A Genomic Compendium of an Island: Documenting Continuity and Change across Irish Human Prehistory

Abstract

This thesis provides an initial demographic scaffold for Irish prehistory based on the palaeogenomic analysis of 93 ancient individuals from all major periods of the island's human occupation, sequenced to a median of 1X coverage. ADMIXTURE and principal component analysis identify three ancestrally distinct Irish populations, whose inhabitation of the island corresponds closely to the Mesolithic, Neolithic and Chalcolithic/Early Bronze Age eras, with large scale migration to the island implied during the transitionary periods. Haplotypic-based sharing methods and Y chromosome analysis demonstrate strong continuity between the Early Bronze Age and modern Irish populations, suggesting no substantial population replacement has occurred on the island since this point in time. The Mesolithic population shares high genetic drift with contemporaries from France and Luxembourg and shows evidence of a severe inbreeding bottleneck, apparent through runs of homozygosity (ROH). Substantial contributions from both Mediterranean farming groups and northwestern hunter-gatherers are evident in the Neolithic Irish population. Moreover, evidence for local Mesolithic survival and introgression in southwestern Ireland, long after the commencement of the Neolithic, is also implied in haplotypic-analysis. Societal complexity during the Neolithic is suggested in patterns of Y chromosome and autosomal structure, while the identification of a highly inbred individual through ROH analysis, retrieved from an elite burial context, strongly suggests the elaboration and expansion of megalithic monuments over the course of the Neolithic was accompanied in some regions by dynastic hierarchies. Haplotypic affinities and distributions of steppe-related introgression among samples suggest a potentially bimodal introduction of Beaker culture to the island from both Atlantic and Northern European sources, with southwestern individuals showing inflated levels of Neolithic ancestry relative to individualised burials from the north and east. Signals of genetic continuity and change after this initial establishment of the Irish population are also explored, with haplotypic diversification evident between both the Bronze Age and Iron Age, and the Iron Age and present day. Across these intervals selection pressures related to nutrition appear to have acted, with variants involved in lactase persistence and skin depigmentation showing steady increases in frequency through time.