Evaluating the Use of ABBA–BABA Statistics to Locate Introgressed Loci
By Simon H. Martin, J. Davey, Chris D. Jiggins. bioRxiv, 2014
643 citations recorded by the source corpus.
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 a modified version of a statistic originally developed to estimate the genome-wide fraction of admixture. is not subject to the same biases as D, and is better at identifying introgressed loci. Finally, we show that both D and 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.
Subfields: Archeology, Computer Vision and Pattern Recognition, Paleontology
View Paper: https://www.semanticscholar.org/paper/931f779f838ef80d2d2e1fcd2d7b38709089d1b6
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Archeology
In Paleontology
Citations in the corpus
- Ancient hybridization fuels rapid cichlid fish adaptive radiations (2017, positive): “…and Upper Nile, whereas BABA represents sites with a derived allele shared between Congolese and Upper Nile lineage taxa. f d is calculated as the difference between ABBA and BABA patterns compared to the maximum possible difference where gene flow between P2 and P3 would equal random mating 78 .”
- The phylogenomic forest of bird trees contains a hard polytomy at the root of Neoaves (2016, background): “On the other hand, postspeciation gene flow can be distinguished from ILS, and there are now a number of methods to do so for single-nucleotide polymorphisms (e.g. Durand et al. 2011; Martin et al. 2015; Pease & Hahn 2015) and retroposon presence/absence patterns (Kuritzin et al. 2016).”
- Dsuite - fast D-statistics and related admixture evidence from VCF files (2020, background): “The first is f d (Martin et al., 2015), which is defined as: Genome-wide tests/statistics Sliding window statistics where ̂ d xy is an estimate of the genetic distance at variable sites be-tween populations x and y, so ̂ d i 13 is the distance between P1 and P3 at site i .”