Feiyun Tu

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.

Complete mitochondrial genome sequence of Nectogale elegans

Abstract The elegant water shrew (Nectogale elegans) belongs to the family Soricidae, and distributes in northern South Asia, central and southern China and northern Southeast Asia. In this study, the complete mitochondrial genome of N. elegans was sequenced. It was determined to be 17,460 bases, and included 13 protein-coding genes (PCGs), 22 tRNA genes, 2 ribosomal RNA genes and one non-coding region, which is similar to other mammalian mitochondrial genomes. Bayesian inference and maximum likelihood methods were used to construct phylogenetic trees based on 12 heavy-strand concatenated PCGs. Phylogenetic analyses further confirmed that Crocidurinae diverged prior to Soricinae, and Sorex unguiculatus differentiated earlier than N. elegans.

The complete mitochondrial genome of the Elongate loach Leptobotia elongata (Cypriniformes: Cobitidae)

The Elongate loach (Leptobotia elongata) belongs to family Cobitidae, which is endemic to the middle and upper reaches of the Yangtze River in China. In this study, the complete mitochondrial genome of L. elongata was sequenced. It was determined to be 16,591 bases. The nucleotide sequence data of 12 heavy-strand protein-coding genes of L. elongata and other 12 Cobitidae species were used for phylogenetic analyses. Trees constructed using Bayesian and maximum parsimony showed a similar topology demonstrating that L. elongate was clustered in subfamily Botiinae being sister to the subfamily Cobitinae. The trees also suggested that the genera Cobitis were polyphyletic.

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.

Complete mitogenome of Chinese shrew mole Uropsilus soricipes (Milne-Edwards, 1871) (Mammalia: Talpidae) and genetic structure of the species in the Jiajin Mountains (China)

The complete mitochondrial genome of the Chinese shrew mole, Uropsilus soricipes (Soricomorpha: Talpidae) was determined (GenBank accession no. JQ658979). The mitogenome is 16,575 base pairs and contains 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes and one control region. Phylogenetic relationship analysis based on 12 concatenated protein-coding genes revealed that Uropsilus occupies a basal position within Talpidae, which is consistent with previous studies. Additionally, low nucleotide diversity (0.0028) and high haplotype diversity (0.936) of U. soricipes in the Jiajin Mountains and the neutrality test statistics (D=−1.59491, p=0.045; Fs=−4.171, p=0.016) suggest that this population experienced a demographic expansion at about 46,600 years ago. The phylogenetic analysis of the combined data (cytochrome b and D-loop) revealed two clades. Divergence of these clades occurred in the middle Pleistocene 0.986 million years ago. Mountains played a substantial role in shaping the geographical populations of this species.

The complete mitochondrial genome sequence of Shrew Gymnure, Neotetracus sinensis

The Shrew Gymnure Neotetracus sinensis belongs to family Erinaceidae, and distributes in China, Myanmar, and northern Vietnam. In this study, the whole mitochondrial genome of N. sinensis was first sequenced and characterized. The genome is 16,982 bases in length. Bayesian inference and maximum likelihood methods were used to construct phylogenetic trees based on 12 concatenated protein-coding genes on the heavy strand. Phylogenetic analyses further confirm the subfamily Galericinae diverged prior to the subfamily Erinaceinae, support the species N. sinensis was in distinct genus Neotetracus rather than Hylomys, and N. sinensis diverged later than Echinosorex gymnura.

Complete mitochondrial genome of blood pheasant (Ithaginis cruentus)

The blood pheasant Ithaginis cruentus belongs to the family Phasianidae and distributes in the eastern Himalayas, India, Nepal, Bhutan and China. In this study, the total mitochondrial genome of I. cruentus was firstly determined. The genome is 16,683 bases in length. Bayesian inference, maximum likelihood and maximum parsimony methods were used to construct phylogenetic trees based on 12 concatenated protein-coding genes on the heavy strand. Phylogenetic analyses further confirmed that Ithaginis clearly diverged later than Arborophila, and Arborophila was a basal branch within Phasianidae.

Taxonomic Status of Tetraophasis obscurus and Tetraophasis szechenyii (Aves: Galliformes: Phasianidae) Based on the Complete Mitochondrial Genome

Tetraophasis szechenyii and T. obscurus are endangered phasianid birds endemic to China. Historically, the question of whether T. obscurus and T. szechenyii are valid species or subspecies has been controversial. In order to clarify their phylogenetic relationship, we sequenced the complete mitochondrial genome of T. obscurus and, using the complete mitochondrial genome of T. szechenyii, which our lab had already sequenced, conducted Bayesian and maximum-likelihood phylogenetic analyses based on the sequences of 12 concatenated heavy-strand encoded protein-coding genes. Genetic distance and divergence time between the two species were also calculated. The complete mitochondrial genome of T. obscurus was 16,707 bases (accession no.: NC_018034), and its structure was similar to mitochondrial genomes reported for other phasianids. The genetic distance between T. obscurus and T. szechenyii was 0.028, and the divergence time of T. obscurus and T. szechenyii was 1.75 Myr. Considering the genetic distance and divergence time, as well as geographical distribution and morphological differences, we suggest that T. obscurus and T. szechenyii are two valid species. The Pleistocene glacial events in the Hengduan Mountains region may have played an important role in the speciation of T. obscurus and T. szechenyii.

Complete mitochondrial genome of Hainan partridge, Arborophila ardens (Galliformes: Phasianidae).

Abstract The Hainan partridge, Arborophila ardens belongs to family Phasianidae, and distributes only in Hainan, China. In this study, the complete mitochondrial genome of A. ardens was first sequenced and characterized. The genome is 16,727 bases in length. Bayesian inference, maximum likelihood and maximum parsimony methods were used to construct phylogenetic trees based on 12 concatenated protein-coding genes located on the heavy strand. Phylogenetic analyses further confirm the Arborophila placed at the root of Phasianidae. Arborophila ardens show closer relationship with A. rufipectus than A. rufogularis and A. gingica which cluster as sister group to A. ardens and A. rufipectus.