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Qi S, Fan S, Li H, He Y, Zhang Y, Zhao W, Xu Q, Chen G. Analysis of Genetic Diversity and Population Structure of Endemic Endangered Goose ( Anser cygnoides) Breeds Based on Mitochondrial CYTB. Animals (Basel) 2024; 14:1480. [PMID: 38791697 PMCID: PMC11117250 DOI: 10.3390/ani14101480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 05/12/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
The analysis of the genetic diversity and historical dynamics of endemic endangered goose breeds structure has attracted great interest. Although various aspects of the goose breed structure have been elucidated, there is still insufficient research on the genetic basis of endemic endangered Chinese goose breeds. In this study, we collected blood samples from Lingxiang White (LX), Yan (YE), Yangjiang (YJ), Wuzong (WZ), Xupu (XP), and Baizi (BZ) geese (Anser cygnoides) and used Sanger sequencing to determine the partial sequence of the cytochrome b (CYTB) gene in a total of 180 geese. A total of 117 polymorphic sites were detected in the 707 bp sequence of the mtDNA CYTB gene after shearing and correction, accounting for approximately 16.55% of the entire sequence. The AT content (51.03%) of the processed sequence was slightly higher than the GC content (48.97%), indicating a preference for purine bases. The YJ, YE, and WZ breeds had the highest population genetic diversity, with a haplotype diversity greater than 0.9 (Hd > 0.9) and average population nucleotide difference of 8.01 (K > 8.01). A total of 81 haplotypes were detected and divided into six major branches. Among the six goose breeds, there were frequent genetic exchanges among LX, YJ, YE, and WZ geese (Nm > 15.00). We analyzed the distribution of base-mismatch differences in goose breeds and tested their historical dynamics for neutrality in Tajima's D and Fu's Fs. For YJ and WZ geese, Tajima's D > 0, but the difference was not significant (p > 0.05). The actual values for the two breeds exhibited multimodal Poisson distributions. The population patterns of the WZ and YJ geese are purportedly relatively stable, and the breeds have not experienced population expansions or bottleneck effects, which is consistent with the neutrality test results. This study provides new insights into the diverse genetic origins and historical dynamics that sustain endemic endangered goose breeds.
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Affiliation(s)
- Shangzong Qi
- Key Laboratory for Evaluation and Utilization of Poultry Genetic Resources, Ministry of Agriculture and Rural Affairs, Yangzhou University, Yangzhou 225009, China; (S.Q.); (S.F.); (H.L.); (Y.H.); (W.Z.); (Q.X.); (G.C.)
- Key Laboratory for Evaluation and Utilization of Livestock and Poultry Resources (Poultry), Ministry of Agriculture and Rural Affairs, Yangzhou 225009, China
| | - Suyu Fan
- Key Laboratory for Evaluation and Utilization of Poultry Genetic Resources, Ministry of Agriculture and Rural Affairs, Yangzhou University, Yangzhou 225009, China; (S.Q.); (S.F.); (H.L.); (Y.H.); (W.Z.); (Q.X.); (G.C.)
| | - Haoyu Li
- Key Laboratory for Evaluation and Utilization of Poultry Genetic Resources, Ministry of Agriculture and Rural Affairs, Yangzhou University, Yangzhou 225009, China; (S.Q.); (S.F.); (H.L.); (Y.H.); (W.Z.); (Q.X.); (G.C.)
| | - Yufan He
- Key Laboratory for Evaluation and Utilization of Poultry Genetic Resources, Ministry of Agriculture and Rural Affairs, Yangzhou University, Yangzhou 225009, China; (S.Q.); (S.F.); (H.L.); (Y.H.); (W.Z.); (Q.X.); (G.C.)
| | - Yang Zhang
- Key Laboratory for Evaluation and Utilization of Poultry Genetic Resources, Ministry of Agriculture and Rural Affairs, Yangzhou University, Yangzhou 225009, China; (S.Q.); (S.F.); (H.L.); (Y.H.); (W.Z.); (Q.X.); (G.C.)
- Key Laboratory for Evaluation and Utilization of Livestock and Poultry Resources (Poultry), Ministry of Agriculture and Rural Affairs, Yangzhou 225009, China
| | - Wenming Zhao
- Key Laboratory for Evaluation and Utilization of Poultry Genetic Resources, Ministry of Agriculture and Rural Affairs, Yangzhou University, Yangzhou 225009, China; (S.Q.); (S.F.); (H.L.); (Y.H.); (W.Z.); (Q.X.); (G.C.)
- Key Laboratory for Evaluation and Utilization of Livestock and Poultry Resources (Poultry), Ministry of Agriculture and Rural Affairs, Yangzhou 225009, China
| | - Qi Xu
- Key Laboratory for Evaluation and Utilization of Poultry Genetic Resources, Ministry of Agriculture and Rural Affairs, Yangzhou University, Yangzhou 225009, China; (S.Q.); (S.F.); (H.L.); (Y.H.); (W.Z.); (Q.X.); (G.C.)
- Key Laboratory for Evaluation and Utilization of Livestock and Poultry Resources (Poultry), Ministry of Agriculture and Rural Affairs, Yangzhou 225009, China
| | - Guohong Chen
- Key Laboratory for Evaluation and Utilization of Poultry Genetic Resources, Ministry of Agriculture and Rural Affairs, Yangzhou University, Yangzhou 225009, China; (S.Q.); (S.F.); (H.L.); (Y.H.); (W.Z.); (Q.X.); (G.C.)
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
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Liao TY, Lu PL, Yu YH, Huang WC, Shiao JC, Lin HD, Jhuang WC, Chou TK, Li F. Amphidromous but endemic: Population connectivity of Rhinogobius gigas (Teleostei: Gobioidei). PLoS One 2021; 16:e0246406. [PMID: 33571236 PMCID: PMC7877787 DOI: 10.1371/journal.pone.0246406] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 01/19/2021] [Indexed: 11/18/2022] Open
Abstract
Rhinogobius gigas is an amphidromous fish endemic to eastern Taiwan. Fishes with the diadromous behavior are expected to have a broader distribution range and higher genetic homogeneity despite that some amphidromous fishes with limited distribution are observed and R. gigas is an additional exception with a limited distribution range. Rhinogobius gigas has been documented to be retained inshore near the river plume with a short pelagic larval duration of 30-40 days, which may account for the endemism of this species. The short marine larval stage of R. gigas may imply a population genetic structure and the aim of the present study is to test whether the population genetic structure is present in R. gigas. To test the population genetic structure, fragments of mitochondrial displacement loop and cytochrome c oxidase subunit I were sequenced to provide molecular inference for genetic structure among populations. Sixty-nine haplotypes were identified among 191 R. gigas from 10 populations of eastern Taiwan and the mean haplotype and nucleotide diversities for all samples were 0.956 and 0.0024, respectively, implying a bottleneck followed by a recent population expansion further supported by Fu's Fs (-26.6; p < 0.001) and Tajima's D (-1.5; p = 0.037) values. The phylogenetic analysis revealed lack of genetic structure and the bush-like median joining network without commonly shared haplotypes supports the same scenario. The genetic homogeneity is probably due to the amphidromous life history providing the opportunity for passive larval transportation among the rivers through coastal currents in eastern Taiwan. The endemism to eastern Taiwan may be a consequence of complicated interactions among short pelagic larval duration, interspecific competition and coastal currents.
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Affiliation(s)
- Te-Yu Liao
- Department of Oceanography, National Sun Yat-sen University, Kaohsiung, Taiwan
- * E-mail: ,
| | - Pei-Luen Lu
- Department of Life Science, National Taitung University, Taitung, Taiwan
| | - Yuan-Huan Yu
- Department of Oceanography, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - 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
| | - Jen-Chieh Shiao
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan
| | - Hung-Du Lin
- Affiliated School of National Tainan First Senior High School, Tainan, Taiwan
| | - Wei-Cheng Jhuang
- Doctoral Degree Program in Marine Biotechnology, National Sun Yat-sen University, Kaohsiung, Taiwan
- Doctoral Degree Program in Marine Biotechnology, Academia Sinica, Taipei, Taiwan
| | - Tak-Kei Chou
- Department of Oceanography, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Fan Li
- Department of Oceanography, National Sun Yat-sen University, Kaohsiung, Taiwan
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Mandal S, Singh A, Sah P, Singh RK, Kumar R, Lal KK, Mohindra V. Genetic and morphological assessment of a vulnerable large catfish, Silonia silondia (Hamilton, 1822), in natural populations from India. JOURNAL OF FISH BIOLOGY 2021; 98:430-444. [PMID: 33044745 DOI: 10.1111/jfb.14587] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 10/07/2020] [Indexed: 06/11/2023]
Abstract
Silonia silondia is a commercially important fish distributed in Asian countries, which is under threat due to overexploitation. This study focuses on the morphological analysis and genetic variation of S. silondia individuals, through truss network and sequencing of two mitochondrial regions, respectively, from six wild populations of the Ganga and Mahanadi river systems in India. A total of 38 haplotypes was observed by analysing combined mitochondrial genes (cytochrome b + ATPase 6/8) in 247 individuals of S. silondia collected from six populations. Average haplotype and nucleotide diversities were 0.8508 and 0.00231, respectively. Genetic structure analysis showed the predominant cause of genetic variation to be within populations. The two clades were observed among the haplotypes and time of divergence from their most probable ancestor was estimated to be around 0.3949 mya. Analysis of combined mitochondrial genes in six populations of S. silondia resulted into three management units or genetic stocks. The truss network analysis was carried out by interconnecting 12 landmarks from digital images of specimens to identify phenotypic stocks. Sixty-five truss morphometric variables were analysed for geometric shape variation which revealed morphological divergence in River Son specimens. The present study presents molecular markers and genetic diversity data which can be critical input for conservation and management of differentiated populations and future monitoring of the genetic bottleneck. The morphological shape analysis clearly shows that variation in the insertion of adipose fin is an important parameter influencing the morphological discrimination.
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Affiliation(s)
- Sangeeta Mandal
- ICAR-National Bureau of Fish Genetic Resources (NBFGR), Lucknow, India
| | - Achal Singh
- ICAR-National Bureau of Fish Genetic Resources (NBFGR), Lucknow, India
| | - Priyanka Sah
- ICAR-National Bureau of Fish Genetic Resources (NBFGR), Lucknow, India
| | - Rajeev K Singh
- ICAR-National Bureau of Fish Genetic Resources (NBFGR), Lucknow, India
| | - Raj Kumar
- ICAR-National Bureau of Fish Genetic Resources (NBFGR), Lucknow, India
| | - Kuldeep K Lal
- ICAR-National Bureau of Fish Genetic Resources (NBFGR), Lucknow, India
| | - Vindhya Mohindra
- ICAR-National Bureau of Fish Genetic Resources (NBFGR), Lucknow, India
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Abstract
Diadromy, the predictable movements of individuals between marine and freshwater environments, is biogeographically and phylogenetically widespread across fishes. Thus, despite the high energetic and potential fitness costs involved in moving between distinct environments, diadromy appears to be an effective life history strategy. Yet, the origin and molecular mechanisms that underpin this migratory behavior are not fully understood. In this review, we aim first to summarize what is known about diadromy in fishes; this includes the phylogenetic relationship among diadromous species, a description of the main hypotheses regarding its origin, and a discussion of the presence of non-migratory populations within diadromous species. Second, we discuss how recent research based on -omics approaches (chiefly genomics, transcriptomics, and epigenomics) is beginning to provide answers to questions on the genetic bases and origin(s) of diadromy. Finally, we suggest future directions for -omics research that can help tackle questions on the evolution of diadromy.
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Affiliation(s)
- M. Lisette Delgado
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Daniel E. Ruzzante
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada
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5
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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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Colihueque N, Estay FJ, Crespo JE, Arriagada A, Baessolo L, Canales-Aguirre CB, Marín J, Carrasco R. Genetic Differentiation and Origin of Naturalized Rainbow Trout Populations From Southern Chile, Revealed by the mtDNA Control Region Marker. Front Genet 2019; 10:1212. [PMID: 31921284 PMCID: PMC6933019 DOI: 10.3389/fgene.2019.01212] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 11/04/2019] [Indexed: 12/03/2022] Open
Abstract
Numerous self-sustaining naturalized or introduced populations of rainbow trout (Oncorhynchus mykiss) are widely distributed throughout the freshwaters of southern Chile. In this study, analysis of the mitochondrial DNA control region (CR) marker was conducted to investigate the level of genetic divergence among populations and their phylogenetic relationships with respect to native lineages. This information provided a framework to interpret the genetic structure and origin that was shaped during historical trout introduction efforts. To this end, we analyzed eleven naturalized populations of lakes and rivers from five basins. The CR marker revealed five haplotypes. The overall haplotype (H) and nucleotide (Π) diversities were 0.684 ± 0.030 and 0.00460 ± 0.00012, respectively. Global FST was 0.169, with several pairwise FST estimates showing significant differences (P < 0.05). The exact test of population differentiation corroborated this result (P < 0.001). Significant geographic structure was found (P < 0.05), with variations explained primarily by differences within populations (61.65%) and among group basins (20.82%). Maximum likelihood phylogenetic analysis resolved two distinct clades with medium bootstrap support when naturalized populations were aligned in conjunction with reference native lineages. The haplotype network revealed a close association between naturalized populations and four main haplotypes representative of three native ecotypes or lineages from western North America (rainbow trout, steelhead trout and redband trout). These results indicate a genetic population structuring for naturalized rainbow trout from southern Chile and an origin probably represented by multiple lineages sources. Thus, mitochondrial DNA data strongly suggest that stocking of rainbow trout from different origins may have occurred during or after the initial introduction efforts.
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Affiliation(s)
- Nelson Colihueque
- Laboratorio de Biología Molecular y Citogenética, Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, Osorno, Chile
| | - Francisco J Estay
- Gerencia de Investigación y Desarrollo, Piscícola Huililco Ltda., Pucón, Chile
| | - Julio E Crespo
- Laboratorio de Ciencias Naturales y Sostenibilidad-Programa IBAM, Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, Osorno, Chile
| | - Aldo Arriagada
- Laboratorio de Biología Molecular y Citogenética, Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, Osorno, Chile
| | | | - Cristian B Canales-Aguirre
- Centro i∼mar, Universidad de Los Lagos, Puerto Montt, Chile.,Núcleo Milenio de Salmónidos Invasores (INVASAL), Concepción, Chile
| | - Javier Marín
- Programa de Pesca Recreativa, Departamento de Acuicultura y Recursos Agroalimentarios, Universidad de Los Lagos, Osorno, Chile
| | - René Carrasco
- Programa de Pesca Recreativa, Departamento de Acuicultura y Recursos Agroalimentarios, Universidad de Los Lagos, Osorno, Chile
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Joshi BD, Johnson JA, Negi T, Singh A, Goyal SP, Negi RK. Understanding genetic diversity and population genetic structure of three Cyprinidae fishes occupying the same habitat from Uttarakhand, India. MITOCHONDRIAL DNA PART B-RESOURCES 2019; 4:2956-2961. [PMID: 33365810 PMCID: PMC7706785 DOI: 10.1080/23802359.2019.1662740] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Different pattern of genetic diversity and population genetic structure among the species are reported due to their different ecological requirements, adaptability and the evolutionary histories. Understanding such patterns in a species and between the populations is important to develop the effective conservation plans. Very limited studies are available, how different factors influencing the gene flow of a species especially in fish communities. Therefore, the present study is aimed to document the genetic diversity and population genetic structure of the three species of Cyprinidae fishes (Puntius sophore, Pethia ticto, and Pethia conchonius) sharing the same kind of habitat using the mitochondrial cytochrome c oxidase subunit 1 (CO1). We used 80 samples of the three species from different river/streams. In which we observed total 4–9 haplotypes in all three species with the intra-species sequenced divergence ranges between 0.002 and 0.019. The nucleotide and haplotype diversity was ranged from 0.002040 to 0.01007 and from 0.251 to 0.822, respectively. Neutrality test values were found to be positive only in the P. ticto but statistically non-significant. The AMOVA variation among the populations was 8.89–84.30% whereas, within the populations, it was ranged from 15.70 to 91.11%. The median-joining haplotype network suggests the stable population size over the time and haplotypes were clustered with respect to their geographic locations except the P. conchonius. Similar pattern observed in the phylogenetic tree.
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Affiliation(s)
- Bheem Dutt Joshi
- Department of Zoology and Environmental Sciences, Gurukula Kangri University, Haridwar, India.,Wildlife Institute of India, Dehradun, India
| | - J A Johnson
- Wildlife Institute of India, Dehradun, India
| | - Tarana Negi
- Department of Zoology, Govt. College, Bahadurgarh, India
| | | | - S P Goyal
- Wildlife Institute of India, Dehradun, India
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Abdou A, Lord C, Keith P, Galzin R. Phylogéographie de Neritina stumpffi Boettger, 1890 et Neritina canalis Sowerby, 1825 (Gastropoda, Cycloneritida, Neritidae). ZOOSYSTEMA 2019. [DOI: 10.5252/zoosystema2019v41a12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Ahmed Abdou
- Unité Biologie des organismes et écosystèmes aquatiques (BOREA), Muséum national d'Histoire naturelle, Sorbonne Université, Université de Caen Normandie, Université des Antilles, CNRS, IRD, case postale 26, 57 rue Cuvier, F-75231 Paris cedex 05 (Fran
| | - Clara Lord
- Unité Biologie des organismes et écosystèmes aquatiques (BOREA), Muséum national d'Histoire naturelle, Sorbonne Université, Université de Caen Normandie, Université des Antilles, CNRS, IRD, case postale 26, 57 rue Cuvier, F-75231 Paris cedex 05 (Fran
| | - Philippe Keith
- Unité Biologie des organismes et écosystèmes aquatiques (BOREA), Muséum national d'Histoire naturelle, Sorbonne Université, Université de Caen Normandie, Université des Antilles, CNRS, IRD, case postale 26, 57 rue Cuvier, F-75231 Paris cedex 05 (Fran
| | - René Galzin
- Laboratoire d'excellence Corail, USR 3278 CNRS-EPHE-UPVD, Centre de Recherches insulaires et Observatoire de l'Environnement (CRIOBE), BP 1013 Papetoai, 98729 Moorea, Polynésie française (France)
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Sandoval-Huerta ER, Beltrán-López RG, Pedraza-Marrón CR, Paz-Velásquez MA, Angulo A, Robertson DR, Espinoza E, Domínguez-Domínguez O. The evolutionary history of the goby Elacatinus puncticulatus in the tropical eastern pacific: Effects of habitat discontinuities and local environmental variability. Mol Phylogenet Evol 2018; 130:269-285. [PMID: 30359746 DOI: 10.1016/j.ympev.2018.10.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 09/05/2018] [Accepted: 10/15/2018] [Indexed: 10/28/2022]
Abstract
Habitat discontinuities, temperature gradients, upwelling systems, and ocean currents, gyres and fronts, can affect distributions of species with narrow environmental tolerance or motility and influence the dispersal of pelagic larvae, with effects ranging from the isolation of adjacent populations to connections between them. The coast of the Tropical Eastern Pacific (TEP) is a highly dynamic environment, with various large gyres and upwelling systems, alternating currents and large rocky-habitat discontinuities, which may greatly influence the genetic connectivity of populations in different parts of the coast. Elacatinus puncticulatus is a cryptic, shallow-living goby that is distributed along the continental shore of virtually the entire TEP, which makes it a good model for testing the influence of these environmental characteristics in the molecular evolution of widespread species in this region. A multilocus phylogeny was used to evaluate the influence of habitat gaps, and oceanographic processes in the evolutionary history of E. puncticulatus throughout its geographical range in the TEP. Two well-supported allopatric clades (one with two allopatric subclades) were recovered, the geographic distribution of which does not correspond to any previously proposed major biogeographic provinces. These populations show strong genetic structure and substantial genetic distances between clades and sub-clades (cytb 0.8-7.3%), with divergence times between them ranging from 0.53 to 4.88 Mya, and recent population expansions dated at 170-130 Kya. The ancestral area of all populations appears to be the Gulf of Panama, while several isolation events have formed the phylogeographic patterns evident in this species. Local and regional oceanographic processes as well as habitat discontinuities have shaped the distribution patterns of the genetic lineages along the continental TEP. Large genetic distances, high genetic differentiation, and the results of species-tree and phylogenetic analyses indicate that E. puncticulatus comprises a complex of three allopatric species with an unusual geographic arrangement.
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Affiliation(s)
- E R Sandoval-Huerta
- Programa Institucional de Maestría en Ciencias Biológicas, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Edificio "R" planta baja, Ciudad Universitaria, Morelia, Michoacán 58030, Mexico; Laboratorio de Biología Acuática, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Edificio "R" planta baja, Ciudad Universitaria, Morelia, Michoacán 58030, Mexico
| | - R G Beltrán-López
- Programa Institucional de Doctorado en Ciencias Biológicas, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Edificio "R" planta baja, Ciudad Universitaria, Morelia, Michoacán 58030, Mexico; Laboratorio de Ictiología, Centro de Investigaciones Biológicas, Universidad Autónoma del Estado de Morelos, Av. Universidad no. 1001, Cuernavaca, Morelos 62209, Mexico.
| | - C R Pedraza-Marrón
- Programa Institucional de Maestría en Ciencias Biológicas, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Edificio "R" planta baja, Ciudad Universitaria, Morelia, Michoacán 58030, Mexico; Laboratorio de Biología Acuática, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Edificio "R" planta baja, Ciudad Universitaria, Morelia, Michoacán 58030, Mexico
| | - M A Paz-Velásquez
- Centro de Estudios del Mar y Acuicultura, Universidad de San Carlos de Guatemala, Guatemala City, Guatemala
| | - A Angulo
- Museo de Zoología y Centro de Investigación en Ciencias del Mar y Limnología, Universidad de Costa Rica. 11501-2060, San Pedro de Montes de Oca, San José, Costa Rica
| | - D R Robertson
- Naos Marine Laboratory, Smithsonian Tropical Research Institute, Balboa, Panama.
| | - E Espinoza
- Dirección del Parque Nacional Galápagos, Puerto Ayora, Islas Galápagos, Ecuador.
| | - O Domínguez-Domínguez
- Laboratorio de Biología Acuática, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Edificio "R" planta baja, Ciudad Universitaria, Morelia, Michoacán 58030, Mexico.
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10
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Mennesson MI, Bonillo C, Feunteun E, Keith P. Phylogeography of Eleotris fusca (Teleostei: Gobioidei: Eleotridae) in the Indo-Pacific area reveals a cryptic species in the Indian Ocean. CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1063-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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11
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Negi RK, Joshi BD, Johnson JA, De R, Goyal SP. Phylogeography of freshwater fish Puntius sophore in India. Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:256-265. [PMID: 28117612 DOI: 10.1080/24701394.2016.1275598] [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: 10/20/2022]
Abstract
Phylogeography and evolutionary history of the freshwater species are poorly known. We document the phylogeography of widely distributed Puntius sophore using cytochrome oxidase subunit I (COI) gene of 650 bp. In the present study, we used 61 individual sequences from known geographic locations across India whereas data are lacking from other parts of its distribution range. Total 20 haplotypes with the intra-species sequence divergence ranging from 0.004 to 0.025 were observed and they were split into two major clades (North and Northeastern to Central India). Two distant geographic (North and Northeastern to Central India) regions shared haplotype suggesting ancient river connectivity or introduction of species from Northeast and Central India. Overall nucleotide and haplotype diversities were 0.00971 and 0.915. The Tajima's D and Fu's Fs values were found negative but non-significant thus rejecting the population expansion model followed by the multimodal mode of mismatch distribution. Bayesian skyline plots from both the clade showed steady population history over time; and start of decline in recent years in the clade B (∼1000-1500 years). The present finding is in support to the 'Satpura hypothesis' proposed to explain species movement patterns from Southeast Asian countries to Indian subcontinent, seconded by P. sophore showing high genetic diversity within Northern India clade (high genetic splits) because of presence of high river network in comparison to other parts of the country.
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Affiliation(s)
- R K Negi
- a Department of Zoology , University of Delhi , Delhi , India
| | - Bheem Dutt Joshi
- b Department of Zoology and Environmental Sciences , Gurukula Kangri University , Haridwar , India.,c Wildlife Institute of India , Dehradun , India
| | - J A Johnson
- c Wildlife Institute of India , Dehradun , India
| | - Rahul De
- c Wildlife Institute of India , Dehradun , India
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Yang JQ, Hsu KC, Zhou XD, Kuo PH, Lin HD, Liu D, Bao BL, Tang WQ. New insights on geographical/ecological populations within Coilia nasus (Clupeiformes: Engraulidae) based on mitochondrial DNA and microsatellites. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 29:158-164. [PMID: 28025897 DOI: 10.1080/24701394.2016.1261850] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The Coilia nasus is an important fish species, which is of commercial values in China. In order to manage the fisheries resources and the development of sustainable fishing strategies to protect this species, 11 microsatellite loci polymorphisms and mtDNA COI sequences were used to examine the genetic diversity of C. nasus in Japan and China. In total, the 40 COI haplotypes and 93 microsatellite alleles were detected. The mtDNA phylogeny did not support population grouping, but the distribution patterns of mtDNA haplotypes and the results of STRUCTURE analysis based on microsatellite indicated a degree of genetic isolation in this species. Our study suggested that the lack of a population genetic structure might result in its amphidromous life cycle, and the geographical distance and habitat fragments might cause isolated populations. Thus, the sampling populations of C. nasus in Japan and China could be divided as four geographical/ecological populations.
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Affiliation(s)
- Jin-Quan Yang
- a Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources , Shanghai Ocean University, Ministry of Education , Shanghai , China
| | - Kui-Ching Hsu
- b Department of Industrial Management , National Taiwan University of Science and Technology , Taipei , Taiwan
| | - Xiao-Du Zhou
- a Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources , Shanghai Ocean University, Ministry of Education , Shanghai , China
| | - Po-Hsun Kuo
- b Department of Industrial Management , National Taiwan University of Science and Technology , Taipei , Taiwan
| | - Hung-Du Lin
- c Department of Biology , The Affiliated School of National Tainan First Senior High School , Tainan , Taiwan
| | - Dong Liu
- a Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources , Shanghai Ocean University, Ministry of Education , Shanghai , China
| | - Bao-Long Bao
- a Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources , Shanghai Ocean University, Ministry of Education , Shanghai , China
| | - Wen-Qiao Tang
- a Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources , Shanghai Ocean University, Ministry of Education , Shanghai , China
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13
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Hidaka H, Kano Y. Morphological and Genetic Variation Between the Japanese Populations of the Amphidromous Snail Stenomelania crenulata (Cerithioidea: Thiaridae). Zoolog Sci 2016; 31:593-602. [PMID: 25186931 DOI: 10.2108/zs140074] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Freshwater gastropods often have limited dispersal capability and small geographic ranges, and face severe threats from habitat loss and degradation. However, in addition to the scarcity of knowledge on their life history traits, species taxonomy has not been adequately resolved and boundaries between intra- and interspecific variation remain unclear for many taxa. One such example of an indeterminate species boundary with implications for conservation issues is the relationship between the thiarid snails Stenomelania crenulata in Okinawa and southwards (ranked as CR+EN in the 2012 Japanese Red List) and S. rufescens in mainland Japan (VU). The results of our multi-disciplinary investigation into variation in the shell morphology and mitochondrial (COI) and nuclear (ITS-1) gene sequences suggest that S. rufescens represents a geographic variant and a junior synonym of S. crenulata. The widespread geographic range of S. crenulata, spanning a few thousand kilometers north to south, is possible due to an amphidromous life cycle that involves a marine planktotrophic larval phase and upstream migration after settlement in estuaries. Nevertheless, there is recognizable morphological and genetic differentiation between distant populations, probably reflecting a relatively short pelagic duration and possibly also infrequent transoceanic dispersal; metamorphic competence is achieved in two weeks in full seawater and even more rapidly in brackish water. The Okinawan population, with only a few known localities, therefore deserves the high conservation priority; conservation efforts need to involve the proper maintenance of migration pathways including all marine, brackish and freshwater environments.
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Affiliation(s)
- Hiroka Hidaka
- 1 Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8564, Japan
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14
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Galván-Quesada S, Doadrio I, Alda F, Perdices A, Reina RG, García Varela M, Hernández N, Campos Mendoza A, Bermingham E, Domínguez-Domínguez O. Molecular Phylogeny and Biogeography of the Amphidromous Fish Genus Dormitator Gill 1861 (Teleostei: Eleotridae). PLoS One 2016; 11:e0153538. [PMID: 27074006 PMCID: PMC4830628 DOI: 10.1371/journal.pone.0153538] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Accepted: 03/28/2016] [Indexed: 11/23/2022] Open
Abstract
Species of the genus Dormitator, also known as sleepers, are representatives of the amphidromous freshwater fish fauna that inhabit the tropical and subtropical coastal environments of the Americas and Western Africa. Because of the distribution of this genus, it could be hypothesized that the evolutionary patterns in this genus, including a pair of geminate species across the Central American Isthmus, could be explained by vicariance following the break-up of Gondwana. However, the evolutionary history of this group has not been evaluated. We constructed a time-scaled molecular phylogeny of Dormitator using mitochondrial (Cytochrome b) and nuclear (Rhodopsin and β-actin) DNA sequence data to infer and date the cladogenetic events that drove the diversification of the genus and to relate them to the biogeographical history of Central America. Two divergent lineages of Dormitator were recovered: one that included all of the Pacific samples and another that included all of the eastern and western Atlantic samples. In contrast to the Pacific lineage, which showed no phylogeographic structure, the Atlantic lineage was geographically structured into four clades: Cameroon, Gulf of Mexico, West Cuba and Caribbean, showing evidence of potential cryptic species. The separation of the Pacific and Atlantic lineages was estimated to have occurred ~1 million years ago (Mya), whereas the four Atlantic clades showed mean times of divergence between 0.2 and 0.4 Mya. The splitting times of Dormitator between ocean basins are similar to those estimated for other geminate species pairs with shoreline estuarine preferences, which may indicate that the common evolutionary histories of the different clades are the result of isolation events associated with the closure of the Central American Isthmus and the subsequent climatic and oceanographic changes.
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Affiliation(s)
- Sesángari Galván-Quesada
- Programa Institucional de Doctorado en Ciencias Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, México
- Laboratorio de Biología Acuática, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, México
- * E-mail: (SGQ); (ODD)
| | - Ignacio Doadrio
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain
| | - Fernando Alda
- Smithsonian Tropical Research Institute, Apartado 2072, Balboa, Republic of Panama
| | - Anabel Perdices
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain
- Smithsonian Tropical Research Institute, Apartado 2072, Balboa, Republic of Panama
| | - Ruth Gisela Reina
- Smithsonian Tropical Research Institute, Apartado 2072, Balboa, Republic of Panama
| | - Martín García Varela
- Instituto de Biología, Universidad Nacional Autónoma de México, Distrito Federal, México
| | | | - Antonio Campos Mendoza
- Laboratorio de Biología Acuática, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, México
| | - Eldredge Bermingham
- Smithsonian Tropical Research Institute, Apartado 2072, Balboa, Republic of Panama
| | - Omar Domínguez-Domínguez
- Laboratorio de Biología Acuática, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, México
- * E-mail: (SGQ); (ODD)
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Moody KN, Hunter SN, Childress MJ, Blob RW, Schoenfuss HL, Blum MJ, Ptacek MB. Local adaptation despite high gene flow in the waterfall-climbing Hawaiian goby,Sicyopterus stimpsoni. Mol Ecol 2015; 24:545-63. [DOI: 10.1111/mec.13016] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 11/12/2014] [Accepted: 11/22/2014] [Indexed: 01/27/2023]
Affiliation(s)
- K. N. Moody
- Department of Biological Sciences; Clemson University; 132 Long Hall Clemson SC 29634 USA
| | - S. N. Hunter
- Department of Biological Sciences; Clemson University; 132 Long Hall Clemson SC 29634 USA
- Department of Ecology and Evolutionary Biology; Tulane University; 400 Lindy Boggs New Orleans LA 70118 USA
| | - M. J. Childress
- Department of Biological Sciences; Clemson University; 132 Long Hall Clemson SC 29634 USA
| | - R. W. Blob
- Department of Biological Sciences; Clemson University; 132 Long Hall Clemson SC 29634 USA
| | - H. L. Schoenfuss
- Aquatic Toxicology Laboratory; St. Cloud State University; 720 Fourth Ave S, WSB-273 St. Cloud MN 56301 USA
| | - M. J. Blum
- Department of Ecology and Evolutionary Biology; Tulane University; 400 Lindy Boggs New Orleans LA 70118 USA
| | - M. B. Ptacek
- Department of Biological Sciences; Clemson University; 132 Long Hall Clemson SC 29634 USA
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