Abstract / Description of output
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 ƒ(d), a modified version of a statistic originally developed to estimate the genome-wide fraction of admixture. ƒ(d) is not subject to the same biases as D, and is better at identifying introgressed loci. Finally, we show that both D and ƒ(d) outliers tend to cluster in regions of low absolute divergence (dXY), which can confound a recently proposed test for differentiating introgression from shared ancestral variation at individual loci.
Original language | English |
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Pages (from-to) | 244-257 |
Number of pages | 14 |
Journal | Molecular Biology and Evolution |
Volume | 32 |
Issue number | 1 |
Early online date | 22 Sept 2014 |
DOIs | |
Publication status | Published - 1 Jan 2015 |
Keywords / Materials (for Non-textual outputs)
- ABBA-BABA
- gene flow
- heliconius
- introgression
- population structure
- simulation
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Simon Martin
- School of Biological Sciences - Royal Society University Research Fellow
Person: Academic: Research Active