Genetic population structure of chum salmon in the Pacific Rim inferred from mitochondrial DNA sequence variation

Sato, Shunpei; Kojima, Hiroyuki; Ando, Junko; Ando, Hironori; Wilmot, Richard L.; Seeb, Lisa W.; Ефремов, В. В.; LeClair, Larry L.; Buchholz, Wally; Jin, Dao‐Chao; Urawa, Shigehiko; Kaeriyama, Masahide; Urano, Akihisa; S, Abe

doi:10.1007/978-94-007-0983-6_4

Cited by 14 publications

(28 citation statements)

References 33 publications

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“…In particular, the lineage of haplotype H1 showed a clear star-like pattern, with the radiating haplotypes mostly region specific, suggesting their recent appearance and rapid expansion (Slatkin and Hudson, 1991;Rodgers and Harpending, 1992) in Japan, Korea, and Russia. This sort of shallow haplotype genealogy has also been reported in some other Pacific salmon and is probably the consequence of population decreases in glacial periods and subsequent recovery during interglacial periods (Mccusker et al, 2000;Churikov and Gharrett, 2002;Sato et al, 2004).…”

Section: Discussionsupporting

confidence: 74%

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

Azuma

Yoon

et al. 2010

Zoological Science

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Section: Discussionsupporting

confidence: 74%

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

Azuma

Yoon

et al. 2010

Zoological Science

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“…Point mutation heteroplasmy has never been reported in fishes, while a huge number of mitochondrial nucleotide sequences have been determined for genetic variation studies in many fish species including chum salmon (Sato et al, 2001(Sato et al, , 2004 and Japanese flounder (Fujii and Nishida 1997;Sekino et al, 2002). Moreover, the positions of the two heteroplasmic sites which we detected were conservative nonsynonymous sites.…”

mentioning

confidence: 64%

Nonsynonymous Site Heteroplasmy in Fish Mitochondrial DNA

et al. 2005

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Heteroplasmic nucleotide polymorphisms are rarely observed in wild animal mitochondrial DNA. The occurrence of such site heteroplasmy is expected to be extremely rare at nonsynonymous sites where the number of nucleotide substitutions per site is low due to functional constraints. This report deals with nonsynonymous mitochondrial heteroplasmy from two wild fish species, chum salmon and Japanese flounder. We detected an A/C nonsynonymous heteroplasmic site corresponding to putative amino acids, Ile or Met, in NADH dehydrogenase subunit-5 (ND5) region of chum salmon. The heteroplasmic site was at the 3rd position of 58th codon. As for Japanese flounder we detected a C/T nonsynonymous heteroplasmic site corresponding to putative amino acids, Leu or Pro, in ND4 region. The heteroplasmic site was at the 2nd position of 450th codon. We also verified heteroplasmy at these sites by sequencing cloned fragments.

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“…; Sato et al . ; Garvin et al . ) was combined with the Eco‐TILLING results and analysed with the software Network 4.613 (fluxus‐engineering.com).…”

Section: Methodsmentioning

confidence: 99%

Potentially adaptive mitochondrial haplotypes as a tool to identify divergent nuclear loci

et al. 2016

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Summary Genetic tools are commonly used for conservation and management of at‐risk species. Individuals are often sampled from mixtures that are composed of many populations, which creates a need to assign individuals to their source. This can be problematic when the genetic divergence among source populations is weak but can be improved using adaptive genetic loci, which should show stronger levels of divergence. We previously reported a signature of positive selection in the mitochondrial‐encoded ND5 subunit of complex I in diverse taxa. The respiratory machinery of the mitochondria in salmonids is composed of more than 80 nuclear genes and there is substantial interaction between nuclear and mitochondrial expressed gene products. Recent studies report adaptive variation in mitochondrial function as well as co‐evolution between mitochondrial and nuclear genomes. We used potentially adaptive ND5‐based mitochondrial haplotypes to identify nuclear loci that would display increased levels of genetic divergence compared to neutral nuclear loci in chum salmon (Oncorhynchus keta). Populations in a geographic area the size of France have previously demonstrated weak genetic divergence even after substantial discovery efforts by multiple laboratories for allozymes, microsatellites and SNPs over the last two decades. We used RAD‐based next‐generation sequencing and identified a nuclear‐encoded subunit of mitochondrial complex I that was a significant FST outlier and 14 other divergent nuclear markers that improve genetic assignment of individuals to their population of origin relative to assignments based on neutral markers alone. This work demonstrates how a known adaptive marker can be leveraged to increase the probability of identifying divergent markers for applied genetics tools that may be biologically linked to it.

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Genetic population structure of chum salmon in the Pacific Rim inferred from mitochondrial DNA sequence variation

Cited by 14 publications

References 33 publications

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

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

Nonsynonymous Site Heteroplasmy in Fish Mitochondrial DNA

Potentially adaptive mitochondrial haplotypes as a tool to identify divergent nuclear loci

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