From Nature Genetics:
A method for genome-wide genealogy estimation for thousands of samples
Leo Speidel, Marie Forest, Sinan Shi & Simon R. Myers
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 have 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 1,000 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.
Sub-Saharan Africans have their own equivalent or equivalents of Neanderthals and Denisovans in their evolutionary past: populations from which they acquired some genes that apparently have proven useful because they are still around. But we don’t have fossils yet from these “archaic ghost” populations of Africa, so it’s still pretty hazy.
Our approach allows more powerful inferences of natural selection than has previously been possible. We identify multiple regions under strong positive selection, and multi-allelic traits including hair color, body mass index and blood pressure, showing strong evidence of directional selection, varying among human groups.