A New Method to Scan Genomes for Introgression in a Secondary Contact Model

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 G min, which is designed to identify genomic regions experiencing introgression in a secondary contact model. G min 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 G min 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 G min to those of the widely used index of population differentiation, F ST, and suggest a simple statistical test for identifying genomic outliers. Extensive computer simulations demonstrate that G min has both greater sensitivity and specificity for detecting recent introgression than does F ST. Furthermore, we find that the sensitivity of G min is robust with respect to both the population mutation and recombination rates. Finally, a scan of G min 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 G min is a biologically straightforward, yet powerful, alternative to F ST, as well as to more computationally intensive model-based methods for detecting gene flow.

Powerful methods for detecting introgressed regions from population genomic data

“…Neither d XY nor F ST are very sensitive to the presence of low‐frequency migrants (Geneva et al . ). This means that analyses using these statistics alone will fail to detect recent introgression (e.g.…”

“…Geneva et al . () introduced a method that is relatively sensitive to recent migration, while still being robust to variation in mutation rates. Their test statistic, G min , is defined as: where d min and d XY are the same as above.…”

“…; Geneva et al . ), and is based on the minimum sequence divergence found between haplotypes in sister taxa. We find that our new statistic offers a modest increase in power over others that use population genetic data, and that it is robust to multiple violations that may confound inferences using other tests.…”

The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication

“…To address this latter concern and look for evidence of introgression of Asian rice alleles into African rice, we first probed the O. glaberrima genome assembly with resequencing reads of 14 O. sativa (7 O Table 23) and 20 O. glaberrima accessions. We then used a newly developed haplotype-based summary statistic that compares the minimum number of nucleotide differences between sequences from two different species to the average number of between-species differences to identify regions of the genome that have experienced recent introgression 42,43 . Our genome-wide analyses were unable to detect any evidence of recent introgression between the sequenced accessions of the two species (Supplementary Fig.…”

“…All reads with a mapping quality score of less than 20 were discarded. The alignment files of the O. sativa and O. glaberrima accessions were then input into POPBAM V0.3 to detect evidence of introgression from O. sativa into O. glaberrima using the recently developed G min statistic 42 .…”