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

Genetic diversity and haplotype distribution patterns analysis of cytb and RAG2 sequences in Rana hanluica from southern China

Rana hanluica: an endemic amphibian of China, is found in the hills and mountains south of the Yangtze River. In this comprehensive study, we collected 162 samples from 14 different localities to delve into the genetic diversity of Rana hanluica using mitochondrial Cytb and nuclear RAG2 as genetic markers. Our findings reveal that the Nanling Mountains, specifically regions like Jiuyi Shan, Jinggang Shan, Mang Shan, and Qiyun Shan, are genetic hotspots harboring remarkable diversity. The research results also indicate that there is gene flow among the various populations of the species, and no distinct population structure has formed, which may be due to migration. Moreover, populations in some regions, as well as the overall population, show signs of a possible genetic bottleneck, which we speculate may have been caused by climate change. However, given the exploratory nature of our study, further investigations are warranted to confirm these observations. Through phylogenetic analyses, we uncovered indications that R. hanluica might have originated within the Nanling region, dispersing along the east-west mountain ranges, with a significant contribution originating from Jiuyi Shan. The genetic distributions uncovered through our research reflect historical migratory patterns, evident in the distinct haplotypes of the RAG2 gene between the western and eastern parts of the studied area. Moreover, Heng Shan and Yangming Shan exhibited unique genetic signatures, possibly influenced by geographic isolation, which has shaped their distinct genotypes. The insights gained from this study hold profound implications for conservation efforts. By identifying regions rich in genetic diversity and crucial gene flow corridors, we can develop more effective conservation strategies. Preserving these genetically diverse areas, especially within the Nanling Mountains, is vital for maintaining the evolutionary potential of R. hanluica. In conclusion, our research has laid a solid foundation for understanding the genetic landscape of R. hanluica, shedding light on its origins, population structures, and evolutionary trajectories. This knowledge will undoubtedly guide future research endeavors and inform conservation strategies for this endemic amphibian.

The complete mitochondrial genome of the Hainan Island Shrew, Crocidura wuchihensis

The Hainan Island Shrew Crocidura wuchihensis is a small-bodied insectivore species belonging to the Soricidae family. In this study, we determined its the complete mitochondrial genome. The whole mitochondrial genome was found to be 17,253 bp in length and comprises 13 protein-coding genes, 22 tRNAs, 2 rRNAs and a control region. The base composition of the C. wuchihensis total mitogenome as follows: A, 32.8%; G, 13.0%; T, 32.1%; and C, 22.1%, with an A + T content of 64.9%. Notably, a tandem repeat sequence (5'-CAC ACG TGT ACA-3') was identified in the control region with 24 copy numbers. Additionally, phylogenetic analysis indicated that C. wuchihensis is closely related to Crocidura tanakae and Crocidura dongyangjiangensis based on the concatenated sequences of the 13 protein-coding genes. The characterization of the shrew's mitogenome will provide the foundation for its use in population genomics and systematic studies of Soricidae.

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.  

The complete mitochondrial genome of the long-tailed mole: Scaptonyx fusicaudus (Eulipotyphla, Talpidae)

The long-tailed mole (Scaptonyx fusicaudus) belongs to a monotypic genus within the family Talpidae. It is a small semi-fossorial mammal mostly distributed in south-western China. In this study, we obtained the complete mitochondrial genome of S. fusicaudus. The genome is a total of 16,602 bp in length, containing 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNA), 2 ribosomal RNA genes (rRNA) and 2 non-coding regions, with a base composition of 33.51% A, 28.73% T, 23.68% C and 14.08% G. The nucleotide sequence data of 13 protein-coding genes of S. fusicaudus and other 14 insectivora species were used to reconstruct a Bayesian phylogenetic tree. The tree shows that S. fusicaudus belongs to the subfamily Talpinae and is closely related to Urotrichus talpoides.

The Effectiveness of Molecular, Karyotype and Morphological Methods in the Identification of Morphologically Conservative Sibling Species: An Integrative Taxonomic Case of the Crocidura attenuata Species Complex in Mainland China

The conservation of morphology has resulted in considerable issues in the taxonomy of small mammals, especially for the identification of sibling species. Moreover, it is often difficult to completely solve such taxonomic problems by relying only on a single research method. The genus Crocidura is one of the genera with a conservative morphology and high species diversity. Among them, Crocidura attenuata has been considered in the field as the most widely distributed and common species. In fact, it is a species complex containing multiple species, and the classification and distribution of this species is controversial. In this study, the species and distribution of the Crocidura attenuata species complex experienced an integrated revision using three different levels of research methods: molecular, karyotype and morphology. The results show that (1) the C. attenuata species complex contains four known species (C. attenuata, C. tanakae, C. anhuiensis and C. dongyangjiangensis) and a cryptic species distributed in Guangxi, which may be the same undescribed species as the "C. attenuata" distributed in Vietnam. (2) C. attenuata is only distributed around the Sichuan Basin, C. tanakae is the most widely distributed throughout Southern China, and C. anhuiensis and C. dongyangjiangensis are almost sympatric in Southeast China. Furthermore, (3) although the molecular method lacks a unified threshold for species classification, it can rapidly and effectively identify the species of the C. attenuata species complex. Although karyotype and morphology methods cannot completely solve the species classification issues in respect of the C. attenuata species complex, they can provide supplemental information for taxonomic purposes. Therefore, the integrated taxonomic method can present the advantages of different methodological levels, and will provide further evidence for the taxonomy of sibling species with a conservative morphology.

Molecular phylogeny reveals distinct evolutionary lineages of the banded krait, Bungarus fasciatus (Squamata, Elapidae) in Asia

The banded krait, Bungarus fasciatus is a widespread elapid snake, likely to comprise several distinct species in different geographic regions of Asia. Therefore, based on molecular phylogenetics and comparative morphology data, we present an overview of the systematic composition of the species to delimit potential biogeographic boundaries. Our phylogenetic analyses, based on four mitochondrial genes, reveal the existence of at least three evolutionary lineages within B. fasciatus, corresponding to Indo-Myanmar, Sundaic and eastern Asian lineages. We are convinced that there are at least three taxonomic entities within the nomen B. fasciatus and restrict the distribution of B. fasciatus sensu stricto to the Indo-Myanmar region. We also provide additional natural history data of the taxon from eastern India. Finally, we advocate further studies to establish the degree of reproductive isolation among these diverging evolutionary lineages and to reassess the systematic status of this species complex especially the Sundaic and eastern Asian lineages.

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.

Dental polymorphisms in Crocidura (Soricomorpha: Soricidae) and evolutionary diversification of crocidurine shrew dentition

The upper dentition of Crocidura exhibits polymorphic characters that were revealed for the first time in this study via high-resolution X-ray computed microtomography. Our analyses of 11 Crocidura species and selected Diplomesodon, Suncus and Sylvisorex species from different geographical regions and size groups revealed the most complex character states of upper dentition in the Ethiopian endemic species Crocidura yaldeni. A three-dimensionally based geometric morphometric analysis revealed the dependence of variation in skull muzzle shape on alterations in general upper dentition, such as a reduction in the number of antemolars. Principal components analysis revealed highly significant shape alterations and morphological trajectories in C. yaldeni (and more moderate ones in Suncus murinus) toward the Sorex-like morphotype in the outgroup, and less significant shape alterations in Crocidura obscurior, Crocidura phanluongi and Crocidura sapaensis with double-rooted third antemolar. Cladistic analysis based on a new data matrix for 20 species and 46 characters allowed us to determine the directions of the morphological trajectories: the apomorphic state of the most complex antemolars of C. yaldeni is associated with deviating skull muzzle shape changes, which we determined to be attributable to neomorphosis, and the less significant alterations in the shape of other Crocidura with complex antemolars are attributable to regional adaptation.

Evolutionary history of Sundaland shrews (Eulipotyphla: Soricidae: Crocidura) with a focus on Borneo

The hyperdiverse shrew genus Crocidura is one of few small mammal genera distributed across Sundaland and all of its boundaries. This represents a rare opportunity to study the geological history of this region through the evolutionary history of these shrews. We generate a phylogeny of all recognized species of Sundaland Crocidura and show that most speciation events took place during the Pleistocene, prior to the inundation of the Sunda Shelf around 400 000 years ago. We find east–west differentiation within two separate lineages on Borneo, and that the current taxonomy of its two endemic species does not reflect evolutionary history, but ecophenotypic variation of plastic traits related to elevation. Sulawesi shrews are monophyletic, with a single notable exception: the black-footed shrew (C. nigripes). We show that the black-footed shrew diverged from its relatives on Borneo recently, suggesting a human-assisted breach of Wallace’s line. Overall, the number of Crocidura species, especially on Borneo, probably remains an underestimate.

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.

Gene Flow Increases Phylogenetic Structure and Inflates Cryptic Species Estimations: A Case Study on Widespread Philippine Puddle Frogs (Occidozyga laevis)

In cryptic amphibian complexes, there is a growing trend to equate high levels of genetic structure with hidden cryptic species diversity. Typically, phylogenetic structure and distance-based approaches are used to demonstrate the distinctness of clades and justify the recognition of new cryptic species. However, this approach does not account for gene flow, spatial, and environmental processes that can obfuscate phylogenetic inference and bias species delimitation. As a case study, we sequenced genome-wide exons and introns to evince the processes that underlie the diversification of Philippine Puddle Frogs-a group that is widespread, phenotypically conserved, and exhibits high levels of geographically-based genetic structure. We showed that widely adopted tree- and distance-based approaches inferred up to 20 species, compared to genomic analyses that inferred an optimal number of five distinct genetic groups. Using a suite of clustering, admixture, and phylogenetic network analyses, we demonstrate extensive admixture among the five groups and elucidate two specific ways in which gene flow can cause overestimations of species diversity: (1) admixed populations can be inferred as distinct lineages characterized by long branches in phylograms; and (2) admixed lineages can appear to be genetically divergent, even from their parental populations when simple measures of genetic distance are used. We demonstrate that the relationship between mitochondrial and genome-wide nuclear p-distances is decoupled in admixed clades, leading to erroneous estimates of genetic distances and, consequently, species diversity. Additionally, genetic distance was also biased by spatial and environmental processes. Overall, we showed that high levels of genetic diversity in Philippine Puddle Frogs predominantly comprise metapopulation lineages that arose through complex patterns of admixture, isolation-by-distance, and isolation-by-environment as opposed to species divergence. Our findings suggest that speciation may not be the major process underlying the high levels of hidden diversity observed in many taxonomic groups and that widely-adopted tree- and distance-based methods overestimate species diversity in the presence of gene flow.

Discovery of a new mammal species (Soricidae: Eulipotyphla) from Narcondam volcanic island, India

We discovered a new Crocidura species of shrew (Soricidae: Eulipotyphla) from Narcondam Island, India by using both morphological and molecular approaches. The new species, Crocidura narcondamica sp. nov. is of medium size (head and body lengths) and has a distinct external morphology (darker grey dense fur with a thick, darker tail) and craniodental characters (braincase is rounded and elevated with weak lambdoidal ridges) in comparison to other close congeners. This is the first discovery of a shrew from this volcanic island and increases the total number of Crocidura species catalogued in the Indian checklist of mammals to 12. The newly discovered species shows substantial genetic distances (12.02% to 16.61%) to other Crocidura species known from the Indian mainland, the Andaman and Nicobar Archipelago, Myanmar, and from Sumatra. Both Maximum-Likelihood and Bayesian phylogenetic inferences, based on mitochondrial (cytochrome b) gene sequences showed distinct clustering of all included soricid species and exhibit congruence with the previous evolutionary hypothesis on this mammalian group. The present phylogenetic analyses also furnished the evolutionary placement of the newly discovered species within the genus Crocidura.

Characterization of the complete mitochondrial genome of Dongyangjiang White-toothed Shrew, Crocidura dongyangjiangensis (Eulipotyphla: Soricidae) and its phylogenetic analysis

The complete mitochondrial genome of the Dongyangjiang White-toothed Shrew (Crocidura dongyangjiangensis), a newly discovered Crocidura species, is sequenced and characterized. The total length of the genome is 16,883 bp, and has similar base composition and gene arrangement to other vertebrates. It contains 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA), 22 transfer RNA (tRNA), a replication origin (OL) and a control region. The phylogenetic tree shows that C. dongyangjiangensis was fully resolved in a clade with three other species of Crocidura and it has a sibling relationship with Crocidura tanakae. This analysis reveals the evolutionary relationship of 16 Crocidura species.