An Ancient Genomic Perspective of Kinship, Disease and Environment

This doctoral research centres on investigating how local-scale processes give rise to longer-term trajectories in a population’s history. This focuses upon considering mid-Holocene hunter-gatherers at Lake Baikal 8000-3000 years ago. Following an Introduction, the second thesis chapter presents a detailed discussion of the progress, current state and future potential of biomolecular archaeology (now a volume chapter in the Oxford Handbooks series). In the third chapter, the long-debated issue of prehistoric hunter-gatherer warfare arises: evidence for this is extremely scarce, with a recently discovered site at Lake Baikal initially interpreted as the only instance in Eurasia. An analysis of the 13 victims' genomes substantially reframes this: one young boy is identi ied as the offspring of a local hunter-gatherer mother and a Steppe pastoralist father. Crucially, this plausibly links the violence to external contemporary pastoralists – for the irst time identifying a speci ic encounter between prehistoric hunter-gatherers and pastoralists. It is clear that some hunter-gatherers survived though: ancient genome-inferred kinship shows their graves arranged according to their biological relationships, with grave goods. Across a wider transect of 288 hunter-gatherers at Lake Baikal, the fourth chapter presents the irst study to integratedly analyse both ancient human genomes and ancient environmental DNA (from lake sediment cores): showing directly how human populations can potentially in luence and be in luenced by ecosystem changes. This demonstrates the considerable potential for this approach to reveal how humans and other species depended on key ecological relationships through time, using Bayesian network analysis. Another major determinant of human demography and adaptation is explored through the origins of a major human pathogen in the ifth chapter. A landmark inding made from sequencing ancient DNA of Baikal hunter-gatherers is the identi ication of phylogenetically basal plague strains, from up to 5500 years ago. This research reveals the earliest outbreaks of plague from zoonotic spillovers, with deadly consequences in hunter-gatherer societies, and explores the genomic, immunological and ecological effects of this in prehistory. In synthesising all these results, focus is placed on what a local understanding of the dynamics and legacies of these ecological and cultural processes can reveal – emphasising that individual events can further provide fundamental

Name dc:type.qualificationname

Doctor of Philosophy (PhD)

Level dc:type.qualificationlevel

Doctoral

Grantor dc:publisher.institution

University of Cambridge

Year dc:date.issued

2024

Author dc:creator

• Macleod, Ruairidh

Advisors dc:contributor.advisor

• Collins, Matthew
• Willerslev, Eske

• ancient DNA

Licence

• https://apollo8-f-pro.lib.cam.ac.uk/bitstreams/4a559ae6-4952-4032-8922-1bb39b10c838/download
• https://creativecommons.org/licenses/by-nc/4.0/

DOI dc:identifier.doi

https://doi.org/10.17863/CAM.119874

OAI identifier oai:identifier

oai:www.repository.cam.ac.uk:1810/386858