Genome-wide assessment of kokanee salmon stock diversity, population history and hatchery representation at the northern range margin

Setzke, Christopher; Wong, Carmen; Russello, Michael A.

doi:10.1007/s10592-021-01418-2

Cited by 6 publications

(3 citation statements)

References 75 publications

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“…The B clade (Figure 5 ) might have been introduced and established in the Korean population through this stocking activity. Despite the enormous efforts, many hatchery populations are challenged by the loss of within‐population genetic diversity due to genetic drift and founder effects, which are the direct outcomes of these stocking activities (Aho et al, 2006 ; Setzke et al, 2022 ), despite some exceptions (e.g., Eldridge & Killebrew, 2008 ). The low diversity in hatchery fish may in turn lead to fitness declines in the wild over a very short period of captive rearing even in only one or two generations (Araki et al, 2008 ; Utter, 1998 ).…”

Section: Discussionmentioning

confidence: 99%

Low genetic diversity, local‐scale structure, and distinct genetic integrity of Korean chum salmon (Oncorhynchus keta) at the species range margin suggest a priority for conservation efforts

Jang

Kim

Yoon³

et al. 2022

Evolutionary Applications

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Chum salmon (Oncorhynchus keta) is an ecologically and economically important species widely distributed across the North Pacific Ocean. However, the population size of this fishery resource has declined globally. Identifying genetic integrity, diversity and structure, and phylogenetic relationships of wild populations of O. keta over an entire species' range is central for developing its effective conservation and management plans. Nevertheless, chum salmon from the Korean Peninsula, which are comprised of its southwestern range margins, have been overlooked. By using mtDNA control region and 10 microsatellite loci, we here assessed the genetic diversity and structure for 16 populations, including 10 wild and six hatchery populations, encompassing the species entire geographic range in South Korea. The analyses showed that genetic diversity is significantly higher for wild than for hatchery populations. Both marker sets revealed significant genetic differentiation between some local populations. Comparisons of six wild and their respective hatchery populations indicated that allele/haplotype frequencies considerably differ, perhaps due to a strong founder effect and/or homogenizing of hatchery populations for stocking practice. Despite its single admixed gene pool for the Korean chum salmon, some local populations housing their own unique lineages should be accorded with a high priority to safeguard their genetic integrities. The results of our comparative analyses of the Korean population with other North Pacific chum salmons (inhabiting regions of Japan, Russia, and North America) revealed a lower diversity but higher contribution to the overall species‐level genetic diversity, and also its unique genetic integrity. These findings advocate for the evolutionary significance of the Korean population for species‐level conservation.

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Section: Discussionmentioning

confidence: 99%

Low genetic diversity, local‐scale structure, and distinct genetic integrity of Korean chum salmon (Oncorhynchus keta) at the species range margin suggest a priority for conservation efforts

Jang

Kim

Yoon³

et al. 2022

Evolutionary Applications

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show abstract

“…The significance of the heterozygote excess was evaluated using Wilcoxon signed‐rank tests under an infinite alleles model (IAM) (Maruyama & Fuerst, 1985). Although IAM is not entirely appropriate for biallelic SNPs, this test was exploratorily conducted following recent studies (Camak et al, 2021; Kogura et al, 2011; Setzke et al, 2022; Stojanova et al, 2020).…”

Section: Methodsmentioning

confidence: 99%

Extremely low level of genetic diversity in Gentiana yakushimensis, an endangered species in Yakushima Island, Japan

Ishii

Hirota

Tsunamoto

et al. 2022

Plant Species Biology

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Rare or endangered species largely contributing to global biodiversity are essential components of ecosystems. Because genetic diversity depends not only on apparent population size but also demographic processes, the conservation priority of endangered species based on population genetics needs to be assessed by comparison with common congeners and demographic events. In this study, we performed population genetic analysis for Gentiana yakushimensis Makino, a rare and endangered plant species with an isolated distribution on Yakushima Island, Japan. We performed comparison of genetic diversity with the congener (Gentiana triflora Pall. var. japonica [Kusn.] H.Hara), demographic inference, and bottleneck test based on genome‐wide single nucleotide polymorphisms. The result was that G. yakushimensis had an extremely low genetic diversity level and a high inbreeding coefficient level compared with those of the congener. The population of G. yakushimensis was estimated to experience an expansion during the Last Glacial Maximum and a recent bottleneck by the demographic inference and the bottleneck test. Therefore, the low level of genetic diversity of this species might have resulted from the impact of the recent bottleneck and the long‐term maintenance of a small population size. Due to the long lifespan of the genus Gentiana, the current level of genetic diversity probably does not reflect a large part of recent demographic events, which requires long‐term monitoring of changes in genetic diversity to identify the time lag between the reduction in apparent population size and genetic diversity as a future outlook.

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“…The significance of the heterozygote excess was evaluated using Wilcoxon signed-rank tests under an infinite alleles model (IAM) (Maruyama & Fuerst, 1985). Although IAM is not entirely appropriate for biallelic SNPs, this test was exploratorily conducted following recent studies (Camak, Osborne, & Turner, 2021; Kogura et al, 2011; Setzke, Wong, & Russello, 2022; Stojanova, Šurinová, Zeisek, Münzbergová, & Pánková, 2020).…”

Section: Methodsmentioning

confidence: 99%

Extremely low level of genetic diversity in Gentiana yakushimensis, an endangered species in Yakushima Island, Japan

Ishii

Hirota

Tsunamoto

et al. 2022

Preprint

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Rare or endangered species largely contributing to global biodiversity are essential components of ecosystems. Because genetic diversity depends not only on apparent population size but also demographic processes, the conservation priority of endangered species based on population genetics needs to be assessed by comparison with common congeners and demographic events. In this study, we performed population genetic analysis for Gentiana yakushimensis, a rare and endangered plant species with an isolated distribution on Yakushima Island, Japan. We also compared genetic diversity with the congener (Gentiana triflora) and demographic inferences based on genome-wide single nucleotide polymorphisms. The result was that G. yakushimensis had an extremely low genetic diversity level and a high inbreeding coefficient level compared to those of the congener. The population of G. yakushimensis was estimated to experience gentle expansion during the Holocene and a bottleneck over the past several decades by demographic inference. Therefore, the low level of genetic diversity of this species might have resulted from the impact of the recent bottleneck and the long-term maintenance of a small population size. Due to the long lifespan of the genus Gentiana, the current level of genetic diversity probably does not reflect a large part of recent demographic events, which requires long-term monitoring of changes in genetic diversity to identify the time lag between the reduction in apparent population size and genetic diversity as a future outlook.

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Genome-wide assessment of kokanee salmon stock diversity, population history and hatchery representation at the northern range margin

Cited by 6 publications

References 75 publications

Low genetic diversity, local‐scale structure, and distinct genetic integrity of Korean chum salmon (Oncorhynchus keta) at the species range margin suggest a priority for conservation efforts

Low genetic diversity, local‐scale structure, and distinct genetic integrity of Korean chum salmon (Oncorhynchus keta) at the species range margin suggest a priority for conservation efforts

Extremely low level of genetic diversity in Gentiana yakushimensis, an endangered species in Yakushima Island, Japan

Extremely low level of genetic diversity in Gentiana yakushimensis, an endangered species in Yakushima Island, Japan

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