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

Abstract

20Medaka is a model organism in medicine, genetics and developmental biology research and in 21 population genetics studies, and lab stocks composed of more than 100 local wild populations 22are available for such research. Thus, medaka represents a potentially excellent bioresource 23 for screening disease-risk-and adaptation-related genes by a genome-wide association study 24 (GWAS). Although a genetic population structure should be known beforehand with 25 practicing a genome-wide association study (GWAS), a comprehensive study on the 26 genome-wide diversity of wild medaka populations has not been performed. Here, we 27 performed Genotyping-by-Sequencing (GBS) for 81 and 12 medakas captured from a 28 bioresource and the wild, respectively. Based on the GBS data, we evaluated the genetic 29 population structure and estimated the demographic parameters using an approximate 30Bayesian computation (ABC) framework. The autosomal data confirmed high 31 differentiation among local populations and supported our previously proposed hypothesis on 32 medaka dispersal that was based on mitochondrial genome (mtDNA) data. A new finding 33 was that a local group thought to be a hybrid between the northern and the southern Japanese 34 groups was actually a sister group of the northern Japanese group. This paper presents the 35 first population-genomic study of medakas and provides information indispensable for a 36 GWAS of this fish. 37 38

DNA methylation site loss for plasticity-led novel trait genetic fixation

“…Medaka in the winter showed significantly shorter guts than did those in the summer, which was observed over that same 2-year period in the Kabe river ( example photos (white bars: 1 cm). Phylogenetic tree and admixture graphs were constructed using genome-wide single nucleotide polymorphisms (SNPs) published in our prior study 11 .…”

“…Why has a genetic fixation of the long gut occurred in the NJPN1 medaka? SJPN and NJPN medaka originate in northern Kyushu and the Tajima-Tango region, respectively 11 . In SJPN medaka, even populations with similar genetic backgrounds differ in their climatic environment habitat.…”

“…5C), the gut length would have been plastically adjusted for efficient digestion and absorption in various foraging environments. On the other hand, an NJPN medaka is a group that has spread rapidly to the north from small habitats where the environment is relatively uniform 11 . In the NJPN2 habitats, both temperature and gut length show minimal variability (Fig.…”

“…To explore the genetically-fixed gut length in medaka populations, we sampled 400 individuals from 40 wild-derived laboratory stocks that originated from wild populations, which had been maintained in a constant environment at an outdoor breeding facility, the University of Tokyo 11,23 Yongcheon, Maegok, Bugang, Sacheon, Shanghai. The subgroup names in parentheses are defined in our prior study 11 . We extracted the gut (from the esophagus to the anus), fixed each one in 4% paraformaldehyde for 1 hour on ice, and took photos of them laid out on glass slides to measure their lengths.…”

“…The medaka (Oryzias latipes), also known as Japanese rice fish, is an excellent model to investigate the molecular mechanism of PFE, because this small, omnivorous freshwater fish inhabits low to high latitudes in East Asia, adapts genetically to the various environments of each region, and shows geographic phenotypic plasticity and latitudinal variations for the traits associated with gut length 9,10 . Moreover, the medakas' evolutionary history is well-studied 11,12 , and various molecular biological techniques can be adapted to medaka 13 . Thus, we aimed to show the PFE process underlying their gut length differences and reveal the molecular basis and evolutionary process from the loss of plasticity to genetic fixation.…”