Genome-wide SNP discovery and phylogeography of sandlances (Ammodytes japonicus and Ammodytes heian) in the Northwest pacific by MIG-Seq with evolutionary implications

This study examined whether the East Sea sandlance is Ammodytes heian at the genomic level.A total of 48 sandlances were analyzed from five regions, "Baengnyeongdo (BA in the Yellow Sea), Tongyeong (TO in the Korea Strait), Gijang (GI in the East Sea), Jumunjin (JU in the East Sea) in Korea, and Wakkanai in Japan (JP in the Okhotsk Sea)".Regional single nucleotide polymorphism (SNP) filtering resulted in a total of 10,545 SNPs, based on which the FST was calculated as follows: 0.501 between JP and TO, 0.446 between JP and BA, 0.003 between GI and JU, and 0.014 between GI and JP.Structure analysis based on 10,545 SNPs had optimal delta K values when K was 3. Two genotypes were dominant: one occurred at BA and TO and the other at GI, JU, and JP; the remaining one occurred in all regions.The PCA scatterplot based on 10,545 SNPs revealed two clear clusters, the Ammodytes japonicus group from BA and TO, and the Ammodytes heian group from GI, JU, and JP, which roughly corresponded to the phylogenetic analysis based on 55,026 SNPs.Our results indicate that the genetic traits based on SNPs are similar to the mt results, but somewhat inconsistent with the ms results, suggesting that the East Sea (GI and JU) sandlance is Ammodytes heian as hybrids are rare.Their complex relationships can be attributed to the accumulation of neutral polymorphism across the species or biases in spatiotemporal gene flow between lineages during glacial-interglacial cycles.