Shunde Chen

Phylogeography of the Large White-bellied Rat Niviventer excelsior Suggests the Influence of Pleistocene Glaciations in the Hengduan Mountains

The Hengduan Mountains, situated in the southeastern Tibetan Plateau, have undergone dramatic geological and climatic changes over the Pleistocene epoch. Several studies have revealed that the mountains served as a refugium during the ice age. The large white-bellied rat Niviventer excelsior is a rodent endemic to the Hengduan Mountains, which makes it an appropriate species for investigating the influence of glacial movements on the genetic structure of mammals. In this study, we sequenced the partial mitochondrial DNA control region from 72 N. excelsior specimens collected from 20 localities. The results revealed very high levels of haplotype diversity (h = 0.947) and nucleotide diversity (&pgr; = 0.101) in this species. No common haplotype was found to be shared in samples from all geographic regions. Demographic analyses suggested that N. excelsior populations had not been subject to either expansion or bottleneck. The phylogenetic relationships among the haplotypes have no correlation with their geographical origins, while topology revealed two major clades. We speculate that the populations of N. excelsior may have been restricted to two separate refugia during the Last Glacial Maximum (0.60–0.17 Mya), with one west and one east of the Shaluli Mountains. Between the two major refugia, there existed a more widely distributed network subrefugia, which conserved genetic variations in N. excelsior. These results indicated that complex topographic configuration in the Hengduan Mountains provided a network of refugia to maintain the high level of genetic diversity in Pleistocene glaciations.

The complete mitogenome of Stripe-Backed Shrew, Sorex cylindricauda (Soricidae)

Abstract The Stripe-Backed Shrew, Sorex cylindricauda belongs to the family Soricidae, and distributes in northwestern Yunnan, central Sichuan, southern Gansu and Shaanxi. In this study, the complete mitochondrial genome sequence of S. cylindricauda was determined. The mitogenome is 17,191 bp in length and contains 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and 1 control region, with a base composition of 33.2% A, 30.2% T, 23.8% C and 12.8% G. The study contributes to illuminating taxonomic status of Stripe-Backed Shrew Sorex cylindricauda.

The complete mitochondrial genome sequence of the Gracile shrew mole, Uropsilus gracilis (Soricomorpha: Talpidae)

The Gracile shrew mole (Uropsilus gracilis) belongs to the family Talpidae, which distributes in southwestern China, extending to northern Myanmar. In this study, the complete mitochondrial genome of U. gracilis was sequenced. It was determined to be of 16,533 bases. The nucleotide sequence data of 12 heavy-strand protein-coding genes of U. gracilis and other 12 insectivores were used for phylogenetic analysis. Phylogenetic trees were constructed by using Bayesian and maximum likelihood methods, which showed that U. gracilis was clustered together with U. soricipes, and Urotrichus should be prior to Galemys.

The complete mitogenome of Asiatic Short-tailed Shrew Blarinella quadraticauda (Soricidae)

Abstract The Asiatic Short-tailed Shrew, Blarinella quadraticauda, is an endemic shrew to China, and is only distributed in Sichuan. In this study, the complete mitochondrial genome sequence of B. quadraticauda was determined. The mitogenome is 17,014 base pairs in length and contains 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and 1 control region, with a base composition of 33.3 % A, 31.8% T, 22.3% C and 12.6% G. This study contributes to illuminating taxonomic status of the Asiatic Short-tailed Shrew, B. quadraticauda.

Molecular phylogenetics and phylogeographic structure of Sorex bedfordiae based on mitochondrial and nuclear DNA sequences

The southeastern margin of the Tibetan Plateau is characterized by complex topography and a discontinuous landscape, creating a sky island situation. However, the way topography shapes genetic structures and demographic histories of endemic species has not been well studied. We examined the phylogeographic pattern and demographic histories of Sorex bedfordiae, a dispersal-limited small mammal, using three nuclear genes [1977bp] and two mitochondrial genes [1794bp] with comprehensive molecular approaches. We recovered five well-supported clades whose distributions are along mountain ridges and roughly subdivided by large rivers. Demographic expansions in the middle Pleistocene were strongly supported by both nuclear and mitochondrial genes. Our results support the hypothesis that sky island topography and river systems strongly affect the genetic structure of non-aquatic terrestrial species. We further clarify that S. bedfordiae and S. cylindricauda are valid sibling species, whereas S. excelsus is most likely a geographic subspecies of S. bedfordiae.

The complete mitogenome of Chinese Mole Shrew, Anourosorex squamipes (Soricidae)

Abstract The Chinese Mole Shrew, Anourosorex squamipes belongs to the family Soricidae, and widely distributes in central and southern China, northern and south Burma, east India, northern Vietnam and Thailand. In this study, the complete mitochondrial genome sequence of Anourosorex squamipes was determined. The mitogenome is 17,121 base pairs in length and contains 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and 1 control region, with base composition of 34.0% A, 31.3% T, 22.0% C, and 12.7% G. The genome organization, nucleotide composition and codon usage did not differ significantly from those of other shrews. The study contributes to illuminating taxonomic status of Chinese Mole Shrew Anourosorex squamipes.

Sequencing and analysis of complete mitochondrial genome of Apodemus draco (Rodentia: Arvicolinae)

Abstract The genus Apodemus are the most common small rodents in fields. They are also one of the best species for biogeographic study and understanding the environmental changes. In this study, the complete mitochondrial genome sequence of Apodemus draco is determined. The mitogenome is 16 220 bp in length and contains 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and a control region, with a base composition of 35.1% A, 29.0% T, 23.8% C and 12.1% G. The nucleotide sequence data of 12 heavy-strand protein-coding genes of Apodemus draco and other 23 rodents were used for mitochondrial genome phylogenetic analyses. The monophyly of the genus Apodemus was well supported with sister to the genus Mus. Bayesian analysis also suggested that Apodemus draco was a sister to Apodemus latronum. The present study may facilitate further investigation of the molecular evolution and biogeographic study of the genus Apodemus.

Morphometric and pelage color variation of two sibling species of shrew (Mammalia: Soricomorpha)

Pelage color variants have been documented in some small mammals, but there is not any reported about coat color variation in shrews. Here, pelage color variants of the two sibling species (Sorex cylindricauda and Sorex bedfordiae) were uncovered in different sampling sites. Our data may initiate new interest to pelage color variants in small mammals. Furthermore, the classification of two striped shrews has been controversial for several decades. We conducted a detailed examination of the morphometric characters for the two sibling shrews. Significant differences between the two species morphologically confirmed the two-species classification status.

Mitochondrial DNA genetic variation and phylogeography of the recently described vole species Proedromys liangshanensis Liu, Sun, Zeng and Zhao, 2007 (Rodentia: Arvicolinae)

A vole species, Proedromys liangshanensis Liu, Sun, Zeng and Zhao, 2007 (Rodentia: Arvicolinae), which is endemic to the Liangshan Mountains, Sichuan, China, was reported in 2007. The species is restricted to a narrow range because of its weak dispersal ability and habitat specificity, and only lives in fir and spruce forests with abundant grass. In this study, the genetic diversity and phylogeographical structure of 42 P. liangshanensis were examined based on analysis of a partial mitochondrial DNA control region. The results revealed low genetic diversity in the P. liangshanensis populations. Twelve nucleotide haplotypes were defined in the 42 collected individuals, and were divided into two major phylogenetic clades, which were obviously related to geographic pattern. Estimates of gene flow (Nm = 0.09) also revealed a genetic divergence between the Jinyang and Meigu populations. Species-specific traits, habitat specificity and geographic events contributed to the genetic divergence of the new vole.

The complete mitogenome of lesser striped shrew Sorex bedfordiae (soricidae).

Abstract The Sorex genus is type genus in Soricidae. Most of them lack comprehensive biological data. In this study, the complete mitochondrial genome sequence of Sorex bedfordiae was determined. The mitogenome is 17 160 base pairs in length and contains 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and one control region. The nucleotide sequence data of 12 heavy-strand protein-coding genes of Sorex bedfordiae and other 10 species in Soricidae were used for phylogenetic analyses. Tree constructed using Bayesian phylogenetic methods demonstrated Sorex bedfordiae as a sister to Sorex cylindricauda. Phylogenetic analyses further confirmed that Blarinella diverged prior to Sorex and Anourosorex, but Episoriculus differentiated earlier than Neomys and Nectogale within subfamily Soricinae.