期刊
MOLECULAR BIOLOGY AND EVOLUTION
卷 32, 期 1, 页码 244-257出版社
OXFORD UNIV PRESS
DOI: 10.1093/molbev/msu269
关键词
ABBA-BABA; gene flow; introgression; population structure; Heliconius; simulation
资金
- Leverhulme Trust [F/09364/E]
- Herchel Smith Fund
- BBSRC [BB/H01439X/1]
- Biotechnology and Biological Sciences Research Council [BB/H01439X/1] Funding Source: researchfish
Several methods have been proposed to test for introgression across genomes. One method tests for a genome-wide excess of shared derived alleles between taxa using Patterson's D statistic, but does not establish which loci show such an excess or whether the excess is due to introgression or ancestral population structure. Several recent studies have extended the use of D by applying the statistic to small genomic regions, rather than genome-wide. Here, we use simulations and whole-genome data from Heliconius butterflies to investigate the behavior of D in small genomic regions. We find that D is unreliable in this situation as it gives inflated values when effective population size is low, causing D outliers to cluster in genomic regions of reduced diversity. As an alternative, we propose a related statistic (f) over cap (d), a modified version of a statistic originally developed to estimate the genome-wide fraction of admixture. (f) over cap (d) is not subject to the same biases as D, and is better at identifying introgressed loci. Finally, we show that both D and (f) over cap (d) outliers tend to cluster in regions of low absolute divergence (d(XY)), which can confound a recently proposed test for differentiating introgression from shared ancestral variation at individual loci.
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