Molecular phylogeny and taxonomy of the genus Vernaya (Mammalia: Rodentia: Muridae) with the description of two new species.

The climbing mouse is a rare, small mammal listed as an endangered species on the China species red list. Molecular phylogenetic analyses and the evolutionary history of the genus remain unexplored because of the extreme difficulty in capturing individuals and their narrow distribution. Here, we collected 44 specimens, sequenced one mitochondrial and eight nuclear genes, and integrated morphological approaches to estimate phylogenetic relationships, delimit species boundaries, and explore evolutionary history. Molecular analyses and morphological results supported the validity of these four species. Here, we describe two new species, Vernaya meiguites sp. nov. and Vernaya nushanensis sp. nov., and recognize Vernaya foramena, previously considered a subspecies of Vernaya fulva, as a valid species. The estimated divergence time suggests that the climbing mouse began to diversify during the Pliocene (3.36 Ma).

Molecular phylogenetics and diversity of the Himalayan shrew ( Soriculus nigrescens Gray, 1842) (Eulipotyphla, Soricidae) in Southwest China.

The Himalayan shrew, Soriculus nigrescens Gray, 1842, belongs to the monotypic genus Soriculus, which is distributed mainly in the Himalayan region. Previous authors have studied its classification based on morphological and molecular data. However, no comprehensive study of the diversity and phylogeny of this species has been performed. In this study, we investigated the molecular phylogeny, genetic diversity, and species divergence of S. nigrescens based on one mitochondrial gene and three nuclear genes. A total of 124 samples from 27 sites in Southwest China were analyzed. Our molecular phylogenetic analyses and species divergence reveal non-monophyly of Soriculus, potentially representing two genera and three clades. Populations from Yunnan (Clade YN) represent the subspecies S. n. minors and should recover the full species status. Populations from Himalayas (Clade A) represent the species S. nigrescens, while populations from southeastern Nyenchen Tanglha Mountains and southern Himalayas (Clade B) represent a new cryptic and unnamed species. Species delimitation analyses and deep genetic distance analysis clearly support the species status of these three evolving clades. The putative new genus and cryptic species should be studied and identified in the future using a more extensive sampling combined with a comprehensive morphological and phylogenetic analysis.

Revalidation and expanded description of Mustela aistoodonnivalis (Mustelidae: Carnivora) based on a multigene phylogeny and morphology.

The lacked-teeth pygmy weasel, Mustela aistoodonnivalis Wu & Kao, 1991, was originally described as being from Taibai Mountain and Zhashui county, Shaanxi, China. Subsequently, it was considered a subspecies or synonym of Mustela nivalis. In a faunal survey of northwestern Sichuan, eight specimens of M. aistoodonnivalis were collected. A molecular phylogenetic analysis of one mitochondrial and six nuclear genes clustered the specimens as a distinct clade and not with M. nivalis. Morphologically, the lack of the second lower molar differentiated them from M. nivalis, and genetic distances were typical of discrete species. These analyses confirmed that M. aistoodonnivalis is an independent species in the genus Mustela.

Complete mitochondrial genome of Cyclopelta obscura (Lepeletier & Serville, 1825) (Hemiptera: Pentatomoidea: Dinidoridae) and phylogenetic analysis of Pentatomoidea species.

Cyclopelta obscura is a crop pest, which mainly damages legumes, especially Robinia pseudoacacia and Cercis chinensis. In recent years, many mitochondrial and nuclear DNA sequences of C. obscura have been sequenced and used for phylogenetic inference. However, the complete mitogenome has not been reported yet and studies on the phylogenetic relationships within Dinidoridae are rare. In this study, we sequenced the mitogenome of C. obscura and conducted comparative mitogenomic analyses of seven Dinidoridae species based on several different factors. The length of the mitogenome is 15,426 bp, which includes 37 typical mitochondrial genes (13 protein-coding genes (PCGs), 22 tRNAs, and 2 rRNAs) and a control region (796 bp long), as well as 13 intergenic spacers and 8 overlapping regions. Most PCGs of C. obscura began with the classical start codon ATN, while cox1 and nad4l used TTG, and nad1 used GTG. The Dinidoridae mitogenomes are highly conserved in terms of nucleotide composition, the codon usage of PCGs, and the secondary structure of tRNA. Phylogenetic analysis based on four datasets with two methods recovered the Dinidoridae as a monophyletic group with strong support values. All results indicate that Dinidoridae formed a sister group to Tessaratomidae, and (Tessaratomidae + Dinidoridae) formed a sister group to Cydnidae in most of the phylogenetic trees. Additionally, seven species within the Dinidoridae, we observed the following relationship: (Eumenotes sp. + (Cyclopelta parva + C. obscura)) + ((Megymenum gracilicorne + Megymenum brevicorne) + (Coridius chinensis + Coridius brunneu)).

Molecular phylogeny and taxonomy of the genus Nectogale (Mammalia: Eulipotyphla: Soricidae).

The elegant water shrew, Nectogale elegans, is one of the small mammal species most adapted to a semi-aquatic lifestyle. The taxonomy of the genus Nectogale has received little attention due to difficulties in specimen collection. In this study, we sequenced one mitochondrial and eight nuclear genes to infer the phylogenetic relationship of Nectogale. Phylogenetic analyses revealed two large clades within Nectogale. One clade represented N. elegans, and the other was regarded as N. sikhimensis. The split between N. elegans and N. sikhimensis dated back to the early Pleistocene (2.15 million years ago [Ma]), which might be relevant to the Qinghai-Tibet Plateau (QTP) uplift. The morphological comparison showed several distinguishing characters within Nectogale: the shape of the mastoids, the first lower unicuspid (a1), and the second upper molar (M2). Overall, the molecular and the morphological evidences supported that the genus Nectogale consists of two valid species: N. elegans and N. sikhimensis.

Multi-locus phylogeny and species delimitations of the striped-back shrew group (Eulipotyphla: Soricidae): Implications for cryptic diversity, taxonomy and multiple speciation patterns.

The striped-back shrew group demonstrates remarkable variation in skull and body size, tail length, and brightness of the dorsal stripe; and karyotypic and DNA variation has been reported in recent years. In this study, we investigated the phylogenetic structure of the group, as well as speciation patterns and demographic history in Mountains of Southwestern China and adjacent mountains, including the southern Himalayas, Mts. Bashan, Wushan, and Qinling. We sequenced a total of 462 specimens from 126 localities in the known range of the group, which were sequenced and analyzed based on 6.2 kb of sequence data from two mitochondrial, six nuclear, and two Y chromosome markers. Phylogenetic analyses of the concatenated mtDNA data revealed 14 sympatric and independently evolving lineages within the striped-back shrew group, including Sorex bedfordiae, S. cylindricauda, S. excelsus, S. sinalis and several cryptic species. All concatenated data (ten genes) showed a consistent genetic structure compared to the mtDNA lineages for the group, whereas the nuclear and the Y chromosome data showed a discordant genetic structure compared to the mtDNA lineages for the striped-back shrew group. Species delimitation analyses and deep genetic distance clearly support the species status of the 14 evolving lineages. The divergence time estimation suggested that the striped-back shrew group began to diversify from the middle Pleistocene (2.34 Ma), then flourished at approximately 2.14 Ma, followed by a series of rapid diversifications through the Pleistocene. Our results also revealed multiple mechanisms of speciation in the Mountains of Southwestern China and Adjacent Mountains with complex landscapes and climate. The uplifting of the Qinghai-Tibetan Plateau, Quaternary climate oscillations, riverine barriers, ecological elevation gradients, topographical diversity, and their own low dispersal capacity may have driven the speciation, genetic structure, and phylogeographic patterns of the striped-back shrew group.

A new species of Tamiops (Rodentia, Sciuridae) from Sichuan, China.

During a small mammal survey in Wanglang National Natural Reserve, Sichuan, China in AugustOctober 2018, we collected four specimens of an Asiatic striped squirrel (genus Tamiops) that could not be assigned morphologically to any described species. Phylogenetic analyses of CYTB and nuDNA sequences strongly supported them in the genus Tamiops. The p-distances of CYTB between these individuals and other species of Tamiops ranged from 17.4 to 19.1%. Morphologically, they differed from their congeners, including T. maritimus, T. mcclellandii, T. rodolphii, and T. swinhoei by pelage, skull, and baculum characteristics. Based on the results of morphological comparisons and molecular analyses, we describe the four specimens as the new species Tamiops minshanica sp. nov.

Neotype designation and redescription of Tropidophorus guangxiensis Wen, 1992 (Squamata: Sauria: Scincidae), with description of a new subspecies from central South China.

The genus Tropidophorus consists of small semi-aquatic lizards that dwell in lowland forest steams (Barbour, 1921; Bauer & Jackman, 2008). Here, we designate the neotype and re-describe T. guangxiensis Wen, 1992 based on newly collected topotypic specimens. We also describe a new subspecies from Xuefeng Mountain, Hongjiang County, Hunan Province, central South China. Based on two mitochondrial genes (12S rRNA and 16S rRNA), the phylogenetic position of T. guangxiensis is allocated for the first time. Additionally, our data strongly support that the new subspecies is phylogenetically closely related to T. g. guangxiensis. We also present a morphological identification key for known species and subspecies of Tropidophorus in China.

The complete mitogenome of Sokolov's Dwarf Hamster (Cricetulus sokolovi) and implication of phylogenetic status.

There is still an obvious lack of information on Sokolov's Dwarf Hamster (Cricetulus sokolovi) which belongs to subfamily Cricetinae because the species is only rarely found in Gobi desert. In this study, we obtained the complete mitochondrial genome sequences of C. sokolovi. The genome is 16,292bp in length and has a base composition of 33.5% A, 30.5% T, 22.9% C, and 13.1% G. The mitogenome structure, consisting of 13 protein-coding genes, two rRNA genes (12S rRNA and 16S rRNA), 22 tRNA genes, and one control region, is similar to that of typical vertebrate mitochondrial genomes of other rodents. We restructured a Bayesian phylogenetic tree by using 12 species belonging to subfamily Cricetinae. As indicated by the phylogenetic tree, genus Cricetulus is polyphyletic group, and C. Sokolovi is the closest relative of Cricetulus griseus. The mitochondrial genome can provide basic data for further study on the phylogenetic relationship of subfamily Cricetinae.

The complete mitochondrial genome of long-tailed red-toothed shrew (Episoriculus leucops) and implication of phylogenetic status.

We determined a complete mitochondrial genome of Episoriculus leucops. This mitogenome is a circular molecule with 16,838 bp in length, containing 13 protein-coding genes, 22 transfer RNA genes (tRNA), and two ribosomal RNA genes (rRNA). This mitochondrial genome has a base composition of 32.8% A, 29.2% T, 24.9% C, and 13.1% G. We reconstructed Bayesian phylogenetic tree by taking advantage of 19 species belonging to subfamily Soricinae. Phylogenetic tree shows that the long-tailed red-toothed shrew belongs to genus Episoriculus, and it is the closest relationship with E. caudatus. This mitochondrial genome provides an important resource for addressing taxonomic issues and studying molecular evolution.

The complete mitochondrial genome of white-tailed mole (Parascaptor leucura).

The white-tailed mole (Parascaptor leucura) belongs to genus Parascaptor, which is a monotypic genus distributed across Southwestern China, Assam (India), Bengal, and Northern Burma, and Laos. In this study, we obtained the complete mitochondrial genome of Parascaptor leucura. The genome is total 16,875 bp in length, containing 13 protein-coding genes, 22 transfer RNA genes (tRNA), two ribosomal RNA genes (rRNA), and two non-coding regions, with a base composition of 33.5% A, 26.4% T, 25.7% C, and 14.3% G. The nucleotide sequence data of 13 protein-coding genes of P. leucura and other nine Eulipotyphla species were used to reconstruct a Bayesian phylogenetic tree. The tree shows that P. leucura belongs to subfamily Talpinae and is closely related to Scaptochirus moschatus.

DNA metabarcoding provides insights into seasonal diet variations in Chinese mole shrew (Anourosorex squamipes) with potential implications for evaluating crop impacts.

Diet analysis of potential small mammals pest species is important for understanding feeding ecology and evaluating their impact on crops and stored foods. Chinese mole shrew (Anourosorex squamipes), distributed in Southwest China, has previously been reported as a farmland pest. Effective population management of this species requires a better understanding of its diet, which can be difficult to determine with high taxonomic resolution using conventional microhistological methods. In this study, we used two DNA metabarcoding assays to identify 38 animal species and 65 plant genera from shrew stomach contents, which suggest that A. squamipes is an omnivorous generalist. Earthworms are the most prevalent (>90%) and abundant (>80%) food items in the diverse diet of A. squamipes. Species of the Fabaceae (frequency of occurrence [FO]: 88%; such as peanuts) and Poaceae (FO: 71%; such as rice) families were the most common plant foods identified in the diet of A. squamipes. Additionally, we found a seasonal decrease in the diversity and abundance of invertebrate foods from spring and summer to winter. Chinese mole shrew has a diverse and flexible diet throughout the year to adapt to seasonal variations in food availability, contributing to its survival even when food resources are limited. This study provides a higher resolution identification of the diet of A. squamipes than has been previously described and is valuable for understanding shrew feeding ecology as well as evaluating possible species impacts on crops.

Multilocus phylogeny and cryptic diversity of white-toothed shrews (Mammalia, Eulipotyphla, Crocidura) in China.

BACKGROUND: Crocidura, the most speciose mammalian genus, occurs across much of Asia, Europe and Africa. The taxonomy of Chinese representatives has been studied primarily based on cursory morphological comparisons and their molecular phylogenetic analyses remain unexplored. In order to understand the phylogeny of this group in China, we estimated the first multilocus phylogeny and conducted species delimitation, including taxon sampling throughout their distribution range. RESULTS: We obtained one mitochondrial gene (cytb) (~ 1, 134 bp) and three nuclear genes (ApoB, BRCA1, RAG1) (~ 2, 170 bp) for 132 samples from 57 localities. Molecular analyses identified at least 14 putative species that occur within two major well-supported groups in China. Polyphyletic C. wuchihensis appears to be composed of two putative species. Two subspecies, C. rapax rapax and C. rapax kurodai should be elevated to full species status. A phylogenetic tree based on mitochondrial gene from Asian Crocidura species showed that the C. rapax rapax is embedded within C. attenuata, making the latter a paraphyletic group. Three strongly supported undescribed species (C. sp.1, C. sp.2 and C. sp.3) are revealed from Zada County of Tibet (Western China), Hongjiang County of Hunan Province (Central China) and Dongyang County of Zhejiang Province (Eastern China), Motuo County of Tibet, respectively. The divergence time estimation suggested that China's Crocidura species began to diversify during the late Pliocene (3.66 Ma) and the Early Pleistocene (2.29 Ma), followed by a series of diversifications through the Pleistocene. CONCLUSIONS: The cryptic diversity found in this study indicated that the number of species is strongly underestimated under the current taxonomy. We propose that the three undescribed species should be evaluated using extensive taxon sampling and comprehensive morphological and morphometric approaches. Climate change since the late Pliocene and the uplift of the Qinghai-Tibet Plateau may result in the diversification and speciation of China's Crocidura species. In short, the underestimated diversity underlines the need for a taxonomic revision of Chinese Crocidura species.

Complete mitochondrial genome of Procapra picticaudata, with phylogenetic implication.

The Tibetan gazelle Procapra picticaudata is endemic to the Tibetan plateau. The species is listed as a Near Threatened (NT) species by the IUCN Red List of Threatened Animals and the Red List of China's Vertebrates. In this study, we sequenced the complete mitochondrial genome of P. picticaudata and examined its phylogenetic position with other nine species in Artiodactyla. The complete mitochondrial genome is 16,620 bp in length and contained 22 transfer RNA genes, 2 ribosomal RNA genes, 13 protein-coding genes, and 1 control region. Our data would provide reference information for further study of this species and be useful for evolutionary and phylogenetics studies for this NT species.

The complete mitochondrial genome of pygmy red-toothed shrew (Chodsigoa parva).

The study of pygmy red-toothed shrew (Chodsigoa parva), which is the smallest species of geuns Chodsigoa, is extremely lacking. Also, it is classified as data deficient (DD) on The IUCN Red List. Here, we obtained a complete mitochondrial genome of Chodsigoa parva. The mitochondrial genome of C. parva is totally 17,216 bp in length and it is composed of 13 protein-coding genes, 22 transfer RNA genes (tRNA), 2 ribosomal RNA genes (rRNA), and 2 non-coding regions. We restructured Bayesian phylogenetic tree by using 19 species those belong to family Soricidae. The mitochondrial genome can provide basic data for further study about the phylogenetic relationship of family Soricidae.

The complete mitogenome of Smith's shrew (Chodsigoa smithii).

The Smith's shrew (Chodsigoa smithii) belongs to subfamily Soricinae, which is an endemic shrew to China. In this study, we obtained the complete mitochondrial genome of the C. smithii. This mitogenome is a circular molecule with 17,108 bp in length, containing 13 protein-coding genes, 22 transfer RNA genes, two ribosome RNA genes, one light strand replication origin (OL), one non-coding region, and with a base composition of 32.5% A, 29.3% T, 24.8% C, and 13.4% G. The nucleotide sequence data of 13 protein-coding genes of C. smithii and other 19 Soricomorpha species were used for phylogenetic analyses. Phylogenetic tree shows that Soricinae includes two major phylogenetic lineages. Chodsigoa smithii is located as a basal position in tribe Nectogalini.

The complete mitochondrial genome of Soriculus nigrescens (Soricomorpha: Soricinae).

The Himalayan Shrew (Soriculus nigrescens) Gray, 1842 belongs to the subfamily Soricinae, which is distributed in southwest China, Nepal, India, and Bhutan. This species is classified as Least Concern on The IUCN Red List. In this study, we sequenced the complete mitochondrial genome of S. nigrescens. This mitogenome is 17,284 bp in length and contains a set of 13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNA), 22 transfer RNA genes (tRNA), one origin of L strand replication, and one control region. In order to explore the molecular phylogenetics evolution of Soricinae, the nucleotide sequence data of 13 PCGs of S. nigrescens and other 17 Insectivores were used for the phylogenetic analysis.

How many species of Apodemus and Rattus occur in China? A survey based on mitochondrial cyt b and morphological analyses.

Apodemus (mice) and Rattus (rats) are the top rodent reservoirs for zoonoses in China, yet little is known about their diversity. We reexamined the alpha diversity of these two genera based on a new collection of specimens from China and their cyt b sequences in GenBank. We also tested whether species could be identified using external and craniodental measurements exclusively. Measurements from 147 specimens of Apodemus and 236 specimens of Rattus were used for morphological comparisons. We analysed 74 cyt b sequences of Apodemus and 100 cyt b sequences of Rattus to facilitate phylogenetic estimations. Results demonstrated that nine species of Apodemus and seven species of Rattus, plus a new subspecies of Rattus nitidus, are distributed in China. Principal component analysis using external and craniodental measurements revealed that measurements alone could not separate the recognized species. The occurrence of Rattus pyctoris in China remains uncertain.

Multilocus approaches reveal underestimated species diversity and inter-specific gene flow in pikas (Ochotona) from southwestern China.

The phylogeny of living pikas (Ochotonidae, Ochotona) remains obscure, and pika species diversity in southwestern China has never been well explored. In this study, 96 tissue samples from 11 valid species in three classified subgenera (Pika, Ochotona and Conothoa) from 23 locations were characterized using multilocus sequences of 7031bp. Two mitochondrial (CYT B and COI) and five nuclear gene segments (RAG1, RAG2, TTN, OXAIL and IL1RAPL1) were sequenced. We analysed evolutionary histories using maximum likelihood (RAxML) and Bayesian analyses (BEAST), and we also used molecular species delimitation analyses (BPP) to explore species diversity. Our study supported O. syrinx (O. huangensis) as a distinct clade from all named subgenera. Relationships among subgenera were not fully resolved, which may be due to a rapid diversification in the middle Miocene (∼13.90Ma). Conflicting gene trees implied mitochondrial introgression from O. cansus to O. curzoniae. We uncovered three cryptic species from Shaanxi, Sichuan and Yunnan with strong support, suggesting an underestimation of species diversity in the "sky-island" mountains of southwest China.