Estimating the timing of multiple admixture pulses during local ancestry inference

TY - JOUR

T1 - Estimating the timing of multiple admixture pulses during local ancestry inference

AU - Medina, Paloma

AU - Thornlow, Bryan

AU - Nielsen, Rasmus

AU - Corbett-Detig, Russell

PY - 2018

Y1 - 2018

N2 - Admixture, the mixing of genetically distinct populations, is increasingly recognized as a fundamental biological process. One major goal of admixture analyses is to estimate the timing of admixture events. Whereas most methods today can only detect the most recent admixture event, here, we present coalescent theory and associated software that can be used to estimate the timing of multiple admixture events in an admixed population. We extensively validate this approach and evaluate the conditions under which it can successfully distinguish one-from two-pulse admixture models. We apply our approach to real and simulated data of Drosophila melanogaster. We find evidence of a single very recent pulse of cosmopolitan ancestry contributing to African populations, as well as evidence for more ancient admixture among genetically differentiated populations in sub-Saharan Africa. These results suggest our method can quantify complex admixture histories involving genetic material introduced by multiple discrete admixture pulses. The new method facilitates the exploration of admixture and its contribution to adaptation, ecological divergence, and speciation.

AB - Admixture, the mixing of genetically distinct populations, is increasingly recognized as a fundamental biological process. One major goal of admixture analyses is to estimate the timing of admixture events. Whereas most methods today can only detect the most recent admixture event, here, we present coalescent theory and associated software that can be used to estimate the timing of multiple admixture events in an admixed population. We extensively validate this approach and evaluate the conditions under which it can successfully distinguish one-from two-pulse admixture models. We apply our approach to real and simulated data of Drosophila melanogaster. We find evidence of a single very recent pulse of cosmopolitan ancestry contributing to African populations, as well as evidence for more ancient admixture among genetically differentiated populations in sub-Saharan Africa. These results suggest our method can quantify complex admixture histories involving genetic material introduced by multiple discrete admixture pulses. The new method facilitates the exploration of admixture and its contribution to adaptation, ecological divergence, and speciation.

KW - Admixture

KW - Drosophila melanogaster

KW - Local ancestry inference

U2 - 10.1534/genetics.118.301411

DO - 10.1534/genetics.118.301411

M3 - Journal article

C2 - 30206187

AN - SCOPUS:85056280164

SN - 1943-2631

VL - 210

SP - 1089

EP - 1107

JO - Genetics

JF - Genetics

IS - 3

ER -