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Uh-Navarrete AE, Valdez-Moreno M, Callejas-Jiménez ME, Vásquez-Yeomans L. Discovering the fish fauna of a lagoon from the southeast of the Yucatan Peninsula, Mexico, using DNA barcodes. PeerJ 2023; 11:e16285. [PMID: 37933260 PMCID: PMC10625761 DOI: 10.7717/peerj.16285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 09/21/2023] [Indexed: 11/08/2023] Open
Abstract
Background Aquatic ecosystems in the tropics are typically environments with a high species richness of fishes. These systems are also among the most vulnerable in the world, threatening the overall biodiversity of tropical regions. As a first step, it is important to enumerate the species in any ecosystem to promote its conservation. This study aims to inventory the ichthyofauna in the Chile Verde Lagoon, Quintana Roo, on the Yucatan Peninsula, a system fortunately well protected in Mexico, based on faunal surveys backed up with mtDNA barcodes. Methods We collected larvae, juveniles, and adults of fishes in the lagoon with a variety of sampling gear targeting various life stages. Species were identified using both morphology and DNA barcodes. The abundance of species and ichthyoplankton biomass (wet weight, suction technique) were calculated from 43 samples. Results We collected 197 adult and juvenile fishes and 3,722 larvae, of which 306 specimens were DNA-sequenced with a success rate of 96.7%. We identified 13 families, 24 genera, and 27 species in our inventory. The species number was estimated to comprise 75% of the potential total richness using the Chao 1 richness estimator. Clupeids and gobiids accounted for 87.9% of the total abundance of fishes, and, together with cyprinodontids, also accounted for the highest ichthyoplankton biomass. Conclusion Adult and juvenile fishes were identified by morphology and meristic values, however larvae required DNA barcoding to identify species. The high biomass and abundance of larvae of clupeids, gobiids and cyprinodontids suggests that the Chile Verde Lagoon may be important for reproduction of these species in the region. Microgobius microlepis, a marine goby species, is reported for the first time in an inland oligohaline system. This study provides a basis for future environmental assessment and biomonitoring of the Chile Verde Lagoon in the Yucatan Peninsula of Mexico.
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Affiliation(s)
| | - Martha Valdez-Moreno
- Department of Aquatic Ecology and Systematics, El Colegio de la Frontera Sur, Chetumal, Quintana Roo, Mexico
| | - Mariana E. Callejas-Jiménez
- Department of Observation and Study of the Land, the Atmosphere and the Ocean, El Colegio de la Frontera Sur, Chetumal, Quintana Roo, Mexico
| | - Lourdes Vásquez-Yeomans
- Department of Aquatic Ecology and Systematics, El Colegio de la Frontera Sur, Chetumal, Quintana Roo, Mexico
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Tsoupas A, Papavasileiou S, Minoudi S, Gkagkavouzis K, Petriki O, Bobori D, Sapounidis A, Koutrakis E, Leonardos I, Karaiskou N, Triantafyllidis A. DNA barcoding identification of Greek freshwater fishes. PLoS One 2022; 17:e0263118. [PMID: 35081163 PMCID: PMC8791500 DOI: 10.1371/journal.pone.0263118] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 01/12/2022] [Indexed: 11/18/2022] Open
Abstract
Biodiversity is a key factor for the functioning and efficiency of an ecosystem. Greece, though covering a relatively small surface area, hosts a great deal of species diversity. This is especially true for freshwater fishes. In recent years, the traditional methods of species identification have been supplemented by the use of molecular markers. The present study therefore aims to extensively produce DNA barcodes for Greek freshwater fish species and investigate thoroughly if the presently accepted species classification is in agreement with molecular data. A 624-bases long fragment of the COI gene was sequenced, from 406 freshwater fish specimens belonging to 24 genera and originating from 18 lake and river sites. These sequences were used along with 596 sequences from the same genera, recovered from BOLD, for the construction of phylogenetic trees and the estimation of genetic distances between individuals. In total, 1002 sequences belonging to 72 species were analyzed. The method was found to be effective for 55 of 72 studied species. 17 closely related species with low interspecific genetic distances were observed, for which further study is proposed. It should also be noted that, in four cases, cryptic diversity was observed, where groups originally identified as one species exhibited genetic distance great enough to be separated into discrete species. Region specific haplotypes were also detected within populations of 14 species, giving the possibility to identify even the geographic origin of a species. Our findings are discussed in the light of the rich history of the Balkan peninsula and provide a significant steppingstone for the further study of Greek and European freshwater fish biodiversity.
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Affiliation(s)
- Alexandros Tsoupas
- Faculty of Sciences, Department of Genetics, Development and Molecular Biology, Laboratory of Animal Population Genetics, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Sofia Papavasileiou
- Faculty of Sciences, Department of Genetics, Development and Molecular Biology, Laboratory of Animal Population Genetics, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Styliani Minoudi
- Faculty of Sciences, Department of Genetics, Development and Molecular Biology, Laboratory of Animal Population Genetics, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
- Bioanalysis and Omics (BIOMIC), Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, Thessaloniki, Greece
| | - Konstantinos Gkagkavouzis
- Faculty of Sciences, Department of Genetics, Development and Molecular Biology, Laboratory of Animal Population Genetics, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
- Bioanalysis and Omics (BIOMIC), Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, Thessaloniki, Greece
| | - Olga Petriki
- Faculty of Sciences, Department of Zoology, Laboratory of Ichthyology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Dimitra Bobori
- Faculty of Sciences, Department of Zoology, Laboratory of Ichthyology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
- * E-mail: (DB); (AT)
| | - Argyrios Sapounidis
- Department of Inland Waters and Lagoons, Fisheries Research Institute, Hellenic Agricultural Organization “DEMETER”, Nea Peramos, Kavala, Greece
| | - Emmanouil Koutrakis
- Department of Inland Waters and Lagoons, Fisheries Research Institute, Hellenic Agricultural Organization “DEMETER”, Nea Peramos, Kavala, Greece
| | - Ioannis Leonardos
- Department of Biological Applications and Technologies, Laboratory of Zoology, School of Health Sciences, University of Ioannina, Ioannina, Greece
| | - Nikoleta Karaiskou
- Faculty of Sciences, Department of Genetics, Development and Molecular Biology, Laboratory of Animal Population Genetics, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
- Bioanalysis and Omics (BIOMIC), Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, Thessaloniki, Greece
| | - Alexandros Triantafyllidis
- Faculty of Sciences, Department of Genetics, Development and Molecular Biology, Laboratory of Animal Population Genetics, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
- Bioanalysis and Omics (BIOMIC), Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, Thessaloniki, Greece
- * E-mail: (DB); (AT)
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DNA barcoding reveals cryptic diversity in the underestimated genus Triplophysa (Cypriniformes: Cobitidae, Nemacheilinae) from the northeastern Qinghai-Tibet Plateau. BMC Evol Biol 2020; 20:151. [PMID: 33183225 PMCID: PMC7663858 DOI: 10.1186/s12862-020-01718-0] [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: 07/06/2020] [Accepted: 11/04/2020] [Indexed: 01/12/2023] Open
Abstract
Background The northeastern part of the Qinghai-Tibet Plateau (QTP) presents a high number of plateau loach species. As one of the three major groups of fishes distributed on the QTP, plateau loach has high ecological value. However, the taxonomy and systematics of these fish are still controversial, and a large number of new species have been reported. The reason for this phenomenon is that the degree of morphological variation is low, the phylogenetic information provided by morphological and anatomical features used for species identification is relatively poor, and many cryptic species are observed. Based on the high-density sampling points from the biodiversity hotspots surveyed, this study aims to evaluate the biodiversity of plateau loach in the northeastern part of the QTP and reveal the hidden diversity by comparing morphological species with molecular operational taxonomic units (MOTUs). Results After careful identification and comparison of the morphology and DNA barcoding of 1630 specimens, 22 species were identified, with 20 considered valid local species and two identified as new species that had not been previously described. Based on the combination of morphological and molecular methods, a total of 24 native species were found, two of which were cryptic species: Triplophysa robusta sp1 and Triplophysa minxianensis sp1. Fourteen of the 24 species form clusters of barcodes that allow them to be reliably identified. The remaining cases involved 10 closely related species, including rapidly differentiated species and species that seemed to have experienced incomplete lineage sorting or showed introgressions. Conclusions The results highlight the need to combine traditional taxonomies with molecular methods to correctly identify species, especially closely related species, such as the plateau loach. This study provides a basis for protecting the biodiversity of plateau loach.
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Evolution of Sri Lanka’s Giant Danios (Teleostei: Cyprinidae: Devario): Teasing apart species in a recent diversification. Mol Phylogenet Evol 2020; 149:106853. [DOI: 10.1016/j.ympev.2020.106853] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 05/05/2020] [Accepted: 05/11/2020] [Indexed: 11/24/2022]
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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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Gu Z, Yang LE, Chen Z, Chen W. Comparative analysis of different DNA barcodes for applications in the identification and production of Pyropia. ALGAL RES 2020. [DOI: 10.1016/j.algal.2020.101874] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Sharpe AE, Inomata T, Triadan D, Burham M, MacLellan J, Munson J, Pinzón F. The Maya Preclassic to Classic transition observed through faunal trends from Ceibal, Guatemala. PLoS One 2020; 15:e0230892. [PMID: 32255773 PMCID: PMC7138325 DOI: 10.1371/journal.pone.0230892] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 03/10/2020] [Indexed: 12/02/2022] Open
Abstract
It is well known that the development of the ancient Maya civilization had significant and long-lasting impacts on the environment. This study assesses a large collection of faunal remains (>35,000 specimens) recovered over a span of several kilometers in and around the archaeological site of Ceibal, Guatemala, in order to determine whether the composition of animal resources was continuous throughout the site’s history between 1000 BC and AD 1200, or whether there were any changes that could be attributed to sociopolitical or environmental causes. Results show a steep uniform decline in the number of freshwater mollusks across the site that occurred during the Preclassic to Classic transition, when large region-wide political changes, including the development of more complex and centralized political organization, took place throughout the Maya region. Evidence of species introductions (e.g., turkeys from central Mexico and possibly the Dermatemys river turtle from the Isthmus of Tehuantepec) and variations in resource exchange (e.g. marine shells) over time indicate that Ceibal was one of likely many communities involved in long-distance animal exchange networks. The results of the faunal analysis at Ceibal show how the ancient Maya had a complex and ever-changing relationship with the local wildlife, with outcomes that can still be observed in the environment today.
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Affiliation(s)
- Ashley E. Sharpe
- Center for Tropical Paleoecology and Archaeology, Smithsonian Tropical Research Institute, Balboa-Ancón, Republic of Panama
- * E-mail:
| | - Takeshi Inomata
- School of Anthropology, University of Arizona, Tucson, Arizona, United States of America
| | - Daniela Triadan
- School of Anthropology, University of Arizona, Tucson, Arizona, United States of America
| | - Melissa Burham
- School of Anthropology, University of Arizona, Tucson, Arizona, United States of America
| | - Jessica MacLellan
- Department of Anthropology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Jessica Munson
- Department of Sociology-Anthropology, Lycoming College, Williamsport, Pennsylvania, United States of America
| | - Flory Pinzón
- Museo Regional de Arqueología la Democracia, Ministerio de Cultura y Deportes de Guatemala, Escuintla, Republic of Guatemala
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Thu PT, Huang WC, Chou TK, Van Quan N, Van Chien P, Li F, Shao KT, Liao TY. DNA barcoding of coastal ray-finned fishes in Vietnam. PLoS One 2019; 14:e0222631. [PMID: 31536551 PMCID: PMC6752846 DOI: 10.1371/journal.pone.0222631] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 09/04/2019] [Indexed: 11/19/2022] Open
Abstract
DNA barcoding based on a fragment of the cytochrome c oxidase subunit I (COI) gene is widely applied in species identification and biodiversity studies. The aim of this study was to establish a comprehensive barcoding database of coastal ray-finned fishes in Vietnam. A total of 3,638 specimens were collected from fish landing sites in northern, central and southern Vietnam. Seven hundred and sixty-five COI sequences of ray-finned fishes were generated, belonging to 458 species, 273 genera, 113 families and 43 orders. A total of 59 species were newly recorded in Vietnam and sequences of six species were new to the Genbank and BOLD online databases. Only 32 species cannot be annotated to species level because difficulty in morphological identifications and their Kimura-2-Parameter (K2P) genetic distances to most similar sequences were more than 2%. Moreover, intra-specific genetic distances in some species are also higher than 2%, implying the existence of putative cryptic species. The mean K2P genetic distances within species, genera, families, orders and classes were 0.34%, 12.14%, 17.39%, 21.42%, and 24.80, respectively. Species compositions are quite different with only 16 common species among northern, central and southern Vietnam. This may attribute to multiple habitats and environmental factors across the 3,260 km Vietnamese coastline. Our results confirmed that DNA barcoding is an efficient and reliable tool for coastal fish identification in Vietnam, and also established a reliable DNA barcode reference library for these fishes. DNA barcodes will contribute to future efforts to achieve better monitoring, conservation, and management of fisheries in Vietnam.
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Affiliation(s)
- Pham The Thu
- Institute of Marine Environment and Resources, Vietnam Academy of Science and Technology, Hai Phong, Vietnam
| | - Wen-Chien Huang
- Doctoral Degree Program in Marine Biotechnology, National Sun Yat-sen University, Kaohsiung, Taiwan
- Doctoral Degree Program in Marine Biotechnology, Academia Sinica, Taipei, Taiwan
- Department of Oceanography, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Tak-Kei Chou
- Department of Oceanography, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Nguyen Van Quan
- Institute of Marine Environment and Resources, Vietnam Academy of Science and Technology, Hai Phong, Vietnam
| | - Pham Van Chien
- Institute of Marine Environment and Resources, Vietnam Academy of Science and Technology, Hai Phong, Vietnam
| | - Fan Li
- Department of Oceanography, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Kwang-Tsao Shao
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Institute of Marine Biology, National Taiwan Ocean University, Keelung, Taiwan
| | - Te-Yu Liao
- Department of Oceanography, National Sun Yat-sen University, Kaohsiung, Taiwan
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Arroyave J, Martinez CM, Stiassny MLJ. DNA barcoding uncovers extensive cryptic diversity in the African long-fin tetra Bryconalestes longipinnis (Alestidae: Characiformes). JOURNAL OF FISH BIOLOGY 2019; 95:379-392. [PMID: 31001832 DOI: 10.1111/jfb.13987] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 04/17/2019] [Indexed: 06/09/2023]
Abstract
To investigate the presence of cryptic diversity in the African longfin-tetra Bryconalestes longipinnis, we employed DNA barcoding in a phylogeographic context, as well as geometric morphometrics, documenting for the first time genetic and body shape variation in the species. Analysis of cytochrome oxidase I gene (coI) sequence variation exposed extremely high levels of genetic differentiation among samples from across the geographic range of the species (up to 18%), certainly much greater than the traditionally employed c. 3% sequence divergence heuristic threshold for conspecifics. Phylogeographic analyses of coI data revealed eight clusters/clades that diverge by >4% and up to 18% (p-distance), potentially representing cryptic members of a species complex. A clear biogeographic pattern was also uncovered, in which the two main coI lineages corresponded geographically with the upper Guinea (UG) and lower Guinea (LG) ichthyofaunal provinces of continental Africa, respectively. Within each of these main lineages, however, no apparent phylogeographic structuring was found. Despite strong genetic differentiation, there is considerable overlap in body shape variation between UG and LG populations. For the most part, morphological variation does not match the strength of the molecular phylogeographic signal. Therefore, the ability to reliably utilise external body shape for regional delimitation remains elusive. Further anatomical investigation appears necessary to establish whether compelling diagnostic morphological features do exist between the divergent lineages of the B. longipinnis complex uncovered in this study.
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Affiliation(s)
- Jairo Arroyave
- Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, México
- Department of Ichthyology, American Museum of Natural History, New York, New York, USA
| | | | - Melanie L J Stiassny
- Department of Ichthyology, American Museum of Natural History, New York, New York, USA
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Valdez-Moreno M, Ivanova NV, Elías-Gutiérrez M, Pedersen SL, Bessonov K, Hebert PDN. Using eDNA to biomonitor the fish community in a tropical oligotrophic lake. PLoS One 2019; 14:e0215505. [PMID: 31009491 PMCID: PMC6476559 DOI: 10.1371/journal.pone.0215505] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 04/04/2019] [Indexed: 12/14/2022] Open
Abstract
Environmental DNA (eDNA) is an effective approach for detecting vertebrates and plants, especially in aquatic ecosystems, but prior studies have largely examined eDNA in cool temperate settings. By contrast, this study employs eDNA to survey the fish fauna in tropical Lake Bacalar (Mexico) with the additional goal of assessing the possible presence of invasive fishes, such as Amazon sailfin catfish and tilapia. Sediment and water samples were collected from eight stations in Lake Bacalar on three occasions over a 4-month interval. Each sample was stored in the presence or absence of lysis buffer to compare eDNA recovery. Short fragments (184–187 bp) of the cytochrome c oxidase I (COI) gene were amplified using fusion primers and then sequenced on Ion Torrent PGM or S5 before their source species were determined using a custom reference sequence database constructed on BOLD. In total, eDNA sequences were recovered from 75 species of vertebrates including 47 fishes, 15 birds, 7 mammals, 5 reptiles, and 1 amphibian. Although all species are known from this region, six fish species represent new records for the study area, while two require verification. Sequences for five species (2 birds, 2 mammals, 1 reptile) were only detected from sediments, while sequences from 52 species were only recovered from water. Because DNA from the Amazon sailfin catfish was not detected, we used a mock eDNA experiment to confirm our methods would enable its detection. In summary, we developed protocols that recovered eDNA from tropical oligotrophic aquatic ecosystems and confirmed their effectiveness in detecting fishes and diverse species of vertebrates.
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Affiliation(s)
| | - Natalia V. Ivanova
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, ON, Canada
- * E-mail:
| | | | - Stephanie L. Pedersen
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, ON, Canada
| | - Kyrylo Bessonov
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, ON, Canada
| | - Paul D. N. Hebert
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, ON, Canada
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de Borba RS, Mariotto S, Centofante L, Henrique Zawadzki C, Pasquali Parise-Maltempi P. Molecular discrimination of Ancistrus lineages (Siluriformes: Loricariidae) using barcode DNA tool. Mitochondrial DNA A DNA Mapp Seq Anal 2019; 30:602-608. [PMID: 30983442 DOI: 10.1080/24701394.2019.1597071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Although several species of Ancistrus have been described from the Amazon and Paraguay river basins in the states of Amazonas and Mato Grosso, Brazil, the taxonomic status of most specimens from these regions remains doubtful. In the present work, cytogenetic and molecular data were used to discriminate and isolate unexpected Ancistrus lineages from the Amazon and Paraguay basins. For that, it was used DNA barcoding based on mitochondrial Cytochrome Oxidase Subunit I (COI) gene and cytogenic data to perform such molecular discrimination. The analyzed sequences had 669 bp, of which 171 bp were conserved and 491 bp were variable. The Neighbor-joining and Bayesian analysis revealed 21 distinct groups in topology. The genetic distances within each group was 0.4%, 21 times smaller than the mean distance observed among groups, which was 8.4%. These values showed seven distinct lineages of Ancistrus from the studied points of the Amazon basin and eight lineages from the Paraguay basin points. Our results illustrate the efficiency of this technique for the discrimination of the Ancistrus lineages once it indicates the occurrence of cryptic species in these regions, which cannot yet be identified either with just chromosomal or morphological analyzes.
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Affiliation(s)
| | | | - Liano Centofante
- c Institute of Biosciences, Mato Grosso Federal University , Cuiabá , Brazil
| | - Claudio Henrique Zawadzki
- d Department of Biology, Center for Research in Limnology, Ichthyology and Aquaculture (Nupélia), Maringá State University , Paraná , Brazil
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Barreto SB, Silva AT, Batalha-Filho H, Affonso PRAM, Zanata AM. Integrative approach reveals a new species of Nematocharax (Teleostei: Characidae). JOURNAL OF FISH BIOLOGY 2018; 93:1151-1162. [PMID: 30306564 DOI: 10.1111/jfb.13834] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Accepted: 10/02/2018] [Indexed: 06/08/2023]
Abstract
An integrative approach based on morphological and multilocus genetic data was used to describe a new species of Nematocharax from the headwaters of the upper Contas River on the Diamantina Plateau, north-eastern Brazil and to infer the relationships among evolutionary lineages within this fish genus. Multispecies coalescent inference using three mitochondrial and five nuclear loci strongly supports a basal split between Nematocharax venustus and the new species, whose distinctive morphological characters include absence of filamentous rays on pelvic fins of maturing and mature males, reduced anal-fin lobe length and lower body depth. The unique morphological and genetic traits of the population from the upper Contas River were supported by previous reports based on cytogenetics, DNA barcode and geometric morphometrics, reinforcing the validation of the new species. The conservation status of this new species is discussed.
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Affiliation(s)
- Silvia B Barreto
- National Institute of Science and Technology in Interdisciplinary and Transdisciplinary Studies in Ecology and Evolution (INCT IN-TREE), Instituto de Biologia, Universidade Federal da Bahia, Salvador, Brazil
| | - André T Silva
- Departamento de Ciências Biológicas, Universidade Estadual do Sudoeste da Bahia, Jequié, Brazil
| | - Henrique Batalha-Filho
- National Institute of Science and Technology in Interdisciplinary and Transdisciplinary Studies in Ecology and Evolution (INCT IN-TREE), Instituto de Biologia, Universidade Federal da Bahia, Salvador, Brazil
| | | | - Angela M Zanata
- Instituto de Biologia, Universidade Federal da Bahia, Salvador, Brazil
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Sales NG, Mariani S, Salvador GN, Pessali TC, Carvalho DC. Hidden Diversity Hampers Conservation Efforts in a Highly Impacted Neotropical River System. Front Genet 2018; 9:271. [PMID: 30087693 PMCID: PMC6066647 DOI: 10.3389/fgene.2018.00271] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 07/03/2018] [Indexed: 11/13/2022] Open
Abstract
Neotropical Rivers host a highly diverse ichthyofauna, but taxonomic uncertainty prevents appropriate conservation measures. The Doce River Basin (DRB), lying within two Brazilian threatened hotspots (Atlantic Forest and Brazilian Savanna) in south-east Brazil, faced the worst ever environmental accident reported for South American catchments, due to a dam collapse that spread toxic mining tailings along the course of its main river. Its ichthyofauna was known to comprise 71 native freshwater fish species, of which 13 endemic. Here, we build a DNA barcode library for the DRB ichthyofauna, using samples obtained before the 2015 mining disaster, in order to provide a more robust biodiversity record for this basin, as a baseline for future management actions. Throughout the whole DRB, we obtained a total of 306 barcodes, assigned to 69 putative species (with a mean of 4.54 barcodes per species), belonging to 45 genera, 18 families, and 5 orders. Average genetic distances within species, genus, and families were 2.59, 11.4, and 20.5%, respectively. The 69 species identified represent over 76% of the known DRB ichthyofauna, comprising 43 native (five endemic, of which three threatened by extinction), 13 already known introduced species, and 13 unknown species (such as Characidium sp., Neoplecostomus sp., and specimens identified only at the sub-family level Neoplecostominae, according to morphological identification provided by the museum collections). Over one fifth of all analyzed species (N = 16) had a mean intraspecific genetic divergence higher than 2%. An integrative approach, combining NND (nearest neighbor distance), BIN (barcode index number), ABGD (automatic barcode gap discovery), and bPTP (Bayesian Poisson Tree Processes model) analyses, suggested the occurrence of potential cryptic species, species complex, or historical errors in morphological identification. The evidence presented calls for a more robust, DNA-assisted cataloging of biodiversity-rich ecosystems, in order to enable effective monitoring and informed actions to preserve and restore these delicate habitats.
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Affiliation(s)
- Naiara G Sales
- Ecosystems and Environment Research Centre, School of Environment & Life Sciences, University of Salford, Salford, United Kingdom
| | - Stefano Mariani
- Ecosystems and Environment Research Centre, School of Environment & Life Sciences, University of Salford, Salford, United Kingdom
| | - Gilberto N Salvador
- Laboratório de Ecologia e Conservação, Universidade Federal do Pará, Belém, Brazil
| | - Tiago C Pessali
- Museu de Ciências Naturais PUC Minas, Pontifícia Universidade Católica de Minas Gerais, Belo Horizonte, Brazil
| | - Daniel C Carvalho
- Programa de Pós-graduação em Biologia de Vertebrados, Pontifícia Universidade Católica de Minas Gerais, Belo Horizonte, Brazil
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14
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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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15
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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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16
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Morais-Silva JP, Oliveira AVD, Fabrin TMC, Diamante NA, Prioli SMAP, Frota A, Graça WJD, Prioli AJ. Geomorphology Influencing the Diversification of Fish in Small-Order Rivers of Neighboring Basins. Zebrafish 2018; 15:389-397. [PMID: 29653071 DOI: 10.1089/zeb.2017.1551] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The current analysis investigates whether the uplift of the Serra da Esperança and the Ponta Grossa Arch in the Serra Geral resulted in ichthyofaunistic changes in adjacent basins. For this, we describe the phylogeographic structure among populations of Trichomycterus collected in hydrographic basins in southern Brazil by using partial nucleotide sequences of the mitochondrial gene Cytochrome C Oxidase subunit I. Analyses revealed that the nomenclature Trichomycterus davisi fails to contain the whole genetic diversity range found in the collected specimens and indicates at least six genetic lineages in Trichomycterus. Diagnostic morphological characteristics not associated to T. davisi could be identified in some specimens from the Iguaçu Piquiri haplogroup, indicating the occurrence of species Trichomycterus stawiarski. The lack of morphological differences among the other clades clearly suggests a cryptic species case. Molecular analyses revealed at least five new species besides T. davisi in the hydrographic basins and support the interpretation that genetic structure in T. davisi species complex is explained by tectonic events intrinsic to the areas of influence of Serra da Esperança and the Ponta Grossa Arch which occurred around 1.7 My.
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Affiliation(s)
- João P Morais-Silva
- 1 Programa de Pós-graduação em Biologia Comparada, Universidade Estadual de Maringá , Maringá, Brazil
| | - Alessandra V de Oliveira
- 2 Departamento de Biotecnologia, Genética e Biologia Celular, Universidade Estadual de Maringá , Maringá, Brazil .,3 Núcleo de Pesquisas em Limnologia, Ictiologia e Aquicultura (Nupélia), Universidade Estadual de Maringá , Maringá, Brazil
| | - Thomaz M C Fabrin
- 4 Programa de Pós-graduação em Ecologia de Ambientes Aquáticos Continentais, Universidade Estadual de Maringá , Maringá, Brazil
| | - Nathália Alves Diamante
- 1 Programa de Pós-graduação em Biologia Comparada, Universidade Estadual de Maringá , Maringá, Brazil
| | - Sônia M A P Prioli
- 2 Departamento de Biotecnologia, Genética e Biologia Celular, Universidade Estadual de Maringá , Maringá, Brazil .,3 Núcleo de Pesquisas em Limnologia, Ictiologia e Aquicultura (Nupélia), Universidade Estadual de Maringá , Maringá, Brazil
| | - Augusto Frota
- 4 Programa de Pós-graduação em Ecologia de Ambientes Aquáticos Continentais, Universidade Estadual de Maringá , Maringá, Brazil
| | - Weferson J da Graça
- 3 Núcleo de Pesquisas em Limnologia, Ictiologia e Aquicultura (Nupélia), Universidade Estadual de Maringá , Maringá, Brazil .,5 Departamento de Biologia, Universidade Estadual de Maringá , Maringá, Brazil
| | - Alberto J Prioli
- 3 Núcleo de Pesquisas em Limnologia, Ictiologia e Aquicultura (Nupélia), Universidade Estadual de Maringá , Maringá, Brazil
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17
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Pérez-Miranda F, Mejía O, Soto-Galera E, Espinosa-Pérez H, Piálek L, Říčan O. Phylogeny and species diversity of the genusHerichthys(Teleostei: Cichlidae). J ZOOL SYST EVOL RES 2017. [DOI: 10.1111/jzs.12197] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Fabian Pérez-Miranda
- Departamento de Zoología; Escuela Nacional de Ciencias Biológicas; Instituto Politécnico Nacional; Mexico City Mexico
| | - Omar Mejía
- Departamento de Zoología; Escuela Nacional de Ciencias Biológicas; Instituto Politécnico Nacional; Mexico City Mexico
| | - Eduardo Soto-Galera
- Departamento de Zoología; Escuela Nacional de Ciencias Biológicas; Instituto Politécnico Nacional; Mexico City Mexico
| | - Héctor Espinosa-Pérez
- Colección Nacional de Peces; Instituto de Biología; Universidad Nacional Autónoma s México; Mexico City Mexico
| | - Lubomír Piálek
- Department of Zoology; Faculty of Science; University of South Bohemia; České Budějovice Czech Republic
| | - Oldřich Říčan
- Department of Zoology; Faculty of Science; University of South Bohemia; České Budějovice Czech Republic
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18
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19
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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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20
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Rossini BC, Oliveira CAM, de Melo FAG, Bertaco VDA, de Astarloa JMD, Rosso JJ, Foresti F, Oliveira C. Highlighting Astyanax Species Diversity through DNA Barcoding. PLoS One 2016; 11:e0167203. [PMID: 27992537 PMCID: PMC5167228 DOI: 10.1371/journal.pone.0167203] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 11/10/2016] [Indexed: 11/18/2022] Open
Abstract
DNA barcoding has been used extensively to solve taxonomic questions and identify new species. Neotropical fishes are found in a wide variety of shapes and sizes, with a large number of species yet to be described, many of which are very difficult to identify. Characidae is the most species-rich family of the Characiformes, and many of its genera are affected by taxonomic uncertainties, including the widely-distributed, species-rich genus Astyanax. In this study, we present an extensive analysis of Astyanax covering almost its entire area of occurrence, based on DNA barcoding. The use of different approaches (ABGD, GMYC and BIN) to the clustering of the sequences revealed ample consistency in the results obtained by the initial cutoff value of 2% divergence for putative species in the Neighbor-Joining analysis using the Kimura-2-parameter model. The results indicate the existence of five Astyanax lineages. Some groups, such as that composed by the trans-Andean forms, are mostly composed of well-defined species, and in others a number of nominal species are clustered together, hampering the delimitation of species, which in many cases proved impossible. The results confirm the extreme complexity of the systematics of the genus Astyanax and show that DNA barcoding can be an useful tool to address these complexes questions.
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Affiliation(s)
- Bruno César Rossini
- Laboratório de Biologia e Genética de Peixes, Departamento de Morfologia, UNESP—Universidade Estadual Paulista, Botucatu, São Paulo, Brazil
- Instituto de Biotecnologia da UNESP, UNESP—Universidade Estadual Paulista, Botucatu, São Paulo, Brazil
- * E-mail:
| | - Carlos Alexandre Miranda Oliveira
- Universidade Estadual de Maringá, Programa de Pós-Graduação em Ecologia de Ambientes Aquáticos Continentais, Maringá, Paraná, Brazil
| | | | - Vinicius de Araújo Bertaco
- Museu de Ciências Naturais, Fundação Zoobotânica do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Juan M. Díaz de Astarloa
- Grupo de Biotaxonomía Morfológica y Molecular de Peces, Instituto de Investigaciones Marinas y Costeras, Universidad Nacional de Mar del Plata. Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Juan J. Rosso
- Grupo de Biotaxonomía Morfológica y Molecular de Peces, Instituto de Investigaciones Marinas y Costeras, Universidad Nacional de Mar del Plata. Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Fausto Foresti
- Laboratório de Biologia e Genética de Peixes, Departamento de Morfologia, UNESP—Universidade Estadual Paulista, Botucatu, São Paulo, Brazil
| | - Claudio Oliveira
- Laboratório de Biologia e Genética de Peixes, Departamento de Morfologia, UNESP—Universidade Estadual Paulista, Botucatu, São Paulo, Brazil
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Lim H, Zainal Abidin M, Pulungan CP, de Bruyn M, Mohd Nor SA. DNA Barcoding Reveals High Cryptic Diversity of the Freshwater Halfbeak Genus Hemirhamphodon from Sundaland. PLoS One 2016; 11:e0163596. [PMID: 27657915 PMCID: PMC5033453 DOI: 10.1371/journal.pone.0163596] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 09/12/2016] [Indexed: 11/18/2022] Open
Abstract
DNA barcoding of the cytochrome oxidase subunit I (COI) gene was utilized to assess the species diversity of the freshwater halfbeak genus Hemirhamphodon. A total of 201 individuals from 46 locations in Peninsular Malaysia, north Borneo (Sarawak) and Sumatra were successfully amplified for 616 base pairs of the COI gene revealing 231 variable and 213 parsimony informative sites. COI gene trees showed that most recognized species form monophyletic clades with high bootstrap support. Pairwise within species comparisons exhibited a wide range of intraspecific diversity from 0.0% to 14.8%, suggesting presence of cryptic diversity. This finding was further supported by barcode gap analysis, ABGD and the constructed COI gene trees. In particular, H. pogonognathus from Kelantan (northeast Peninsular Malaysia) diverged from the other H. pogonognathus groups with distances ranging from 7.8 to 11.8%, exceeding the nearest neighbor taxon. High intraspecific diversity was also observed in H. byssus and H. kuekanthali, but of a lower magnitude. This study also provides insights into endemism and phylogeographic structuring, and limited support for the Paleo-drainage divergence hypothesis as a driver of speciation in the genus Hemirhamphodon.
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Affiliation(s)
- HongChiun Lim
- School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia
- School of Biological Sciences, Faculty of Integrative Sciences and Technology, Quest International University Perak, Ipoh, Perak, Malaysia
- * E-mail:
| | - Muchlisin Zainal Abidin
- Department of Aquaculture, Faculty of Marine and Fisheries, Syiah Kuala University, Banda Aceh, Indonesia
| | - Chaidir Parlindungan Pulungan
- Department of Aquatic Resources Management, Faculty of Fisheries and Marine Science, Riau University, Pekanbaru, Indonesia
| | - Mark de Bruyn
- School of Biological Sciences, Bangor University, Bangor, United Kingdom
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Siti Azizah Mohd Nor
- School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia
- Centre for Marine and Coastal Studies, Universiti Sains Malaysia, Penang, Malaysia
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22
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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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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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24
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Yan S, Lai G, Li L, Xiao H, Zhao M, Wang M. DNA barcoding reveals mislabeling of imported fish products in Nansha new port of Guangzhou, Guangdong province, China. Food Chem 2016; 202:116-9. [PMID: 26920274 DOI: 10.1016/j.foodchem.2016.01.133] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Revised: 01/23/2016] [Accepted: 01/29/2016] [Indexed: 11/20/2022]
Abstract
In the present study, we employed a DNA barcoding approach to authenticate the species of fish imported via one port in China. The fish were identified as smallmouth scad based on morphological characteristics, Alepes apercna (Perciformes, Carangidae), but were labeled as Rastrelliger brachysoma (Perciformes, Scombridae). Fragments of the partial mitochondrial cytochrome c oxidase 1 (COI) gene were sequenced from 12 specimens, and their phylogenetic relationship was subsequently examined. The phylogenetic analysis demonstrated that all of the individuals formed a monophyletic cluster with high bootstrap values and were placed in a sister group with the ancestor of Alepes vari and Alepes melanoptera. The K2P genetic distances at an intraspecific level were significantly smaller than those at an interspecific level. Our results indicated that the fish were A. apercna, rather than R. brachysoma, which confirms the morphological analysis. This study presents a practical demonstration of the use of DNA barcoding to prevent fraud in international trade.
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Affiliation(s)
- Shuai Yan
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, PR China
| | - Guiyan Lai
- Nansha Entry-Exit Inspection and Quarantine Bureau, Guangzhou 511457, PR China
| | - Li Li
- Nansha Entry-Exit Inspection and Quarantine Bureau, Guangzhou 511457, PR China
| | - Hao Xiao
- Nansha Entry-Exit Inspection and Quarantine Bureau, Guangzhou 511457, PR China
| | - Ming Zhao
- Nansha Entry-Exit Inspection and Quarantine Bureau, Guangzhou 511457, PR China
| | - Ming Wang
- Nansha Entry-Exit Inspection and Quarantine Bureau, Guangzhou 511457, PR China; Guangdong Institute of Standardization, Guangzhou 510220, PR China.
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Ahmed MI, Sabrah MM, Heneish RA, El-Alwany M. DNA Barcoding Uncover Cryptic Diversity in Goat Fishes (Family: Mullidae) Across the Egyptian Coastal Waters. Pak J Biol Sci 2016; 19:65-70. [PMID: 29023041 DOI: 10.3923/pjbs.2016.65.70] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Despite ongoing efforts to protect species and ecosystems in the egyptian costs of the Red Sea and Mediterranean Sea, habitat degradation, overfishing and pollution have posed serious challenges to marine natural resources. In spite of the accumulated knowledge on the systematics of commercial fishes in Egypt recent results suggested that we are far from having a complete picture of egyptian fish diversity. The accurate identification of species is a very important component in many fields of biological research and conservation efforts. The high level of expertise and time consuming process needed means a loss in biodiversity. Successful species identification is now frequently based on a combination of approaches including morphometrics and the sequencing of the mitochondrial COI gene known as the DNA barcoding. This study employed COI sequencing alongside traditional taxonomic identification methods and uncovered cryptic diversity within the goat fish species of Family Mullidae, four species collected from both the Red Sea and the Mediterranean Sea. Upeneus pori, Upeneus vittatus, Mullus surmuletus and Mullus barbatus samples from the Red Sea and the Mediterranean were clustered separately in a NJ tree indicating the possibility of the presence of cryptic species complex. All species could be differentiated by their COI sequence.
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Affiliation(s)
- Mohammed I Ahmed
- Department of Marine Science, Faculty of Science, Suez Canal University, Ismailia, Egypt
| | - Manal M Sabrah
- Department of Fisheries, National Institute of Oceanography and Fisheries (NIOF), Suez, Egypt
| | - Rasha A Heneish
- Department of Fisheries, National Institute of Oceanography and Fisheries (NIOF), Suez, Egypt
| | - Magdy El-Alwany
- Department of Marine Science, Faculty of Science, Suez Canal University, Ismailia, Egypt
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Lakra WS, Singh M, Goswami M, Gopalakrishnan A, Lal KK, Mohindra V, Sarkar UK, Punia PP, Singh KV, Bhatt JP, Ayyappan S. DNA barcoding Indian freshwater fishes. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4510-4517. [PMID: 26703324 DOI: 10.3109/19401736.2015.1101540] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
DNA barcoding is a promising technique for species identification using a short mitochondrial DNA sequence of cytochrome c oxidase I (COI) gene. In the present study, DNA barcodes were generated from 72 species of freshwater fish covering the Orders Cypriniformes, Siluriformes, Perciformes, Synbranchiformes, and Osteoglossiformes representing 50 genera and 19 families. All the samples were collected from diverse sites except the species endemic to a particular location. Species were represented by multiple specimens in the great majority of the barcoded species. A total of 284 COI sequences were generated. After amplification and sequencing of 700 base pair fragment of COI, primers were trimmed which invariably generated a 655 base pair barcode sequence. The average Kimura two-parameter (K2P) distances within-species, genera, families, and orders were 0.40%, 9.60%, 13.10%, and 17.16%, respectively. DNA barcode discriminated congeneric species without any confusion. The study strongly validated the efficiency of COI as an ideal marker for DNA barcoding of Indian freshwater fishes.
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Affiliation(s)
- Wazir Singh Lakra
- a Central Institute of Fisheries Education , Versova , Mumbai , India
| | - M Singh
- b National Bureau of Fish Genetic Resources , Lucknow , India
| | - Mukunda Goswami
- a Central Institute of Fisheries Education , Versova , Mumbai , India
| | | | - K K Lal
- b National Bureau of Fish Genetic Resources , Lucknow , India
| | - V Mohindra
- b National Bureau of Fish Genetic Resources , Lucknow , India
| | - U K Sarkar
- b National Bureau of Fish Genetic Resources , Lucknow , India
| | - P P Punia
- b National Bureau of Fish Genetic Resources , Lucknow , India
| | - K V Singh
- b National Bureau of Fish Genetic Resources , Lucknow , India
| | - J P Bhatt
- c Department of Zoology and Biotechnology , HNB Garhwal University , Uttarakhand , India , and
| | - S Ayyappan
- d Indian Council of Agricultural Research , New Delhi , India
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Bashir A, Bisht BS, Mir JI, Patiyal RS, Kumar R. Morphometric variation and molecular characterization of snow trout species from Kashmir valley, India. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4492-4497. [PMID: 26486012 DOI: 10.3109/19401736.2015.1101537] [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
There is a significant taxonomic ambiguity among snow trout species due to their morphometric similarities. In view of this, a morphometric and molecular study was conducted on five different species of genus Schizothorax that have been reported from Kashmir valley. Morphometric data analyzed using multivariate statistics (Principal component analysis and cluster analysis) indicated the significant grouping of species to individual clusters. Mitochondrial DNA cytochrome oxidase I (COI) gene analysis revealed 0.2%-4.5% genetic divergence among the five species. This study confirms that utility of cytochrome oxidase I in species delineation along with morphometric data. Phylogenetic tree obtained using Neighbor-Joining method revealed that all the five species represented distinct species group. The Schizothorax genus formed two distinct clades; one containing S. niger, S. curvifrons and S. plagiostomus, while other clade containing S. esocinus and S. labiatus. This phlogeny trend was also supported by cluster analysis of morphometric characters. The phylogenetic analysis with other published COI sequences revealed distinct nature of these five species. The study may aid in the taxonomic identification of snow trout species in India. This may further increase the knowledge of the ichthyologists in planning conservation and management strategies for these important fish species along with their natural habitat.
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Affiliation(s)
- Amir Bashir
- a Department of Zoology , Badshahithaul Campus, HNB Garhwal University , Tehri Garhwal , Uttarakhand , India and
| | - Balwant Singh Bisht
- a Department of Zoology , Badshahithaul Campus, HNB Garhwal University , Tehri Garhwal , Uttarakhand , India and
| | - Javaid Iqbal Mir
- b Directorate of Coldwater Fisheries Research, Anusandhan Bhawan , Bhimtal , Uttarakhand , India
| | - Rabindar Singh Patiyal
- b Directorate of Coldwater Fisheries Research, Anusandhan Bhawan , Bhimtal , Uttarakhand , India
| | - Rohit Kumar
- b Directorate of Coldwater Fisheries Research, Anusandhan Bhawan , Bhimtal , Uttarakhand , India
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Muhammad Tahir H, Akhtar S. Services of DNA barcoding in different fields. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4463-4474. [DOI: 10.3109/19401736.2015.1089572] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
| | - Samreen Akhtar
- Department of Zoology, University of Sargodha, Sargodha, Pakistan
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Maranan JBD, Basiao ZU, Quilang JP. DNA barcoding of feral tilapias in Philippine lakes. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4302-4313. [PMID: 26457820 DOI: 10.3109/19401736.2015.1089478] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Tilapia (Oreochromis mossambicus) was first introduced to the Philippines in 1950 for aquaculture. Since then, other species of tilapia have been introduced to the country and some of them (mainly Oreochromis niloticus) have become established in lakes and other water bodies. In this study, DNA barcoding using the mitochondrial cytochrome c oxidase subunit I (COI) gene was done to assess the reliability of morphological identification and the degree of introgression among feral tilapias (Oreochromis spp.) in seven major Philippine lakes, namely Laguna de Bay, Lake Lanao, Taal Lake, Lake Mainit, Lake Naujan, Lake Bato, and Lake Buhi. Specimens were also collected from a private hatchery in Sual, Pangasinan to serve as reference. Morphological traits, Nucleotide BLAST (BLASTn), and Translated BLAST (BLASTx) analyses were used to classify the specimens. A Neighbor-Joining tree was constructed using the Kimura 2-Parameter method, incorporating 66 COI sequences generated from the study and 20 additional reference sequences obtained from GenBank. Three Oreochromis clusters were obtained and were classified as the O. niloticus group, O. mossambicus group, and O. aureus group, with bootstrap support values of 99%, 74%, and 99%, respectively. The mean K2P genetic distances within each group were 0.008%, 0.959%, and 0.086%, respectively. The clustering of COI sequences generated from this study corresponded with the results of the BLASTn analysis. Oreochromis hybrids were also found in all the lakes. The study highlights the usefulness of DNA barcoding for molecular identification and detection of introgressed individuals, with potential applications in management of feral stocks.
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Affiliation(s)
- Justin Bryan D Maranan
- a Molecular Population Genetics Laboratory, Institute of Biology, College of Science, University of the Philippines , Diliman , Quezon City , Philippines
| | - Zubaida U Basiao
- a Molecular Population Genetics Laboratory, Institute of Biology, College of Science, University of the Philippines , Diliman , Quezon City , Philippines
| | - Jonas P Quilang
- a Molecular Population Genetics Laboratory, Institute of Biology, College of Science, University of the Philippines , Diliman , Quezon City , Philippines
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Mejía O, Pérez-Miranda F, León-Romero Y, Soto-Galera E, Luna ED. Morphometric variation of the Herichthys bartoni (Bean, 1892) species group (Teleostei: Cichlidae): How many species comprise H. labridens (Pellegrin, 1903)? NEOTROPICAL ICHTHYOLOGY 2015. [DOI: 10.1590/1982-0224-20140067] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cichlids of the tribe Heroini have long been a source of taxonomical conflict. In particular, the species included in the Herichthys bartoni group have failed to be recovered as monophyletic in different molecular studies. In this paper we use traditional and geometric morphometrics to evaluate morphological variation in the species included in the H. bartoni complex in order to evaluate the number of species it contains. An update of a previously published DNA barcoding study suggests the existence of three genetic clusters that included the six recognized species analyzed in this study, none of them recovered as monophyletic. On the other hand, geometric morphometrics arise as a useful tool to discriminate species due that traditional morphometrics showed a high overlap in the characters analyzed that prevents the proposal of diagnostic characters.
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Frantine-Silva W, Sofia SH, Orsi ML, Almeida FS. DNA barcoding of freshwater ichthyoplankton in the Neotropics as a tool for ecological monitoring. Mol Ecol Resour 2015; 15:1226-37. [PMID: 25655460 DOI: 10.1111/1755-0998.12385] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 01/30/2015] [Accepted: 02/02/2015] [Indexed: 11/26/2022]
Abstract
Quantifying and classifying ichthyoplankton is one of the most effective ways of monitoring the recruitment process in fishes. However, correctly identifying the fish based on morphological characters is extremely difficult, especially in the early stages of development. We examined ichthyoplankton from tributaries and reservoirs along the middle stretch of the Paranapanema River, one of the areas most impacted by hydroelectric projects in the Neotropics. Matching DNA sequences of the COI gene (628-648 bp) allowed us to identify 99.25% of 536 samples of eggs (293) and larvae (243) subjected to BOLD-IDS similarity analysis with a species-level threshold of 1.3%. The results revealed 37 species in 27 genera, 15 families and four orders, some 23.8% of documented fish species in the Paranapanema River. Molecular identification meant that we could include data from egg samples that accounted for about 30% of the species richness observed. The results in this study confirm the efficacy of DNA barcoding in identifying Neotropical ichthyoplankton and show how the data produced provide valuable information for preparing plans for conserving and managing inland waters.
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Affiliation(s)
- W Frantine-Silva
- Departamento de Biologia Geral, Universidade Estadual de Londrina, Centro de Ciências Biológicas, Campus Universitário, Rodovia Celso Garcia Cid, PR 445 km 380, 86057-970, Londrina-PR, Brasil
| | - S H Sofia
- Departamento de Biologia Geral, Universidade Estadual de Londrina, Centro de Ciências Biológicas, Campus Universitário, Rodovia Celso Garcia Cid, PR 445 km 380, 86057-970, Londrina-PR, Brasil
| | - M L Orsi
- Departamento de Biologia Animal e Vegetal, Universidade Estadual de Londrina, Centro de Ciências Biológicas, Campus Universitário, Rodovia Celso Garcia Cid, PR 445 km 380, 86057-970, Londrina-PR, Brasil
| | - F S Almeida
- Departamento de Biologia Geral, Universidade Estadual de Londrina, Centro de Ciências Biológicas, Campus Universitário, Rodovia Celso Garcia Cid, PR 445 km 380, 86057-970, Londrina-PR, Brasil
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Benzaquem DC, Oliveira C, da Silva Batista J, Zuanon J, Porto JIR. DNA barcoding in pencilfishes (Lebiasinidae: Nannostomus) reveals cryptic diversity across the Brazilian Amazon. PLoS One 2015; 10:e0112217. [PMID: 25658694 PMCID: PMC4320009 DOI: 10.1371/journal.pone.0112217] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Accepted: 10/11/2014] [Indexed: 11/24/2022] Open
Abstract
Nannostomus is comprised of 20 species. Popularly known as pencilfishes the vast majority of these species lives in the flooded forests of the Amazon basin and are popular in the ornamental trade. Among the lebiasinids, it is the only genus to have undergone more than one taxonomic revision. Even so, it still possesses poorly defined species. Here, we report the results of an application of DNA barcoding to the identification of pencilfishes and highlight the deeply divergent clades within four nominal species. We surveyed the sequence variation in the mtDNA cytochrome c oxidase subunit I gene among 110 individuals representing 14 nominal species that were collected from several rivers along the Amazon basin. The mean Kimura-2-parameter distances within species and genus were 2% and 19,0%, respectively. The deep lineage divergences detected in N. digrammus, N. trifasciatus, N. unifasciatus and N. eques suggest the existence of hidden diversity in Nannostomus species. For N. digrammus and N. trifasciatus, in particular, the estimated divergences in some lineages were so high that doubt about their conspecific status is raised.
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Affiliation(s)
- Denise Corrêa Benzaquem
- Laboratório de Genética Animal, Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo, 2.936, Petrópolis, CEP 69067-375, Manaus, AM, Brazil
| | - Claudio Oliveira
- Instituto de Biociências, Departamento de Morfologia, UNESP, CEP 18618-970 Botucatu, SP, Brazil
| | - Jaqueline da Silva Batista
- Laboratório de Fisiologia Comportamental e Evolução, Laboratório Temático de Biologia Molecular, Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo, 2.936, Petrópolis, CEP 69067-375, Manaus, AM, Brazil
| | - Jansen Zuanon
- Laboratório de Sistemática e Ecologia de Peixes, Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo, 2.936, Petrópolis, CEP 69067-375, Manaus, AM, Brazil
| | - Jorge Ivan Rebelo Porto
- Laboratório de Genética Animal, Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo, 2.936, Petrópolis, CEP 69067-375, Manaus, AM, Brazil
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Henriques JM, Silva GJC, Ashikaga FY, Hanner R, Foresti F, Oliveira C. Use of DNA barcode in the identification of fish species from Ribeira de Iguape Basin and coastal rivers from São Paulo State (Brazil). ACTA ACUST UNITED AC 2015. [DOI: 10.1515/dna-2015-0015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractSpecies identification is a difficult task, ranging from the definition of the species concept itself to the definition of the threshold for speciation. DNA Barcode technology uses a fragment of the Cytochrome Oxidase I (COI) gene as a molecular tool that many studies have already validated as a tool for species identification. DNA barcode sequences for COI were generated and analyzed from 805 specimens. The General Mixed Yule Coalescent (GMYC) analysis recognized 99 independent evolution units, and the Barcode Index Numbers (BIN) approach pointed to the existence of 104 BINs (interpreted as distinct species). By cross-tabulating the results of all approaches, we identified 109 Molecular Operational Taxonomic Units (MOTU) by at least one methodology. In most cases (89 MOTUs), the genetic approaches are in agreement with morphological identification, and the discrepant results of MOTUs are in the complex groups, which have many morphological similarities but may represent species complexes.
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Roxo FF, Ochoa LE, Costa-Silva GJ, Oliveira C. Species delimitation in Neoplecostomus (Siluriformes: Loricariidae) using morphologic and genetic approaches. ACTA ACUST UNITED AC 2015. [DOI: 10.1515/dna-2015-0014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractIn the present study, we compare the results of alpha taxonomy (based on morphology), DNA Barcoding method with a 2% genetic divergence threshold, and the GMYC (General Model Yule Coalescent) technique to identify species clusters in Neoplecostomus. We used partial sequences of mitochondrial COI (Cytochrome oxidase subunit I) for 59 specimens representing 13 valid species (Neoplecostomus bandeirante, N. jaguari, N. langeanii, N. paranensis, N. yapo, N. botucatu, N. selenae, N. doceensis, N. corumba, N. ribeirensis, N. microps, N. espiritosantensis and N. franciscoensis) of Neoplecostomus collected in all its distribution area. For the analysis we used Bayesian inference of phylogeny with relaxed clock methods on an arbitrary timescale, using BEAST. The ultrametrics genes trees obtained for each tree prior evaluated (Yule, Birth-death and coalescent Population Size) were used in the GMYC analysis to identify a time in the tree when the branching rate shifts (in forward time) from Yule and Birth-Death (species) to a coalescent (population) process. We found that the GMYC model using the Yule prior identified 11 groups, closer to the current taxonomy (13 species). GMYC analyses using other ultrametric gene trees estimated under alternative prior such as Birth-Death and Coalescent Population Size, identified 9 groups, results observed in the traditional 2% genetic distance threshold, resulting in a low number of species recognized compared to the number of species identified with current taxonomy. Based on these results we conclude that the molecular approaches are helpful to distinguish species of Neoplecostomus, nevertheless it is important to combine molecular methodologies with current taxonomy in order to identify correctly species that recently originated.
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Dhar B, Ghosh SK. Genetic assessment of ornamental fish species from North East India. Gene 2015; 555:382-92. [DOI: 10.1016/j.gene.2014.11.037] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 11/04/2014] [Accepted: 11/15/2014] [Indexed: 02/07/2023]
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Alves-Silva AP, Dergam JA. Cryptic speciation within the Neotropical cichlid Geophagus brasiliensis (Quoy & Gaimard, 1824) (Teleostei Cichlidae): a new paradigm in karyotypical and molecular evolution. Zebrafish 2014; 12:91-101. [PMID: 25495140 DOI: 10.1089/zeb.2014.0999] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The family Cichlidae is one of the most species-rich taxa in the Neotropics. However, the factors that determine these high levels of biodiversity remain unexplored. We have analyzed the morphological, cytogenetic, and molecular data from 62 specimens of a widespread cichlid, Geophagus brasiliensis, from three adjacent basins in southeastern Brazil. Morphological analyses did not show differences among specimens. The cytogenetic data indicate the occurrence of multiple nucleolar organizer regions and four sympatric karyotypes that differ in the first pair of chromosome morphology, in the Doce River Basin; whereas the karyotype from the Paraíba do Sul Basin is widely divergent. The molecular data--616 bp fragment of cytochrome oxidase subunit I--revealed two haplogroups with the deepest genetic divergence (6.4%) ever reported within a nominal species in the Neotropical Region: One of the haplogroups is restricted to the quaternary lakes in the middle portion of the Doce Basin and the Mucuri River, whereas the other haplogroup is composed of haplotypes from elsewhere in the Doce Basin and the Paraíba do Sul Basin. These patterns suggest that G. brasiliensis undergoes a cryptic speciation process involving three major lineages that differ from the African explosive cichlid radiation.
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Affiliation(s)
- Ana Paula Alves-Silva
- Laboratório de Sistemática Molecular-Beagle, Departamento de Biologia Animal, Universidade Federal de Viçosa , Viçosa, Minas Gerais State, Brazil
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Elías-Gutiérrez M, León-Regagnon V. DNA barcoding in Mexico: an introduction. Mol Ecol Resour 2013; 13:1093-6. [PMID: 23919390 DOI: 10.1111/1755-0998.12149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Revised: 05/30/2013] [Accepted: 06/24/2013] [Indexed: 11/30/2022]
Abstract
DNA barcoding has become an important current scientific trend to the understanding of the world biodiversity. In the case of mega-diverse hot spots like Mexico, this technique represents an important tool for taxonomists, allowing them to concentrate in highlighted species by the barcodes instead of analyzing entire sets of specimens. This tendency resulted in the creation of a national network named Mexican Barcode of Life (MEXBOL) which main goals are to train students, and to promote the interaction and collective work among researchers interested in this topic. As a result, the number of records in the Barcode of Life Database (BOLD) for some groups, such as the Mammalia, Actinopterygii, Polychaeta, Branchiopoda, Ostracoda, Maxillopoda, Nematoda, Pinophyta, Ascomycota and Basidiomycota place Mexico among the top ten countries in the generation of these data. This special number presents only few of the many interesting findings in this region of the world, after the use of this technique and its integration with other methodologies.
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Affiliation(s)
- M Elías-Gutiérrez
- El Colegio de la Frontera Sur, Av. Centenario Km 5.5, Chetumal, Quintana Roo, 77014, Mexico
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38
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Development of a DNA chip to identify the place of origin of hairtail species. BIOCHIP JOURNAL 2013. [DOI: 10.1007/s13206-013-7206-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Silva GSC, Melo BF, Oliveira C, Benine RC. Morphological and molecular evidence for two new species of Tetragonopterus (Characiformes: Characidae) from central Brazil. JOURNAL OF FISH BIOLOGY 2013; 82:1613-1631. [PMID: 23639157 DOI: 10.1111/jfb.12094] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Accepted: 02/06/2013] [Indexed: 06/02/2023]
Abstract
The combination of morphological and molecular data of Tetragonopterus species collected in the Rio Araguaia basin allows the recognition of two undescribed species that are presented in this article. These species are distinguished from their congeners (Tetragonopterus anostomus, Tetragonopterus argenteus, Tetragonopterus carvalhoi, Tetragonopterus chalceus and Tetragonopterus rarus) by characters related to the number and morphology of the teeth, the numbers of gill rakers on the upper and lower limbs of the first gill arch, the number of predorsal scales and the overall colour pattern. In addition, the analysis of mitochondrial DNA sequences identified an accentuated genetic distance between these two new species and their congeners. A discussion of the phylogenetic relationships within Tetragonopterus is provided.
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Affiliation(s)
- G S C Silva
- Laboratório de Biologia e Genética de Peixes, Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista-UNESP, Rubião Jr., s/n, 18618-970 Botucatu, SP, Brazil
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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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García-Morales AE, Elías-Gutiérrez M. DNA barcoding of freshwater Rotifera in Mexico: Evidence of cryptic speciation in common rotifers. Mol Ecol Resour 2013; 13:1097-107. [DOI: 10.1111/1755-0998.12080] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Revised: 06/27/2012] [Accepted: 07/04/2012] [Indexed: 11/27/2022]
Affiliation(s)
- A. E. García-Morales
- El Colegio de la Frontera Sur; Av. Centenario km 5.5; Chetumal; Quintana Roo; 77014; Mexico
| | - M. Elías-Gutiérrez
- El Colegio de la Frontera Sur; Av. Centenario km 5.5; Chetumal; Quintana Roo; 77014; Mexico
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42
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Galimberti A, De Mattia F, Losa A, Bruni I, Federici S, Casiraghi M, Martellos S, Labra M. DNA barcoding as a new tool for food traceability. Food Res Int 2013. [DOI: 10.1016/j.foodres.2012.09.036] [Citation(s) in RCA: 155] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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43
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Puckridge M, Andreakis N, Appleyard SA, Ward RD. Cryptic diversity in flathead fishes (
S
corpaeniformes:
P
latycephalidae) across the
I
ndo‐
W
est
P
acific uncovered by
DNA
barcoding. Mol Ecol Resour 2012; 13:32-42. [DOI: 10.1111/1755-0998.12022] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Revised: 08/16/2012] [Accepted: 08/20/2012] [Indexed: 11/29/2022]
Affiliation(s)
- Melody Puckridge
- Institute for Marine and Antarctic Studies University of Tasmania Private Bag 129 Hobart Tas. 7001 Australia
- CSIRO Marine and Atmospheric Research Wealth from Oceans Flagship Castray Esplanade Hobart Tas. 7000 Australia
| | - Nikos Andreakis
- Australian Institute of Marine Science PMB No. 3 Townsville Qld 4810 Australia
| | - Sharon A. Appleyard
- CSIRO Marine and Atmospheric Research Wealth from Oceans Flagship Castray Esplanade Hobart Tas. 7000 Australia
| | - Robert D. Ward
- CSIRO Marine and Atmospheric Research Wealth from Oceans Flagship Castray Esplanade Hobart Tas. 7000 Australia
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44
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León‐Romero Y, Mejía O, Soto‐Galera E. DNA
barcoding reveals taxonomic conflicts in the
H
erichthys bartoni
species group (
P
isces:
C
ichlidae). Mol Ecol Resour 2012; 12:1021-6. [DOI: 10.1111/1755-0998.12018] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Revised: 08/21/2012] [Accepted: 08/23/2012] [Indexed: 12/30/2022]
Affiliation(s)
- Yatzil León‐Romero
- Laboratorio de Variación Biológica y Evolución Departamento de Zoología Escuela Nacional de Ciencias Biológicas‐IPN Carpio esq. Plan de Ayala s/n Col. Casco de Santo Tomás Mexico City DF C.P. 11340 México
| | - Omar Mejía
- Laboratorio de Variación Biológica y Evolución Departamento de Zoología Escuela Nacional de Ciencias Biológicas‐IPN Carpio esq. Plan de Ayala s/n Col. Casco de Santo Tomás Mexico City DF C.P. 11340 México
| | - Eduardo Soto‐Galera
- Laboratorio de Ictiología y Limnología Departamento de Zoología Escuela Nacional de Ciencias Biológicas‐IPN Carpio esq. Plan de Ayala s/n Col., Casco de Santo Tomás Mexico City DF C.P. 11340 México
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45
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Rosso JJ, Mabragaña E, González Castro M, Díaz de Astarloa JM. DNA
barcoding
N
eotropical fishes: recent advances from the
P
ampa
P
lain,
A
rgentina. Mol Ecol Resour 2012; 12:999-1011. [DOI: 10.1111/1755-0998.12010] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Revised: 07/24/2012] [Accepted: 07/28/2012] [Indexed: 11/28/2022]
Affiliation(s)
- J. J. Rosso
- Grupo de Biotaxonomía Morfológica y Molecular de Peces (BIMOPE) Instituto de Investigaciones Marinas y Costeras (IIMyC, CONICET‐UNMDP) Funes 3350 Mar del Plata 7600 Argentina
| | - E. Mabragaña
- Grupo de Biotaxonomía Morfológica y Molecular de Peces (BIMOPE) Instituto de Investigaciones Marinas y Costeras (IIMyC, CONICET‐UNMDP) Funes 3350 Mar del Plata 7600 Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) Av. Rivadavia 1917, CABA C1033AAJ Buenos Aires Argentina
| | - M. González Castro
- Grupo de Biotaxonomía Morfológica y Molecular de Peces (BIMOPE) Instituto de Investigaciones Marinas y Costeras (IIMyC, CONICET‐UNMDP) Funes 3350 Mar del Plata 7600 Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) Av. Rivadavia 1917, CABA C1033AAJ Buenos Aires Argentina
| | - J. M. Díaz de Astarloa
- Grupo de Biotaxonomía Morfológica y Molecular de Peces (BIMOPE) Instituto de Investigaciones Marinas y Costeras (IIMyC, CONICET‐UNMDP) Funes 3350 Mar del Plata 7600 Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) Av. Rivadavia 1917, CABA C1033AAJ Buenos Aires Argentina
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46
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Mejía O, León-Romero Y, Soto-Galera E. DNA barcoding of the ichthyofauna of Pánuco-Tamesí complex: evidence for taxonomic conflicts in some groups. ACTA ACUST UNITED AC 2012; 23:471-6. [PMID: 22917217 DOI: 10.3109/19401736.2012.710207] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The Pánuco-Tamesí complex in eastern Mexico is globally recognized as an important ecoregion due to its high level of endemism. In this study, DNA barcodes were generated for 152 individuals of 31 species. Additionally, 170 DNA barcodes for the related species available in the Barcode of Life Database (BOLD) system were included to test the ability of barcoding technique to discriminate between the closely related species. DNA barcoding allowed the discrimination of 79.2% of the analyzed species; poor resolution was observed in four genera in which the levels of resolution ranged from 16.6% in the genus Herichthys to 77.7% in the genus Xiphophorus. The results of this study demonstrate that DNA barcoding is a useful exploratory tool but fails to discriminate between closely related species.
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Affiliation(s)
- Omar Mejía
- Laboratorio de Variación Biológica y Evolución, Departamento de Zoología, Escuela Nacional de Ciencias Biológicas-IPN, Carpio esq. Plan de Ayala s/n Col. Casco de Santo Tomás, México DF C.P. 11340, Mexico.
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47
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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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Pazian MF, Pereira LHG, Shimabukuru-Dias CK, Oliveira C, Foresti F. Cytogenetic and molecular markers reveal the complexity of the genus Piabina Reinhardt, 1867 (Characiformes: Characidae). NEOTROPICAL ICHTHYOLOGY 2012. [DOI: 10.1590/s1679-62252012005000015] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Cytogenetic and molecular analyses were carried out in fish representative of the genus Piabina. This study specifically involved the species P. argentea and P. anhembi collected from areas of the Paranapanema and Tietê River basins, Brazil. Our findings suggest that fish classified as Piabina argentea in the Paranapanema and Tietê Rivers may represent more than one species. The samples analyzed differed by cytogenetic particularities and molecular analyses using partial sequences of the genes COI and CytB as genetic markers revealed three distinct groups of P. argentea with genetic distances sufficient to support the conclusion that the three samples analyzed are three distinct taxonomic units.
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Affiliation(s)
| | | | | | | | - Fausto Foresti
- Universidade Estadual Paulista Júlio de Mesquita Filho, Brazil
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49
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Deep phylogenetic divergence and lack of taxonomic concordance in species of astronotus (cichlidae). INTERNATIONAL JOURNAL OF EVOLUTIONARY BIOLOGY 2012; 2012:915265. [PMID: 22779032 PMCID: PMC3388587 DOI: 10.1155/2012/915265] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2012] [Accepted: 04/14/2012] [Indexed: 11/18/2022]
Abstract
The neotropical cichlid genus Astronotus currently comprises two valid species: A. ocellatus Agassiz, 1831 and A. crassipinnis Heckel, 1840. The diagnosis is based on color pattern and meristics counts. However, body color pattern is highly variable between regions and the meristic counts show a considerable overlap between populations differing in color patterning. They do not represent true synapomorphies that diagnose species. Purportedly the only truly diagnostic character is the presence or absence of one or more ocelli at the base of the dorsal fin, diagnosing A. ocellatus and A. crassipinnis, respectively. Using the 5' portion of the mitochondrial COI gene and EPIC nuclear markers, the validity of the dorsal ocelli as diagnostic character was tested in individuals sampled from ten localities in the Amazon basin. Analyses rejected the hypothesis that dorsal ocelli are diagnostic at the species level. However, they revealed the existence of five hypothetical, largely allopatrically distributed morphologically cryptic species. The phylogeographic structure is not necessarily surprising, since species of the genus Astronotus have sedentary and territorial habits with low dispersal potential. The distribution of these hypothetical species is coincident with patterns observed in other Amazonian aquatic fauna, suggesting the role of common historical processes in generating current biodiversity patterns.
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50
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Collins RA, Armstrong KF, Meier R, Yi Y, Brown SDJ, Cruickshank RH, Keeling S, Johnston C. Barcoding and border biosecurity: identifying cyprinid fishes in the aquarium trade. PLoS One 2012; 7:e28381. [PMID: 22276096 PMCID: PMC3262790 DOI: 10.1371/journal.pone.0028381] [Citation(s) in RCA: 111] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Accepted: 11/07/2011] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Poorly regulated international trade in ornamental fishes poses risks to both biodiversity and economic activity via invasive alien species and exotic pathogens. Border security officials need robust tools to confirm identifications, often requiring hard-to-obtain taxonomic literature and expertise. DNA barcoding offers a potentially attractive tool for quarantine inspection, but has yet to be scrutinised for aquarium fishes. Here, we present a barcoding approach for ornamental cyprinid fishes by: (1) expanding current barcode reference libraries; (2) assessing barcode congruence with morphological identifications under numerous scenarios (e.g. inclusion of GenBank data, presence of singleton species, choice of analytical method); and (3) providing supplementary information to identify difficult species. METHODOLOGY/PRINCIPAL FINDINGS We sampled 172 ornamental cyprinid fish species from the international trade, and provide data for 91 species currently unrepresented in reference libraries (GenBank/Bold). DNA barcodes were found to be highly congruent with our morphological assignments, achieving success rates of 90-99%, depending on the method used (neighbour-joining monophyly, bootstrap, nearest neighbour, GMYC, percent threshold). Inclusion of data from GenBank (additional 157 spp.) resulted in a more comprehensive library, but at a cost to success rate due to the increased number of singleton species. In addition to DNA barcodes, our study also provides supporting data in the form of specimen images, morphological characters, taxonomic bibliography, preserved vouchers, and nuclear rhodopsin sequences. Using this nuclear rhodopsin data we also uncovered evidence of interspecific hybridisation, and highlighted unrecognised diversity within popular aquarium species, including the endangered Indian barb Puntius denisonii. CONCLUSIONS/SIGNIFICANCE We demonstrate that DNA barcoding provides a highly effective biosecurity tool for rapidly identifying ornamental fishes. In cases where DNA barcodes are unable to offer an identification, we improve on previous studies by consolidating supplementary information from multiple data sources, and empower biosecurity agencies to confidently identify high-risk fishes in the aquarium trade.
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Affiliation(s)
- Rupert A Collins
- Bio-Protection Research Centre, Lincoln University, Canterbury, New Zealand.
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