Divergence, Selection, and Demographic History of Wolves in Eurasia using Genomic Data

• Main Author: Hennelly, Lauren Mae
• Other Authors: Sacks, Benjamin N
• Format: Thesis
• Language: English
• Published: eScholarship, University of California 2022
• Subjects: Biology; Ecology; Genetics; Conservation; Evolutionary genomics; Genomics; Gray wolf; Phylogeography; Canis lupus; gray wolf
• Online Access: https://escholarship.org/uc/item/9022h7qv

Species are often composed of evolutionarily distinct populations and lineages. Deciphering the evolutionary history of recently diverged species with multiple lineages remains challenging because genealogical discordance is common across the genome. Emerging genomic and statistical tools are allowing unprecedented insight into the evolutionary history of complicated species that have been notoriously difficult to resolve. The gray wolf exemplifies this challenge as it has multiple recognized lineages and has only recently diverged from other canids. In this dissertation, I use genome-wide data to study the evolutionary history of gray wolves in Eurasia, with a focus on investigating the phylogenomics, demographic history, and role of adaptive introgression. For my first chapter, I investigate the genomic distinctiveness of wolves corresponding to two deeply divergent mitochondrial clades restricted to the Indian subcontinent and the Tibetan plateau, respectively. Using the first whole genome sequences of four Indian wolves along with those of two newly sequenced Tibetan wolves and 31 additional canids, I demonstrate Indian and Tibetan wolves are the two most deeply divergent wolf lineages and highly distinct from broadly distributed wolf populations corresponding to the mitochondrial Holarctic clade. Low-recombination regions of the genome provided evidence that the Indian wolf is the most basal wolf lineage, in contrast to the mitochondrial DNA, showing the Tibetan wolf as the most basal lineage. Our findings imply that southern regions of Asia have been important centers for gray wolf evolution and that the Indian wolf represents one of the world’s most endangered and evolutionarily distinct wolf lineages. My second chapter focuses on distinguishing secondary contact zones and investigating adaptive introgression among wolf lineages in Asia. I used 5 newly and 7 recently sequenced wolf (Canis lupus) genomes from the lowland plains and high-altitude mountains of Pakistan, India, and Kyrgyzstan, along with 79 ...