Genomic analysis of hybridization between the spruce budworm species Choristoneura fumiferana, C. occidentalis, and C. biennis (Lepidoptera: Tortricidae)

Bryan TM Brunet
The spruce budworm (Choristoneura fumiferana) species complex is a destructive group of insect defoliators of North American conifers that have a remarkable propensity to hybridize ex situ despite little evidence for hybridization in nature. Introgression between species is increasingly identified as a source for adaptive genetic variation. Hybridization between these species could have important implications in the management of forest resources. In addition, hybrid zones can reveal important
more » ... n reveal important insights about the evolutionary processes that underlie species divergence. In this thesis, I use a combination of traditional and more recent molecular approaches to investigate a putative hybrid zone between three spruce budworm species, C. fumiferana, C. biennis, and C. occidentalis, that straddles the Rocky Mountains of Alberta and British Columbia. Using mitochondrial COI DNA and nuclear microsatellite gene markers, I identify an outbreaking population of C. occidentalis in southwestern Alberta occurring on alternative host trees in the area (Chapter 2). This work confirmed the presence of hybrid individuals with C. fumiferana in the area and noted similarities in the phenology of budworms on Douglas-fir and a hybrid spruce species. I then turned to genomic methods and exploited a large EST sequence resource to develop a suite of EST-based microsatellite loci suitable for genetic analysis of C. fumiferana (Chapter 3). After that, by using an even newer genome-wide marker discovery approach called 'Genotyping-By-Sequencing (GBS)', I investigated the population structure and gene flow between the three spruce budworm species that interact along the northern Rocky Mountains (Chapter 4). I concluded that recent hybridization between eastern (C. fumiferana) and western (C. biennis/C. occidentalis) populations is not extensive, although there is evidence for historical gene flow. However, whereas three species were expected, we find overwhelming support for a two-species (eastern and western) dynamic in this region. iii Populations of C. biennis and C. occidentalis identified on the basis of life history traits were only weakly supported as genetically identifiable subpopulations within a western lineage. I compare the patterns of differential introgression between C. biennis and C. occidentalis (recent divergence) with those between C. fumiferana and C. occidentalis (deep divergence) to determine if there was correspondence among the loci subject to selection, as well as the modes of selection in each comparison (Chapter 5). Clines between the deeply diverged species were steep and highly concordant across loci, suggesting strong selection against hybrids, whereas those between the recently diverged species were linear and gradual. However, directional selection was found to be the predominant mode of selection in each comparison. Finally, I developed a preliminary linkage map for an outbred hybrid backcross between C. biennis and C. occidentalis to assist in establishing linkage relationships between unassembled scaffolds in a spruce budworm genome assembly that is currently in development (Chapter 6). Ultimately, this work highlights the usefulness of genome-wide approaches for marker discovery and development. Where hybridization between C. fumiferana and the western species was presumed to be rampant, these results reveal that it is not. On the other hand, these results also call into question the validity of C. biennis as a species distinct from C. occidentalis. Overall, this work provides a foundation for future work to elucidate the mechanisms responsible for maintaining reproductive isolation between these species, as well as the genomic architecture of species differences. iv
doi:10.7939/r3p55dn7j fatcat:abm7dw254jai5e54geyyyyaapu