Investigations into the Adaptive Value and Biological Consequences of Positively-Selected Neanderthal Introgressed Genetic Variation in Modern Humans

Abstract

The sequencing of ancient genomes has revealed that modern humans interbred with at least two different archaic hominin populations, Neanderthals and Denisovans. Some of this introgressed variation appears to have been under positive selection, yet the adaptive phenotypes driving this selection, as well as the timescales and locations of these positive selection sweeps, remain unclear. The goal of this dissertation is to explore why some archaically introgressed variation has been under positive selection in modern humans and what the biological consequences of this introgression are for human populations today. Over three data chapters, I will approach this question in several ways: (1) investigating the dynamics of the positive selection on introgressed haplotypes genome-wide, (2) identifying adaptively introgressed variants genome-wide that modulate genes in the human immune system and probing their phenotypic effects, and (3) identifying Neanderthal introgressed variants on a locus-specific level that are putative drivers of an increased risk of severe COVID-19. In the second chapter, I conduct a computational analysis of the timescale and location of positive selection sweeps on introgressed variation present in the genomes of contemporary humans from the Estonian Genome Diversity Project. I show that the vast majority of these sweeps took place after East and West Eurasian human populations split from one another — i.e., not immediately after they entered they human gene pool via interbreeding. Therefore, the adaptive value of these introgressed haplotypes is best considered in the context of the local Eurasian environments over the last , rather than in the Middle East ~55kya when they were initially introgressed. Following the multitude of past research highlighting the human immune system as a potential phenotypic target of Neanderthal adaptive introgression, in the third chapter, I conduct a Multiple Parallel Reporter Assay on a set of 5,353 putative adaptively introgressed variants in a multi-potent human immune cell line to test their ability to modulate gene expression. I identified 2,548 variants in active cis-regulatory elements (CREs) and 292 expression-modulating variants (emVars). These emVars are predicted to regulate genes that are enriched for function in innate immune pathways including interferon signaling, toll-like receptor pathways, and anti-viral response. One emVar is significantly associated with protection against severe COVID-19 response. To explore these variants functionally, I endogenously deleted two CREs containing emVars linked to immune function, rs11624425 and rs80317430, identifying their primary genic targets as ELMSAN1, and PAN2 and STAT2 respectively, three genes differentially expressed during influenza infection. Overall, I present the first database of directly identified expression-modulating Neanderthal-introgressed alleles contributing to potential immune response in modern humans. Finally, as a specific example of the critically important effects of Neanderthal introgressed variation in living humans today, in chapter four, I investigate an introgressed haplotype that drives the strongest genetic association with increased risk for severe COVID-19 illness, which was putatively under positive selection in South Asian populations. I assessed the variants present on the risk haplotype for their likelihood of driving the severe COVID-19 phenotype. I do this by first exploring their impact on the regulation of genes involved in COVID-19 infection using a variety of population genetics and functional genomics tools. I then perform a locus-specific massively parallel reporter assay to individually assess the regulatory potential of each allele on the haplotype in a multipotent immune-related cell line. We ultimately reduce the set of over 600 linked genetic variants to identify four introgressed alleles that are strong functional candidates for driving the association between this locus and severe COVID-19. These variants likely drive the locus’ impact on severity by putatively modulating the regulation of two critical chemokine receptor genes: CCR1 and CCR5. These alleles are ideal targets for future functional investigations into the interaction between host genomics and COVID-19 outcomes. They further point the potentially critically important biological consequences of Neanderthal introgressed genetic variation in human populations today.