Abstract
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.
Highlights
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)
From over 224 million raw single-end reads obtained from single-digest restriction-site-associated DNA sequencing (RAD-Seq) using the EcoRI, 187 million reads were retained after quality filtering with an average of 3.6 million reads per pooled sample (Supplementary Table S1)
The results of Principal component analysis (PCA), multidimensional scaling (MDS), gene-level phylogenetic tree, and admixture analyses using nuclear DNA data show that 52 accessions of L. cruciata are separated into three groups, East-Honshu, West-Honshu, and Kyushu types (Figs. 2, 3, and 6 and Supplementary Fig. S1)
Summary
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 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[5,6,7] 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)[7]. The two types were genetically differentiated at the subspecies level (Nei’s genetic distance by allozymes was 0.09)[9]
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