A population genetic study on the relationship between medaka fish and the spread of wet-rice cultivation across the Japanese archipelago

Abstract

It has been generally thought that a tiny freshwater fish, medaka (Oryzias latipes), has expanded its habitat into the Japanese archipelago as wet-rice cultivation spread across the region, and hence the distribution of medaka should be a matter of anthropological interest. However, there has been no study to verify this popular belief. To address the issue, we sampled wild medaka, and undertook genetic analyses of its populations. We collected 976 individual medaka from 13 local wild sites, which included 11 paddy-field irrigation channels and two ponds. The gene tree constructed based on nucleotide sequences of mitochondrial genome D-loop region showed no discrepancy in the topology, which is presumed to reflect the northern Kyushu origin of the southern Japanese medaka. Population genetic statistics indicated that the medaka populations in west Japan have greater genetic diversity (heterozygosity) than those in east Japan, supporting the hypothesis that the medaka originate from northern Kyushu. Hence, we argue that the current medaka distribution can be attributed to their past migration event(s) following the expansion of paddy fields from northern Kyushu to the eastern part of the Japanese archipelago.

Medaka population genome structure and demographic history described via genotyping-by-sequencing

“…The fifth was the "Local" dataset, including two Kyushu deme samples: one was 182 Umeshiro (US), which was sampled in the northern part of the Saga prefecture, and the other 183 was Ogi (SO), which was sampled in the southern part of the Saga prefecture. These samples 184 were used to estimate the time of Honshu's population divergence from Kyushu to infer the 185 timing of the "Out of Northern Kyushu" event (Katsumura et al 2012). 186…”

Medaka Population Genome Structure and Demographic History Described via Genotyping-by-Sequencing

“…The phylogenetic data from these studies also suggested that N.JPN and S.JPN have been spreading in the Japanese archipelago at different times. Particularly, the origin of S.JPN, which has the largest habitat, has been suggested to be the northern part of Kyushu Island based on mtDNA (“Out of Northern Kyushu” hypothesis) (Katsumura et al 2012). However, mtDNA is insufficient to describe the population structure and history because of its single locus.…”

“…To unravel the population structure based on chromosomes, we comprehensively performed a population-genetic analysis based on chromosomal single-nucleotide polymorphisms (SNPs) using all 81 local populations maintained as wild lab stocks at the University of Tokyo. We examined an individual sampled from each population stock and 12 wild individuals captured from the northern part of Kyushu Island, where (Katsumura et al 2012) the medakas currently distributed along the entire Pacific side of the Japanese archipelago originated, to estimate each population’s time of expansion from Northern Kyushu. To obtain SNP data, we conducted genotyping-by-sequencing (GBS) (Elshire et al 2011; Narum et al 2013) using a high-throughput sequencer.…”

Natural Allelic Variations of Xenobiotic Enzymes Pleiotropically Affect Sexual Dimorphism inOryzias latipes

“…To unravel this paradox, we performed experiments using medaka fish (Oryzias latipes) that are prevalent throughout East Asia [12,13] (Figure 1A) because they are an excellent animal model for studies on phenotypic variations [14]. Specifically, this model allows functional genetic comparisons among geographically local populations with abundant genetic diversity [15,16], according to geographical differences in sexual dimorphisms of anal fin morphology [17,18] Figure 1C).…”