Assessing the impact of realized relatedness on primate sociality using whole genome sequencing

快速的技术进步，如全基因组测序（WGS），为广泛的物种基因组研究开辟了令人兴奋的新途径。受到这一进展重大影响的主题之一是亲属驱动行为对社会关系的影响，这对人类的健康和健身也至关重要。正如亲缘选择理论所预测的那样，许多分类群中的个体经常根据共有等位基因的比例，将其社会行为偏向于同种个体。然而，观察到的模式是高度可变的，这可能是由于对遗传关系的不精确估计。衡量社会偏好（如裙带关系）和反对亲缘关系（如避免近亲繁殖）需要对亲缘关系（或血统认同，IBD）进行准确的估计。值得注意的是，由于减数分裂期间的随机过程，近亲共享的基因组数量变化很大，导致IBD值的梯度，而以前使用的方法的亲缘关系估计只能很好地反映这种梯度。例如，谱系或短串联重复（STR）标记要么提供分类平均值，要么提供基于部分基因组的相当不精确的估计。另一方面，WGS分析了整个基因组中的所有单核苷酸变异，从而提供了最权威的亲缘关系估计，并为解决亲缘驱动行为问题提供了前所未有的能力。到目前为止，灵长类动物的亲缘关系主要是在分类水平上进行研究，而不是在IBD中沿着梯度进行研究。这给我们对社会性及其进化的理解留下了重大空白。WGS关于自由放养灵长类动物的数据仍然很少，但填补这些空白是必要的。在这里，我们将利用圣地亚哥岛（波多黎各）自由放养的恒河猴（Macaca mulatta）的特殊种群，对其人口统计、生殖、行为和其他表型数据进行了数十年的收集。我们将把这些数据与来自WGS的800只动物的IBD数据联系起来，以评估IBD梯度对支持和反对亲属的社会偏好的影响。通过这种综合的方法，我们将追求三个主要目标：1。我们将量化IBD在亲族内部和亲族之间的变异，并比较WGS数据、家系和STR标记对IBD估计的差异。2. 我们将确定社会偏好是否可以通过IBD的梯度来预测。为了理解亲属偏见的机制，我们将把表型相似性与IBD的变异联系起来，并评估表型线索是否根据共同的IBD被感知。3. 我们将研究是否可以从WGS数据中检测到近交和近交抑制，以及共同的IBD是否会影响个体的交配偏好和繁殖。通过将WGS的IBD与大量个体的广泛社会数据相结合，该项目将为揭示人类进化史上已实现的亲缘关系对社会性的影响做出重大贡献。

Rapid technological advances such as whole genome sequencing (WGS) have opened up exciting new avenues for genomic studies in a wide range of species. One of the topics that will be substantially impacted by this progress is the influence of kin-driven behaviour on social relationships, which are of crucial importance for health and fitness even in humans. As predicted by kin selection theory, individuals in many taxa frequently bias their social behaviour towards conspecifics depending upon the proportion of alleles shared. Yet the observed patterns are highly variable, which may be due to imprecise estimates of genetic relatedness.Measuring social preferences for (e.g. nepotism) and against kin (e.g. inbreeding avoidance) requires accurate estimates of relatedness (or identity-by-descent, IBD). Notably, the amount of the genome shared by relatives varies considerably due to stochastic processes during meiosis, resulting in a gradient of IBD values that is only poorly reflected by relatedness estimates from previously used methods. Pedigrees or Short Tandem Repeat (STR) markers, for instance, provide either categorical averages or rather imprecise estimates based on parts of the genome. WGS, on the other hand, assays all single-nucleotide variants across the entire genome, thus providing the most authoritative relatedness estimates and unprecedented power for addressing questions on kin-driven behaviour. Primate relatedness has so far mainly been examined at the categorical level but not along a gradient in IBD. This leaves major gaps in our understanding of sociality and its evolution. WGS data on free-ranging primates remain scarce, but are imperative to fill these gaps. Here we will take advantage of an exceptional population of free-ranging rhesus macaques (Macaca mulatta) at Cayo Santiago (Puerto Rico), for which demographic, reproductive, behavioural, and other phenotypic data have been collected over decades. We will link these data with IBD from WGS in 800 animals to assess the impact of the gradient in IBD on social preferences for and against kin. With this integrative approach, we will pursue three main aims: 1. We will quantify variation in IBD within and between kin classes and will compare differences between IBD estimates from WGS data, pedigrees and STR markers. 2. We will determine whether social preferences are predicted by the gradient in IBD. To understand the mechanisms of kin bias, we will relate phenotypic similarities to variation in IBD and assess whether phenotypic cues are perceived according to shared IBD. 3. We will investigate whether inbreeding and inbreeding depression can be detected from WGS data, and whether shared IBD affects individual mating preferences and breeding. By combining IBD from WGS with extensive social data on a large set of individuals, the project will contribute significantly to unravelling the impact of realized relatedness on sociality in our evolutionary history.