Phylogeographic analysis of Ligidium japonicum (Isopoda: Ligiidae) and its allied species reveals high biodiversity and genetic differentiation in the Kanto region, Japan

Abstract

Research of the diversity and evolutionary history of Japanese soil invertebrates is scarce. Molecular data analysis can help to elucidate species classifications and evolutionary processes. We analyzed the mitochondrial cytochrome oxidase subunit I (COI) and nuclear 28S rDNA genes and the morphology of the male pleopod 2 endopod of Ligidium japonicum and its allied species from 67 sites in Hokkaido, Honshu and Shikoku, where only L. japonicum is thought to occur. We found males of the L. japonicum complex with a pleopod 2 endopod morphology matching that of the L. japonicum syntype specimens, except for the number of denticles at the inner margin. There were also more than five species that differed morphologically from the L. japonicum complex, and most of these species had allopatric distributions despite the absence of obvious barriers. A time‐calibrated molecular phylogeny implied that the L. japonicum complex of the Kanto region first differentiated allopatrically in the mountains; this was followed by independent dispersal of three lineages to the Kanto Plain and Boso Peninsula, where secondary contact occurred. Two of the three sympatrically distributed L. japonicum complex lineages had a significant difference in the number of denticles at the inner margin of male pleopod 2 endopods. This variation implies the presence of cryptic species within the L. japonicum complex.

History of the terrestrial isopod genus Ligidium in Japan based on phylogeographic analysis

“…Kanozan_h8 (LC565946; 1), Owasi_i9 (LC565990; 1) ✓ 17 33 34 Harigai et al, 2020 [ 14 ] Niigata4 (LC534813; 33), Niigata5 (LC534814; 1) 18 ST02 8 this study ST021 (LC711283; 4), ST0202 (LC711279; 1), ST0204 (LC711280; 1), ST0206 (LC711281; 1), ST0208 (LC711282; 1) 19 55, 57, Amigasamori-Forest, Aomori 12 this study and Yoshino & Kubota, 2022 [ 15 ] A4a (LC711155; 1), A4b (LC711156; 3), A4c (LC711157, 2), A4d (LC711158; 1), A4e (LC711159, 3), A4f (LC711160; 1), Amigasamori-Forest_a1 (LC565844; 1) ✓ 20 Yuzawa-shi, Akita 1 Yoshino & Kubota, 2022 [ 15 ] Yuzawa-shi_b2 (LC566057; 1) 21 48, 50, 54, 55 33 this study A3a (LC711147; 17), A3b (LC711148; 1), A3c (LC711149; 1), A3d (LC711150; 1), A3e (LC711151; 10), A3f (LC711152; 1), A3g (LC711153; 1), A3h (LC711154; 1) ✓ 22 Dakigaeri-Valley, Akita 1 Yoshino & Kubota, 2022 [ 15 ] Dakigaeri-Valley_a1 (LC565848; 1) 23 Boso peninsula, Chiba 12 Yoshino & Kubota, 2022 [ 15 ] Owasi_d4 (LC565985; 1), Chiba_Owasi1 (LC565982, LC565983, LC565988, LC565989, LC565991; 5), Owasi_c3 (LC565984; 1), Owasi_e5 (LC565987; 1), Owasi_Kanozan1 (LC565941, LC565944, LC565945; 3), Tozaki_3 (LC566043; 1) ✓ 24 Boso peninsula, Chiba 6 Yoshino & Kubota, 2022 [ ...…”

“…Kanozan1 (LC565943, LC565947; 2) ✓ 44 Kawayatu, Chiba 1 Yoshino & Kubota, 2022 [ 15 ] Kawayatu_l12 (LC565910; 1) 45 Midori-ku, Chiba 1 Yoshino & Kubota, 2022 [ 15 ] Midori-ku_c3 (LC565932; 1) 46 Boso peninsula, Chiba 7 Yoshino & Kubota, 2022 [ 15 ] Ishigami_a1 (LC565876, LC565877, LC565880, LC565882, LC565885; 5), Ishigami_f6 (LC565881; 1), Ishigami_d4 (LC565879; 1) ✓ 47 Takataki, Chiba 2 Yoshino & Kubota, 2022 [ 15 ] Takataki3 (LC566025, LC566036; 2) 48 Boso peninsula, Chiba 9 Yoshino & Kubota, 2022 [ 15 ] Takataki1 (LC566026, LC566028, LC566030, LC566031, LC566032, LC566035; 6), Takataki2 (LC566027, LC566029; 2), Takataki_j10 (LC566034; 1) ✓ 49 Sosa-shi, Chiba 1 Yoshino & Kubota, 2022 [ 15 ] Sosa-shi_a1 (LC566019; 1) 50 Tateyama, Chiba 2 Yoshino & Kubota, 2022 [ 15 ] Tateyama1 (LC566037, LC566038; 2) 51 Kawasaki-shi, Kanagawa 8 Yoshino & Kubota, 2022 [ 15 ] Ikuta-Ryokuchi-Park_d4 (LC565870; 1), Kanagawa_Ikuta1 (LC565867, LC565868; 2), Kanagawa_h...…”

“…SHIZU2 (LC496507) and Ligidium sp. SHIZU1 (LC496506) collected in Shizuoka, a prefecture central to the Pacific Ocean side of Honshu, 213 sequences of individuals sampled mainly in the regions around Tokyo, Japan, that were previously published by Yoshino and Kubota [ 15 ], Ligidium species from Europe, and Oniscidea sp. collected in Shanghai, China.…”

“…Table S 4 lists the accession numbers for the downloaded data. Data from Yoshino and Kubota [ 15 ] were also used in the population genetics analyses.…”

“…Our preliminary analysis showed that the Hokkaido population in northern Japan experienced a bottleneck caused by the Last Glacial Maximum (LGM) [ 14 ], suggesting that this genus is sensitive to glacial cycles. Furthermore, the phylogeography of independent lineages of L. japonicum reflects its dispersal history from the mountains to the plains and peninsulas in the Kanto Plain of Japan [ 15 ].…”