Evolutionary history of Early-Middle and Late Pleistocene equids, revealed by analysis of their paleogenomes

• Main Author: Vershinina, Alisa
• Other Authors: Shapiro, Beth
• Format: Thesis
• Language: English
• Published: eScholarship, University of California 2020
• Subjects: Genetics; Evolution & development; Biology; ancient DNA; equids; Equus; population genetics; Bering Land Bridge; Beringia
• Online Access: https://escholarship.org/uc/item/2dn2j38w; https://escholarship.org/content/qt2dn2j38w/qt2dn2j38w.pdf

DNA from archaeological, paleontological, and museum samples (ancient, or aDNA) provides a unique opportunity to trace eco-evolutionary history of populations affected by environmental shifts on geological time scale. Yet it is still unclear how climate-driven environmental change and biogeographical barriers affect diversification, population size and population structure of large-bodied herbivores inhabiting northern regions of the Northern Hemisphere. The goal of this dissertation is to fill in this gap by utilizing ancient DNA techniques and population genetic analysis to reveal the demographic and population history of extinct and present-day equids, genus Equus, focusing on their key ancient dispersal corridor - the Bering Land Bridge. In the following chapters, I explore the links between paleoenvironments and population history of various equid groups using high coverage paleogenomes recovered from fossil horse specimens sampled across Beringia. In my first chapter, I use in-solution DNA capture enrichment and mitochondrial genome assembly to reconstruct a whole mitochondrial genome of a specimen found in Western Beringia and initially identified as E. hemionus, or an Asiatic wild ass. With molecular phylogenetic analysis I demonstrate that the specimen belongs to a group of caballoid horses, E. ferus, rather than stenonid wild asses. The results obtained in Chapter 1 highlight the utility of ancient DNA studies in identification of incomplete, juvenile, or otherwise problematic museum specimens. In my second chapter I discover that Beringia was a key contact zone for populations of Late Pleistocene caballoid horses, E. ferus. I use new high coverage nuclear and mitochondrial paleogenomes, isolated from fossils of caballoid horses sampled across the Northern Hemisphere to infer that North American and Eurasian caballoid horse populations diverged around 0.8-1 million years ago. With coalescent simulations and genome-wide adamixtude inference I show that evolution of caballoid horses after this divergence ...