1
|
Bektas Y, Aksu İ, Kaya C, Bayçelebi E, Turan D. DNA barcoding and species delimitation of the genus Oxynoemacheilus (Teleostei: Nemacheilidae) in Anatolia. JOURNAL OF FISH BIOLOGY 2022; 101:505-514. [PMID: 35607971 DOI: 10.1111/jfb.15114] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 05/17/2022] [Indexed: 06/15/2023]
Abstract
The DNA barcoding approach was used for the determination of evolutionary relationships and species delimitation of the genus Oxynoemacheilus (Teleostei: Nemacheilidae). The COI barcode region (615 bp amplicon) was used to barcode 444 individuals from 64 morphologically identified species in the genus Oxynoemacheilus and 189 haplotypes were identified. The average of the interspecific p distance (9.59%) was about 21-fold higher than the average intraspecific distance (0.44%). A general genetic threshold of 1.46% sequence divergence was defined for species delimitation. The multiple species delimitation methods (BCM, GMYC, bPTP and TCS) revealed a total of 62 molecular operational taxonomic units for 64 morphospecies with a new loach species from the BuyukMelen River. Neighbour-joining, maximum likelihood and Bayesian inference analyses indicated that all haplotypes were clustered into 62 clades, which corresponded to Oxynoemacheilus species, with strong bootstrap support (≥95%). Furthermore, all samples grouped in concurrence with the taxonomic status of the species except for species groups (O. germencicus-O. cinicus-O. mesudae and O. leontinae-O. namiri) that were showed intraspecific overlap in genetic diversity for COI-based barcodes. In conclusion, our analyses indicate that COI-based barcodes provide reliable species discrimination. Therefore, we currently recommend COI barcodes as the suitable barcode for genus Oxynoemacheilus.
Collapse
Affiliation(s)
- Yusuf Bektas
- Deparment of Biology, Faculty of Arts and Sciences, Recep Tayyip Erdogan University, Rize, Turkey
| | - İsmail Aksu
- Faculty of Fisheries and Aquatic Sciences, Recep Tayyip Erdogan University, Rize, Turkey
| | - Cüneyt Kaya
- Faculty of Fisheries and Aquatic Sciences, Recep Tayyip Erdogan University, Rize, Turkey
| | - Esra Bayçelebi
- Faculty of Fisheries and Aquatic Sciences, Recep Tayyip Erdogan University, Rize, Turkey
| | - Davut Turan
- Faculty of Fisheries and Aquatic Sciences, Recep Tayyip Erdogan University, Rize, Turkey
| |
Collapse
|
2
|
Chen W, Hubert N, Li Y, Xiang D, Cai X, Zhu S, Yang J, Zhou C, Li X, Li J. Large scale DNA barcoding of the subfamily Culterinae (Cypriniformes: Xenocyprididae) in East Asia unveils geographic scale effect, taxonomic warnings and cryptic diversity. Mol Ecol 2022; 31:3871-3887. [PMID: 35593525 PMCID: PMC9542215 DOI: 10.1111/mec.16540] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 03/29/2022] [Accepted: 04/11/2022] [Indexed: 11/28/2022]
Abstract
Geographical scale might be expected to impact significantly the efficiency of DNA barcoding as spatially comprehensive sampling provides opportunities to uncover intricate relationships among closely related species and to detect cryptic diversity for widespread taxa. Here, we present a DNA barcoding study on a Xencyprididae subfamily (Culterinae) involving the production of 998 newly generated DNA barcodes from East Asian drainages (80 localities). Together with 513 barcodes mined from BOLD and GenBank, a reference library consisting of 1511 DNA barcodes (116 localities) for 42 species was assembled, accounting for 66% of known Culterinae species. Intraspecific genetic distances are positively correlated to geographical scale, while a negative correlation is detected between interspecific genetic distances and geographical scale. The present study demonstrates that geographical scale influences the efficiency of DNA barcoding by narrowing the width of the barcoding gap. DNA‐based species delimitation analyses delimited 44 molecular operational taxonomic units (MOTUs). Rampant cryptic diversity is detected within eight species with multiple MOTUs, whereas 25 species present mismatch between morphological and molecular delimitations. A total of 18 species are lumped into nine MOTUs due to low interspecific divergence and/or mixed lineages. Several MOTU divergences are hypothesized to relate to known biogeographical barriers and geological events during the Pliocene and Pleistocene. This study provides new insights into the taxonomy and phylogeography of the subfamily Culterinae.
Collapse
Affiliation(s)
- Weitao Chen
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou, Guangdong, China.,Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Guangzhou, China.,Guangzhou Scientific Observing and Experimental Station of National Fisheries Resources and Environment, Guangzhou, Guangdong, China
| | - Nicolas Hubert
- Institut de Recherche pour le Développement, UMR 226 ISEM (UM-CNRS-IRD), Montpellier cedex 05, France
| | - Yuefei Li
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou, Guangdong, China.,Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Guangzhou, China.,Guangzhou Scientific Observing and Experimental Station of National Fisheries Resources and Environment, Guangzhou, Guangdong, China
| | - Denggao Xiang
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou, Guangdong, China
| | - Xingwei Cai
- Hainan Academy of Ocean and Fisheries Sciences, Haikou, Hainan, China
| | - Shuli Zhu
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou, Guangdong, China.,Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Guangzhou, China.,Guangzhou Scientific Observing and Experimental Station of National Fisheries Resources and Environment, Guangzhou, Guangdong, China
| | - Jiping Yang
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou, Guangdong, China.,Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Guangzhou, China.,Guangzhou Scientific Observing and Experimental Station of National Fisheries Resources and Environment, Guangzhou, Guangdong, China
| | - Chuanjiang Zhou
- College of Fisheries, Henan Normal University, Xinxiang, Henan, China
| | - Xinhui Li
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou, Guangdong, China.,Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Guangzhou, China.,Guangzhou Scientific Observing and Experimental Station of National Fisheries Resources and Environment, Guangzhou, Guangdong, China
| | - Jie Li
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou, Guangdong, China.,Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Guangzhou, China.,Guangzhou Scientific Observing and Experimental Station of National Fisheries Resources and Environment, Guangzhou, Guangdong, China
| |
Collapse
|
3
|
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.
Collapse
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)
| |
Collapse
|
4
|
Adeoba MI, Yessoufou K. Analysis of temporal diversification of African Cyprinidae (Teleostei, Cypriniformes). Zookeys 2018:141-161. [PMID: 30588160 PMCID: PMC6302146 DOI: 10.3897/zookeys.806.25844] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Accepted: 10/02/2018] [Indexed: 11/12/2022] Open
Abstract
Recent evidence that freshwater fishes diversify faster than marine fishes signifies that the evolutionary history of biodiversity in freshwater system is of particular interest. Here, the evolutionary diversification events of African Cyprinidae, a freshwater fish family with wide geographic distribution, were reconstructed and analysed. The overall diversification rate of African Cyprinidae is 0.08 species per million year (when extinction rate is very high, i.e., ε = 0.9) and 0.11 species per million year (when ε = 0). This overall rate is lower than the rate reported for African Cichlids, suggesting that African freshwaters might be less conducive for a rapid diversification of Cyprinidae. However, the observed diversification events of African Cyprinidae occurred in the last 10 million years. The temporal pattern of these events follows a non-constant episodic birth-death model (Bayes Factor > 28) and the rate-constant model never outperformed any of the non-constant models tested. The fact that most diversification events occurred in the last 10 million years supports the pattern reported for Cyprinidae in other continent, e.g., Asia, perhaps pointing to concomitant diversification globally. However, the diversification events coincided with major geologic and paleo-climatic events in Africa, suggesting that geological and climatic events may have mediated the diversification patterns of Cyprinidae on the continent.
Collapse
Affiliation(s)
- Mariam I Adeoba
- Department of Zoology, University of Johannesburg, Kingsway Campus PO Box 524, Auckland Park 2006, South Africa University of Johannesburg Johannesburg South Africa
| | - Kowiyou Yessoufou
- Department of Geography, Environmental management and Energy studies, University of Johannesburg, Kingsway Campus PO Box 524, Auckland Park 2006, South Africa University of Johannesburg Johannesburg South Africa
| |
Collapse
|
5
|
Müller MI, Morais DH, Costa-Silva GJ, Aguiar A, Ávila RW, da Silva RJ. Diversity in the genusRhabdias(Nematoda, Rhabdiasidae): Evidence for cryptic speciation. ZOOL SCR 2018. [DOI: 10.1111/zsc.12304] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Maria I. Müller
- Department of Parasitology, Rua Professor Doutor Antônio Celso Wagner Zanin; Institute of Biosciences, São Paulo State University (UNESP); Botucatu São Paulo Brazil
| | - Drausio H. Morais
- Universidade Federal Rural da Amazônia (UFRA); Parauapebas Pará Brazil
| | - Guilherme J. Costa-Silva
- Department of Morphology, Rua Professor Doutor Antônio Celso Wagner Zanin; Institute of Biosciences, São Paulo State University (UNESP); Botucatu São Paulo Brazil
- Universidade Santo Amaro, Rua Prof. Enéas de Siqueira Neto, Jardim das Imbuias; São Paulo Brazil
| | - Aline Aguiar
- Department of Parasitology, Rua Professor Doutor Antônio Celso Wagner Zanin; Institute of Biosciences, São Paulo State University (UNESP); Botucatu São Paulo Brazil
| | - Robson W. Ávila
- Departamento de Química Biológica, Laboratório de Herpetologia; Universidade Regional do Cariri (URCA); Crato Ceará Brazil
| | - Reinaldo J. da Silva
- Department of Parasitology, Rua Professor Doutor Antônio Celso Wagner Zanin; Institute of Biosciences, São Paulo State University (UNESP); Botucatu São Paulo Brazil
| |
Collapse
|