Local adaptation shapes pattern of mitochondrial population structure in Sebastiscus marmoratus

Xu, Shengyong; Sun, Donglin; Song, Na; Gao, Tianxiang; Han, Zhiqiang; Shui, Bonian

doi:10.1007/s10641-017-0602-5

Cited by 17 publications

(17 citation statements)

References 74 publications

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“…Overall, our results indicated that the entire S. marmoratus population shared one gene pool, although some weak genetic differentiation was observed among several populations. In addition, our results were superficially different from the estimation obtained using SNPs in mtDNA ATPase 6 and cytochrome b genes (Xu, Song, et al, ; Xu, Sun, et al, ). The overall result of weak genetic differentiation was based on all SNPs.…”

Section: Discussioncontrasting

confidence: 99%

“…Recently, several studies on S. marmoratus population genetics have been conducted using amplified fragment length polymorphism (AFLP), mitochondrial DNA (mtDNA) and single nucleotide polymorphisms (SNPs) (Xu, Song, et al, ; Xu, Sun, et al, ; Zhang, ). However, there are no reports on the genetic structure of S. marmoratus populations that cover most of the habitat, from Japan to China.…”

Section: Introductionmentioning

confidence: 99%

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Genetic structure in the marbled rockfish(Sebastiscus marmoratus)across most of the distribution in the northwestern Pacific

Liu

Song

et al. 2019

J Appl Ichthyol

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The marbled rockfish (Sebastiscus marmoratus) is an important species that is widely distributed across the marginal seas of the northwestern Pacific. Several kinds of DNA markers, such as amplified fragment length polymorphisms (AFLP), mitochondrial DNA (mtDNA) and single nucleotide polymorphisms (SNPs), have been used to assess the population genetic characteristics of this species in previous studies. However, there have been no genetic profiling studies to cover the entire distribution. Here, six highly polymorphic microsatellite markers were applied to 18 populations across a spatially large area (from the Sea of Japan in the north to the South China Sea in the south). The results showed that the whole population exhibits high, stable genetic diversity, low relatedness and large effective population size. There was very weak genetic differentiation overall and no isolation by distance occurred among the populations, which may be attributed to significant contemporary gene flow, each generation. The above results may lead us to infer that the recent S. marmoratus population structure could be considered as one large integrated population. The present study will be beneficial to population conservation and fisheries management of S. marmoratus and will lead to better insights into the genetic characteristics of other species that belong to the Sebastidae family.

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Section: Discussioncontrasting

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Genetic structure in the marbled rockfish(Sebastiscus marmoratus)across most of the distribution in the northwestern Pacific

Liu

Song

et al. 2019

J Appl Ichthyol

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“…S. marmoratus has strong site fidelity and appears within narrow home ranges [14]. Several studies have been conducted on S. marmoratus germplasm resources due to the decline in wild populations [15][16][17]. However, inconsistent results were demonstrated given the insufficient resolution of molecular markers.…”

Section: Introductionmentioning

confidence: 99%

Whole genome survey analysis and microsatellite motif identification of Sebastiscus marmoratus

Song

Xiao

et al. 2020

Bioscience Reports

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The marbled rockfish Sebastiscus marmoratus is an ecologically and economically important marine fish species distributed along the northwestern Pacific coast from Japan to the Philippines. Here, next-generation sequencing was used to generate a whole genome survey dataset to provide fundamental information of its genome and develop genome-wide microsatellite markers for S. marmoratus. The genome size of S. marmoratus was estimated as approximate 800 Mb by using K-mer analyses, and its heterozygosity ratio and repeat sequence ratio were 0.17% and 39.65%, respectively. The preliminary assembled genome was nearly 609 Mb with GC content of 41.3%, and the data were used to develop microsatellite markers. A total of 191,592 microsatellite motifs were identified. The most frequent repeat motif was dinucleotide with a frequency of 76.10%, followed by 19.63% trinucleotide, 3.91% tetranucleotide, and 0.36% pentanucleotide motifs. The AC, GAG, and ATAG repeats were the most abundant motifs of dinucleotide, trinucleotide, and tetranucleotide motifs, respectively. In summary, a wide range of candidate microsatellite markers were identified and characterized in the present study using genome survey analysis. High-quality whole genome sequence based on the “Illumina+PacBio+Hi-C” strategy is warranted for further comparative genomics and evolutionary biology studies in this species.

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“…In marine fishes, different dimensions of natural selection between populations may be related to temperature adaptation and aerobic exercise associated with individual size (Bélanger-Deschênes et al 2013;Jacobsen et al 2016;Zhang et al 2016). These results have also been validated in studies of Sebastiscus marmoratus (Xu et al 2017). Currently, P. minor has a wide thermal amplitude.…”

Section: Discussionmentioning

confidence: 72%

Pleistocene isolation caused by sea-level fluctuations shaped genetic characterization of Pampus minor over a large-scale geographical distribution

Li¹,

Liu²,

Lin³

et al. 2020

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The southern lesser pomfret (Pampus minor) is an economically important fish, and its numbers are declining because of overfishing and environmental pollution. In addition, owing to the similarities of its external morphological characteristics to other species in the genus Pampus, it is often mistaken for grey pomfret (P. cinereus) or silver pomfret (P. argenteus) juveniles. In this study, the genetic diversity and structure of 264 P. minor individuals from 11 populations in China and Malaysia coastal waters were evaluated for the first time, to the best of our knowledge, using mitochondrial cytochrome b fragments. The results showed that P. minor had moderate haplotype diversity and low nucleotide diversity. Furthermore, two divergent lineages were detected within the populations, but the phylogenetic structure corresponded imperfectly with geographical location; thus, the populations may have diverged in different glacial refugia during the Pleistocene low sea levels. Analysis of molecular variation (AMOVA) showed that genetic variation originated primarily from individuals within the population. Pairwise FST results showed significant differentiation between the Chinese and Malaysian populations. Except for the Xiamen population, which was classified as a marginal population, the genetic differentiation among the other Chinese populations was not significant. During the Late Pleistocene, P. minor experienced a population expansion event starting from the South China Sea refugium that expanded outward, and derivative populations quickly occupied and adapted to the new habitat. The results of this study will provide genetic information for the scientific conservation and management of P. minor resources.

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Local adaptation shapes pattern of mitochondrial population structure in Sebastiscus marmoratus

Cited by 17 publications

References 74 publications

Genetic structure in the marbled rockfish(Sebastiscus marmoratus)across most of the distribution in the northwestern Pacific

Genetic structure in the marbled rockfish(Sebastiscus marmoratus)across most of the distribution in the northwestern Pacific

Whole genome survey analysis and microsatellite motif identification of Sebastiscus marmoratus

Pleistocene isolation caused by sea-level fluctuations shaped genetic characterization of Pampus minor over a large-scale geographical distribution

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