About Medaka
The Medaka Fish
Medaka Fish in an Aquarium.
The Medaka fish (Oryzias latipes) is a slender, largely transparent Teleost of up to 4 cm in length that occurs naturally in slow moving water including rice paddies throughout much of East Asia. Medaka have been kept in aquaria in Japan since the 17th Century, and are now a common aquarium fish worldwide. In the wild they are able to migrate back and forth bewteen between fresh and sea water (amphidromous). They are also known as Japanese killifish, Rice Fish, and Ricefish.
The physiology, embryology and genetics of medaka have been extensively studied in Japan from the turn of the 20th Century. Mendelian inheritance in vertebrates was demonstrated in Medaka and in 1921 Medaka was the first vertebrate in which crossing over between the X and Y chromosomes was detected (Toyama 1916; Aida 1921).Over the last decade, Medaka (Oryzias latipes) has been rediscovered outside Japan (Wittbrodt et al. 2002; Takeda and Shimada 2010). Standard transgenesis protocols, a 700MB reference genome sequence combined with a detailed linkage map (Kasahara et al. 2007), and tools for enhancer and chromatin analysis (Sasaki et al. 2009; Mongin et al. 2011) make Medaka a powerful model vertebrate organism for developmental and molecular studies. A large number of wild Medaka catches have been collected to establish laboratory strains and highly inbred lines, which form a unique repository for genomic and population genetic studies. The long history of medaka research, its amenability to inbreeding and its easily accessible habitat make this species very well suited for genetic studies and especially for establishing a reference panel of inbred lines.
Medaka Populations and Phylogeny
The distribution of Medaka across Asia.
Medaka are found across East Asia including China, Korea, Taiwan and Japan. In Japan there are two divergent wild populations of Medaka separated by the Japanese Alps dividing the main island of Honshu (the Northern and Southern populations, see right). These two populations do not overlap in the wild and have many different phenotypic features. However they can produce fertile offspring when mated in the laboratory. The reference Medaka genome sequence was generated from a HdrR, and inbred line of Southern Japanese origin.
We have used high throughput short read sequencing to characterize the genomes of four inbred lines derived from three different locations in East Asia (Northern Japan (HNI and Kaga), South Korea (HSOK) and Taiwan (Nilan)) compared to the Southern Japanese HdrR line. The phylogeny of the strains based on the sequence data was consistent with their geographical origins as below. 
Fish in Space
Medaka have travelled in space on several occassions, including on board space shuttles and the International Space Station (ISS). Medaka were the first first vertebrate to mate in orbit on board the space shuttle Columbia in 1994. The Japanese Space Agency recently launched the Aquatic Habitat on board the ISS to study the effects of orbit on various aspects of vertebrate physiology.