Whole-genome sequencing of Tarim red deer (Cervus elaphus yarkandensis) reveals demographic history and adaptations to an arid-desert environment

Abstract

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.

Revealing the coexistence of differentiation and communication in an endemic hare, Lepus yarkandensis (Mammalia, Leporidae) using specific-length amplified fragment sequencing

“…The divergence time of Yarkand hare (0.86 Mya) estimated herein is in agreement with the results obtained from mitochondrial genes (0.83 Mya [ 8 ]; 0.84 Mya [ 83 ]), combined with numerous accurate fossil datasets. Notably, this divergence time is similar to that of other species currently living around the Tarim Basin, including Cervus elaphus yarkandensis (0.8–2.2 Mya [ 73 ]; 0.98 Mya [ 84 ]), and with the timing of the most recent common ancestor Phrynocephalus axillaris (0.88 Mya) and the appearance of Phrynocephalus forsythii in the Tarim Basin (0.94 Mya) [ 85 ].…”

Admixture mapping reveals loci for carcass mass in red deer x sika hybrids in Kintyre, Scotland

“…It would also be interesting to look at sequence divergence between red deer and sika for each of the 45 genes that we have identified here. While there is a sika genome ( Xing et al 2021 ) and a Hungarian red deer genome ( Ababaikeri et al 2020 ), neither of these is from Scottish red deer nor Scottish sika, which would be ideal for comparing divergence within this system, particularly given that introgression is occurring and selection is possible. Additionally, future work could look at gene expression at these genes to estimate whether expression differences are correlated with carcass mass ( Todd et al 2016 ).…”

Life in Deserts: The Genetic Basis of Mammalian Desert Adaptation

“…Other methods can be applied to a single desert population and identify genomic regions of reduced diversity, skewed allele frequency distribution, increased haplotype homozygosity (haplotype-based) [14,15], or combinations thereof, all of which could be signatures of selective sweeps [9,10]. These approaches have been used to detect selection in different desert-dwelling mammals [12,13,[16][17][18], and we highlight some specific examples herein.…”

“…Several studies of different desert mammals have identified genes, and functional classes of genes and pathways, involved in fat metabolism [17,21,32,39,55], thyroid-induced metabolism [12], salt metabolism and prevention of high blood pressure [13,16,34], insulin signaling Box 1. Endurer-Evader-Evaporator Concept Aiming to summarize and categorize decades of classic literature on desert adaptations in species occupying distinct ecological niches, Willmer et al [2] proposed a classification system relative to extreme temperatures and body size.…”

“…While past investigations of adaptive phenotypes underlying increased water retention at the kidney have focused on endocrine systems (e.g., vasopressin and/or RAAS-mediated osmoregulation) [65][66][67][68], significant shared evidence of selection across genomic studies (e.g., [13,[16][17][18]34]) points to the arachidonic acid metabolism pathway as perhaps the most important adaptive water-retention mechanism driving convergent evolution in desert mammals and birds [69]. Some genes from this pathway putatively under selection (Figure 1D) may be involved in the production of vasodilators of renal preglomerular vessels [19(S)-HETE] that simulate water reabsorption at the kidney.…”