GEDIMAP: a database of genetic diversity for Japanese freshwater fishes

Abstract

Genetic diversity is a key component of biodiversity, and thus represents important information for evolutionary and conservation biology. DNA sequence data are primary sources of information on genetic diversity and are now accumulated and managed in international databases, such as the DNA Data Bank of Japan (DDBJ), the European Molecular Biology Laboratory (EMBL) Nucleotide Sequence Database, and GenBank of the US National Center for Biotechnology Information (NCBI). Such databases provide basic information that is used in most areas of contemporary bioscience (Brunak et al. 2002). MitoFish (Nishida 2009), a DNA database devoted to the mitochondrial DNA (mtDNA) genomes of fish, supports research into fish biology, and contains links to other international DNA databases and general fish databases (e.g., FishBase; Froese and Pauly 2009). Genetic diversity and divergence within and among local populations within a species are primary elements of biodiversity at the genetic level and are of essential conceptual and practical importance (Avise 2004). Genetic data from population genetic and phylogeographic studies based on various genetic markers, especially mtDNA sequences, are increasingly being reported. However, the DNA databases mentioned above do not provide effective functions for accumulating and searching for population genetic data, which are based on allele frequencies in each population with geographical data. Thus, when researchers want to browse or reuse data from previous studies, they typically need to reconstruct such a dataset by combining information described in original papers with that deposited in the DNA databases. Further, probably because of the lack of a platform for accumulating such information, a significant proportion of the papers do not provide fundamental information for reconstructing the population genetic data analyzed in those papers. Thus, it is difficult for anyone to use these valuable data secondarily. This situation impedes evolutionary and biogeographic research and applications in biodiversity conservation based on comprehensive population genetic data, and it leads to a waste of human, monetary, and wildlife resources. To improve this situation, we have constructed a comprehensive database for genetic diversity in Japanese freshwater fish. Freshwater fish are good targets for studying evolution and biogeography because of their restricted dispersal ability and conspicuous intraspecific divergence (Avise 2000; Watanabe et al. 2006). Research in this area will benefit from accumulated population genetic data. Here, we outline and describe the application of the database. ‘‘GEDIMAP’’ (genetic diversity and distribution map) is a public database primarily for mtDNA genetic diversity data within populations of freshwater fish in and around Japan (URL: http://gedimap.zool.kyoto-u.ac.jp/). The beta version was released in January 2008, and the current K. Watanabe (&) R. Kakioka K. Tominaga Department of Zoology, Division of Biological Science, Graduate School of Science, Kyoto University, KitashirakawaOiwakecho, Sakyo-ku, Kyoto 606-8502, Japan e-mail: watanak@terra.zool.kyoto-u.ac.jp

DOI: 10.1007/s10228-009-0129-7

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Cite this paper

@article{Watanabe2009GEDIMAPAD, title={GEDIMAP: a database of genetic diversity for Japanese freshwater fishes}, author={Katsutoshi Watanabe and Yuichi Kano and Hiroshi Takahashi and Takahiko Mukai and Ryo Kakioka and Koji Tominaga}, journal={Ichthyological Research}, year={2009}, volume={57}, pages={107-109} }