RT Journal Article
SR Electronic
T1 A method for genome-wide genealogy estimation for thousands of samples
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 550558
DO 10.1101/550558
A1 Speidel, Leo
A1 Forest, Marie
A1 Shi, Sinan
A1 Myers, Simon R.
YR 2019
UL http://biorxiv.org/content/early/2019/02/14/550558.abstract
AB Knowledge of genome-wide genealogies for thousands of individuals would simplify most evolutionary analyses for humans and other species, but has remained computationally infeasible. We developed a method, Relate, scaling to > 10,000 sequences while simultaneously estimating branch lengths, mutational ages, and variable historical population sizes, as well as allowing for data errors. Application to 1000 Genomes Project haplotypes produces joint genealogical histories for 26 human populations. Highly diverged lineages are present in all groups, but most frequent in Africa. Outside Africa, these mainly reflect ancient introgression from groups related to Neanderthals and Denisovans, while African signals instead reflect unknown events, unique to that continent. Our approach allows more powerful inferences of natural selection than previously possible. We identify multiple novel regions under strong positive selection, and multi-allelic traits including hair colour, BMI, and blood pressure, showing strong evidence of directional selection, varying among human groups.