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Abdulmalik-Labe OP, Eduardo AJL, Quilang JP. Genetic diversity and divergence among native and translocated populations of the golden flathead goby Glossogobius aureus (Gobiiformes: Gobiidae) in Philippine lakes. PLoS One 2023; 18:e0293076. [PMID: 38096142 PMCID: PMC10721109 DOI: 10.1371/journal.pone.0293076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 10/03/2023] [Indexed: 12/17/2023] Open
Abstract
The golden flathead goby Glossogobius aureus is a native species in the Philippines, Australia, Japan, Taiwan, and many other countries in Asia. In the Philippines, it is an important food fish as it is commonly caught in major lakes. In this study, a total of 307 specimens morphologically identified as G. aureus were sampled from nine major lakes in the Philippines and were sequenced for their mitochondrial cytochrome b (cyt b) gene. Two hundred sixty of the 307 cyt b sequences had sequence similarities of ≥ 99% with G. aureus reference sequence in GenBank, while the remaining 47 (all from Lake Lanao) had sequence similarities of only 95% and were thus designated as Glossogobius cf. aureus and treated as a separate population. The sequences were then analyzed to examine the pattern of genetic diversity, relatedness, divergence, and demographic history among native and translocated populations of the species. Twenty-nine haplotypes were recovered, of which four haplotypes were shared among three to seven populations. Only one haplotype each was found in the native population in Lake Buhi and translocated population in Lake Paoay. Low haplotype and low nucleotide diversities were found for the populations in Laguna de Bay, Lanao, Bato, Buhi, Paoay, and Sebu lakes, which indicate founder event for the introduced populations in Lanao, Paoay, and Sebu lakes and recent genetic bottleneck for the native populations in Laguna de Bay, Bato, and Buhi. In contrast, high haplotype but low nucleotide diversities were found for the native populations of Taal, Naujan, and Buluan lakes, signifying a recent bottleneck followed by population expansion. Pairwise FST values showed generally large (FST = 0.168-0.249) to very large (FST = 0.302-1.000) genetic divergence between populations except between Laguna de Bay and Lake Bato, Laguna de Bay and Lake Buhi, and Lake Bato and Lake Buhi populations, which showed nonsignificant genetic differentiation. Lake Buluan and Lake Sebu populations showed moderate genetic differentiation (FST = 0.098). Neutrality tests showed significant negative Tajima's D and Fu's FS values only for the population from Laguna de Bay, which suggests that the population is undergoing expansion. These results are important for establishing scientifically sound strategies for effective conservation and sustainable exploitation of G. aureus in the Philippines.
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Affiliation(s)
- Onaya P. Abdulmalik-Labe
- Institute of Biology, College of Science, University of the Philippines Diliman, Quezon City, Philippines
- Biology Department, College of Natural Sciences and Mathematics, Mindanao State University, Marawi City, Philippines
| | - Andrew Jason L. Eduardo
- Institute of Biology, College of Science, University of the Philippines Diliman, Quezon City, Philippines
| | - Jonas P. Quilang
- Institute of Biology, College of Science, University of the Philippines Diliman, Quezon City, Philippines
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Canoglu H, Aksu I, Turan D, Bektas Y. DNA barcoding of the genus Alburnoides Jeitteles, 1861 (Actinopterygii, Cyprinidae) from Anatolia, Turkey. ZOOSYST EVOL 2023. [DOI: 10.3897/zse.99.94333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023] Open
Abstract
The present study investigated the ability of DNA barcoding to reliably identify the endemic freshwater species in Turkey, known as biodiversity hotspots. The barcode region (652 bp) of the mitochondrial cytochrome c oxidase subunit I (COI) was used to barcode 153 individuals from 13 morphologically identified species of the genus Alburnoides. Based on the Kimura two-parameter (K2P) evolution model, the average interspecific distance (0.0595) was 31-fold higher than the average intraspecific distance (0.0019). There was a clear-cut barcode gap (0.0158–0.0187) between maximum intraspecific distance (A. tzanevi and A. velioglui) and minimum nearest-neighbour distance (A. freyhofi and A. kurui) for Anatolian Alburnoides species and a common genetic threshold of 0.0158 sequence divergence was defined for species delimitation. The multiple species delimitation methods (ABGD, ASAP, GMYC and bPTP) revealed a total of 11 molecular operational taxonomic units (MOTUs) for 13 morphospecies. Neighbour-joining (NJ), Maximum Likelihood (ML) and Bayesian Inference (BI) tree analysis indicated that all haplotypes were clustered into two major clades, which corresponded to eleven Alburnoides species clusters, with strong bootstrap support. Furthermore, all the specimens clustered in concurrence with the morpho-taxonomic status of the species, except for two species (A. coskuncelebii and A. emineae) that were morphologically differentiated, but showed overlap in variation for COI-based DNA barcode data with other species. Overall, present results identified that COI-based DNA barcoding is effective for species identification and cataloguing of genus Alburnoides in Turkey.
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Pragmatic applications of DNA barcoding markers in identification of fish species – a review. ANNALS OF ANIMAL SCIENCE 2023. [DOI: 10.2478/aoas-2022-0073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Abstract
DNA barcoding and mini barcoding involve Cytochrome Oxidase Subunit I (COI) gene in mitochondrial genome and is used for accurate identification of species and biodiversity. The basic goal of the current study is to develop a complete reference database of fishes. It also evaluates the applicability of COI gene to identify fish at the species level with other aspects i.e., as Kimura 2 parameter (K2P) distance. The mean observed length of the sequence was ranging between 500 to 700 base pairs for fish species in DNA barcoding and 80 to 650 base pairs for DNA mini barcoding. This method describes the status of known to unknown samples but it also facilitates the detection of previously un-sampled species at distinct level. So, mini-barcoding is a method focuses on the analysis of short-length DNA markers has been demonstrated to be effective for species identification of processed food containing degraded DNA. While DNA meta-barcoding refers to the automated identification of multiple species from a single bulk sample. The may contain entire organisms or a single environmental sample containing degraded DNA. Despite DNA barcoding, mini barcoding and meta-barcoding are efficient methods for species identification which are helpful in conservation and proper management of biodiversity. It aids researchers to take an account of genetic as well as evolutionary relationships by collecting their morphological, distributional and molecular data. Overall, this paper discusses DNA barcoding technology and how it has been used to various fish species, as well as its universality, adaptability, and novel approach to DNA-based species identification.
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Li H, Yang F, Wang X, Li Y, Zhang N, Zhang R, Liu C, Zhang H, Lin L, Song P. Demersal fish diversity and molecular taxonomy in the Bering Sea and Chukchi Sea. CONSERV GENET RESOUR 2021. [DOI: 10.1007/s12686-021-01241-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Karabanov DP, Kodukhova YV, Pashkov AN, Reshetnikov AN, Makhrov AA. “Journey to the West”: Three Phylogenetic Lineages Contributed to the Invasion of Stone Moroko, Pseudorasbora parva (Actinopterygii: Cyprinidae). RUSSIAN JOURNAL OF BIOLOGICAL INVASIONS 2021. [DOI: 10.1134/s2075111721010070] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Ağdamar S, Baysal Ö, Yıldız A, Tarkan AS. Genetic differentiation of non-native populations of Gibel Carp, Carassius gibelio in Western Turkey by ISSR and SRAP markers. ZOOLOGY IN THE MIDDLE EAST 2020. [DOI: 10.1080/09397140.2020.1835215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Sevan Ağdamar
- Gökçeada School of Applied Sciences, Çanakkale Onsekiz Mart University, Çanakkale, Turkey
| | - Ömür Baysal
- Department of Molecular Biology and Genetics, Faculty of Science, Muğla Sıtkı Koçman University, Muğla, Turkey
| | - Ayşegül Yıldız
- Department of Molecular Biology and Genetics, Faculty of Science, Muğla Sıtkı Koçman University, Muğla, Turkey
| | - Ali Serhan Tarkan
- Faculty of Fisheries, Muğla Sıtkı Koçman University, Muğla, Turkey
- Department of Ecology and Vertebrate Zoology, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland
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Distribution Revised-Fifteen Years of Changes in the Invasion of a Freshwater Fish, Pseudorasbora parva (Temminck and Schlegel, 1846) in Turkey. TRANSYLVANIAN REVIEW OF SYSTEMATICAL AND ECOLOGICAL RESEARCH 2020. [DOI: 10.2478/trser-2019-0013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Abstract
The aim of the present paper is to revise the distribution range of the invasive freshwater fish species, topmouth gudgeon Pseudorasbora parva (Temminck and Schlegel, 1846) in Turkey, based on the literature review. After the first report of the species from the Meriç River in Thrace (European part of Turkey) in 1982, it has spread across the country mainly through human-mediated accidental introductions. The species has now been reported from 66 water bodies in total. Besides the introduction pathways, we also present chronological distribution pattern of the species. This information is useful especially for conservation endemic ichthyofauna due to the negative impact of Pseudorasbora parva, particularly through introducing an emerging infectious eukaryotic intracellular pathogen on the fungal-animal boundary, Sphaerothecum destruens Arkush et al., 2003.
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Shen Y, Hubert N, Huang Y, Wang X, Gan X, Peng Z, He S. DNA barcoding the ichthyofauna of the Yangtze River: Insights from the molecular inventory of a mega‐diverse temperate fauna. Mol Ecol Resour 2019; 19:1278-1291. [DOI: 10.1111/1755-0998.12961] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 09/07/2018] [Accepted: 09/24/2018] [Indexed: 01/04/2023]
Affiliation(s)
- Yanjun Shen
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology Chinese Academy of Sciences Wuhan China
- University of Chinese Academy of Sciences Beijing China
| | - Nicolas Hubert
- Institut de Recherche pour le Développement UMR 226 ISEM (UM2‐CNRS‐IRD) Montpellier cedex 05 France
| | - Yan Huang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education) Southwest University School of Life Sciences Chongqing China
| | - Xuzheng Wang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology Chinese Academy of Sciences Wuhan China
| | - Xiaoni Gan
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology Chinese Academy of Sciences Wuhan China
| | - Zuogang Peng
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education) Southwest University School of Life Sciences Chongqing China
| | - Shunping He
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology Chinese Academy of Sciences Wuhan China
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Shen Y, Guan L, Wang D, Gan X. DNA barcoding and evaluation of genetic diversity in Cyprinidae fish in the midstream of the Yangtze River. Ecol Evol 2016; 6:2702-13. [PMID: 27066250 PMCID: PMC4798831 DOI: 10.1002/ece3.2060] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 01/31/2016] [Accepted: 02/02/2016] [Indexed: 11/29/2022] Open
Abstract
The Yangtze River is the longest river in China and is divided into upstream and mid-downstream regions by the Three Gorges (the natural barriers of the Yangtze River), resulting in a complex distribution of fish. Dramatic changes to habitat environments may ultimately threaten fish survival; thus, it is necessary to evaluate the genetic diversity and propose protective measures. Species identification is the most significant task in many fields of biological research and in conservation efforts. DNA barcoding, which constitutes the analysis of a short fragment of the mitochondrial cytochrome c oxidase subunit I (COI) sequence, has been widely used for species identification. In this study, we collected 561 COI barcode sequences from 35 fish from the midstream of the Yangtze River. The intraspecific distances of all species were below 2% (with the exception of Acheilognathus macropterus and Hemibarbus maculatus). Nevertheless, all species could be unambiguously identified from the trees, barcoding gaps and taxonomic resolution ratio values. Furthermore, the COI barcode diversity was found to be low (≤0.5%), with the exception of H. maculatus (0.87%), A. macropterus (2.02%) and Saurogobio dabryi (0.82%). No or few shared haplotypes were detected between the upstream and downstream populations for ten species with overall nucleotide diversities greater than 0.00%, which indicated the likelihood of significant population genetic structuring. Our analyses indicated that DNA barcoding is an effective tool for the identification of cyprinidae fish in the midstream of the Yangtze River. It is vital that some protective measures be taken immediately because of the low COI barcode diversity.
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Affiliation(s)
- Yanjun Shen
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of SciencesInstitute of HydrobiologyChinese Academy of SciencesWuhan430072HubeiChina
- University of Chinese Academy of SciencesBeijing100039China
| | - Lihong Guan
- College of Life Science and TechnologyXinxiang Medical UniversityHe'nan Xinxiang453003China
| | - Dengqiang Wang
- The Key Laboratory of Freshwater Biodiversity ConservationMinistry of AgricultureYangtze River Fisheries Research InstituteChinese Academy of Fishery SciencesWuhanChina
| | - Xiaoni Gan
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of SciencesInstitute of HydrobiologyChinese Academy of SciencesWuhan430072HubeiChina
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Doğaç E, Ağdamar S, Keskin E, Tarkan AS, Yapıcı S, Acar Ü. Mitochondrial genetic variations of an introduced freshwater fish, goldfish Carassius auratus at the frontier between Europe and Asia (western Anatolia, Turkey): proximity to Europe rather than East Asia? Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4008-4014. [PMID: 25648924 DOI: 10.3109/19401736.2014.1003820] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Carassius auratus is one of the most significant ornamental and food fishes of the world that is globally distributed and well known. Although it is known to have existed at least for six decades and expanding its distribution range in Turkish waters, there is a dearth of information on genetic structure and variations of goldfish in Turkey. In this study, four mitochondrial genes (Cytochrome b, cytochrome oxidase II, 12S ribosomal RNA, and 16S ribosomal RNA) were used to infer the genetic variations of goldfish populations sampled from western part of Anatolia, Turkey. Three populations were clustered under three haplotypes for each gene and all haplotypes were special. Cytochrome b was found to have more variable sites and higher genetic diversity than other genes. According to the haplotype networks, goldfish populations in Turkey showed high level of genetic structuring and originated from the common haplotype known in native East Asian populations of the species. Extensive sampling scheme covering whole Anatolia should provide better understanding on the dispersal pattern of the species.
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Affiliation(s)
- Ersin Doğaç
- a Department of Medicinal and Aromatic Plants , Köyceğiz Vocational School, Muğla Sıtkı Koçman University , Muğla , Turkey
| | - Sevan Ağdamar
- b Faculty of Fisheries , Muğla Sıtkı Koçman University , Muğla , Turkey , and
| | - Emre Keskin
- c Department of Fisheries and Aquaculture, Faculty of Agriculture , Ankara University , Ankara , Turkey
| | - Ali Serhan Tarkan
- b Faculty of Fisheries , Muğla Sıtkı Koçman University , Muğla , Turkey , and
| | - Sercan Yapıcı
- b Faculty of Fisheries , Muğla Sıtkı Koçman University , Muğla , Turkey , and
| | - Ümit Acar
- b Faculty of Fisheries , Muğla Sıtkı Koçman University , Muğla , Turkey , and
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Ağdamar S, Tarkan AS, Keskin E, Top N, Doğaç E, Baysal Ö, Emiroğlu Ö. The role of environmental factors and genetic diversity on colonization success of a non-native fish, Lepomis gibbosus from western part of Turkey. BIOCHEM SYST ECOL 2015. [DOI: 10.1016/j.bse.2014.12.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Simmons MP, Norton AP. Divergent maximum-likelihood-branch-support values for polytomies. Mol Phylogenet Evol 2014; 73:87-96. [DOI: 10.1016/j.ympev.2014.01.018] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 01/09/2014] [Accepted: 01/21/2014] [Indexed: 10/25/2022]
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