Data from: Population transcriptomes reveal synergistic responses of DNA polymorphism and RNA expression to extreme environments on the Qinghai-Tibetan Plateau in a predatory bird

Low oxygen and temperature pose key physiological challenges for endotherms living on the Qinghai-Tibetan Plateau (QTP). Molecular adaptations to high-altitude living have been detected in the genomes of Tibetans, their domesticated animals and a few wild species, but the contribution of transcriptional variation to altitudinal adaptation remains to be determined. Here we studied a top QTP predator, the saker falcon, and analysed how the transcriptome has become modified to cope with the stresses of hypoxia and hypothermia. Using a hierarchical design to study saker populations inhabiting grassland, steppe/desert and highland across Eurasia, we found that the QTP population is already distinct despite having colonised the Plateau less than 2,000 years ago. Selection signals are limited at the cDNA level, but of only seventeen genes identified, three function in hypoxia and four in immune response. Our results show a significant role for RNA transcription: 50% of upregulated transcription factors were related to hypoxia responses, differentiated modules were significantly enriched for oxygen transport, and importantly, divergent <i></i>EPAS1<i></i> functional variants with a refined co-expression network were identified. Conservative gene expression and relaxed immune gene variation may further reflect adaptation to hypothermia. Our results exemplify synergistic responses between DNA polymorphism and RNA expression diversity in coping with common stresses, underpinning the successful rapid colonization of a top predator onto the QTP. Importantly, molecular mechanisms underpinning highland adaptation involve relatively few genes, but are nonetheless more complex than previously thought and involve fine-tuned transcriptional responses and genomic adaptation.低氧与低温对栖息于青藏高原（Qinghai-Tibetan Plateau，QTP）的恒温动物（endotherm）构成了核心生理挑战。针对高原栖息的分子适应性已在藏族人群、其驯养动物以及少数野生物种的基因组中被发现，但转录组变异对海拔适应的贡献仍有待阐明。本研究以青藏高原顶级捕食者——猎隼（saker falcon）为研究对象，解析其转录组如何重塑以应对低氧与低温胁迫。本研究采用分层设计，对欧亚大陆不同生境（草原、草原荒漠与高原）的猎隼种群进行分析，结果显示：尽管青藏高原种群的定居历史不足2000年，但其转录组已与其他种群产生显著分化。在cDNA层面筛选到的选择信号较为有限，仅鉴定出17个相关基因，其中3个参与低氧应答，4个参与免疫应答。本研究结果凸显了RNA转录的关键作用：上调的转录因子（transcription factor）中有50%与低氧应答相关，分化的共表达模块显著富集于氧运输通路；且重要的是，我们鉴定出了具有精细调控共表达网络的分化型EPAS1功能变异体。保守的基因表达谱与受选择放松作用的免疫基因变异，或进一步反映了猎隼对低温环境的适应性机制。本研究结果阐明了DNA多态性与RNA表达多样性在应对共同胁迫时的协同应答模式，为顶级捕食者快速成功定植青藏高原奠定了分子基础。值得注意的是，支撑高原适应的分子机制仅涉及相对较少的基因，但其复杂程度远超此前认知，且包含精细调控的转录应答与基因组适应性演化。