Shamshidin Abduriyim

The goitered gazelle, Gazella subgutturosa, is a conservation priority globally, one of the important ungulates in the arid and semiarid ecosystem. We produced Illumina short reads, PacBio HiFi long reads and Hi-C sequencing data of a road-killed male individual of this species to assemble its whole genome at the chromosome level. Consequently, the assembly is a 3.13 Gb in size, consisting of 16 pseudochromosomes (14 autosomes + X chromosome + partial Y chromosome), with a scaffold N50 length of 186.56 Mb. The quality value and Benchmarking Universal Single-Copy Ortholog score were 47.6% and 99.3%, respectively, indicating that our genomes sequence is of high quality and completeness. A total of 20,896 protein-coding genes were predicted in the genome, with an average gene length of 38,012 bp and an average coding sequence length of 1,291 bp. Comparison with other Bovidae genome revealed that each of the pseudochromosome of G. subgutturosa corresponds to two chromosomes of Bovidae species, suggesting multiple whole-chromosome fusions. Notably, the X chromosome corresponds to a fusion of the Bos taurus X chromosome and BTA5, consistent with a known X-autosomal translocation in the tribe Antilopini. However, the underlying molecular mechanism of this chromosome fusion has yet to be elucidated in future studies. In summary, the whole genome generated provides a high-quality reference for conservation genomics and genome evolution studies of Gazella species, especially of G. subgutturosa.

Understanding how environmental heterogeneity drives spatially varying selection is key to deciphering adaptive evolution. The Major Histocompatibility Complex (MHC) provides an ideal model to study this process. We investigated the MHC class II DQA gene across seven subspecies of wild argali sheep (Ovis ammon) in China. High-throughput sequencing of 98 individuals revealed high diversity (25 alleles), with balancing selection maintaining allelic richness and trans-species polymorphism indicating long-term balancing selection. Molecular evolutionary analyses uncovered heterogeneous positive selection on antigen-binding sites among subspecies (ω = 1.181-3.000), mirroring variable pathogen-driven pressures. Mantel tests detected no significant isolation-by-distance or isolation-by-environment. However, Spearman correlations identified significant associations between specific alleles (e.g., Ovam-DQA*08) and climatic variables, as well as between allele frequencies and MaxEnt-predicted suitability. Redundancy analysis showed that temperature and precipitation explained 54.7% of allele frequency variance. Ecological niche modeling suggested that annual mean temperature was associated with allele distribution, indicating that abiotic factors may shape immunogenetic variation, likely by structuring pathogen communities. Our study provides the first MHC characterization in argali and elucidates how balancing and positive selection interact to maintain functional diversity, offering a foundation for predicting evolutionary responses to environmental change.

During a Chiroptera resource survey conducted in 2023 on the Pamir Plateau of China’s Xinjiang Uygur Autonomous Region, two adult male bat individuals were captured. External morphology examination revealed small-sized individuals characterized by long, narrow ears with straight tragus structures tapering to sharp tips—features diagnostic of the genus Myotis . Concurrently, we obtained free-flight echolocation calls from the bats: the signals showed an initial frequency of 65.12 ± 2.12 kHz, terminal frequency of 42.78 ± 1.27 kHz, peak energy frequency of 47.41 ± 1.46 kHz, pulse duration of 2.52 ± 0.26 ms, and inter-pulse interval of 94.01 ± 31.41 ms. Based on skull morphological traits and bioacoustic data, the specimens were preliminarily identified as Myotis aurascens . However, our phylogenetic analysis based on the mitochondrial cytochrome b ( Cytb ) gene revealed that sequences attributed to M. aurascens and M. davidii formed a single strongly supported clade, underscoring the unresolved taxonomic status of these species. Irrespective of the exact species assignment, this discovery constitutes the first documented occurrence of the M. davidii / aurascens complex on the Pamir Plateau, thereby extending the known distribution range in China. Notably, these specimens represent the highest-elevation record for this group to date (3200 m). Our study provides the first comprehensive description of cranial morphology and echolocation signatures for this taxon in a high-altitude habitat. These findings significantly enhance regional biodiversity inventories and offer critical baseline data for plateau ecosystem research.

During a Chiroptera resource survey conducted in 2023 on the Pamir Plateau of China's Xinjiang Uygur Autonomous Region, two male bat specimens were captured. External morphology examination revealed small-sized individuals characterized by long, narrow ears with straight tragus structures tapering to sharp tips—features diagnostic of the genus Myotis . Echolocation call parameters were as follow: omitted signals exhibited a start frequency of 65.12 ± 2.12 kHz, end frequency of 42.78 ± 1.27 kHz, peak energy frequency of 47.41 ± 1.46 kHz, pulse duration of 2.52 ± 0.26 ms, and inter-pulse interval of 94.01 ± 31.41 ms. Integrated analyses incorporating mitochondrial cytochrome b (Cytb) gene sequencing, (skull) morphological traits, and bio-acoustic data conclusively identified the specimens as the steppe whiskered bat, Myotis aurascens . This discovery constitutes the first documented occurrence of M. aurascens in Xinjiang, thereby expanding the confirmed distribution range of this species in China. Notably, these specimens represent the highest-altitude record for the species at 3,200 m above sea level. Our study provides the inaugural comprehensive description of cranial morphology and echolocation signatures for this species in high-altitude habitats. These findings significantly enhance regional biodiversity inventories and contribute critical baseline data for plateau ecosystem research.

The Caspian barbastelle, Barbastella caspica, has spread widely in the Caspian region, Iran, and Central Asia; however, there is no evidence of its occurrence in China so far. During a field investigation, we collected a single specimen of B. caspica in China’s Xinjiang Uyghur Autonomous Region. At the same time, we obtained the free-flight echolocation calls of the bat. It omitted signals with start frequency of 33.15 ± 1.43 kHz, end frequency of 29.82 ± 0.40 kHz, frequency of most energy 31.48 ± 0.40 kHz, duration of 2.43 ± 0.24 ms, and a pulse interval of 246.57 ± 9.48 ms, which are probably type-I sounds emitted through the mouth. We also sequenced its entire mitochondrial genome to elucidate the genomic structure and its evolutionary relationships with closely related Barbastella. The mitochondrial genome of B. caspica spans 16,933 bp, comprising 13 protein-encoding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a displacement loop/control region. Consistent with previous bat mitogenome reports, the majority of mitochondrial genes are encoded on the heavy chain. A phylogenetic analysis based on 13 protein-coding genes revealed that Rhogeessa, Plecotus, and B. caspica formed a clade within Vespertilionidae. Barbastella caspica was found to be a sister species to B. beijingensis and B. leucomelas in phylogenetic trees using the cytochrome b and ND1 gene sequences. This is the first report of the mitogenome of a member of the genus Barbastella, as well as the first record of the distribution of B. caspica in China and first documentation of its echolocation calls.

Argali, also known as wild sheep ( Ovis ammon ), is a prominent alpine mammal found in Central Asia. It is of conservation concern globally and domestically in China. Our study aims to unveil the genetic diversity and phylogenetic relationships among argali populations in China using the mitochondrial cytochrome b ( Cytb ) and control region (CR) sequences. We noninvasively collected a total of 77 fecal or tissue samples from various locations within Xinjiang, covering most of its range. Consequently, we identified 22 distinct haplotypic sequences for Cytb (1140 bp) and 36 for CR (1107–1260 bp). In our phylogenetic analyses, all sequences from China and abroad were grouped into 10 different clades, labeled as clade A through clade J. The network clustering pattern was consistent with the phylogenetic topology. The genetic distance and genetic divergence between clades ranged from 1.21% to 9.25% and from 0.30 to 0.94, respectively. Our analysis of molecular variation (AMOVA) analysis also revealed that more than 70% of the variation was accounted for among the clades. The genetic differentiation between populations was positively corelated with geography distances ( r = 0.472, p < 0.01). We observed significant differences in genetic diversity among the various populations. The mismatch distribution analysis showed a multimodal distribution for all clades. Fu’s Fs and Tajima’s D values were not statistically significant. In conclusion, we genetically identified 10 matrilineal populations, which may represent subspecies of argali population, eight of which were in China. The demographic history analyses suggest that the population size of all argali evolutionary populations remained relatively stable. Nonetheless, some populations need special attention due to their low level of genetic diversity.

Bat populations are highly diverse, making bat species taxonomy and phylogenetic relationships an important research topic. Mitochondrial DNA, a form of maternal inheritance, has been extensively used in species relationship research. Barbastella caspica has spread widely in the Caspian region, Iran, and Central Asia, however there is no evidence of its occurrence in China. During a field investigation, we obtained a single specimen of the B. caspica species for the first time in China’s Xinjiang Uyghur Autonomous Region. We sequenced the entire mitochondrial genome, presented its genomic structure and features, and examined its evolutionary position in relation to its congenerous. The mitochondrial genome of B. caspica spans 16,933 bp, composing 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a displacement loop/control region. Consistent with previous bat mitogenome reports, the majority of mitochondrial genes are encoded on the heavy chain. With the exception of the DHU arm in tRNA-Ser1, all other tRNAs exhibit a “cloverleaf” secondary structure. Phylogenetic analysis based on 13 protein-coding genes revealed that Rhogeessa, Plecotus, and B. caspica formed one clade within the Vespertilionidae. B. caspica was found to be a sister species to B. beijingensis and B. leucomelas in the phylogenetic trees using the cytochrome b and ND1 gene sequences, respectively. This is the first report of the Barbastella genus’ mitogenome, as well as the first record of a B. caspica species from China.

The major histocompatibility complex (MHC) genes are the most polymorphic genes in vertebrates, and their proteins play a critical role in adaptive immunity for defense against a variety of pathogens. MHC diversity was lost in many species after experiencing a decline in size. To understand the variation and evolution of MHC genes in the Siberian ibex, Capra sibirica, which has undergone a population decline, we analyzed the variation of the second exon of MHC class II DRB genes in samples collected from five geographic localities in Xinjiang, China, that belong to three diverged mitochondrial clades. Consequently, we identified a total of 26 putative functional alleles (PFAs) with 260 bp in length from 43 individuals, and found one (for 27 individuals) to three (for 5 individuals) PFAs per individual, indicating the presence of one or two DRB loci per haploid genome. The Casi-DRB1*16 was the most frequently occurring PFA, Casi-DRB1*22 was found in only seven individuals, 14 PFAs occurred once, 7 PFAs twice, implying high frequency of rare PFAs. Interestingly, more than half (15) of the PFAs were specific to clade I, only two and three PFAs were specific to clades II and III, respectively. So, we assume that the polygamy and sexual segregation nature of this species likely contributed to the allelic diversity of DRB genes. Genetic diversity indices showed that PFAs of clade II were lower in nucleotide, amino acid, and supertype diversity compared to those of the other two clades. The pattern of allele sharing and F_ST values between the three clades was to some extent in agreement with the pattern observed in mitochondrial DNA divergence. In addition, recombination analyses revealed no evidence for significant signatures of recombination events. Alleles shared by clades III and the other two clades diverged 6 million years ago, and systematic neighbor grids showed Trans-species polymorphism. Together with the PAML and MEME analyses, the results indicated that the DRB gene in C. sibirica evolved under balancing and positive selection. However, by comparison, it can be clearly seen that different populations were under different selective pressures. Our results are valuable in understanding the diversity and evolution of the DRB gene in a mountain living C. sibirica and in making decisions on future long-term protection strategies.

Maternal lineages of mitochondrial DNA (mtDNA) are recognized as important components of intra and interspecific biodiversity and help us to disclose the phylogeny and divergence times of many taxa. Species of the genus Capra are canonical mountain dwellers. Among these is the Siberian ibex (Capra sibirica), which is regarded as a relic species whose intraspecific classification has been controversial so far. We collected 58 samples in Xinjiang, China, and analyzed the mtDNA genes to shed light on the intraspecific relationships of the C. sibirica populations and estimate the divergence time. Intriguingly, we found that the mtDNA sequences of C. sibirica split into two main lineages in both phylogenetic and network analyses: the Southern lineage, sister to Capra falconeri, consisting of samples from Ulugqat, Kagilik (both in Xinjiang), India, and Tajikistan; and the Northern lineage further divided into four monophyletic clades A–D corresponding to their geographic origins. Samples from Urumqi, Sawan, and Arturk formed a distinct monophyletic clade C within the Northern lineage. The genetic distance between the C. sibirica clades ranges from 3.0 to 8.6%, with values of F_ST between 0.839 and 0.960, indicating notable genetic differentiation. The split of the genus Capra occurred approximately 6.75 Mya during the late Miocene. The Northern lineage diverged around 5.88 Mya, followed by the divergence of Clades A–D from 3.30 to 1.92 Mya during the late Pliocene and early Pleistocene. The radiation between the Southern lineage and C. falconeri occurred at 2.29 Mya during the early Pleistocene. Our results highlight the importance of extensive sampling when relating to genetic studies of alpine mammals and call for further genomic studies to draw definitive conclusions.

The major histocompatibility complex (MHC) genes are the most polymorphic genes in vertebrates, and their proteins play a critical role in adaptive immunity for defense against a variety of pathogens. MHC diversity was lost in many species after experiencing a decline in size. To understand the variation and evolution of MHC genes in the Siberian ibex, Capra sibirica, which has undergone a population decline, we analyzed the variation of the second exon of MHC class II DRB genes in samples collected from five geographic localities in Xinjiang, China, that belong to three diverged mitochondrial clades. Consequently, we identified a total of 26 putative functional alleles (PFAs) with 260 bp in length from 43 individuals, and found one (for 27 individuals) to three (for 5 individuals) PFAs per individual, indicating the presence of one or two DRB loci per haploid genome. The Casi-DRB1*16 was the most frequently occurring PFA, Casi-DRB1*22 came after found in only seven individuals, 14 PFAs occurred once (7 PFAs twice), implying high frequency of rare PFAs. Interestingly, more than half of the (15) PFAs were specific to clade I, only one and three PFAs were specific to clades II and III, respectively. So, we assume that the polygamy and sextual segregation nature of this species likely contributed to the allelic diversity of DRB genes. Genetic diversity indices showed that PFAs of clade II were lower in nucleotide, amino acid, and supertype diversity compared to those of the other two clades. The way of allele sharing and FST values between three clades were to some extent in agreement with pattern observed in mitochondrial DNA divergence. In addition, recombination analyses revealed no evidence for significant signatures of recombination events. Alleles shared by clades III and the other two clades diverged 6 million years ago, and systematic neighbor grids showed cross-species polymorphisms. Together with the PAML and MEME analyses, the results indicated that the DRB gene in C. sibirica evolved under balancing and positive selection. However, by comparison, it can be clearly seen that different populations were under different selective pressures. Our results are valuable in understanding the diversity and evolution of the DRB gene in a mountain living C. sibirica and in making decisions on future long-term protection strategies.