A new method to scan genomes for introgression in a secondary contact model

13Citations
Citations of this article
109Readers
Mendeley users who have this article in their library.

Abstract

Secondary contact between divergent populations or incipient species may result in the exchange and introgression of genomic material. We develop a simple DNA sequence measure, called Gmin, which is designed to identify genomic regions experiencing introgression in a secondary contact model. Gmin is defined as the ratio of the minimum between-population number of nucleotide differences in a genomic window to the average number of between- population differences. Although it is conceptually simple, one advantage of Gmin is that it is computationally inexpensive relative to model-based methods for detecting gene flow and it scales easily to the level of whole-genome analysis. We compare the sensitivity and specificity of Gmin to those of the widely used index of population differentiation, FST, and suggest a simple statistical test for identifying genomic outliers. Extensive computer simulations demonstrate that Gmin has both greater sensitivity and specificity for detecting recent introgression than does FST. Furthermore, we find that the sensitivity of Gmin is robust with respect to both the population mutation and recombination rates. Finally, a scan of Gmin across the X chromosome of Drosophila melanogaster identifies candidate regions of introgression between sub-Saharan African and cosmopolitan populations that were previously missed by other methods. These results show that Gmin is a biologically straightforward, yet powerful, alternative to FST, as well as to more computationally intensive model-based methods for detecting gene flow.

Cite

CITATION STYLE

APA

Geneva, A. J., Muirhead, C. A., Kingan, S. B., & Garrigan, D. (2015). A new method to scan genomes for introgression in a secondary contact model. PLoS ONE, 10(4). https://doi.org/10.1371/journal.pone.0118621

Register to see more suggestions

Mendeley helps you to discover research relevant for your work.

Already have an account?

Save time finding and organizing research with Mendeley

Sign up for free