Liang-Kong Lin

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.

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.

Molecular phylogenetic reconstructions identify East Asia as the cradle for the evolution of the cosmopolitan genus Myotis (Mammalia, Chiroptera)

Sequences of the mitochondrial cytochrome b (1140 bp) and nuclear Rag 2 (1148 bp) genes were used to assess the evolutionary history of the cosmopolitan bat genus Myotis, based on a worldwide sampling of over 88 named species plus 7 species with uncertain nomenclature. Phylogenetic reconstructions of this comprehensive taxon sampling show that most radiation of species occurred independently within each biogeographic region. Our molecular study supports an early divergence of species from the New World, where all Nearctic and Neotropical species plus a lineage from the Palaearctic constitute a monophyletic clade, sister to the remaining Old World taxa. The major Old World clade includes all remaining Eurasian taxa, most Oriental species, one Oceanian, and all Ethiopian species. Another lineage, including M. latirostris from Taiwan, appears at the base of these two major biogeographic clades and, because it bears nyctalodont molars, could be considered as a distinct genus. However, this molar configuration is also found in crown-group species, indicating that these dental characters are variable in the genus Myotis and may confound interpretation of the fossil record. Molecular datings suggest an origin of all recent Myotis in the early Miocene (about 21MYA with 95% highest posterior density interval 23-20MYA). This period was characterized by a global climatic cooling that reduced the availability of tropical habitats and favoured the development of more temperate vegetation. This sharp climatic change might have triggered the evolution of Myotis in the Northern continents, because Myotis ancestors seem to have been well adapted and successful in such temperate habitats. Ancestral area reconstructions based on the molecular phylogeny suggest that the eastern portion of the Asian continent was an important center of origin for the early diversification of all Myotis lineages, and involved relatively few subsequent transcontinental range expansions.

Phylogenetic Relationships among Asian species of Petaurista (Rodentia, Sciuridae), Inferred from Mitochondrial Cytochrome b Gene Sequences.

Abstract To elucidate the phylogenetic relationships among four species belonging to the genus Petaurista (P. alborufus castaneus, P. alborufus lena, P. leucogenys leucogenys, P. leucogenys nikkonis, P. petaurista melanotus, and P. philippensis grandis), we investigated the partial sequences (1,068 bp) of the mitochondrial cytochrome b gene for these giant flying squirrels. Phylogenetic trees (NJ, MP, and ML trees) constructed from cytochrome b sequences indicated that P. leucogenys was grouped independently with other species, and that P. philippensis was most closely related to P. petaurista with 99–100% bootstrap values. In addition, two subspecies of P. alborufus did not form a single clade: P. alborufus castaneus from China was most distantly related to the other species, whereas P. alborufus lena from Taiwan was closely related to P. petaurista and P. philippensis with 82–90% bootstrap values. This result suggests that it is reasonable to regard P. alborufus lena as a distinct species from P. alborufus castaneus.

A multi-locus phylogeny of Nectogalini shrews and influences of the paleoclimate on speciation and evolution.

Nectogaline shrews are a major component of the small mammalian fauna of Europe and Asia, and are notable for their diverse ecology, including utilization of aquatic habitats. So far, molecular phylogenetic analyses including nectogaline species have been unable to infer a well-resolved, well-supported phylogeny, thus limiting the power of comparative evolutionary and ecological analyses of the group. Here, we employ Bayesian phylogenetic analyses of eight mitochondrial and three nuclear genes to infer the phylogenetic relationships of nectogaline shrews. We subsequently use this phylogeny to assess the genetic diversity within the genus Episoriculus, and determine whether adaptation to aquatic habitats evolved independently multiple times. Moreover, we both analyze the fossil record and employ Bayesian relaxed clock divergence dating analyses of DNA to assess the impact of historical global climate change on the biogeography of Nectogalini. We infer strong support for the polyphyly of the genus Episoriculus. We also find strong evidence that the ability to heavily utilize aquatic habitats evolved independently in both Neomys and Chimarrogale+Nectogale lineages. Our Bayesian molecular divergence analysis suggests that the early history of Nectogalini is characterized by a rapid radiation at the Miocene/Pliocene boundary, thus potentially explaining the lack of resolution at the base of the tree. Finally, we find evidence that nectogalines once inhabited northern latitudes, but the global cooling and desiccating events at the Miocene/Pliocene and Pliocene/Pleistocene boundaries and Pleistocene glaciation resulted in the migration of most Nectogalini lineages to their present day southern distribution.

Phylogeography of Pallas's Squirrel in Taiwan: Geographical Isolation in an Arboreal Small Mammal

Abstract To. test for isolation by mountain ranges in small arboreal mammals, phylogeography of Pallass squirrel .Callosciurus erythraeus) was investigated using complete mitochondrial control region sequences (1,079–1,081 bases). This common species is distributed in the low and middle elevations of Taiwan, Republic of China. We examined 71 specimens from 6 sites in 3 study regions divided by mountain ranges in Taiwan. The 43 haplotypes found in the Taiwan populations revealed association with geography. There were 4 main mitochondrial DNA phylogroups (northern, western, southern, and eastern), but 4 haplotypes were not included in any phylogroup. Distribution range of each phylogroup was similar to defined geological categories, suggesting mountain range isolation influenced populations of C. erythraeus. The 4 phylogroups may be the result of glacial refugia during the Pleistocene.

Phylogeography of the mole-shrew (Anourosorex yamashinai) in Taiwan: implications of interglacial refugia in a high-elevation small mammal

To test the Pleistocene interglacial refugia hypothesis with a high‐elevation mammal, we studied the phylogeography of the mole‐shrew (Anourosorex yamashinai) using partial mitochondrial cytochrome b gene sequences (737 bases). This shrew is endemic to Taiwan. It is mainly distributed in the highlands from 1000 to 2500 m in elevation. We examined 103 specimens from 24 localities in three mountain ranges of Taiwan and found 36 haplotypes. These haplotypes separated into two major phylogroups (Northern and Southern) plus a minor phylogroup (Houhuan) of only one haplotype. This demonstrated strong association with geography. The formation of these three phylogroups may be the result of interglacial refugia during the middle Pleistocene. Distinct sublineages were not found within each major phylogroup, suggesting that the populations (phylogroups) explosively expanded from the interglacial refugia of ancestral founder haplotypes. The present distribution pattern of haplotypes suggests that Mount Houhuan is an effective refugium in central Taiwan. It was not possible to specify the refugia for the Northern and Southern phylogroups.

Phylogenetic Relationships among Six Flying Squirrel Gener,a Inferred from Mitochondrial Cytochrome b Gene Sequences

Abstract Petauristinae (flying squirrels) consists of 44 extant species in 14 recent genera, and their phylogenetic relationships and taxonomy are unsettled questions. We analyzed partial mitochondrial cyto-chrome b gene sequences (1,068 base pairs) to investigate the phylogenetic relationships among six flying squirrel genera (Belomys, Hylopetes, Petaurista, Petinomys, and Pteromys from Asia and Glaucomys from North America). Molecular phylogenetic trees, constructed by neighbor-joining and maximum likelihood methods, strongly indicated the closer relationship between Hylopetes and Petinomys with 100% bootstrap values. Belomys early split from other flying squirrels. Petaurista was closely related to Pteromys, and Glaucomys was most closely related to the cluster consisting of Hylopetes and Petinomys. The bootstrap values supporting branching at the deeper nodes were not always so high, suggesting the early radiation in the evolution of flying squirrels.

Taxonomic status of the Senkaku mole, Nesoscaptor uchidai, with special reference to variation in Mogera insularis from Taiwan (Mammalia : Insectivora)

Abstract The taxonomic status of the Senkaku mole,Nesoscaptor uchidai Abe, Shiraishi et Arai, 1991 (Mammalia: Insectivora: Talpidae), described from Uotsurijima in the Senkaku Group, Ryukyu Archipelago, was re-evaluated. Morphological analyses suggest that N. uchidai is most similar to Mogera insularis from Taiwan, although several morphological characters, such as the number of premolars and the shapes of the anterior portion of the palate, zygomatic arch, auditory bulla, and coronoid process, differentiate N. uchidai from M. insularis. Therefore, we synonymize the monotypic genus Nesoscaptor Abe, Shiraishi et Arai, 1991 with the genus Mogera Pomel, 1848, and define Mogera uchidai (Abe, Shiraishi et Arai, 1991) as a valid species endemic to Uotsurijima. In addition, we analyzed morphological variation within M. insularis, such as variation in the second upper premolar pair, overall cranial size, and the breadth of the rostrum and palate. Some of this variation may be associated with topographical and environmental factors in its habitat.

Pattern of X-Y chromosome pairing in the Taiwan vole, Microtus kikuchii.

Pairing of X and Y chromosomes at meiotic prophase and the G- and C-banding patterns and nucleolar organizer region (NOR) distribution were analyzed in Microtus kikuchii. M. kikuchii is closely related to M. oeconomus and M. montebelli, karyologically and systematically. The formation of a synaptonemal complex between the X and Y chromosomes at pachytene and end-to-end association at diakinesis--metaphase I are only observed in three species in the genus Microtus; M. kikuchii, M. oeconomus, and M. montebelli. All the other species that have been studied so far have had asynaptic X-Y chromosomes. These data confirm that M. kikuchii, M. oeconomus, and M. montebelli are very closely related, and support the separation of asynaptic and synaptic groups on the phylogenetic tree.