Molecular analysis of Korean Apodemus mitochondrial genome and possible historical migration routes of A. chejuensis

Abstract

Chapter 1. Comparative analysis of the complete mitochondrial genome sequences of Korean Apodemus

The complete mitochondrial (mt) genomes of Apodemus agrarius, A. chejuensis, and A. peninsulae were determined to be 16,260, 16,261, and 16,266 base pairs (bp) long, respectively, and have been deposited in the GenBank database (Accession Nos. HM034866, HM034867, and HQ660074, respectively). Like other vertebrate mt genomes, the 3 mt genomes contain 13 protein-coding genes, 22 tRNAs, 2 rDNAs and a noncoding control region. The mt genomes of A. agrarius and A. chejuensis had protein-coding genes that use the most common initiation codon, ATG, and 2 unusual initiation codons: GTG and ATA. However, A. peninsulae had an additional unusual ATC codon for initiation in the NADH dehydrogenase subunit (ND) 2 gene. Overall, the nucleotide frequencies of all analyzed mt protein-coding genes were similar. Codon usage patterns based on mt protein-coding genes were similar in A. agrarius and A. chejuensis, while the mt protein-coding genes of A. peninsulae were slightly different. The 12S rRNA gene sequences were 955, 955, and 956 bp long in A. agrarius, A. chejuensis, and A. peninsulae, respectively, and the 16S rRNA gene sequences were 1,572, 1,573, and 1,571 bp long, respectively. tRNA-Leu and tRNA-Ser were identified two distinct forms, respectively. The Three tRNA clusters, IQM (isoleucine, glutamine, and methionine), WANCY (tryptophan, alanine, asparagine, cysteine, and tyrosine), and HSL (histidine, serine, and leucine), were conserved in A. agrarius, A. chejuensis, and A. peninsulae, as in the typical mt genomes of Rodentia. Generally, the mt genomes of mammals have 2 noncoding regions: OL and CR, which is also called the displacement loop (D-loop). The CR sequences spanned 854, 857, and 866 bp in A. agrarius, A. chejuensis, and A. peninsulae, respectively, and was positioned between the tRNA-Pro and tRNA-Phe genes. The phylogenetic analysis of Rodentia using mt 13 protein-coding genes suggested that Sciurus and Myoxus was diverged earlier than other rodents, and Rattus consisted of two distinct clades. Korean Apodemus was closely related to Mus as sister group. Although phylogenetic relationships of Apodemus spp. have been studied by many researchers, some species remain controversial owing to wide distribution, subspecies problems, and fragmentary data. Thus, the mt genome of Korean Apodemus spp. will be useful information to clarify rodent, especially the Apodemus, phylogeny.

Chapter 2. Possible historical migration routes of Apodemus chejuensis

Nineteen CYTB sequence haplotypes were defined in 24 Apodemus agrarius individuals, and 25 were defined in 49 A. chejuensis individuals. The most frequent haplotype group was Hap27, which was shared by 6 A. chejuensis individuals. The most frequent haplotype group in the A. agrarius was Hap15, which was shared by 3 individuals. Fu's Fs test showed that COR-II and CHE had significantly negative Fs values (-4.462 and -5.703, respectively), whereas the COR-I had a positive value (0.613). Mismatch distribution analyses suggested population expansion in COR-II and CHE and a stable COR-I population. Median-joining network data indicated that A. chejuensis is a clearly separate species containing 4 subgroups, but these subgroups did not correspond to local distribution patterns on Jeju Island. Interestingly, Hap42 of the CHE population was closely related to Hap9 of the COR-I. In addition, molecular clock calculations that estimate the time of divergence of A. agrarius and A. chejuensis suggest that those species diverged at approximately 0.3 million years ago (Mya). Based on these data, three historical migration routes were hypothesized. (1) The ancestral lineage of A. agrarius might migrate into the Korean Peninsula via North Korea; then, a group migrated to Jeju Island via the Yellow Sea basin when the sea level was lower. (2) The ancestral lineage of A. chejuensis might migrate to Jeju Island via the Yellow Sea basin, followed by a second migration into the western islet of the Korean Peninsula via the Yellow Sea basin when the sea level was lower. (3) The common ancestor of A. agrarius and A. chejuensis might have originated in eastern China, where it split into 2 lineages; one lineage moved to the western islet of the Korean Peninsula, and the other moved to Jeju Island. The estimation of divergence time suggested that A. agrarius and A. chejuensis diverged at approximately 0.3 Mya. Because A. chejuensis has been geographically and reproductively isolated from A. agrarius since the last glacial age, many researchers have proposed that populations diverged as species. This study supports the notion that A. chejuensis should be treated as a species; however, further study of North Korea and Chinese samples is needed to understand their biogeographic history fully.