A total of 120 individuals of 11 native Japanese chicken breeds were used. They are 8 Ingie, 13 Nagoya, 12 Oh-Shamo, 11 Tosa-Jidori, 10 Tosa-Kukin, 7 Ukokkei, 16 White Leghorn G line, 10 White Leghorn
Wild-caught Syngnathus scovelli from 16 populations. A total of 719 individuals were sequenced using ddRAD-seq with the enzymes PstI and MboI. Other archived data can be found on Dryad: doi:10.5061/dr
