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Author ORCID Identifier

https://orcid.org/0009-0006-4596-6791

Date Available

4-30-2026

Year of Publication

2026

Document Type

Doctoral Dissertation

Degree Name

Doctor of Philosophy (PhD)

College

Agriculture, Food and Environment

Department/School/Program

Veterinary Science

Faculty

Ted Kalbfleisch

Faculty

Emma Adam

Abstract

The evolution of modern horses has a well-documented fossil record and has long been of interest to the genetics community. Although non-caballine equids (e.g. zebras, donkeys, and asses) can hybridize with horses, the resulting offspring are typically infertile. Despite these reproductive barriers, genomic analyses reveal regions of high sequence similarity among equid species. This dissertation investigates the role of historical introgression in the evolution of modern Equus species. The first chapter re-evaluates earlier findings derived from a limited horse population and a single reference genome. The variants of the identified regions were pushed through Ensembl’s Variant Effect Predictor to assess the possible consequences. Three consistent patterns emerged: an overrepresentation of conserved regions on chromosome 20, which contains the major histocompatibility complex (MHC), a higher density of conserved regions on smaller chromosomes, and many of the conserved regions occurred in introns. Building on these patterns, the following chapter examined the functional consequences of MHC alleles identified within regions of high sequence similarity. Of the 50 loci identified within the MHC superlocus, 12 had the assumed pattern of introgression. A region in DR-beta2 gene (Thoroughbred T2T with donkeys only) dataset had coding consequences. The other 11 loci are hypothesized to be involved with expression of the complexes. However, timing of the introgression event(s) is still unknown and are part of a future project. The final chapter investigates chromosomal rearrangements in equids using pan-genome graph representations. Previous work was able to decipher the large rearrangements between species at the karyotypic level and SNVs gave more information about their evolutionary relationships. However, the pan-genome graphs were able to compare three publicly available reference genomes and verify previous results. Another aspect of the pan-genome graphs is the ability to study large structural variants to single nucleotide polymorphisms between species for molecular evolution. Together, these analyses provide new insight into the molecular evolution of equids—particularly at the DR-beta2 locus—and establish a framework for applying evolutionary genomics to conservation and future gene-editing efforts.

Digital Object Identifier (DOI)

https://doi.org/10.13023/etd.2026.280

Archival?

Archival

Funding Information

Keeley M. Hagan & Louis D. Lieto Fellowship, 2022-2026

Additional Files
panSpeciesPlots.pdf (1032 kB)
DeSilvaChap4_Methods.Rationale.pdf (1872 kB)
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