Evaluation of population genetics of Acanthogobius ommaturus using genotyping by sequencing technology

Abstract

Recent high-throughput genotyping technologies allow for comprehensive genomic analyses on an unprecedented scale. In order to evaluate the pattern of genetic structure, 112 individuals from 4 Acanthogobius ommaturus populations over the coastal waters of China were analyzed by genotyping-by-sequencing method. A total of 48.96 Gb of high-quality sequencing data were obtained, and 19159 SNP loci were identified, 1088 of which were outlier loci. The largest genetic differentiation (Fst) occurred between population Zhoushan and other populations based on all SNP loci and outlier loci. The admixture analysis based on outlier loci showed population Zhoushan formed a separate cluster, while the results based on total SNPs did not show consistent clustering evidence. Additionally, the results of principal component analysis (PCA) showed more obvious grouping information, supporting the above admixture results. Across all populations, the genome-wide distribution patterns for π, He and Tajima’s D were greatly similar. Notably, the range of Tajima’s D values fluctuated sharply, revealing that A. ommaturus genomic sites might be subjected to natural selection. Consequently, together with previous works, the present results further suggested that the genetic differentiation pattern might be caused by biogeographical isolation and the divergent evolution of specific gene sites. The local adaptive evolution may play an important role in the genetic differentiation of population Zhoushan.