The Genji firefly, Luciola cruciata, is widely distributed throughout the major Japanese islands (Honshu, Shikoku, and Kyushu) and distinguished into two ecological types on the basis of the flash interval of the mate-seeking males (4-sec slow-flash or 2-sec fast-flash intervals). The boundary of the ecological types corresponds to the Fossa Magna, a great rupture zone that separates eastern and western Japan. Although the degree of genetic differentiation of the two types has been evaluated using allozyme and mitochondrial DNA sequence data, it has not been evaluated using genome-wide data. Based on the genome-wide data obtained using single-end restriction-site-associated DNA (RAD-Seq), principal component, gene-level phylogenetic tree, admixture, and Wright's fixation index analyses, we identified three phylogenetic groups in L. cruciata: East-Honshu, West-Honshu, and Kyushu. This grouping corresponds to the ecological types: East-Honshu to the slow-flash type and West-Honshu and Kyushu to the fast-flash type. Although introgression was exceptionally observed around adjacent or artificially transplanted areas, gene flow among the groups was almost absent in the natural populations. The phylogenetic tree under the coalescent model also evaluated differentiation among the East-Honshu, West-Honshu and Kyushu groups. Furthermore, because the distribution patterns of the three groups are consistent with the geological history of Japanese islands, a vicariant speciation scenario of L. cruciata is concluded. In addition, we identified genetic markers that can be used to distinguish the three genetic groups for genetic management of firefly transplantation in nature conservation and regeneration.The fantastic light of fireflies has been attractive to nearly all peoples. This attraction is particularly strong in Japan, where the firefly has appeared in the oldest Japanese history book, "Nihon Shoki, " compiled during the Nara period of the 8th century.Light emission in adult fireflies is a mating adaptation 1-3 , and species-specific and mating-related flash signals play a major role in reproductive isolation 4 . Therefore, it is presumed that the flash signal differentiation and speciation processes are closely correlated. The Genji firefly, Luciola cruciata, is a species that shows synchronous flashes, and its flash communication and mating behaviour have been intensively studied 5,6 . The communication system is described in several phases: after sunset, the males begin to fly and seek females with synchronous flashing lights; the females emit single-pulsed flashes of light (not synchronized) on grasses; when a male finds the female's flashed light, the male approaches the female; the male emits flashes with various patterns while approaching and walking around the female; thereafter, they copulate 5-7 .This species is distributed throughout the three major islands of Japan, i.e., Honshu, Shikoku, and Kyushu, and two ecological types have been recognized based on the synchronous flashing behaviours of males (Fig. 1)...

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We performed mitogenome analysis of Japanese firefly Luciola cruciata (Coleoptera: Lampyridae), which is unique species in Japan. It is classified into six haplotypes based on the difference of COII sequence on mitochondrial DNA. The complete mitogenome sequence of Tohoku group has been registered so far, we newly analysed West Japan groups which belong to different haplotype. The total length of analysed mitogenome was 15,990 bp, being one base longer than the case of Tohoku’s firefly. The base substitution was found at 273 positions over the whole mitochondrial sequence, while amino acid substitution accompanying it was observed at only 11 positions.

We will report the complete mitochondrial genome sequence of Japanese firefly 'Heike Botaru', Luciola lateralis (Coleoptera: Lampyridae). Total length of this mitogenome was 16,719 bp and the composition of each base was A (42.50%), C (9.01%), G (14.16%), T (34.33%), respectively. The obtained sequence fulfils general mitogenome composition of metazoan (13 protein coding sequences (CDSs), 22 tRNA genes, two rRNA subunits, and an AT-rich region). From the phylogenetic tree analysis using 25 kinds of insect mitogenome including firefly family was found that L. lateralis is the closest to the genus Aquatica.