Genetic Characterization and Insular Habitat Enveloping of Endangered Leaf-Nosed Bat, Hipposideros nicobarulae (Mammalia: Chiroptera) in India: Phylogenetic Inference and Conservation Implication.

The Nicobar leaf-nosed Bat (Hipposideros nicobarulae) was described in the early 20th century; however, its systematic classification has been debated for over 100 years. This endangered and endemic species has achieved species status through morphological data in the last 10 years. However, the genetic information and phylogenetic relationships of H. nicobarulae remain neglected. The generated mitochondrial cytochrome b gene (mtCytb) sequences (438 bp) of H. nicobarulae contains 53.42-53.65% AT composition and 1.82% variable sites. The studied species, H. nicobarulae maintains an 8.1% to 22.6% genetic distance from other Hipposideros species. The genetic divergence estimated in this study is congruent with the concept of gene speciation in bats. The Bayesian and Maximum-Likelihood phylogenies clearly discriminated all Hipposideros species and showed a sister relationship between H. nicobarulae and H. cf. antricola. Current mtCytb-based investigations of H. nicobarulae have confirmed the species status at the molecular level. Further, the MaxEnt-based species distribution modelling illustrates the most suitable habitat of H. nicobarulae (294 km2), of which the majority (171 km2) is located on Great Nicobar Island. The present study suggests rigorous sampling across the range, taxonomic coverage, the generation of multiple molecular markers (mitochondrial and nuclear), as well as more ecological information, which will help in understanding population genetic structure, habitat suitability, and the implementation of appropriate conservation action plans for H. nicobarulae and other Hipposideros species.

Matrilineal phylogeny and habitat suitability of the endangered spotted pond turtle (Geoclemys hamiltonii; Testudines: Geoemydidae): a two-dimensional approach to forecasting future conservation consequences.

The spotted pond turtle (Geoclemys hamiltonii) is a threatened and less explored species endemic to Bangladesh, India, Nepal, and Pakistan. To infer structural variation and matrilineal phylogenetic interpretation, the present research decoded the mitogenome of G. hamiltonii (16,509 bp) using next-generation sequencing technology. The mitogenome comprises 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and one AT-rich control region (CR) with similar strand symmetry in vertebrates. The ATG was identified as a start codon in most of the PCGs except Cytochrome oxidase subunit 1 (cox1), which started with the GTG codon. The non-coding CR of G. hamiltonii was determined to have a unique structure and variation in different domains and stem-loop secondary structure as compared with other Batagurinae species. The PCGs-based Bayesian phylogeny inferred strong monophyletic support for all Batagurinae species and confirmed the sister relationship of G. hamiltonii with Pangshura and Batagur taxa. We recommend generating more mitogenomic data for other Batagurinae species to confirm their population structure and evolutionary relationships. In addition, the present study aims to infer the habitat suitability and habitat quality of G. hamiltonii in its global distribution, both in the present and future climatic scenarios. We identify that only 58,542 km2 (7.16%) of the total range extent (817,341 km2) is suitable for this species, along with the fragmented habitats in both the eastern and western ranges. Comparative habitat quality assessment suggests the level of patch shape in the western range is higher (71.3%) compared to the eastern range. Our results suggest a massive decline of approximately 65.73% to 70.31% and 70.53% to 75.30% under ssp245 and ssp585 future scenarios, respectively, for the years between 2021-2040 and 2061-2080 compared with the current distribution. The present study indicates that proper conservation management requires greater attention to the causes and solutions to the fragmented distribution and safeguarding of this endangered species in the Indus, Ganges, and Brahmaputra (IGB) river basins.

Morphology and Mitochondrial Lineage Investigations Corroborate the Systematic Status and Pliocene Colonization of Suncus niger (Mammalia: Eulipotyphla) in the Western Ghats Biodiversity Hotspot of India.

The Indian highland shrew, Suncus niger (Horsfield, 1851), is the least studied soricid species from its original range distribution in Southern India, with several systematics conundrums. Following its discovery in 1851, the species was synonymized with Suncus montanus (Kelaart, 1850) (endemic to Sri Lanka) and subsequently identified as a separate Indian population. However, the systematic status of S. niger from topotype specimens in Southern India has yet to be determined through an integrated approach. Both taxonomy and mitochondrial genetic data (Cytochrome b and 16S ribosomal RNA) were used to re-examine the systematics of S. niger. The mtCytb gene clearly distinguished topotypic S. niger from other Suncus species, with high genetic divergences varying from 8.49% to 26.29%. Further, the Bayesian and maximum likelihood topologies clearly segregated S. niger from other congeners and corroborated the sister relationship with S. stoliczkanus with expected divergence in the late Pliocene (2.62 MYA). The TimeTree analysis also exhibits a strong matrilineal affinity of S. dayi (endemic to India) toward the African species. The current study hypothesizes that the ancestor of the soricids evolved in Africa and that genetic lineages were subsequently shifted by plate tectonic events that subsequently colonized different continents as distinct species during the late Miocene (Tortonian) to the Holocene era. In addition to the new range expansion and elevation records of S. niger in the Central Western Ghats, we propose that additional sampling across its distribution, as well as the use of multiple genetic markers, may be useful in determining the genetic diversity and population structure of this endemic species. The present study also recommends that more molecular data on the Soricomorphs lineages, and estimates of their divergence times, will shed light on the evolution of these small mammals on Earth.

Complete mitogenome of the endangered and endemic Nicobar treeshrew (Tupaia nicobarica) and comparison with other Scandentians.

The Nicobar treeshrew (Tupaia nicobarica) is an endangered small mammal endemic to the Nicobar Island of the Andaman Sea, India regarded as an alternative experimental animal model in biomedical research. The present study aimed to assemble the first mitochondrial genome of T. nicobarica to elucidate its phylogenetic position with respect to other Scandentians. The structure and variation of the novel mitochondrial genome were analyzed and compared with other Scandentians. The complete mitogenome (17,164 bp) encodes 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNAs), two ribosomal RNA (rRNAs), and one control region (CR). Most of the genes were encoded on majority strand, except nad6 and eight tRNAs. The nonsynonymous/synonymous ratio in all PCGs indicates strong negative selection among all Tupaiidae species. The comparative study of CRs revealed the occurrence of tandem repeats (CGTACA) found in T. nicobarica. The phylogenetic analyses (Maximum Likelihood and Bayesian Inference) showed distinct clustering of T. nicobarica with high branch supports and depict a substantial divergence time (12-19 MYA) from the ancestor lineage of Tupaiidae. The 16S rRNA dataset corroborates the taxonomic rank of two subspecies of T. nicobarica from the Great and Little Nicobar Islands. In the future, whole nuclear genome sequencing is necessary to further improve our understanding of evolutionary relationships among treeshrews, and will have implications for biomedical research.

Complete mitochondrial genome of critically endangered Crocidura nicobarica (Soricidae: Eulipotyphla) from the Great Nicobar Island, India.

The mitogenome (17,388 bp) of the Nicobar shrew, Crocidura nicobarica was determined in the present study. The mitogenome comprises 13 PCGs (11,427 bp), 22 tRNAs (1507 bp), two rRNAs (2538 bp), and a major non-coding control region (1932 bp). The Maximum Likelihood phylogeny clearly discriminates all the studied Crocidura species with high bootstrap support by concatenated PCGs. The studied species, C. nicobarica shows a close relationship with Crocidura orientalis, distributed in Java, Indonesia. The lineage diversification and zoogeographic patterns are congruent in the present analyses and encouraged further sampling and more molecular data to elucidate their in-depth evolutionary relationship.

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.