Origin and diversification of pheretimoid megascolecid earthworms in the Japanese Archipelago as revealed by mitogenomic phylogenetics

• Published in: Molecular phylogenetics and evolution Vol. 182; p. 107735
• Main Authors: Sato, Chika, Nendai, Noriko, Nagata, Nobuaki, Okuzaki, Yutaka, Ikeda, Hiroshi, Minamiya, Yukio, Sota, Teiji
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01-05-2023
• Subjects: Amynthas; Animals; Biological Evolution; Character evolution; Distribution; DNA; Ecosystem; Japan; Metaphire; Native species; Nuclear ribosomal DNA; Oligochaeta - anatomy & histology; Oligochaeta - classification; Phylogeny; Phylogeography; Japan; Amynthas; Character evolution; Native species; Distribution; Nuclear ribosomal DNA; Metaphire
• ISSN: 1055-7903; 1095-9513
• DOI: 10.1016/j.ympev.2023.107735

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•Pheretimoid megascolecids are the major component of earthworm fauna in Japan.•Their phylogenetic relationships were studied using mitogenome sequence data.•Multiple Japan-endemic groups originated from Taiwan Island and continental China.•Distribution ranges within the Japanese Archipelago differed among the endemic groups.•The endemic groups may have diversified during the Miocene or later.
Megascolecid earthworms of the pheretimoid group are dominant detritivores of soil ecosystems in the Japanese Archipelago and East Asia. However, their diversity and phylogenetic relationships are poorly understood. We assembled whole mitogenome sequences for 197 megascolecid earthworms collected throughout Japan to study the phylogenetic relationships, phylogeography, divergence times, and diversification of important morphological characteristics among pheretimoid earthworms. Using 197 mitogenome sequences and 24 published mitogenome sequences from the East Asian mainland (221 sequences in total), we constructed a maximum likelihood tree and found that the pheretimoid earthworms currently assigned to Amynthas, Metaphire, Duplodicodrilus, and Manus are involved in the most senior genus Amynthas; thus, Amynthas can be treated as the sole genus encompassing all of the above genera. Within the Amynthas group, we identified three major lineages that led to four groups of endemic species in Japan. These lineages originated from different lineages on the East Asian mainland and Taiwan Island, indicating multiple colonization events from the East Asian mainland by different ancestral lineages, possibly after the Miocene. We also assembled nuclear ribosomal DNA sequences encompassing the 18S to 28S rRNA genes. The nuclear gene tree showed major groups consistent with the mitogenome tree except for different (and not well-resolved) relationships among major clades. Our molecular data covered 115–158 native and 7 non-native Amynthas group species in Japan in terms of DNA-based species delimitation. Our findings provide a basis for understanding the evolutionary relationships among diversified megascolecid earthworms in the Amynthas group in Japan and adjacent regions.