Identification and interpretation of introgressed hominin DNA in modern human genomes

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Summary Over the past decade, advances in ancient DNA (aDNA) have provided striking new insights into human history, including conclusive proof that modern humans admixed with now extinct hominins, such as Neandertals and Denisovans. In the last cycle of funding, we pioneered methods to identify and interpret introgressed hominin DNA that still segregates in the genomes of modern humans. Analyses of these surviving archaic lineages shows that admixture among hominins was common, there was both positive and negative fitness consequences to gene flow, and introgressed sequences have functional and phenotypic effects. Despite these insights, there are many fundamentally important questions that remain to be addressed. The major barriers to a more comprehensive understanding of archaic hominin admixture include the need for further development of computationally efficient methods to find introgressed sequences, their application to more globally diverse populations, and experimental studies to delineate the molecular and functional consequences of gene flow. We will address each of these issues in the renewal project. Specifically, in Aim 1, we will extend and refine methods for identifying introgressed DNA sequences. Such further methodological development is necessary to improve power, reduce false positive rates, and be computationally efficient enough to analyze massively large sequencing data sets. In Aim 2, we will leverage our access to several large-scale sequencing projects and apply these novel methods to whole-genome sequence data from over 100,000 geographically diverse individuals. Importantly, by specifically constructing a diverse panel of individuals, particularly from understudied populations, we will be able to make inferences about archaic hominin admixture not previously possible. We will also develop methods to comprehensively analyze the population genetics characteristics of introgressed sequences and test hypotheses such as the fitness effects of admixture, sex-biased patterns of gene flow, and admixture with unknown (or “ghost”) lineages. Finally, in Aim 3, we will perform the first systematic and comprehensive experimental analysis of adaptively introgressed loci using cutting-edge gene editing and functional genomics technologies. The successful completion of the proposed project will extend our understanding of admixture events between archaic and modern humans, provide insight into how introgression has shaped extant patterns of human genomic diversity, and facilitate the molecular discovery and characterization of previously unknown archaic groups that have contributed to the modern gene pool.