Electronic Thesis and Dissertation Repository

Thesis Format

Integrated Article

Degree

Doctor of Philosophy

Program

Biology

Supervisor

Coltman, David W.

Abstract

The increased accessibility of complete DNA sequences from individual organisms, i.e., nuclear whole-genome sequences (WGS), allows us to explore evolutionary processes, including hybridization events. The North American wild thinhorn (Ovis dalli) and bighorn (Ovis canadensis) sheep are interesting systems for studying such patterns. The former comprises the dark pelage Stone (O. d. stonei) and the pure white Dall (O. d. dalli) subspecies. These species diverged due to geographical separation and isolation, with potential hybridization leading to adaptive features. No recent hybridization is expected, given their non-overlapping distributions. Here, I aimed to study the WGS of fossil and modern sheep to shed new light on their mosaic genomic patterns shaped by various evolutionary processes. The dataset consisted of WGS of fossils from the Yukon (Canada) and Wyoming (USA), and WGS and mitogenomes of modern thinhorn and bighorn sheep. I explored their evolution in the following data chapters: (2) fossils versus modern species using nuclear WGS data, and contemporary thinhorn and bighorn with (3) mitogenomes, (4) low-quality nuclear and (5) high-quality nuclear WGS data. Concerning the first comparison (2), I identified hybridization signals between missing lineages and the Yukon and Wyoming fossils and found evidence that might support the Wyoming sample as a hybrid lineage between the ancestors of thinhorn and bighorn sheep. In chapters 3 and 4, I observed potential ancient hybridization signals between Stone and bighorn sheep. Nuclear genomic fragments showing hybridization had coat-colour genes often present, suggesting that hybridization somehow contributed to Stone’s darker pelage. Finally, I used high-quality genomes (5) to investigate evolutionary processes and WGS reference choice, confirming previous results and providing new insights into their evolution. Dall and Stone sheep presented similar effective population size fluctuations over time. I also observed that Stone had, on average, higher cumulative length and count for runs of homozygosity (ROH) than Dall and bighorn sheep, likely due to their restricted geographic distribution. The WGS reference used impacted ROH, demonstrating the need to reassess which references should be used. By using WGS of ancient and modern species, this project more fully illuminated the ancient hybridization signals between these North American species.

Summary for Lay Audience

The recent exponential increase in the accessibility of complete DNA (i.e., genome) sequencing power brings the "genomics revolution" to wildlife conservation. New technologies have allowed the rapid and inexpensive whole-genome sequencing of numerous organisms. However, only a small fraction of the genomes available come from wild species, especially mammals. Most non-model species have not yet been analyzed through a whole-genome approach, notably thinhorn (Ovis dalli) and bighorn sheep (Ovis canadensis), iconic wild sheep of western North America. Thinhorn includes the pure white Dall (Ovis dalli dalli) and the dark coat-colour Stone subspecies (Ovis dalli stonei). These species have a complex evolutionary history due to past encounters between bighorn and thinhorn sheep, which are no longer occurring since they do not have current overlapping distributions. I aimed to apply whole-genome sequencing to better understand their evolution. I used the complete nuclear DNA sequences of sheep fossils from the Yukon/CAN and Wyoming/USA, along with the complete nuclear and mitochondrial DNA of modern thinhorn and bighorn sheep. My thesis included four data chapters that focused on the evolutionary relationships among these species, especially ancient hybridization events. These events occur when different species can breed with each other (i.e., hybridize), possibly resulting in new genetic information from the other species being incorporated into their genomes. Here, nuclear DNA sequences from sheep fossils show hybridization between the ancestors of modern mountain sheep, and some of this ancient hybridization occurred with unsampled and now extinct “ghost” lineages. I also observed that nuclear and mitochondrial DNA sequences revealed ancient hybridization between the ancestors of Stone and bighorn sheep. Finally, I explored other evolutionary aspects of how these wild sheep evolved over time using high-quality nuclear DNA sequences. The ancestors of Stone and Dall had similar ancient population trends during the last ice age compared to bighorn sheep, which were located in the southernmost part of major ice sheets. From these genomes, I shed more light on how these species evolved over time and improved the whole-genome database of wild species.

Creative Commons License

Creative Commons Attribution-Noncommercial-No Derivative Works 4.0 License
This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 4.0 License.

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