Genomic signatures of reproductive isolation in a primate hybrid system

灵长类杂交系统中生殖隔离的基因组特征

• 批准号: 1517701
• 负责人: Liliana Cortes-Ortiz
• 金额: $ 30.39万
• 依托单位: Regents of the University of Michigan - Ann Arbor
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-06-15 至 2019-05-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1517701&HistoricalAwards=false
• 关键词: Genomic; signatures; reproductive; isolation; primate

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.

本计画将研究两种相近的吼猴，以增进我们对灵长类动物物种形成遗传学的了解。当两个密切相关的物种相互繁殖时，它们产生的杂交个体具有两个物种的遗传特征。然而，在这些杂交种中可能存在某些遗传区域，它们不是随机混合的，并且可能对局部适应、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的基因组所涉及的机制，面对最近的证据表明，在古人类进化过程中，现代人和古代人之间发生了杂交。该项目还将通过支持代表性不足的少数群体的研究人员和学生，并通过为当地社区学龄儿童开展教育活动，促进灵长类动物自然种群的保护，来增加科学的多样性。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）的研究为我们提供了一个极好的机会，以提高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吼猴的纯种群和混合种群。全基因组数据的分析将用于首先确定亲本物种的非杂交群体之间具有高于预期水平的分歧的基因组区域的数量和分布。此外，还将进行基因组渐变群分析，以确定异地种群中的这些趋异基因座是否也显示杂交区中渐渗水平降低（与生殖隔离相关基因座的预期相同）。将估计基因渗入减少的基因座的连锁不平衡水平，并将基因座定位到公开可用的参考基因组，以确定它们是否聚集或分散在整个基因组中。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/或与调控区域的关联。最后，将估计位于X染色体中的非渐渗基因座相对于位于常染色体区域中的基因座的比例，以检验涉及生殖隔离的基因座在X染色体中积累的假设。