Natural Selection Signatures in the Hondo and Ryukyu Japanese Subpopulations

Natural selection signatures across Japanese subpopulations are under-explored. Here we conducted genome-wide selection scans with 622,926 single nucleotide polymorphisms for 20,366 Japanese individuals, who were recruited from the main-islands of Japanese Archipelago (Hondo) and the Ryukyu Archipelago (Ryukyu), representing two major Japanese subpopulations. The integrated haplotype score (iHS) analysis identified several signals in one or both subpopulations. We found a novel candidate locus at IKZF2, especially in Ryukyu. Significant signals were observed in the major histocompatibility complex region in both subpopulations. The lead variants differed and demonstrated substantial allele frequency differences between Hondo and Ryukyu. The lead variant in Hondo tags HLA-A*33:03-C*14:03-B*44:03-DRB1*13:02-DQB1*06:04-DPB1*04:01, a haplotype specific to Japanese and Korean. While in Ryukyu, the lead variant tags DRB1*15:01-DQB1*06:02, which had been recognized as a genetic risk factor for narcolepsy. In contrast, it is reported to confer protective effects against type 1 diabetes and human T lymphotropic virus type 1-associated myelopathy/tropical spastic paraparesis. The FastSMC analysis identified 8 loci potentially affected by selection within the past 20-150 generations, including 2 novel candidate loci. The analysis also showed differences in selection patterns of ALDH2 between Hondo and Ryukyu, a gene recognized to be specifically targeted by selection in East Asian. In summary, our study provided insights into the selection signatures within the Japanese and nominated potential sources of selection pressure.

Small Mammalian Remains from the Late Holocene Deposits on Ishigaki and Yonaguni Islands, Southwestern Japan

Yuichiro Nishioka, Ryohei Nakagawa, Shin Nunami, and Satoshi Hirasawa (2016) Small mammalian remains were newly discovered from the Late Quaternary sediments of the Yaeyama region (Ishigaki and Yonaguni Islands) in the southwestern-most part of Japan. We examined these materials based on taxonomical and chronological approaches, in order to reconstruct the past fauna in this region. Accelerator Mass Spectrometry radiocarbon dating indicates that the mammalian assemblages from Ishigaki and Yonaguni Islands are composed mainly of late Holocene fossils. The fossil assemblage from Ishigaki Island comprises five species of small mammals belonging to Soricomorpha (Suncus murinus), Chiroptera (Pteropus sp., Hipposideros turpis, and Rhinolophus perditus), and Rodentia (Niviventer sp.). One rodent bone, collected from the fissure sediments near Sabichi-do Cave, Ishigaki Island, is dated at 230 ± 20 yBP (ca. AD 1,700), and is considered part of the recent remain. Furthermore, the fossil assemblage from Umabana-zaki Fissure, on Yonaguni Island, is dated at 1,760 ± 20 yBP (ca. AD 300) and comprises three species of small mammals belonging to Chiroptera (Pipistrellus cf. abramus) and Rodentia (Niviventer sp. and Mus musculus). Niviventer is not currently distributed in Japan. Only domestic rats (Rattus rattus and R. norvegicus) live on Ishigaki and Yonaguni Islands at the present time. However, the fossil assemblage from Umabana-zaki Fissure is dominated completely by Niviventer sp. Most fossils of small mammals found from the late Holocene Ishigaki and Yonaguni Islands represented species that are currently endemic to the Yaeyama region. Niviventer sp. from these islands is unique because this form has never been found from neighboring regions, such as Taiwan and Miyako Islands, and because it likely existed in the late Holocene. These discoveries support the hypothesis that the Yaeyama region had been isolated zoogeographically from the continent even during the Last Glacial Maximum, when the sea level had drastically fallen.

Part I: ascidian-dwellers

Commensal leucothoid amphipods have been collected from the branchial chambers of their ascidian hosts throughout the Ryukyu Archipelago, Japan. Seven new species are described in two genera with valuable location data and host records. An identification key to ascidian-dwelling Leucothoidae of the Ryukyu Archipelago is provided.