Shafer, Aaron BA

Animal migrations are ubiquitous and one of the most threatened ecological processes globally. Because of the multifaceted nature of migration – seasonal movements between home ranges – it can be difficult to tease apart the underlying mechanisms influencing this behaviour. It is necessary to understand these mechanisms, not only to deepen our fundamental understanding of migration in animals, but also because migrations in many species are vulnerable to environmental change. In Chapter 2, I first systematically identify the broad proximate drivers of migration and offer generalities across vertebrate taxa. I quantitatively reviewed 45 studies and extracted 132 observations of effect sizes for internal and external proximate drivers that influenced migration propensity. Through this meta-analysis, I found that internal and external drivers had a medium and large effect, respectively, on migration propensity. Predator abundance and predation risk had a large effect on migration propensity, as did individual behaviour. Of the studies that examined genetic divergence between migrant and resident populations, 64% found some genetic divergence between groups. In Chapter 3, I explore the genetic basis for migration and identified genes associated with migration direction from pooled genome-wide scans on a population of 233 migrating female mule deer (Odocoileus hemionus) where I identified genomic regions including FITM1, a gene linked to the formation of lipids, and DPPA3, a gene linked to epigenetic modifications of the maternal line. These results are consistent with the underlying genetic basis for a migratory trait which contributes to the additive genetic variance influencing migratory behaviours and can affect the adaptive potential of a species. Finally, in Chapter 4 I used a pedigree-free quantitative genetic approach to estimate heritability and sources of environmental variation in migration distance, timing, and movement rate of the same population of mule deer. I found low heritability for broad patterns of migration timing, and greater variation in heritability for behaviours during migration, with low heritability for distance and duration and high heritability for movement rate along the route. Insights into the genetic and environmental sources of variation for migration are critical both for the eco-evolutionary dynamics of migration behaviour, and for the conservation of species whose migrations may be vulnerable to environmental change. My thesis reveals that broad patterns of migration are driven largely by environmental effects while within these broad patterns, migration behaviour is driven to a measurable degree by genetic variation.

Author Keywords: heritability, migration, Odocoileus hemionus, reduced representation sequencing, whole genome sequencing

Understanding the complex genomic architecture underlying quantitative traits can provide valuable insight for the conservation and management of wildlife. Despite improvements in sequencing technologies, few empirical studies have identified quantitative trait loci (QTL) via whole genome sequencing in free-ranging mammal populations outside a few well-studied systems. This thesis uses high-depth whole genome pooled re-sequencing to characterize the molecular basis of the natural variation observed in two sexually selected, heritable traits in white-tailed deer (Odocoileus virginianus, WTD). Specifically, sampled individuals representing the phenotypic extremes from an island population of WTD for antler and body size traits. Our results showed a largely homogenous genome between extreme phenotypes for each trait, with many highly differentiated regions throughout the genome, indicative of a quantitative model for polygenic traits. We identified and validated several potential QTL of putatively small-to-moderate effect for each trait, and discuss the potential for real-world application to conservation and management.

Author Keywords: evolution, extreme phenotypes, genetics, genomics, quantitative traits, sexual selection