The origin and maintenance of genetic variation are central topics to evolutionary biology. This dissertation investigates three forms of genetic variations, de novo mutations (DNMs), structural variants (SVs) and intersexual mutational variations using the guppy (Poecilia reticulata), a model system of rapid adaptation. By integrating laboratory pedigree-based analyses with wild population genomics, it investigates how genetic variation arises, is maintained, and contributes to adaptation. First, I used pedigree-based approaches to estimate germline DNMs in three large guppy families. The results demonstrate DNMs are randomly distributed throughout the genome and guppy exhibits remarkable variation across individuals and families. Most DNMs are shared across multiple siblings, suggesting they arose during early embryonic development. Second, structural variants (SVs) were characterised from three replicated rivers, each of which has high- and low-predation populations. SVs were widespread across the genome and predate the colonization of each river. Three SVs that are associated with local adaptation syndromes in high- and low-predation populations, however none are reciprocally fixed throughout all three replicate rivers. Additionally, seven SVs were maintained in all three rivers without evidence of local adaptation. Simulations reveal that the observed level of SV polymorphism is far greater than expected under neutral models. Many polymorphic SVs captures loci associated with guppy male pattern variation, which subject to negative frequency-dependent selection driven by female preference. This suggests sexual selection might explain the maintenance of SV polymorphism. Third, analysis of inter-sexual mutational variation identified seven autosomal genes that show allelic differences between the sexes. Five of these genes show clear evidence of whole or partial gene duplication between the Y chromosome and the autosomes. The remaining two genes show evidence of partial homology to the Y. This suggests that the guppy Y chromosome, despite its small ancestral size and recent origin, may nonetheless accumulate genes with male-specific functions, contributing to the sex genetic difference and genetic diversity in the natural populations. Together, this dissertation shows that germline mutations, structural variants, and sex-linked gene duplications shape genetic diversity and adaptive potential in guppies.
Yuying Lin (Fri,) studied this question.