The genomes of archaic and early modern humans offer a unique window into their histories. However, the sequencing and analysis of DNA from archaic humans is complicated by DNA degradation, chemical modifications and contamination

The genomes of archaic and early modern humans offer a unique window into their histories. However, the sequencing and analysis of DNA from archaic humans is complicated by DNA degradation, chemical modifications and contamination. Recent technological advances have made it possible to recover nuclear DNA sequences from a number of archaic and early modern humans and a number of important insights have been obtained from the whole genome sequences that have been generated. Comparison of archaic genome sequences to the genome sequences of present-day humans has allowed us to identify sequence differences that have come to fixation or reached high frequency in modern humans since their divergence from Neandertals and Denisovans, some of which may have important functional effects in modern humans.  Further, ancient genomes have provided direct evidence that interbreeding between archaic humans and early modern humans occurred and that it resulted in between 1-6% archaic human DNA in the genomes of present day non-Africans. This introgressed DNA has been shown to have both positive and negative outcomes for present-day carriers: underlying apparently adaptive phenotypes as well as influencing disease risk.  I will discuss recent work in which we have identified Neandertal haplotypes that are likely of archaic origin and determined the likely functional consequences of these haplotypes using public genome, gene expression, and phenotype datasets.