Phylogenomics and Spatiotemporal Dynamics of Bovine Leukemia Virus Focusing on Asian Native Cattle: Insights Into the Early Origin and Global Dissemination.

Bovine leukemia virus (BLV), the causative agent of enzootic bovine leukosis, is currently one of the most important pathogens affecting the cattle industry worldwide. Determining where and in which host it originated, and how it dispersed across continents will provide valuable insights into its historical emergence as the cattle pathogen. Various species in the Bos genus were domesticated in Asia, where they also diversified. As native cattle (taurine cattle, zebu cattle, yak, and water buffalo) are indigenous and adapted to local environments, we hypothesized that Asian native cattle could have harbored BLV and, therefore, that they were important for virus emergence, maintenance, and spread. In this study, phylogeographic and ancestral trait analyses-including sequences obtained from Asian native cattle-were used to reconstruct the evolutionary history of BLV. It was shown that, since its probable emergence in Asia, the virus spread to South America and Europe via international trade of live cattle. It was inferred that zebu cattle were the hosts for the early origin of BLV, while taurine cattle played the significant role in the transmission worldwide. In addition, the results of positive selection analysis indicate that yak had a substantially minor role in the transmission of this virus. In this study, endogenous deltaretrovirus sequences in bats, collected in Asian countries, were also analyzed on whether these sequences were present in the bat genome. Endogenous deltaretrovirus sequences were detected from bat species endemic to specific regions and geographically isolated for a long time. Endogenous deltaretrovirus sequences from these geographically isolated species represent ancient exogenous deltaretroviruses distributions. The phylogenetic analysis revealed that these newly obtained endogenous deltaretrovirus sequences were closely related to those of BLV from Asian native cattle, indicating that BLV-related ancient deltaretroviruses circulated in Asia long before the emergence of BLV. Together, our analyses provide evidence for origin and spatiotemporal dynamics of BLV.

Taxonomic status of the barbastelles (Chiroptera: Vespertilionidae: Barbastella) from the Japanese archipelago and Kunashir Island.

Until recently, almost all barbastelle populations inhabiting Asia, from Iran to Japan and Taiwan, were recognized as a single species, Barbastella darjelingensis. However, in recent years, it was shown that the taxonomic diversity within the genus Barbastella was underestimated, and B. darjelingensis sensu lato is highly variable, both morphologically and genetically. Transcaucasian and Central Asian populations were already raised to the species level as B. caspica. Populations from eastern and south-eastern Asia are still understudied and likely encompass undescribed species. Comparing results from mtDNA sequences, skull morphometry and baculum shape, we concluded that one of these putative species is represented by populations inhabiting Honshu, Hokkaido and Kunashir Islands, and provide a scientific description of this new species. Populations from Taiwan, southern China and Indochina represent a sister mitochondrial clade to this new species. However, available morphological material from these areas did not demonstrate a significant difference from the Himalayan B. darjelingensis. Therefore, we refuse to give this form any taxonomic status until further studies of more vast material are done.

Refugia in glacial ages led to the current discontinuous distribution patterns of the dark red-backed vole Myodes rex on Hokkaido, Japan.

The terrestrial mammalian fauna of the North Japanese island, Hokkaido, is more similar to that of Southern Siberia than to the main island of Japan, Honshu. Three species of the genus Myodes (Muridae, Rodentia) are found on Hokkaido, but not on Honshu. While Myodes rufocanus and M. rutilus are widely distributed across Hokkaido as well as the Eurasian continent, M. rex, which is endemic to Hokkaido and its adjacent islands, shows a discontinuous distribution pattern. We analyzed the phylogeographic history of M. rex using the mitochondrial DNA control region in order to interpret their discontinuous distribution pattern. Phylogenetic relationships among 54 distinct haplotypes showed that M. rex can be divided into four clades that occur on the northern, central, and southern regions of the Hokkaido mainland and on Rishiri Island, respectively. The phylogroups in the northern and central regions were largely separated in space, although several areas of sympatry were found. The phylogroup in the southern region, which was clearly separated from other phylogroups, showed markedly low genetic variability. All analyzed individuals from the population on Rishiri belonged to a separate lineage. Across a range of divergence rate estimates, we dated the basal divergence of all phylogroups to the mid to late Pleistocene, with subsequent signals of population expansion within lineages. We conclude that current phylogeographic structure in M. rex likely reflects Pleistocene survival in several separate refugia in situ. Past glacial ages have thus played an important role in shaping the current distribution patterns of mammalian species on Hokkaido.

DNA Barcoding and Molecular Phylogeny of Drosophila lini and Its Sibling Species.

Drosophila lini and its two sibling species, D. ohnishii and D. ogumai, are hardly distinguishable from one another in morphology. These species are more or less reproductively isolated. The mitochondrial ND2 and COI-COII and the nuclear ITS1-ITS2 regions were sequenced to seek for the possibility of DNA barcoding and to reconstruct the phylogeny of them. The character-based approach for DNA barcoding detected some diagnostic nucleotides only for monophyletic D. ogumai, but no informative sites for the other two very closely species, D. lini and D. ohnishii, of which strains intermingled in the molecular phylogenetic trees. Thus, this study provides another case of limited applicability of DNA barcoding in species delineation, as in other cases of related Drosophila species. The molecular phylogenetic tree inferred from the concatenated sequences strongly supported the monophyly of the cluster of the three species, that is, the lini clade. We propose some hypotheses of evolutionary events in this clade.

Strong purifying selection on the Odysseus gene in two clades of sibling species of the Drosophila montium species subgroup.

The Odysseus (OdsH) gene was duplicated from its ancestral neuron-expressed gene, unc-4, and then evolved very rapidly under strong positive Darwinian selection as a speciation gene causing hybrid-male sterility between closely related species of the Drosophila simulans clade. Has OdsH also experienced similar positive selection between Drosophila sibling species other than those of the simulans clade? We cloned and sequenced OdsH and unc-4 from two clades of the Drosophila montium species subgroup, the Drosophila lini and the Drosophila kikkawai clades. The ratios of Ka/Ks for OdsH were remarkably low between sibling species of these two clades, suggesting that OdsH has been subjected to strong purifying selection in these two clades.

The status of the Japanese and East Asian bats of the genus Myotis (Vespertilionidae) based on mitochondrial sequences.

The genus Myotis includes the largest number of species in the family Vespertilionidae (Chiroptera), and its members are distributed throughout most of the world. To re-evaluate the phylogenetic position of East Asian Myotis species with respect to Myotis species worldwide, we analyzed mitochondrial gene sequences of NADH dehydrogenase subunit 1 and cytochrome b from 24 East Asian individuals as well as 42 vespertilionid bats determined previously. The results suggest that: (1) some individuals having the same species name in Europe and Japan do not form a monophyletic clade, indicating that some bat species exhibit morphological convergence, (2) Japanese Myotis mystacinus forms a sister relationship with Myotis brandtii (Palaearctic), and both species are included in the American clade implying that an ancestor of these species originated in North America, and (3) the Black whiskered bat, Myotis pruinosus, is endemic to Japan and forms sister relationships with Myotis yanbarensis and Myotis montivagus collected from Okinawa (Japan) and Selangor (Malaysia), respectively, implying that M. pruinosus originated from the south. The systematics of Japanese and East Asian Myotis bats were revisited by considering their phylogenetic relationships. Our study provides the first extensive phylogenetic hypothesis of the genus Myotis that includes East Asian and Japanese species.

Intra- and interfamily relationships of Vespertilionidae inferred by various molecular markers including SINE insertion data.

The family Vespertilionidae comprises the largest number of species in the order Chiroptera, and its members are distributed over most of the world. We collected sequences of the mitochondrial NDI (NADH dehydrogenase subunit 1) gene from 38 species as well as 20 sequences of exon28 of the vWF (von Willebrand Factor) gene and analyzed phylogenetic relationships in Vespertilionidae using maximum-likelihood analyses and SINE (short interspersed elements) insertions. Our data strongly suggest the following: (1) Murininae and Myotis, each of which is classified into different subfamilies, are monophyletic; (2) the monophyly of Murininae, Myotis, Pipistrellini, and Plecotini is supported by our analyses of the NDI and nuclear vWF as well as data from SINE insertions, while Miniopterinae was not included in this group; and (3) Rhinolophoidea (microchiroptera) is separated from all the other microchiropteran species. Our study represents the most comprehensive phylogenetic model of Vespertilionidae to date.