Genetic adaptation and demography of chimpanzees (Pan troglodytes)

黑猩猩正濒临灭绝，其数量还在继续减少。种群基因组学提高了我们对黑猩猩长期人口和适应历史的理解，但对最近种群规模的变化和对当地环境的遗传适应知之甚少。最近的种群规模趋势对于评估濒危种群很重要，而当地适应模式可以为保护适应性遗传多样性提供信息，并确定影响生存和繁殖的关键环境压力。这个项目将分析一个新出现的数据集，该数据集包含800个野生黑猩猩的外显子组，分布在所有四个亚种的已知地点。新的基于连锁不平衡的方法将被用来推断最近(100代)有效种群数量的变化。病原体驱动的选择，特别是SIVcpz(HIV-1的前身)，将通过识别免疫和SIV相关基因的高度分化基因来进行研究。每个样本地点的环境数据将被整合到分析中，以确定所选的基因座和负责的环境因素。近似贝叶斯计算将允许详细研究关键基因座的进化历史，使我们能够推断选择性扫描的年龄、强度和模式。总而言之，这些方法将为黑猩猩的人口学和局部适应提供更完整的图景。

Chimpanzees are endangered and their numbers continue to decline. Population genomics has improved our understanding of the long-term demographic and adaptive history of chimpanzees but very little is known about recent changes in population size and genetic adaptation to local environments. Recent population size trends are important for the assessment of endangered populations while patterns of local adaptation can inform the conservation of adaptive genetic diversity and identify key environmental pressures influencing survival and reproduction. This project will analyse an emerging dataset of 800 exomes from wild chimpanzees at known locations across the range of all four subspecies. New linkage disequilibrium-based methods will be used to infer recent (<100 generations) changes in effective population size. Pathogen-driven selection, particularly SIVcpz (the precursor to HIV-1), will be investigated by identifying highly differentiated loci at immunity and SIV-related genes. Environmental data from each sample location will be integrated into the analysis to identify loci under selection and the environmental factors responsible. Approximate Bayesian computation will allow detailed investigation of the evolutionary history of key loci, allowing us to infer the age, strength and mode of selective sweeps. Together, these methods will provide a more complete picture of demography and local adaptation in chimpanzees.