Genomic signatures of reproductive isolation in a primate hybrid system

这个项目将研究吼猴的两个密切相关的物种，以提高我们对灵长类动物模型中物种形成的遗传学的理解。当两个亲缘关系很近的物种相互繁殖时，它们会产生混合了两个物种遗传特征的杂交个体。然而，在这些杂交种中可能有某些遗传区域不是随机混合的，这些遗传区域可能对局部适应、生殖隔离和物种形成起重要作用。研究灵长类杂交系统中生殖隔离的遗传机制可以作为一个活的模型来理解塑造我们自己基因组的机制，面对人类进化过程中现代和古人类群体之间杂交的最新证据。该项目还将通过支持未被充分代表的少数民族的研究人员和学生，以及通过对当地社区学龄儿童的教育活动促进灵长类动物自然种群的保护，从而增加科学的多样性。对基因渗入模式（等位基因通过杂交从一个基因库移动到另一个基因库）的研究为我们了解物种形成过程中不同基因组区域的数量、分布和功能提供了一个绝佳的机会。为了探索灵长类动物生殖隔离的遗传机制，这项工作将分析在墨西哥杂交的两种吼猴的纯种和混合种群。全基因组数据分析将首先用于确定亲本物种非杂交种群间差异高于预期水平的基因组区域的数量和分布。此外，还将进行基因组突变分析，以确定异域种群中的这些分化位点在杂交区是否也表现出较低的基因渗入水平（正如所预期的与生殖隔离有关的位点）。将对基因渗入减少的位点的连锁不平衡水平进行估计，并将这些位点映射到公开可用的参考基因组中，以确定它们在整个基因组中是聚集还是分散。序列还将通过与NCBI非冗余蛋白和核苷酸数据库的比较进行注释，以确定这些区域与已知功能的基因区域和/或调控区域的关联。最后，估计位于X染色体上的非渗入位点相对于位于常染色体区域的位点的比例，以检验与生殖隔离有关的位点在X染色体上积累的假设。

This project will study two closely-related species of howler monkey in order to improve our understanding of the genetics of speciation in a primate model. When two closely-related species reproduce with one another, they produce hybrid individuals that have a mixture of genetic characteristics of both species. However, there are likely to be certain genetic regions in those hybrids that are not randomly mixed and that may play be important for local adaptation, reproductive isolation, and speciation. Studying genetic mechanisms that underlie reproductive isolation in a primate hybrid system can serve as a living model to understand the mechanisms involved in shaping our own genome, in the face of recent evidence of the occurrence of hybridization between modern and archaic human populations during hominin evolution. This project will also increase diversity in science by supporting the researchers and students who are underrepresented minorities and by promoting the conservation of natural populations of primates through educational activities for school-age children in local communities. Studies of patterns of introgression (the movement of alleles from one gene pool to another through hybridization) provide an outstanding opportunity to improve our understanding of the number, distribution and function of differentiated genomic regions during the process of speciation. To explore the genetic mechanisms that underlie reproductive isolation in primates, the proposed work will analyze pure and admixed populations of two species of howler monkeys that hybridize in Mexico. Analyses of genome-wide data will be used to first determine the number and distribution of genomic regions that have higher than expected levels of divergence between non-hybridizing populations of parental species. In addition, genomic cline analyses will be performed to determine whether or not these divergent loci in allopatric populations also show reduced levels of introgression in the hybrid zone (as expected for loci involved in reproductive isolation). Levels of linkage disequilibrium will be estimated for loci with reduced introgression and the loci will be mapped to publicly available reference genomes to determine whether they are clumped or scattered throughout the genome. Sequences will also be annotated through comparison with the NCBI non-redundant protein and nucleotide databases to determine the association of these regions to genic regions with known functions and/or to regulatory regions. Finally, the proportion of non-introgressing loci located in the X chromosome relative to loci located in autosomal regions will be estimated to test the hypothesis that loci involved in reproductive isolation have accumulated in the X chromosome.