Baowei Zhang

Species Delimitation in the Genus Moschus (Ruminantia: Moschidae) and Its High-Plateau Origin

The authenticity of controversial species is a significant challenge for systematic biologists. Moschidae is a small family of musk deer in the Artiodactyla, composing only one genus, Moschus. Historically, the number of species in the Moschidae family has been debated. Presently, most musk deer species were restricted in the Tibetan Plateau and surrounding/adjacent areas, which implied that the evolution of Moschus might have been punctuated by the uplift of the Tibetan Plateau. In this study, we aimed to determine the evolutionary history and delimit the species in Moschus by exploring the complete mitochondrial genome (mtDNA) and other mitochondrial gene. Our study demonstrated that six species, M. leucogaster, M. fuscus, M. moschiferus, M. berezovskii, M. chrysogaster and M. anhuiensis, were authentic species in the genus Moschus. Phylogenetic analysis and molecular dating showed that the ancestor of the present Moschidae originates from Tibetan Plateau which suggested that the evolution of Moschus was prompted by the most intense orogenic movement of the Tibetan Plateau during the Pliocene age, and alternating glacial-interglacial geological eras.

Mitochondrial genome of the Anas falcata (Anatidae: Anas)

Abstract Anas falcate, near threatened species, has very wide geographical range with an estimated global extent of occurrence. Here, the complete mitochondrial genome of A. falcate (16,601 bp in length) was been analyzed for building the database. Similar to the typical mtDNA of vertebrates, it contained 37 genes (13 protein-coding genes, 2 rRNA genes and 22 tRNA genes) and a non-coding region (D-loop). All the genes in A. falcata were distributed on the H-strand, except for the ND6 subunit gene and 10 tRNA genes which were encoded on the L-strand.

Mitochondrial genome of the Emberiza pusilla (Emberizidae: Emberiza)

Abstract Emberiza rutila is a passerine bird of eastern Asia which belongs to the genus Emberiza in the bunting family Emberizidae. The complete mitochondrial genome of E. rutila was obtained for the first time in this study. The circular genome (16,803 bp in length) consists of 37 typical animal mitochondrial genes (13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes) and 1 control region. Overall base composition of the complete mitochondrial DNA was 30% A, 22.8% T, 32.8% C and 14.3% G. Except for 8 tRNA genes and ND6 gene, the relative position and orientation of all the genes were identical to those of most vertebrates.

Mitochondrial genome of theEmberiza aureola(Emberizidae:Emberiza)

The Emberiza pusilla is a common bunting with very wide geographical range. Here, the complete mitochondrial genome of E. pusilla (16,790 bp in length) has been analyzed for building the database. The results showed that it consisted of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 control region. The base composition of mtDNA was A (29.6%), G (14.8%), C (32.8%), and T (22.9%), so the percentage of A and T (52.5%) was slightly higher than G and C. All the genes in E. pusilla were distributed on the H-strand, except for the ND6 subunit gene and 10 tRNA genes, which were encoded on the L-strand.

Mitochondrial genome of Protobothrops dabieshanensis (Squamata: Viperidae: Crotalinae)

Abstract Protobothrops dabieshanensis is new species snake which is only distributed in Dabie Mountain of Anhui China at present. In this study, the complete mitochondrial genome of P. dabieshanensis (AHU 2013-EE-Hp01) had been determined. The circle genome with the 17,193 bp total length contained 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 2 control regions. Overall base composition of the complete mtDNA was 33.20% A, 25.13% T, 29.22% C and 12.45% G. All the genes in P. dabieshanensis were distributed on the H-strand, except for the ND6 subunit gene and eight tRNA genes which were encoded on the L-strand.

Mitochondrial genome of the black-faced bunting (Emberiza spodocephala)

Abstract Black-faced bunting (Emberiza spodocephala) is a common small songbird with widely geographical range. In this study, the complete mitochondrial genome of the Emberiza spodocephala was determined. The study showed that the total length of the mitogenome was 16,796 bp as a circular DNA consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 1 control region (CR). Overall base composition of the complete mitochondrial DNA was 29.81% A, 23.12% T, 32.51% C, and 14.56% G. The CR is 1215 bp in length and was located between the tRNAGln and tRNAPhe genes. The mitochondrial genes from Emberiza spodocephala were overlapped in a total of 29 bp at 6 locations, as well as interleaved with a total of 96 bp intergenic spacers at 18 locations.

Mitochondrial genome of Dasyatis bennettii (Chondrichthyes: Dasyatidae)

Dasyatis bennettii is a bottom-dweller that inhabits in the coastal waters of the Indian and Pacific Oceans as well as the freshwaters of Southern China. In this study, we determined the complete mitochondrial genome of this species of stingrays. The results showed that the total length of the mitogenome was 17,668 bp as a circular DNA and contained 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 control region. The base composition of the complete mitochondrial DNA was 31.1% A, 28.7% T, 26.7% C, and 13.5% G. All the genes in D. bennettii were distributed on the H-strand, except for the ND6 subunit gene and eight tRNA genes which were encoded on the L-strand.

Mitochondrial genome ofProtobothrops mangshanensis(Squamata: Viperidae: Crotalinae)

Abstract Protobothrops mangshanensis is a venomous pit viper species endemic to Hunan province in China. In this study, the complete mitochondrial genome of P. mangshanensis had been determined. The circle genome with the 17,230 bp total length contained 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 2 control regions. Overall base composition of the complete mtDNA was 32.27% A, 24.16% T, 30.34% C and 13.23% G. All the genes in P. mangshanensis were distributed on the H-strand, except for the ND6 subunit gene and eight tRNA genes which were encoded on the L-strand.

Mitochondrial genome of the Alpine musk deer Moschus chrysogaster (Artiodactyla: Ruminantia: Moschidae)

The Alpine musk deer (Moschus chrysogaster) is an endangered species, which is distributed on the plateau and mountains, mainly in Neimenggu, Ningxia, Qinghai, Gansu, Sichuan, Tibet, Yunnan, Xinjiang, and other places. In this study, we determined the complete mitochondrial genome of M. chrysogaster. The circle genome was 16,354 bp and consists of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 1 control region (CR). The CR was located between the tRNAPro and tRNAPhe genes and is 924 bp in length. Overall base composition of the complete mitochondrial DNA was 34.0% A, 28.0% T, 25.1% C, and 12.9% G. The M. chrysogaster mitochondrial genome had 21 tRNA genes folded in the typical cloverleaf structure, with a unique exception of tRNASer.

The Phylogeography and Population Demography of the Yunnan Caecilian (Ichthyophis bannanicus): Massive Rivers as Barriers to Gene Flow

Ichthyophis bannanicus is the only caecilian species in China. In this study, the phylogeography and population demography of I. bannanicus were explored, based on the mitochondrial DNA genes (cyt b and ND2) and 15 polymorphic microsatellite loci. Altogether 158 individuals were collected from five populations in Yunnan province, Guangxi province, Guangdong province, and Northern Vietnam. Phylogeographical and population structure analysis identified either two groups (Xishuangbanna, Northern Vietnam-Yulin-Yangchun-Deqing) or three groups (Xishuangbanna, Northern Vietnam-Yulin-Yangchun, and Deqing), indicating that the Red River and Pearl River systems may have acted as gene-flow barriers for I. bannanicus. Historical population expansion that happened 15–17 Ka ago was detected for mtDNA data and was possibly triggered by warmer weather after the Last Glacial Maximum. However, the Bayesian simulations of population history based on microsatellite data pinpointed population decline in all populations since 19,123 to 1,029 years ago, demonstrating a significant influence of anthropogenic habitat alteration on I. bannanicus.