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

A brighter shade of future climate on Himalayan musk deer Moschus leucogaster

Himalayan musk deer (Moschus leucogaster) is classified as an endangered species by IUCN with a historically misunderstood distribution due to misidentification with other species of musk deer, Moschus spp. Taking advantage of recent genetic analyses confirming the species of various populations in Nepal and China, we produced an accurate estimate of the species' current and future distribution under multiple climate change scenarios. We collected high-quality occurrence data using systematic surveys of various protected areas of Nepal to train species distribution models. The most influential determinants of the distribution of Himalayan musk deer were precipitation of the driest quarter, temperature seasonality, and annual mean temperature. These variables, and precipitation in particular, determine the vegetation type and structure in the Himalaya, which is strongly correlated with the distribution of Himalayan musk deer. We predicted suitable habitats between the Annapurna and Kanchenjunga region of Nepal Himalaya as well as the adjacent Himalaya in China. Under multiple climate change scenarios, the vast majority (85-89%) of current suitable sites are likely to remain suitable and many new areas of suitable habitat may emerge to the west and north of the current species range in Nepal and China. Two-thirds of current and one-third of future suitable habitats are protected by the extensive network of protected areas in Nepal. The projected large gains in suitable sites may lead to population expansion and conservation gains, only when the threat of overexploitation and population decline is under control.

Empirical Data Suggest That the Kashmir Musk Deer (Moschus cupreus, Grubb 1982) Is the One Musk Deer Distributed in the Western Himalayas: An Integration of Ecology, Genetics and Geospatial Modelling Approaches

Insufficient research has been conducted on musk deer species across their distribution range, primarily because of their elusive behaviour and the fact they occupy remote high-altitude habitats in the Himalayas above 2500 m. The available distribution records, primarily derived from ecological studies with limited photographic and indirect evidence, fail to provide comprehensive information on the species distribution. Consequently, uncertainties arise when attempting to determine the presence of specific taxonomic units of musk deer in the Western Himalayas. This lack of knowledge hampers species-oriented conservation efforts, as there need to be more species-specific initiatives focused on monitoring, protecting, and combatting the illegal poaching of musk deer for their valuable musk pods. We used transect surveys (220 trails), camera traps (255 cameras), non-invasive DNA sampling (40 samples), and geospatial modelling (279 occurrence records) to resolve the taxonomic ambiguity, and identify the suitable habitat of musk deer (Moschus spp.) in Uttarkashi District of Uttarakhand and the Lahaul-Pangi landscape of Himachal Pradesh. All the captured images and DNA-based identification results confirmed the presence of only Kashmir musk deer (KDM) (Moschus cupreus) in Uttarakhand and Himachal Pradesh. The results suggest that KMD inhabit a narrow range of suitable habitats (6.9%) of the entire Western Himalayas. Since all evidence indicates that only KMD are present in the Western Himalayas, we suggest that the presence of other species of musk deer (Alpine musk deer and Himalayan musk deer) was wrongly reported. Therefore, future conservation plans and management strategies must focus only on KMD in the Western Himalayas.

Genetic evidence indicates the occurrence of the Endangered Kashmir musk deer Moschus cupreus in Uttarakhand, India

The Endangered Kashmir musk deer Moschus cupreus occurs in the western Himalayan region from Nepal to Afghanistan, but there is a lack of comprehensive and reliable information on its range. The region also harbours the Endangered Himalayan musk deer Moschus leucogaster, and this range overlap may have led to misidentification of the two musk deer species and errors in the delimitation of their ranges. Here, using genetic analysis of the mitochondrial DNA control region, we examined the phylogenetic relationship among musk deer samples from three regions in India: Ganderbal District in Jammu and Kashmir, and Kedarnath Wildlife Sanctuary and Nanda Devi Biosphere Reserve, both in Uttarakhand. The Bayesian phylogenetic analysis indicated a close genetic relationship between samples from Jammu and Kashmir, Kedarnath Wildlife Sanctuary and Nanda Devi Biosphere Reserve, validated by previously published sequences of Kashmir musk deer from Nepal. Our analyses confirmed the samples from Uttarakhand to be from the Kashmir musk deer, which was not previously known from this region. Therefore, we recommend further research in this area, to validate species identification and confirm the geographical distribution of the various species of musk deer. In addition, we recommend revision of the range of M. cupreus in the IUCN Red List assessment, to facilitate effective conservation and management of this Endangered species.

Mitochondrial genome of captive Alpine musk deer, Moschus chrysogaster (Moschidae), and phylogenetic analyses with its coordinal species

Alpine musk deer, Moschus chrysogaster, a solitary, primitive ungulate inhabiting high elevation areas (3000–4500 m) is an endangered species facing threat of extinction globally due to excessive hunting for its musk. In this study, we determined the complete mitochondrial genome of M. chrysogaster, which was 16,354 bp in length, and revealed the same gene order and genomic organization as typical Moschidae mitochondrial DNA. Start codons in 13 protein-coding genes (PCGs) were all typical ATGs except ATA for ND2 and ND3 and ATT for ND5. Stop codons were all typical types except an incomplete stop codon T for COX3, ND2, ND3, and ND4. Secondary structures in 22 transfer RNA genes all showed typical cloverleaf except tRNA-Ser (AGY), in which the dihydrouridine arm formed a simple loop. No repeat units were found in the control region. The topology structure indicated that M. cupreus was primitive and located at the root of the Moschidae clade. Phylogenetic reconstruction placed M. chrysogaster as a distinct lineage, closely related to the branch of M. leucogaster, M. berezovskii (wild) and predicted a sister relationship with M. moschiferus, M. anhuiensis, and M. berezovskii (captive). However, we suggested that the genetic resources of M. chrysogaster_JQ608470 should be further investigated.

Complete mitogenome of Kashmir musk deer (Moschus cupreus) and its comparative phylogenetic relationships

Kashmir musk deer, Moschus cupreus (KMD) is one the most threatened species endemic to the Himalayan region of Kashmir, Pakistan and Afghanistan. Herein, we have sequenced, annotated and characterized the complete mitogenome of M. cupreus. The investigation and comparison of the mitogenome provide crucial information for phylogenetic analysis to understand the evolutionary relationships. The mitogenome of KMD was 16,354 bp long, comprising 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and non-coding control region. Its composition was highly A+T biased 68.42%, and exhibited a positive AT-skew (0.082) and negative GC-skew (- 0.307). The phylogenetic analysis suggested that KMD was a primitive and extant species in the genus Moschus, whereas Alpine musk deer (M. chrysogaster) and Himalayan musk deer (M. leucogaster) were the closest relatives. It indicated the placement of M. cupreus within the monotypic family Moschidae of musk deer. Hence, it provides a better understanding of lineage identification and musk deer evolution for further research.

Dynamics behind disjunct distribution, hotspot-edge refugia, and discordant RADseq/mtDNA variability: insights from the Emei mustache toad

Background

The distribution of genetic diversity and the underlying processes are important for conservation planning but are unknown for most species and have not been well studied in many regions. In East Asia, the Sichuan Basin and surrounding mountains constitute an understudied region that exhibits a “ring” of high species richness overlapping the eastern edge of the global biodiversity hotspot Mountains of Southwest China. We examine the distributional history and genetic diversification of the Emei mustache toad Leptobrachium boringii, a typical “ring” element characterized by disjunct ranges in the mountains, by integrating time-calibrated gene tree, genetic variability, individual-level clustering, inference of population splitting and mixing from allele frequencies, and paleoclimatic suitability modeling.

Results

The results reveal extensive range dynamics, including secondary contact after long-term isolation via westward dispersal accompanied by variability loss. They allow the proposal of a model that combines recurrent contractions caused by Quaternary climatic changes and some failed expansions under suitable conditions for explaining the shared disjunct distribution pattern. Providing exceptional low-elevation habitats in the hotspot area, the eastern edge harbors both long-term refugial and young immigrant populations. This finding and a synthesis of evidence from other taxa demonstrate that a certain contributor to biodiversity, one that preserves and receives low-elevation elements of the east in this case, can be significant for only a particular part of a hotspot. By clarifying the low variability of these refugial populations, we show that discordant mitochondrial estimates of diversity can be obtained for populations that experienced admixture, which would have unlikely left proportional immigrant alleles for each locus.

Conclusions

Dispersal after long-term isolation can explain much of the spatial distribution of genetic diversity in this species, while secondary contact and long-term persistence do not guarantee a large variation. The model for the formation of disjunct ranges may apply to many other taxa isolated in the mountains surrounding the Sichuan Basin. Furthermore, this study provides insights into the heterogeneous nature of hotspots and discordant variability obtained from genome-wide and mitochondrial data.

Whole-genome sequencing of wild Siberian musk deer (Moschus moschiferus) provides insights into its genetic features

Background

Siberian musk deer, one of the seven species, is distributed in coniferous forests of Asia. Worldwide, the population size of Siberian musk deer is threatened by severe illegal poaching for commercially valuable musk and meat, habitat losses, and forest fire. At present, this species is categorized as Vulnerable on the IUCN Red List. However, the genetic information of Siberian musk deer is largely unexplored.

Results

Here, we produced 3.10 Gb draft assembly of wild Siberian musk deer with a contig N50 of 29,145 bp and a scaffold N50 of 7,955,248 bp. We annotated 19,363 protein-coding genes and estimated 44.44% of the genome to be repetitive. Our phylogenetic analysis reveals that wild Siberian musk deer is closer to Bovidae than to Cervidae. Comparative analyses showed that the genetic features of Siberian musk deer adapted in cold and high-altitude environments. We sequenced two additional genomes of Siberian musk deer constructed demographic history indicated that changes in effective population size corresponded with recent glacial epochs. Finally, we identified several candidate genes that may play a role in the musk secretion based on transcriptome analysis.

Conclusions

Here, we present a high-quality draft genome of wild Siberian musk deer, which will provide a valuable genetic resource for further investigations of this economically important musk deer.

Projected distribution and climate refugia of endangered Kashmir musk deer Moschus cupreus in greater Himalaya, South Asia

Kashmir musk deer Moschus cupreus (KMD) are the least studied species of musk deer. We compiled genetically validated occurrence records of KMD to construct species distribution models using Maximum Entropy. We show that the distribution of KMD is limited between central Nepal on the east and north-east Afghanistan on the west and is primarily determined by precipitation of driest quarter, annual mean temperature, water vapor, and precipitation during the coldest quarter. Precipitation being the most influential determinant of distribution suggests the importance of pre-monsoon moisture for growth of the dominant vegetation, Himalayan birch Betula utilis and Himalayan fir Abies spectabilis, in KMD's preferred forests. All four Representative Concentration Pathway Scenarios result an expansion of suitable habitat in Uttarakhand, India, west Nepal and their associated areas in China in 2050s and 2070s but a dramatic loss of suitable habitat elsewhere (Kashmir region and Pakistan-Afghanistan border). About 1/4th of the current habitat will remain as climate refugia in future. Since the existing network of protected areas will only include a tiny fraction (4%) of the climatic refugia of KMD, the fate of the species will be determined by the interplay of more urgent short-term forces of poaching and habitat degradation and long-term forces of climate change.

mtDNA analysis confirms the endangered Kashmir musk deer extends its range to Nepal

Musk deer Moschus spp. are endemic to the high mountain forests of central Asia. The taxonomic status of musk deer in the central and western Himalayas is poorly understood. We investigated the phylogenetic relationship of musk deer from the central and western Himalayas based on mitochondrial genomic data of Cytochrome b (380 bps) and D-loop (1000 bps). Our results distinguished two divergent lineages using higher bootstrap support (bs) values from the Maximum likelihood and Bayesian posterior probabilities (bpp). Both the Manang and Kaski lineages from central Nepal are confirmed as Himalayan musk deer Moschus leucogaster and represent a species complex widespread throughout the central and eastern Himalayan region. The musk deer Mustang lineage was confirmed as Kashmir musk deer Moschus cupreus and has wide distribution in the western Himalayas (from central Nepal to Afghanistan). Our analysis validates that Kashmir musk deer is a genetically distinct species and it clarifies that Himalayan musk deer and Kashmir musk deer are confirmed instead of Alpine musk deer Moschus chrysogaster which has been previously described from the southern parts of Himalayas of Nepal, India and Pakistan.

Species dilemma of musk deer (Moschus spp) in India: molecular data on cytochrome c oxidase I suggests distinct genetic lineage in Uttarakhand compared to other Moschus species

Musk deer are of high conservation priority owing to poaching pressure because of its musk pod. Representation of musk deer status using genetics is poorly documented in India, and it is not confirmed as to how many species of musk deer are present. We characterize for the first time, the genetic diversity of musk deer from Uttarakhand using Cytochrome Oxidase sub-unit (COI) gene (486 bp) and compared with the data available for other species. Results revealed the presence of six haplotypes in the Uttarakhand population amongst 17 sequences. Of these, 12 sequences shared the single haplotype. The intra-species sequences divergence was 0.003-0.017, whereas divergence with other species of musk deer was 0.071-0.081. Bayesian phylogenetic tree revealed that samples from Uttarakhand formed a separate clade with respect to other species of musk deer, whereas three species distributed in China clustered in the same clade and showed low sequences divergence, i.e., 0.002-0.061. Because of different ecomorph reported, we suggest using the barcoding based approach for inter and intra-species distinction and delineating species boundaries across the range for effective conservation. Besides, systematic classification, DNA barcoding would also help in dealing wildlife offence cases for disposal of the legal report in court.

Multiple independent structural dynamic events in the evolution of snake mitochondrial genomes

BACKGROUND

Mitochondrial DNA sequences have long been used in phylogenetic studies. However, little attention has been paid to the changes in gene arrangement patterns in the snake's mitogenome. Here, we analyzed the complete mitogenome sequences and structures of 65 snake species from 14 families and examined their structural patterns, organization and evolution. Our purpose was to further investigate the evolutionary implications and possible rearrangement mechanisms of the mitogenome within snakes.

RESULTS

In total, eleven types of mitochondrial gene arrangement patterns were detected (Type I, II, III, III-A, III-B, III-B1, III-C, III-D, III-E, III-F, III-G), with mitochondrial genome rearrangements being a major trend in snakes, especially in Alethinophidia. In snake mitogenomes, the rearrangements mainly involved three processes, gene loss, translocation and duplication. Within Scolecophidia, the O_L was lost several times in Typhlopidae and Leptotyphlopidae, but persisted as a plesiomorphy in the Alethinophidia. Duplication of the control region and translocation of the tRNA^Leu gene are two visible features in Alethinophidian mitochondrial genomes. Independently and stochastically, the duplication of pseudo-Pro (P*) emerged in seven different lineages of unequal size in three families, indicating that the presence of P* was a polytopic event in the mitogenome.

CONCLUSIONS

The WANCY tRNA gene cluster and the control regions and their adjacent segments were hotspots for mitogenome rearrangement. Maintenance of duplicate control regions may be the source for snake mitogenome structural diversity.

Next generation sequencing yields the complete mitogenome of captive forest musk deer, Moschus berezovskii (Ruminantia: Moschidae)

Moschus berezovskii is an endangered species, but its captive populations are valuable on musk secretions in traditional Chinese medicine and perfume manufacture. The mitogenome of M. berezovskii was 16,353 bp in size. Stop codons in 13 PCGs were all typical types except incomplete stop codon T for COX3, ND2 and ND4, and TA for ND3. No tandem repeat was found in control region. Phylogenetic analysis indicated that Moschidae has the closest relationship with Bovidae. We supported that M. berezovskii should be categorized into two subspecies, and suggested that the status of M. chrysogaster JQ608470 should be further investigated.

Complete mitochondrial genome of Siberian musk deer Moschus moschiferus (Artiodactyla: Moschidae) and phylogenetic relationship with other moschus species

The Siberian musk deer, Moschus moschiferus, is an Endangered species in South Korea due to its decreasing population size caused by illegal hunting and habitat destruction. In this study, the complete mitochondrial genome of M. moschiferus was determined using next-generation sequencing. Total length of its mitogenome is 16,356 bp in length, encoding 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and one control region. Its AT contents are 62.4%, which are higher than its GC contents (37.7%) (A, 34.1%; C, 24.9%; G, 12.8%; and T, 28.3%). Phylogenetic relationship of genus Moschus showed topologies similar to those reported in previous studies. Sequence comparison between two M. moschiferus from South Korea indicated high sequence variations with 122 nucleotide differences. These results provide useful information necessary for further phylogenetic studies of Moschus species.

The complete mitochondrial genome of Anthus hodgsoni (Passeriformes: Motacillidae)

Anthus hodgsoni is a species of small passerine bird in the family Motacillidae, which is widely distributed. In this study, we determined the complete mitochondrial genome of A. hodgsoni. The result showed that the total length of the mitochondrial genome was 16,886 bp and contained 2 ribosomal RNA genes, 22 transfer RNA genes, 13 protein-coding genes and 1 control region. The phylogenetic tree was reconstructed using the Bayesian analysis method and divided into four genera, Anthus, Dendronanthus, Motacilla and Tmetothylacus. The A. hodgsoni which we determined was clustered into genus Anthus and received strong support.

Systematics of the Artiodactyla of China in the 21(st) century

In this paper, I have introduced the concept of the Evolutionary Species, and shown how it affects the taxonomy of the Artiodactyla of China. The "traditional" taxonomy of the Artiodactyla, which has remained almost unchanged for 100 years, relies on ill-formulated notions of species and subspecies, only slightly modified by the population-thinking of the 1930s. Species are populations (or metapopulations) differentiated by the possession of fixed heritable differences from other such populations (or metapopulations). In the Artiodactyla, there are many more species than "traditionally" recognised; this is by no means a drawback, as it enables the units of biodiversity to be identified in a testable fashion, and brings the taxonomy of large mammals into line with that long practised for small mammals. Species are likely to differentiate where there are natural gaps in the distribution of a genus, such as mountain blocks (for example in the genus Budorcas) or otherwise dissected habitat (for example in the genus Cervus). Natural hybridisation between distinct species is not an uncommon phenomenon, again illustrated well in the genus Cervus, where hybridisation between the elaphus and nippon groups occurs today and evidently occurred in the past, as shown by the distribution of mtDNA.

The complete mitochondrial genome of Lycodon liuchengchaoi (squamata: colubridae)

Lycodon liuchengchaoi is a new species discovered in recent years which is widely distribute in Anhui, Hubei and Sichuan Province. In this study, we determined the complete mitochondrial genome of L. liuchengchaoi. The result shows that the complete mitogenome of L. liuchengchaoi is 17,171bp. It is similar with the typical mtDNA of Serpentes, which contains 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, 2 control regions, and a stem-loop region. The phylogenetic tree, contains 17 Serpentiforms species, is divided into two clades which correspond to six genera in Colubridae. The L. liuchengchaoi which appeared into Clade A, clustered within Lycodon.