Analysis of the genomes of archaic hominins, such as Neandertals, has revealed that these groups have contributed to the genetic variation of modern human populations. Yet, we know little about the impact of these ancient mixtures on human phenotypes. To answer these questions systematically, we need a map of Neandertal local ancestry i.e., a map that labels whether each region of an individual genome is descended from Neandertals. 

 

We propose a statistical model that infers Neandertal local ancestry from patterns of genetic variation. We inferred a map of Neandertal local ancestry in modern humans using data from the 1000 Genome project combined with a high-coverage Neandertal genome. Analyses of this map document the effects of positive and purifying selection on Neandertal variants.