Abstract
BackgroundThe 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.ResultsWe 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.ConclusionsOur 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.
Highlights
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
Based on the high-quality sequence data, the genomic GC content averaged 44.03% for the Tarim red deer (TRD) (Additional file 3: Table S3) and 41.55% for the Tule elk [34], which are typical values comparable to those observed in the genomes of other mammals, including ungulates [25, 28,29,30], indicating that our sequencing data were not affected by GC bias
The Tule elk Selective sweep and gene ontology (GO) enrichment analyses We considered the top 5% of FST values and the θπ ratio cut-off values, Z(FST) > 0.734 and log2 > 0.827 (Fig. 4c) for the Tule elk population / TRD population, to be potentially selected regions associated with adaptation to
Summary
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. Adaptation to diverse and changing environments is a fundamental principle in evolutionary biology, and estimating the potential for adaptive evolution is critical when identifying populations/species at risk of extinction due to environmental change [1]. Species in the genus show a broad range of morphological features (i.e. antler and body size; coat colour) in different climatic conditions, and show considerable biological adaptations for survival under diverse environmental conditions—for example, extreme cold, hot, or moderate temperatures; extremely dry or wet conditions; high altitude; steppe-like habitats, forests, and swampy river plains [8]. Honored as “the flower of Asia” in the international market owing to its large quantities of velvet antler with good quality [11, 12], and being the main large-
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