Background: The initiation of desert conditions in the Tarim Basin in China since the late Miocene has led to the significant genetic structuring of local organisms. Tarim Red Deer (Cervus elaphus yarkandensis, TRD) have adapted to the harsh environmental conditions in this basin, including high solar radiation and temperature, aridity, and poor nutritional conditions. However, the underlying genetic basis of this adaptation is poorly understood. Results: We sequenced the whole genomes of 13 TRD individuals, conducted comparative genomic analyses, and estimated demographic fluctuation. The ∂a∂i model estimated that the TRD and Tule elk (Cervus canadensis nannodes) populations diverged approximately 0.98 Mya. Analyses revealed a substantial influence of the Earth’s climate on the effective population size of TRD, associated with glacial advances and retreat, and human activities likely underlie a recent serious decline in population. A marked bottleneck may have profoundly affected the genetic diversity of TRD populations. We detected a set of candidate genes, pathways, and GO categories related to oxidative stress, water reabsorption, immune regulation, energy metabolism, eye protection, heat stress, respiratory system adaptation, prevention of high blood pressure, and DNA damage and repair that may directly or indirectly be involved in the adaptation of TRD to an arid-desert environment. Conclusions: Our analyses highlight the role of historical global climates in the population dynamics of TRD. In light of ongoing global warming and the increasing incidence of droughts, our study offers insights into the genomic adaptations of animals, especially TRD, to extreme arid-desert environments and provides a valuable resource for future research on conservation design and biological adaptations to environmental change.

Major histocompatibility complex (MHC) genes in vertebrates are vital in defending against pathogenic infections. To gain new insights into the evolution of MHC Class I (MHCI) genes and test competing hypotheses on the origin of the MHCI region in eutherian mammals, we studied available genome assemblies of nine species in Afrotheria, Xenarthra, and Laurasiatheria, and successfully characterized the MHCI region in six species. The following numbers of putatively functional genes were detected: in the elephant, four, one, and eight in the extended class I region, and κ and β duplication blocks, respectively; in the tenrec, one in the κ duplication block; and in the four bat species, one or two in the β duplication block. Our results indicate that MHCI genes in the κ and β duplication blocks may have originated in the common ancestor of eutherian mammals. In the elephant, tenrec, and all four bats, some MHCI genes occurred outside the MHCI region, suggesting that eutherians may have a more complex MHCI genomic organization than previously thought. Bat‐specific three‐ or five‐amino‐acid insertions were detected in the MHCI α1 domain in all four bats studied, suggesting that pathogen defense in bats relies on MHCIs having a wider peptide‐binding groove, as previously assayed by a bat MHCI gene with a three‐amino‐acid insertion showing a larger peptide repertoire than in other mammals. Our study adds to knowledge on the diversity of eutherian MHCI genes, which may have been shaped in a taxon‐specific manner.

Occurrence of copy number variation (CNV) of gene loci is important in the adaptation of species and populations to their environments. High copy numbers of mammalian genes encoding the digestive enzyme amylase, which plays a role in starch digestion, have been associated with adaptation to high‐starch foods. Here, we investigated CNV in the pancreatic amylase gene (AMY2) in Eurasian badgers (Meles species) and related taxa using real‐time quantitative PCR. We found that Meles anakuma and M. meles, as well as the other mustelids Mustela sibirica, Martes melampus and Martes zibellina, had only one copy of the AMY2 locus, whereas in Meles leucurus the copy number varied between one and four. The AMY2 copy number also varied significantly among M. leucurus populations. This suggests that M. leucurus is better adapted to a diet rich in starch and/or glycogen than its congeners. As Meles spp. are basically omnivorous but favor a carnivoran diet, for example, earthworms and amphibians, we speculate that the CNV is related to the dearth of animal food in the range of M. leucurus, which enforces a more vegetal diet. This in turn would favor more efficient digestion of dietary starch, which could be achieved by increasing the copy number of AMY2 .

Major histocompatibility complex (MHC) genes encode proteins that play a key role in the adaptive immune system of vertebrates and are generally highly polymorphic for defence against various pathogens. To understand the diversity and evolution of MHC variation in badgers in the genus Meles (Carnivora, Mustelidae), we analysed sequence variation of the MHC class II DRB gene exon 2 in the Japanese (Meles anakuma), Asian (Meles leucurus), European (Meles meles) and Southwest Asian (Meles canescens) badgers. Variation was higher in the Meles species than in other species in Mustelidae, and altogether 60 alleles were isolated from 28 individuals. The variable number of three to eight putative alleles per individual was observed, indicating the presence of two to four DRB loci per haploid genome. Non-synonymous substitutions exceeded synonymous substitutions at putative antigen-binding sites. Selection analyses of PAML models, fixed-effect likelihood and mixed-effect model evolution, together with the single breakpoint recombination, indicated that recombination and selection could be responsible for driving and maintaining the diversity of Meles DRBs. In a phylogenetic analysis, the DRB sequences from Meles were distributed in several clusters, which were dispersed among sequences of other mustelid family, even five alleles comprised a monophyletic group of Meles DRBs within a canid clade. The data demonstrate trans-species polymorphisms at different taxonomic and temporal scales, transgressing family-, genus- and species-level splits. Some allele sequences were shared by two to four of the Meles species, in line with a close phylogenetic relationship among these species.