Genomic signatures of reproductive isolation in a primate hybrid system

这个项目将研究两个密切相关的咆哮猴物种，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。当两个密切相关的物种彼此繁殖时，他们产生的杂交个体具有两个物种的混合遗传特征。然而，在这些杂交种中，可能有一些不是随机混合的特定遗传区域，这些区域可能对局部适应、生殖隔离和物种形成起重要作用。最近有证据表明，在古人类进化过程中，现代人和古代人之间发生了杂交，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。该项目还将通过支持研究人员和代表不足的少数群体的学生，以及通过在当地社区为学龄儿童开展教育活动，促进保护灵长类自然种群，从而增加科学多样性。对导入模式的研究(通过杂交将等位基因从一个基因库转移到另一个基因库)为我们提供了一个极好的机会来改善我们对物种形成过程中分化基因组区域的数量、分布和功能的理解。为了探索灵长类动物生殖隔离的遗传机制，拟议的工作将分析在墨西哥杂交的两种咆哮猴的纯种群和混合种群。对全基因组数据的分析将首先用来确定在亲本物种的非杂交种群之间具有高于预期水平的差异的基因组区域的数量和分布。此外，还将进行基因组临床分析，以确定在异地种群中，这些不同的基因座是否也显示出杂交区内渗水平的降低(正如涉及生殖隔离的基因座所预期的那样)。导入减少的基因座的连锁不平衡程度将被估计，这些基因座将被映射到公开可用的参考基因组，以确定它们是成簇的还是散布在整个基因组中。还将通过与NCBI非冗余蛋白质和核苷酸数据库的比较来注释序列，以确定这些区域与具有已知功能的基因区域和/或调控区域的关联。最后，将估计位于X染色体上的非导入基因座相对于位于常染色体区域的基因座所占的比例，以检验与生殖隔离有关的基因座已在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.