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

Abstract

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.

Exploring the phylogeography of a hexaploid freshwater fish by RAD sequencing

“…The relatively high transition/transversion ratio of 2.04 after filtering for paralogs and mitochondrial loci may indicate a bias toward genic regions, as SNPs occur more frequently as transitions in exons than in introns (Park, Yu, Mun, & Lee, 2010). This value may also reflect effective filters to reduce sequencing error in the final SNP dataset (Pujolar et al., 2013; Rašić, Filipović, Weeks, & Hoffmann, 2014; Zhang et al., 2015). Initial examination of the SNP data, prior to filtering, showed many SNPs in the last few base pairs of reads (Figure S2) that may reflect sequencing errors rather than true variants (Pujolar et al., 2013).…”

Genomic evidence for local adaptation in the ovoviviparous marine fish Sebastiscus marmoratus with a background of population homogeneity

“…Recent studies have shown that high-throughput sequencing technology provides a novel approach for investigating local adaptation in natural populations of marine fishes 15, 22, 40 . In contrast to previous work that found a lack of genetic structure in populations of S. marmoratus , on the basis of mitochondrial control region sequences and AFLP markers 31 , the most important finding of this study was the detection of the high degree of population differentiation among three sampling sites by using 329 candidate adaptive SNPs (Figs 3b and 5, see Supplementary Fig.…”

“…Although the marine environment is relatively homogeneous compared with freshwater, numerous studies have revealed that differential thermal tolerance may result in ecological adaptation in marine species 5, 20 . Moreover, with the development of sequencing techniques, a growing number of studies using a high number of genome-wide polymorphic makers suggest that marine populations are not as connected as might be presumed 21, 22 . Hence, these techniques allow for inference of neutral population structure and also provide information on local adaptation or speciation events 19, 22, 23 .…”

“…Moreover, with the development of sequencing techniques, a growing number of studies using a high number of genome-wide polymorphic makers suggest that marine populations are not as connected as might be presumed 21, 22 . Hence, these techniques allow for inference of neutral population structure and also provide information on local adaptation or speciation events 19, 22, 23 . Consequently, local adaptation in marine fish species with little intraspecific population structure may commonly arise through ecologically different environments.…”

“…For instance, the GBS technique and related approaches have been used to investigate the genetic structure and local adaptation in marine fish species, such as sailfin molly Poecilia latipinna 25 , ide Leuciscus idus 26 , threespine stickleback Gasterosteus aculeatus 27, 28 , small yellow croaker Larimichthys polyactis 22 , and Atlantic mackerel Scomber scombrus L 21 . Using such methods to investigate populations undergoing ecological divergence is particularly useful because these techniques provide good opportunities to detect genomic loci under divergence selection 5 , and such loci are expected to stand out with high F st estimates against a background of low genetic divergence 29 .…”