Divergence time of the two regional medaka populations in Japan as a new time scale for comparative genomics of vertebrates

Abstract

The southern and northern Japanese populations of the medaka fish provide useful tools to gain insights into the comparative genomics and speciation of vertebrates, because they can breed to produce healthy and fertile offspring despite their highly divergent genetic backgrounds compared with those of human-chimpanzee. Comparative genomics analysis has suggested that such large genetic differences between the two populations are caused by higher molecular evolutionary rates among the medakas than those of the hominids. The argument, however, was based on the assumption that the two Japanese populations diverged approximately at the same time (4.0-4.7 Myr ago) as the humanchimpanzee lineage (5.0-6.0 Myr ago). This can be misleading, because the divergence time of the two populations was calculated based on estimated, extremely higher molecular evolutionary rates of other fishes with an implicit assumption of a global molecular clock. Here we show that our estimate, based on a Bayesian relaxed molecular-clock analysis of whole mitogenome sequences from 72 rayfinned fishes (including 14 medakas), is about four times older than that of the previous study (18 Myr). This remarkably older estimate can be reconciled with the vicariant events of the Japanese archipelago, and the resulting rates of molecular evolution are almost identical between the medaka and hominid lineages. Our results further highlight the fact that reproductive isolation may not evolve despite a long period of geographical isolation.

Complete mitochondrial genome and the phylogenetic position of the Lake Eyre hardyhead (Craterocephalus eyresii), a freshwater atherinid fish endemic to Lake Eyre Basin, South Australia

“…The resulting phylogeny was congruent with previous mitogenome (e.g. Kawahara et al 2008;Setiamarga et al 2008Setiamarga et al , 2009) and nuclear gene marker (e.g. Betancur et al 2013) studies.…”

Transspecies dimorphic allelic lineages of the proteasome subunit β-type 8 gene ( PSMB8 ) in the teleost genus Oryzias

“…Both PSMB8d and PSMB8N lineages were retained in NP and SP although the allelic frequency of the PSMB8d lineage (73-100%) was much higher than that of the PSMB8N lineage (0-27%) in all the populations we analyzed. These findings suggest that the dichotomous allelic lineages were established before the divergence between NP and SP and have been maintained in each group for 5-18 million years (18,19).…”

“…These species most likely were generated by allopatric speciation, and the few hybridization experiments among them performed thus far showed the presence of reproductive isolation resulting in abortive embryonic development in the case of O. latipes x O. javanicus (25) or sterile F1 males in the case of O. latipes x O. celebensis (26) and O. latipes x O. curvinotus (27). The Oryzias species are divided into three species groups, the latipes, javanicus, and celebensis groups, based on mitochondrial DNA sequences (18,19), corresponding to the biarmed, monoarmed, and fused chromosome groups of karyological grouping. The divergence time among these three species groups was estimated as 29-32 Mya, based on the molecular clock assumption using the mitochondrial 12S and 16S rRNA sequences (18), or as 58-65 Mya, based on a Bayesian relaxed molecular clock analysis of whole-mitogenome sequences (19).…”

“…These subunit substitutions enhance the chymotrypsin-like activity of the immunoproteasomes, which are responsible for generation of peptides with a hydrophobic residue at the C terminus suitable for binding to MHC class I molecules. In particular, PSMB8, with its chymotrypsin-like activity, is a critical component for supplying MHC class I-binding peptides, because PSMB8-knockout mice show reduced expression of MHC class I molecules on the cell surface (17).The Japanese population of medaka, Oryzias latipes, is divided into two subpopulations, the Northern Population (NP) and the Southern Population (SP), which diverged [5][6][7][8][9][10][11][12][13][14][15][16][17][18]19). Using BAC clones, we determined the complete nucleotide sequences of the approximately 400-kb MHC class I region of two inbred strains, HNI (derived from the NP) and Hd-rR (derived from the SP) (20,21).…”

“…The Japanese population of medaka, Oryzias latipes, is divided into two subpopulations, the Northern Population (NP) and the Southern Population (SP), which diverged 5-18 Mya (18,19). Using BAC clones, we determined the complete nucleotide sequences of the approximately 400-kb MHC class I region of two inbred strains, HNI (derived from the NP) and Hd-rR (derived from the SP) (20,21).…”