The genetic divergence between two closely related rockfishes, Sebastes longispinis and Sebastes hubbsi, was inferred from both mitochondrial DNA (mtDNA) sequence variations and amplified fragment length polymorphism (AFLP) markers. The two species were placed into two distinct clades in a neighbour-joining tree based on the AFLP data, clearly indicating that they represented separate species. Although this evidence, together with a previous morphological study, revealed clear differences between the two species, no obvious clustering of haplotypes by species was detected in the minimum spanning network inferred from sequence variations in the mtDNA control region (c. 500 base pairs). In fact, the significant Φ(ST) estimates indicated only a restriction of gene flow between the two species. Uncorrected pairwise sequence differences in mtDNA between two species were small (1·8% at maximum, on the lower end of the range of control region divergence between previously studied sister species pairs), suggesting their speciation event as having been fairly recent. The incongruent results of AFLP and mtDNA phylogenies suggested incomplete lineage sorting and introgression of mtDNA in the course of the evolution of the two species. Differences in their main distributional ranges and the small level of sequence divergence in mtDNA suggests that speciation and dispersal may have been associated with glacio-eustatic sea level fluctuations between the Japanese Archipelago and the Korean Peninsula during the past 0·4 million years.

Jeju horse (Natural Monument number 347) is a breed of horse that has experienced long-term isolation and domestication in Jeju Island, South Korea. We evaluated genetic features of this breed, including SNP, by whole-genome resequencing using an Illumina HiSeq 2000. A total of 5,986,852 SNP were identified in 4 Jeju horses and were divided into homozygous and heterozygous SNP (2,357,099 and 3,629,753 SNP, respectively). It revealed that 63.8% of these SNP resided in intergenic regions. Immune response genes with nonsynonymous SNP were overrepresented in Jeju horses as evidenced by Gene Ontology clustering. Among these genes, Toll-like receptors (TLR) are highly enriched. Comparing TLR genes between Jeju horses and the Przewalski's horse, and genes showed "possibly damaging" mutations in several regions by analysis with PolyPhen-2. These results provide a framework for further genetic studies in Jeju horse by domestication. Furthermore, research on functions of SNP-associated genes would aid in understanding the molecular genetic variation of horse breeds.