AbstractThe giant water bug Kirkaldyia deyrolli is one of the most well‐known endangered aquatic insects in Japan. The population of this species in Kyushu, one of the four major islands of the Japanese Archipelago, is extremely limited. In the present study, we identified a new population of K. deyrolli and undertook population genetic structure analyses based on genome‐wide nuclear DNA single nucleotide polymorphisms (SNPs). We collected samples using a nonlethal sampling method and obtained 59,279 SNPs. The results of our study confirm that sufficient SNP data for population genetic structure analysis can be obtained through nonlethal sampling. We determined that the newly identified population is genetically differentiated from a previously identified population on Kyushu. Therefore, this population is considered highly important for the conservation of K. deyrolli in Kyushu.
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