Genetic information and demographic history: What can we learn about a species' past from its current genetic structures

We investigated evolutionary and biogeographic history of Peromyscus species in the Pacific Northwest of North America and Apodemus species in the Hengduan Mountains of southwest China. Sequences of mitochondrial cytochrome-b gene and control region were collected and analyzed. For the Peromyscus species, two distinct clades were found, consistent with the morphological designation of the two species. The sequence divergence between the two clades was 0.0484 substitutions per site for cyt-b and 0.0396 for control region, suggesting that divergence of the two clades occurred during the middle to late Pleistocene. For the Apodemus species, four distinct clades were found, partly different from the morphological identification of the species. The substantial and significant genetic divergences of 9% to 20% suggest a long history of differentiation for these species within the Hengduan Mountains. Population genetic analysis for the Apodemus species revealed differential migration across rivers and mountain ranges.; We further tested an approach to obtaining single-nucleotide polymorphism (SNP) data on natural populations of four species of field mice of the genus Apodemus. We designed exon-primed intron-crossing loci by comparing the mouse and human genomes. Two loci eventually generated high quality sequence data for the Apodemus species. These are intron 5 of the M2 subunit of the ribonucleotide reductase gene (RRM2-5) and intron 5 of the histone binding protein gene NASP (NASP-5). Cloned PCR products from all mice tested were heterozygous at RRM2-5, with pairwise differences within individuals ranging from 0.3% to 0.9%, and distances between individuals ranging from 1.1% to 6.5%. For the NASP-5 locus, one individual was heterozygous and the other two were homozygous, with a Jukes-Cantor distance between alleles of one individual at 0.1% and distances between individuals ranging from 0.4% to 2.8%. The genealogy recovered from the RRM2-5 locus was different from that of previously analyzed mitochondrial DNA but was consistent with morphological identification. These overall results show that population genetic studies of natural species can greatly benefit from genome information from model organisms, and that introgression of mitochondrial genomes might have indeed happened between Apodemus species.