期刊
GENETICS
卷 211, 期 3, 页码 1059-1073出版社
GENETICS SOCIETY AMERICA
DOI: 10.1534/genetics.118.301831
关键词
ABBA-BABA; admixture; gene flow; homoploid hybrid speciation
资金
- National Science Foundation [MCB-1127059]
Introgression is a pervasive biological process, and many statistical methods have been developed to infer its presence from genomic data. However, many of the consequences and genomic signatures of introgression remain unexplored from a methodological standpoint. Here, we develop a model for the timing and direction of introgression based on the multispecies network coalescent, and from it suggest new approaches for testing introgression hypotheses. We suggest two new statistics, D-1 and D-2, which can be used in conjunction with other information to test hypotheses relating to the timing and direction of introgression, respectively. D-1 may find use in evaluating cases of homoploid hybrid speciation (HHS), while D-2 provides a four-taxon test for polarizing introgression. Although analytical expectations for our statistics require a number of assumptions to be met, we show how simulations can be used to test hypotheses about introgression when these assumptions are violated. We apply the D-1 statistic to genomic data from the wild yeast Saccharomyces paradoxus-a proposed example of HHS-demonstrating its use as a test of this model. These methods provide new and powerful ways to address questions relating to the timing and direction of introgression.
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