Sociology

Population

Genetic variation

Evolutionary biology

Biology

1000 Genomes Project

Gene

Genotype

Demography

Genome

Allele

Single-nucleotide polymorphism

Artificial intelligence

Human genome

Haplotype

Computer science

Natural selection

Introgression

Genetics

Selection (genetic algorithm)

Directional selection

Nature Genetics

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 &gt;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. 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. Relate is a new method for evolutionary analysis of large genetic datasets that can estimate branch lengths, mutational ages and variable historical population sizes.

A method for genome-wide genealogy estimation for thousands of samples