Molecular phylogeny of Japanese Leporidae, the Amami rabbit Pentalagus furnessi, the Japanese hare Lepus brachyurus, and the mountain hare Lepus timidus, inferred from mitochondrial DNA sequences.

Abstract

We determined mitochondrial 12S ribosomal RNA (rRNA) and cytochrome b (cyt b ) gene sequences in three leporid species of Japan, the Amami rabbit Pentalagus furnessi from the Ryukyu Islands, the Japanese hare Lepus brachyurus from Honshu, and a Japanese form of the mountain hare Lepus timidus ainu from Hokkaido. We compared the sequences with those of other taxa of leporids available in databases. Phylogenetic trees of the 12S rRNA gene sequences indicated that the lineage of P. furnessi diversified during the generic radiation of the leporids at an ancient time, which was estimated to have been the middle Miocene. Cyt-b gene trees revealed that the lineage of L. brachyurus branched off at an early stage in the speciation of Lepus , probably at the beginning of the Pliocene. The cyt b sequences of L. t. ainu were somewhat distinct from those of continental conspecific populations; this lineage divergence is likely to have occurred during the middle or late Pleistocene. The results show that the three regions of the Japanese archipelago, Ryukyu, Honshu-Shikoku-Kyushu, and Hokkaido, now preserve their own leporid taxa, each with a different extent of genetic endemicity. It is possible that the zoogeographic traits of the Japanese leporids are a consequence of the evolutionary dynamics of leporids in East Asia, in that the radiation centers of leporids are likely to have shifted from tropical, through temperate, to arctic zones.

Colonization history of the sableMartes zibellina(Mammalia, Carnivora) on the marginal peninsula and islands of northeastern Eurasia

“…The present study and Sato et al (2011) suggest that the mtDNA lineage of the sable in Hokkaido was established during the Late Pleistocene. This migration time estimate is consistent with that for the Korean field mouse (Sakka et al 2010), but not with those for the Eurasian flying squirrel, the gray redbacked vole, and the mountain hare, whose migration times were estimated to occur during the late Middle Pleistocene (Yamada et al 2002;Oshida et al 2005;Abramson et al 2012;Kinoshita et al 2012). On the other hand, the brown bear Ursus arctos and the red fox Vulpes vulpes possess several distinctive mtDNA lineages on Hokkaido, suggesting repeated colonizations since the Middle to Late Pleistocene (Matsuhashi et al 1999(Matsuhashi et al , 2001Inoue et al 2007;Korsten et al 2009;Hirata et al 2013).…”

Evolution and Biogeography of Talpid Moles from Continental East Asia and the Japanese Islands Inferred from Mitochondrial and Nuclear Gene Sequences

“…Conversely, peripheral parts of the continent, especially the nearby island chains, helped to preserve these distinct mole lineages over time. A similar procession has been documented in other small mammal groups from continental to insular regions of East Asia (Suzuki et al, 1997(Suzuki et al, , 1999Iwasa et al, 2000;Serizawa et al, 2000;Iwasa and Suzuki 2002;Yamada et al, 2002). Consequently, the Japanese Islands, home to six talpid species, can best be regarded as a species refugia, preserving important biological materials integral to tracing the biogeographical and evolutionary history of the family Talpidae.…”

“…900 bp) was obtained using the universal primer pair L-613 (Mindell et al ., 1991) and H-1478 (Kocher et al ., 1989). Following this step, a heminested PCR was carried out using two primer pair sets: (1) R-L613 (Yamada et al ., 2002) and U-H1066 (Suzuki et al ., 1997) and (2) R-L 946 (5'-CAGGAAACAGCTATGACCGACATACGGCGTAAAGAG-TGT-3') and U-H1478 (Suzuki et al ., 1997).…”

Phylogenetic position of the Malaysian mole, Euroscaptor micrura (Mammalia: Eulipotyphla), inferred from three gene sequences

“…900 bp) was obtained using the universal primer pair L-613 (Mindell et al 1991) and H-1478 (Kocher et al 1989). Nested PCR was carried out with two primer pair sets: (1) R-L613 (Yamada et al 2002) and U-H1066 (Suzuki et al 1997) and (2) R-L 946 ) and U-H1478 (Suzuki et al 1997). A partial exon sequence of the RAG-1 gene was amplified using the primer pair RAG1-F1851 (Sato et al 2004) and RAG1-R2951 (5'-GAGCCATCCCTCTC-AATAATTTCAGG-3'; = RAG1-R2864, Teeling et al 2000).…”