Investigating the population structure of small yellow croaker (Larimichthys polyactis) using internal and external features of otoliths

Recent advances in high-throughput sequencing technologies have offered the possibility to generate genomewide sequence data to delineate previously unidentified genetic structure, obtain more accurate estimates of demographic parameters and to evaluate potential adaptive divergence. Here, we identified 27 556 single nucleotide polymorphisms for the small yellow croaker (Larimichthys polyactis) using restriction-site-associated DNA (RAD) sequencing of 24 individuals from two populations. Significant sources of genetic variation were identified, with an average nucleotide diversity (π) of 0.00105 ± 0.000425 across individuals, and long-term effective population size was thus estimated to range between 26 172 and 261 716. According to the results, no differentiation between the two populations was detected based on the SNP data set of top quality score per contig or neutral loci. However, the two analysed populations were highly differentiated based on SNP data set of both top FST value per contig and the outlier SNPs. Moreover, local adaptation was highlighted by an FST -based outlier tests implemented in LOSITAN and a total of 538 potentially locally selected SNPs were identified. blast2go annotation of contigs containing the outlier SNPs yielded hits for 37 (66%) of 56 significant blastx matches. Candidate genes for local adaptation constituted a wide array of biological functions, including cellular response to oxidative stress, actin filament binding, ion transmembrane transport and synapse assembly. The generated SNP resources in this study provided a valuable tool for future population genetics and genomics studies of L. polyactis.

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“…; Zhang et al . ). Here, we applied a RAD‐seq approach to produce orders of magnitude more markers than previously possible.…”

Section: Discussionmentioning

confidence: 97%

Development and preliminary evaluation of a genomewide single nucleotide polymorphisms resource generated by RAD‐seq for the small yellow croaker (Larimichthys polyactis)

Zhang

Xue

Wang

et al. 2015

Molecular Ecology Resources

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“…The subpopulations structure, i.e. the so‐called ‘local adaption’, of the East China Sea has been confirmed by analyses of otolith features and neutral microsatellites (Wang et al., ; Zhang et al., ). The relationship of the HZB stock with the other stocks has differed across previous studies, and the morphometric results of this work are consistent with the results of previous studies that have employed meristic characteristics (Liu, ); furthermore, the morphometric results of this work also demonstrated the temporal variation in body shape.…”

Section: Discussionmentioning

confidence: 86%

“…). These differences provide further evidence for the complexity of the stock structure, which includes individuals from two wintering grounds located near Cheju Island and offshore the central Yellow Sea (Liu, ; Zhang et al., ). These differences may be attributable to spatial variation in environmental factors during wintering.…”

Section: Discussionmentioning

confidence: 98%

A morphometric investigation of the small yellow croaker (Larimichthys polyactis Bleeker, 1877): evidence for subpopulations on the Chinese coast

Zhang

Jiang

et al. 2015

J. Appl. Ichthyol.

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Summary In this study the morphometric characteristics based on the truss network system were constructed from the body shapes and used to investigate the population structure of the small yellow croaker (Larimichthys polyactis Bleeker, 1877). From April to June 2013, a total of 431 fish samples were collected from commercial catches acquired with bottom trawlers (20 × 20 mm) in seven main spawning grounds along the coast of China. The results of principal component and discriminant function analyses indicated a clear distinction among the regional stocks and within the Haizhou Bay (HZB) stock. Observed differences primarily involved head measurements, body length and tail size, which were associated with environmental factors. Latitudinal gradient of the stock distribution and the relationship among the stocks provided further evidence for the existence of subpopulations and the re‐division of the East China Sea group. Moreover, the temporal inter‐structure of the HZB stock is a potential reason for the contrast in results from previous studies. Additional thorough studies of migration trajectories are required for a conclusive and improved understanding of the population structure.

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“…Otolith morphometric measurements were obtained using IMAGE-PRO PLUS 6.0 software (Media Cybernetics, Inc.), including measurements of the maximum length and width of the otolith, the otolith perimeter in mm and area in mm 2 , the aspect (the ratio between the major and minor axes of the ellipse equivalent to the otolith), roundness [perimeter 2 /(4 9 pi9area)] and area/box (ratio between the otolith area and area of its boundary). The aspect, roundness and area/box were calculated following the formulas of Tuset et al (2003a,b), Pothin et al (2006) and Zhang et al (2014).…”

Section: Otolith Shape Analysismentioning

confidence: 99%

“…The small yellow croaker ( Larimichthys polyactis ) is a sciaenid fish with straddling, migratory, demersal habits and is endemic to the Northwest Pacific, extensively distributed throughout the East China Sea, Yellow Sea, Bohai Sea, and waters west of Korea (Wang et al., ; Zhang et al., ). This fish primarily inhabits temperate waters to depths of less than 150 m (Li et al., ; Lin et al., ).…”

Section: Introductionmentioning

confidence: 99%

Factors affecting morphological development of the sagittal otolith in juvenile and adult small yellow croaker (Larimichthys polyactisBleeker, 1877)

et al. 2015

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The morphology and morphometrics of the sagittal otoliths of small yellow croaker (Larimichthys polyactis) from the southern Yellow Sea were investigated. Study objectives were to evaluate the shape variability and morphometric variables of sagittae of juveniles and adults as related to developmental changes and habit shift. A total of 152 fish were sampled from April to June of 2012 and 2013, along the coastal waters of the L€ usi spawning ground in the southern Yellow Sea. Changes in otolith shapes from the juvenile to the adult were presented with the rim development through the entire-lobed-entire transition and with the curvature of the cauda toward the ventral margin. The otolith elongation in the juvenile stage occurred at 10-20 mm standard length (SL) and was likely associated with the formation of otolith accessory growth centers from larvae to juvenile. The L. polyactis sagittal otoliths acquired their definitive shape at 130 mm SL maturity. Ontogeny on otolith shape might be related, for example, to the factors of metamorphic development, feeding habitat, and ambient water salinity, which varied throughout the growth of L. polyactis.U.S.

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Investigating the population structure of small yellow croaker (Larimichthys polyactis) using internal and external features of otoliths

Cited by 33 publications

References 22 publications

Development and preliminary evaluation of a genomewide single nucleotide polymorphisms resource generated by RAD‐seq for the small yellow croaker (Larimichthys polyactis)

Development and preliminary evaluation of a genomewide single nucleotide polymorphisms resource generated by RAD‐seq for the small yellow croaker (Larimichthys polyactis)

A morphometric investigation of the small yellow croaker (Larimichthys polyactis Bleeker, 1877): evidence for subpopulations on the Chinese coast

Factors affecting morphological development of the sagittal otolith in juvenile and adult small yellow croaker (Larimichthys polyactisBleeker, 1877)

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