable in cryptically patterned coral-reef lineages. We identified 16 orders, 50 families, 105 genera, and more than 180 species of biofluorescent fishes. We have also reconstructed our current understanding of the phylogenetic distribution of biofluorescence for ray-finned fishes. The presence of yellow long-pass intraocular filters in many biofluorescent fish lineages and the substantive color vision capabilities of coral-reef fishes suggest that they are capable of detecting fluoresced light. We present species-specific emission patterns among closely related species, indicating that biofluorescence potentially functions in intraspecific communication and evidence that fluorescence can be used for camouflage. This research provides insight into the distribution, evolution, and phenotypic variability of biofluorescence in marine lineages and examines the role this variation may play.
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Affiliation(s)
- John S. Sparks
- Department of Ichthyology, American Museum of Natural History, Division of Vertebrate Zoology, New York, New York United States of America
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, United States of America
| | - Robert C. Schelly
- Department of Ichthyology, American Museum of Natural History, Division of Vertebrate Zoology, New York, New York United States of America
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, United States of America
| | - W. Leo Smith
- Biodiversity Institute, University of Kansas, Lawrence, Kansas, United States of America
| | - Matthew P. Davis
- Biodiversity Institute, University of Kansas, Lawrence, Kansas, United States of America
| | - Dan Tchernov
- Marine Biology Department, The Leon H. Charney School of Marine Sciences, University of Haifa, Mount Carmel, Haifa, Israel
| | - Vincent A. Pieribone
- Department of Ichthyology, American Museum of Natural History, Division of Vertebrate Zoology, New York, New York United States of America
- Department of Cellular and Molecular Physiology, The John B. Pierce Laboratory, Inc., Yale University, New Haven, Connecticut, United States of America
| | - David F. Gruber
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, United States of America
- Department of Natural Sciences, Baruch College, City University of New York, New York, New York, United States of America
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Quilang JP, Yu SCS. DNA barcoding of commercially important catfishes in the Philippines. ACTA ACUST UNITED AC 2013; 26:435-44. [PMID: 24274093 DOI: 10.3109/19401736.2013.855897] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Many species of catfish are important resources for human consumption, for sport fishing and for use in aquarium industry. In the Philippines, some species are cultivated and some are caught in the wild for food and a few introduced species have become invasive. In this study, DNA barcoding using the mitochondrial cytochrome c oxidase I (COI) gene was done on commercially and economically important Philippine catfishes. A total of 75 specimens belonging to 11 species and 5 families were DNA barcoded. The genetic distances were computed and Neighbor-Joining (NJ) trees were constructed based on the Kimura 2-Parameter (K2P) method. The average K2P distances within species, genus, family and order were 0.2, 8.2, 12.7 and 21.9%, respectively. COI sequences clustered according to their species designation for 7 of the 11 catfishes. DNA barcoding was not able to discriminate between Arius dispar and A. manillensis and between Pterygoplichthys disjunctivus and P. pardalis. The morphological characters that are used to distinguish between these species do not complement molecular identification through DNA barcoding. DNA barcoding also showed that Clarias batrachus from the Philippines is different from the species found in India and Thailand, which supports earlier suggestions based on morphology that those found in India should be designated as C. magur and those in mainland Southeast Asia as C. aff. batrachus "Indochina". This study has shown that DNA barcoding can be used for species delineation and for tagging some species for further taxonomic investigation, which has implications on proper management and conservation strategies.
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Affiliation(s)
- Jonas P Quilang
- Molecular Population Genetics Laboratory, Institute of Biology, College of Science, University of the Philippines , Diliman, Quezon City , Philippines
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16
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García-Dávila C, Duponchelle F, Castro-Ruiz D, Villacorta J, Quérouil S, Chota-Macuyama W, Núñez J, Römer U, Carvajal-Vallejos F, Renno JF. Molecular identification of a cryptic species in the Amazonian predatory catfish genus Pseudoplatystoma (Bleeker, 1962) from Peru. Genetica 2013; 141:347-58. [PMID: 24008811 DOI: 10.1007/s10709-013-9734-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Accepted: 08/31/2013] [Indexed: 10/26/2022]
Abstract
Pseudoplatystoma species are highly prized South American Pimelodid migratory catfishes. Until recently, their taxonomy was not clearly established, with discrepancies between morphological and molecular analyses. Here, Pseudoplatystoma species from the Peruvian Amazon were characterized at the molecular level from a sample representing the observed range of their color pattern variations in the study area. Analyses were performed using seven microsatellite loci for 103 specimens and, for part of them (52), using sequences of two regions of their mitochondrial genome [Cytochrome Oxidase subunit I (COI) and Control Region (CR)]. Factorial correspondence analysis and assignment tests based on microsatellite polymorphism showed that the specimens originally identified as P. punctifer belonged to two different gene pools highly differentiated from P. tigrinum. Morphological examination identified two different morphotypes (with and without black stripes), suggesting the existence of two distinct taxa within P. punctifer. This result was corroborated by the ML tree based on CR sequences, where all individuals but four clustered in a similar way as in the FCA and Bayesian assignment tests. For these four individuals, mitochondrial introgression or retention of ancestral polymorphism was likely. In contrast, the ML tree based on COI sequences showed that reciprocal monophyly was not yet achieved for this marker for the two P. punctifer taxa. The existence of three sympatric species of Pseudoplatystoma in the Peruvian Amazon is discussed in relation to their molecular characteristics, color patterns and ecology. Evolutionary scenarios regarding their divergence are hypothesized.
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Affiliation(s)
- Carmen García-Dávila
- Laboratoire Mixte International-Evolution et Domestication de l'Ichtyofaune Amazonienne (LMI-EDIA), Iquitos, Peru,
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Pereira LHG, Hanner R, Foresti F, Oliveira C. Can DNA barcoding accurately discriminate megadiverse Neotropical freshwater fish fauna? BMC Genet 2013; 14:20. [PMID: 23497346 PMCID: PMC3608943 DOI: 10.1186/1471-2156-14-20] [Citation(s) in RCA: 156] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Accepted: 03/05/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The megadiverse Neotropical freshwater ichthyofauna is the richest in the world with approximately 6,000 recognized species. Interestingly, they are distributed among only 17 orders, and almost 80% of them belong to only three orders: Characiformes, Siluriformes and Perciformes. Moreover, evidence based on molecular data has shown that most of the diversification of the Neotropical ichthyofauna occurred recently. These characteristics make the taxonomy and identification of this fauna a great challenge, even when using molecular approaches. In this context, the present study aimed to test the effectiveness of the barcoding methodology (COI gene) to identify the mega diverse freshwater fish fauna from the Neotropical region. For this purpose, 254 species of fishes were analyzed from the Upper Parana River basin, an area representative of the larger Neotropical region. RESULTS Of the 254 species analyzed, 252 were correctly identified by their barcode sequences (99.2%). The main K2P intra- and inter-specific genetic divergence values (0.3% and 6.8%, respectively) were relatively low compared with similar values reported in the literature, reflecting the higher number of closely related species belonging to a few higher taxa and their recent radiation. Moreover, for 84 pairs of species that showed low levels of genetic divergence (<2%), application of a complementary character-based nucleotide diagnostic approach proved useful in discriminating them. Additionally, 14 species displayed high intra-specific genetic divergence (>2%), pointing to at least 23 strong candidates for new species. CONCLUSIONS Our study is the first to examine a large number of freshwater fish species from the Neotropical area, including a large number of closely related species. The results confirmed the efficacy of the barcoding methodology to identify a recently radiated, megadiverse fauna, discriminating 99.2% of the analyzed species. The power of the barcode sequences to identify species, even with low interspecific divergence, gives us an idea of the distribution of inter-specific genetic divergence in these megadiverse fauna. The results also revealed hidden genetic divergences suggestive of reproductive isolation and putative cryptic speciation in some species (23 candidates for new species). Finally, our study constituted an important contribution to the international Barcoding of Life (iBOL.org) project, providing barcode sequences for use in identification of these species by experts and non-experts, and allowing them to be available for use in other applications.
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Affiliation(s)
- Luiz H G Pereira
- Laboratory of Biology and Genetic of Fish, Department of Morphology, Biosciences Institute, State University of São Paulo, São Paulo, Brazil.
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DNA barcoding reveals cryptic diversity within commercially exploited Indo-Malay Carangidae (Teleosteii: Perciformes). PLoS One 2012; 7:e49623. [PMID: 23209586 PMCID: PMC3510217 DOI: 10.1371/journal.pone.0049623] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Accepted: 10/11/2012] [Indexed: 11/19/2022] Open
Abstract
Background DNA barcodes, typically focusing on the cytochrome oxidase I gene (COI) in many animals, have been used widely as a species-identification tool. The ability of DNA barcoding to distinguish species from a range of taxa and to reveal cryptic species has been well documented. Despite the wealth of DNA barcode data for fish from many temperate regions, there are relatively few available from the Southeast Asian region. Here, we target the marine fish Family Carangidae, one of the most commercially-important families from the Indo-Malay Archipelago (IMA), to produce an initial reference DNA barcode library. Methodology/Principal Findings Here, a 652 bp region of COI was sequenced for 723 individuals from 36 putative species of Family Carangidae distributed within IMA waters. Within the newly-generated dataset, three described species exhibited conspecific divergences up to ten times greater (4.32–4.82%) than mean estimates (0.24–0.39%), indicating a discrepancy with assigned morphological taxonomic identification, and the existence of cryptic species. Variability of the mitochondrial DNA COI region was compared within and among species to evaluate the COI region's suitability for species identification. The trend in range of mean K2P distances observed was generally in accordance with expectations based on taxonomic hierarchy: 0% to 4.82% between individuals within species, 0% to 16.4% between species within genera, and 8.64% to 25.39% between genera within families. The average Kimura 2-parameter (K2P) distance between individuals, between species within genera, and between genera within family were 0.37%, 10.53% and 16.56%, respectively. All described species formed monophyletic clusters in the Neighbour-joining phylogenetic tree, although three species representing complexes of six potential cryptic species were detected in Indo-Malay Carangidae; Atule mate, Selar crumenophthalmus and Seriolina nigrofasciata. Conclusion/Significance This study confirms that COI is an effective tool for species identification of Carangidae from the IMA. There were moderate levels of cryptic diversity among putative species within the central IMA. However, to explain the hypothesis of species richness in the IMA, it is necessary to sample the whole family across their broad geographic range. Such insights are helpful not only to document mechanisms driving diversification and recruitment in Carangidae, but also to provide a scientific framework for management strategies and conservation of commercially-important fisheries resources.
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Weigt LA, Baldwin CC, Driskell A, Smith DG, Ormos A, Reyier EA. Using DNA barcoding to assess Caribbean reef fish biodiversity: expanding taxonomic and geographic coverage. PLoS One 2012; 7:e41059. [PMID: 22815912 PMCID: PMC3398874 DOI: 10.1371/journal.pone.0041059] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Accepted: 06/16/2012] [Indexed: 11/18/2022] Open
Abstract
This paper represents a DNA barcode data release for 3,400 specimens representing 521 species of fishes from 6 areas across the Caribbean and western central Atlantic regions (FAO Region 31). Merged with our prior published data, the combined efforts result in 3,964 specimens representing 572 species of marine fishes and constitute one of the most comprehensive DNA barcoding "coverages" for a region reported to date. The barcode data are providing new insights into Caribbean shorefish diversity, allowing for more and more accurate DNA-based identifications of larvae, juveniles, and unknown specimens. Examples are given correcting previous work that was erroneous due to database incompleteness.
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Affiliation(s)
- Lee A Weigt
- Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States of America.
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Schoelinck C, Cruaud C, Justine JL. Are all species of Pseudorhabdosynochus strictly host specific? — A molecular study. Parasitol Int 2012; 61:356-9. [DOI: 10.1016/j.parint.2012.01.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Revised: 01/25/2012] [Accepted: 01/27/2012] [Indexed: 10/14/2022]
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