Population Genetic Structure and Phylogeography of Masu Salmon (Oncorhynchus Masou Masou) Inferred from Mitochondrial and Microsatellite DNA Analyses

Yu, Jeong Nam; Azuma, Noriko; Yoon, Moongeun; Брыков, Вл. А.; Urawa, Shigehiko; Nagata, Mitsuhiro; Jin, Dae Ho; S, Abe

doi:10.2108/zsj.27.375

Cited by 19 publications

(21 citation statements)

References 40 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The mitochondrial COI and nuclear ITS-1 displayed significantly different levels of genetic diversity which are often seen in phylogeographical studies with multiple markers [67], [68]. Generally, animal mitochondrial DNA accumulates nucleotide substitutions severalfold faster than does nuclear DNA (see review by Avise [69]).…”

Section: Discussionmentioning

confidence: 99%

Phylogeography of Bivalve Cyclina sinensis: Testing the Historical Glaciations and Changjiang River Outflow Hypotheses in Northwestern Pacific

Kong

et al. 2012

PLoS ONE

View full text Add to dashboard Cite

BackgroundThe marginal seas of northwestern Pacific are characterized by unique topography and intricate hydrology. Two hypotheses have been proposed to explain genetic patterns of marine species inhabiting the region: the historical glaciations hypothesis suggests population genetic divergence between sea basins, whereas the Changjiang River outflow hypothesis suggests genetic break in line with the Changjiang Estuary. Here the phylogeography of bivalve Cyclina sinensis was investigated to test the validity of these two hypotheses for intertidal species in three marginal seas—the East China Sea (ECS), the South China Sea (SCS), and the Japan Sea (JPS).Methodology/Principal FindingsFragments of two markers (mitochondrial COI and nuclear ITS-1) were sequenced for 335 individuals collected from 21 populations. Significant pairwise ΦST were observed between different marginal sea populations. Network analyses illustrated restricted distribution of haplogroups/sub-haplogroups to sea basins, with a narrow secondary contact zone between the ECS and SCS. Demographic expansion was inferred for ECS and SCS lineages using mismatch distributions, neutral tests, and extended Bayesian Skyline Plots. Based on a molecular clock method, the divergence times among COI lineages were estimated dating from the Pleistocene.ConclusionsThe phylogeographical break revealed for C. sinensis populations is congruent with the historical isolation of sea basins rather than the putative Changjiang River outflow barrier. The large land bridges extending between seas during glaciation allowed accumulation of mutations and subsequently gave rise to deep divergent lineages. The low-dispersal capacity of the clam and coastal oceanography may facilitate the maintenance of the historical patterns as barriers shift. Our study supports the historical glaciations hypothesis for interpreting present-day phylogeographical patterns of C. sinensis, and highlights the importance of historical glaciations for generating genetic structure of marine coastal species especially those with low-dispersal abilities in northwestern Pacific.

show abstract

Section: Discussionmentioning

confidence: 99%

Phylogeography of Bivalve Cyclina sinensis: Testing the Historical Glaciations and Changjiang River Outflow Hypotheses in Northwestern Pacific

Kong

et al. 2012

PLoS ONE

View full text Add to dashboard Cite

show abstract

“…The ND5 region (1,597 bp) was amplified with the primer pair ND5-F1 and ND5-R ( The relationships among haplotypes were estimated using the TCS program implemented in PopART [28]. To determine the relationships between haplotypes in past studies and the current study, we also analyzed the haplotype network including data of Kitanishi et al [10] and Yu et al [16]. number of samples with each determined MT haplotype are shown for each sampling site in Table 4.…”

Section: Dna Sequence and Genetic Analysismentioning

confidence: 99%

“…[10] and Yu et al [16] (S3 Table and S1 Fig). KS1, KS2, and KS13, were new haplotypes in this region of ND5 in the current study.…”

Section: Haplotype Network Analysismentioning

confidence: 99%

“…To conserve the indigenous O. m. masou resource in a river, their genetic information is required. Genetic study of O. m. masou in Japan has focused mainly on northern Hokkaido Island and some areas of Honshu Island and its surrounding waters (e.g., [10,13,16,17]); studies of this species in Kyushu Island are scarce [18,19]. The Kase River system is located in northwestern Kyushu Island (Fig 1).…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Fingerprinting of hatchery haplotypes by whole-mitogenome sequencing improves genetic studies of masu salmonOncorhynchus masou masou

Kato-Unoki

Umemura

Tashiro

2020

Preprint

View full text Add to dashboard Cite

AbstractStocking hatchery fish can lead to disturbance and extinction of the local indigenous population. Stocking similar lineages to the indigenous population makes it difficult to conduct genetic studies to determine conservation units. We considered that, due to the length of the mitogenome, whole-mitogenome analysis might overcome this problem by enabling identification of hatchery haplotypes. Here, to provide basic information for conservation of indigenous masu salmon Oncorhynchus masou masou, a commonly stocked fish in the Kase River system, Japan, we used whole-mitogenome analysis of fish to identify hatchery haplotypes in the river and in several hatcheries that might be used for stocking. Whole-mitogenome sequencing clearly identified hatchery haplotypes like fingerprints, identifying the tributaries contaminated with hatchery haplotypes. The results suggest that informal stocking of O. m. masou has been performed widely across the Kase River system. Non-hatchery haplotypes mainly belonged to clade I, which was not found in northern Hokkaido Island. Sites without hatchery haplotypes were estimated three, suggesting that these sites are suitable for conservation of the indigenous fish. This study demonstrated that the resolution of the conventional analysis using partial mitogenome is insufficient to distinguish hatchery haplotype from similar lineages. The whole-mitogenome sequences provided accurate information that was not available in the partial sequences, enabling various inferences: e.g., estimation of the origin of stocked fish and circulation of the reared strains. We conclude that whole-mitogenome analysis is useful for the genetic study of this species. The whole-mitogenome data produced will contribute to the conservation, resource management, and further study of O. m. masou.

show abstract

“…SHI a , four yearly collections (SHI97, SHI98, SHI99 and SHI00); MOR b , three hatchery collections (Line 1, Line 2 and Line 3-RR) PCR products were directly sequenced after sequencing reaction with an ABI PRISM BigDye Terminator Cycle Sequencing Ready Reaction Kit version 3.1 on an ABI PRISM 3130XL genetic analyzer (Applied Biosystems). Primers for direct sequencing included the ND5-1F primer and newly designed reverse primers, ND5-R1 and ND5-R2, which were nested to the ND5-3R primer (Yu et al 2010a).…”

Section: Fish Samples and Dna Extractionmentioning

confidence: 99%

Genetic differentiation between collections of hatchery and wild masu salmon (Oncorhynchus masou) inferred from mitochondrial and microsatellite DNA analyses

Azuma

2011

Environ Biol Fish

Self Cite

View full text Add to dashboard Cite

There has been very little effort to understand genetic divergence between wild and hatchery populations of masu salmon (Oncorhynchus masou). In this study, we used mitochondrial (mt) NADH dehydrogenase subunit 5 gene (ND5) and six polymorphic nuclear microsatellite DNA loci to compare the genetic variability in three hatchery broodstocks of masu salmon with the variability in eight putative wild masu populations sampled in five rivers including one known source river for the hatchery broodstocks. Both ND5 and microsatellites showed no significant genetic divergence (based on F ST estimates) between four annual collections from the source river population, suggesting no change in genetic diversity over this time period. The F ST estimates, an analysis of molecular variance (AMOVA), and a neighbor-joining tree using both DNA markers suggested significant differentiation between the three hatchery and all eight putative wild populations. We conclude that genetic diversity of hatchery populations are low relative to putative wild populations of masu salmon, and we discuss the implications for conservation and fisheries management in Hokkaido.

show abstract

Population Genetic Structure and Phylogeography of Masu Salmon (Oncorhynchus Masou Masou) Inferred from Mitochondrial and Microsatellite DNA Analyses

Cited by 19 publications

References 40 publications

Phylogeography of Bivalve Cyclina sinensis: Testing the Historical Glaciations and Changjiang River Outflow Hypotheses in Northwestern Pacific

Phylogeography of Bivalve Cyclina sinensis: Testing the Historical Glaciations and Changjiang River Outflow Hypotheses in Northwestern Pacific

Fingerprinting of hatchery haplotypes by whole-mitogenome sequencing improves genetic studies of masu salmonOncorhynchus masou masou

Genetic differentiation between collections of hatchery and wild masu salmon (Oncorhynchus masou) inferred from mitochondrial and microsatellite DNA analyses

Contact Info

Product

Resources

About