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

Takafumi Katsumura, Shoji Oda, Hiroshi Mitani, Hiroki Oota
doi: https://doi.org/10.1101/233411
Takafumi Katsumura
Okayama University;
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  • For correspondence: tk@med.kitasato-u.ac.jp
Shoji Oda
University of Tokyo;
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Hiroshi Mitani
University of Tokyo;
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Hiroki Oota
Kitasato University School of Medicine
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Abstract

Medaka is a model organism in medicine, genetics, developmental biology and population genetics. Lab stocks composed of more than 100 local wild populations are available for research in these fields. Thus, medaka represents a potentially excellent bioresource for screening disease-risk- and adaptation-related genes in genome-wide association studies. Although the genetic population structure should be known before performing such an analysis, a comprehensive study on the genome-wide diversity of wild medaka populations has not been performed. Here, we performed genotyping-by-sequencing (GBS) for 81 and 12 medakas captured from a bioresource and the wild, respectively. Based on the GBS data, we evaluated the genetic population structure and estimated the demographic parameters using an approximate Bayesian computation (ABC) framework. The autosomal data confirmed that there were substantial differences between local populations and supported our previously proposed hypothesis on medaka dispersal based on mitochondrial genome (mtDNA) data. A new finding was that a local group that was thought to be a hybrid between the northern and the southern Japanese groups was actually a sister group of the northern Japanese group. Thus, this paper presents the first population-genomic study of medaka and reveals its population structure and history based on autosomal diversity.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted June 11, 2018.
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Medaka population genome structure and demographic history described via genotyping-by-sequencing
Takafumi Katsumura, Shoji Oda, Hiroshi Mitani, Hiroki Oota
bioRxiv 233411; doi: https://doi.org/10.1101/233411
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Medaka population genome structure and demographic history described via genotyping-by-sequencing
Takafumi Katsumura, Shoji Oda, Hiroshi Mitani, Hiroki Oota
bioRxiv 233411; doi: https://doi.org/10.1101/233411

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