Liu, Zuyao (2023). Exploring the Evolutionary Significance of Chromosomal Fusions and Inversions: Implications for Adaptive Evolution and Sex Chromosome Evolution. (Thesis). Universität Bern, Bern
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Abstract
For several decades, identifying the genetic basis of evolutionary changes has been a primary focus of evolutionary biology. While empirical studies have largely concentrated on single nucleotide polymorphisms (SNPs), chromosomal rearrangements have garnered less attention due to the challenges associated with accurate detection via traditional sequencing approaches. Nevertheless, it is predicted that chromosomal rearrangements can have a greater impact on evolutionary processes since they affect more genomic regions and elements. Further, due to the ability of chromosomal rearrangements to modify the recombination landscape, they have been hypothesized to play a significant role in various evolutionary processes, such as adaptation to distinct environments and the evolution of sex chromosomes. This thesis first utilized stickleback species (Gasterosteidae) as a model system to explore the role of chromosomal fusion in adaptive evolution. Sticklebacks, particularly threespine sticklebacks (Gasterosteus aculeatus), have gained attention for their ability to colonize and adapt to freshwater environments from ancestral marine habitats over the past several million years. Notably, repeated patterns of phenotypic variation between the marine and freshwater ecotypes have been observed, making sticklebacks a unique and valuable system for identifying the genetic changes underlying adaptive evolution. In Chapter 1, I generated a fourspine stickleback (Apeltes quadracus) genome assembly and identified two fusion events in G. aculeatus by comparative genomics. On the two fused chromosomes, I also found an enrichment of adaptive quantitative trait loci (QTL) and population genomic signals of selection between marine and freshwater ecotypes of G. aculeatus. My research suggests that adaptive clusters on the fused chromosomes in G. aculeatus have more likely arisen from new mutations that occurred after the fusion rather than the linking of pre-existing adaptive alleles. Aside from their recognized role as a model system to study adaptive evolution, sticklebacks have remarkable variation in sex chromosome composition, even among closely-related species. Furthermore, chromosomal inversions have been observed on the sex chromosomes of G. aculeatus and are believed to have contributed to the formation of distinct evolutionary strata. In Chapter 2, I investigated the sex chromosome system of A. quadracus and identified a recent sex chromosome turnover in the identity of the sex chromosome and sex determination gene. Utilizing linked-read sequencing data, I found two polymorphic inversions on the X and Y chromosomes across different populations. In Chapter 3, I developed a novel pipeline to assemble the Y chromosome of blackspotted stickleback (G. wheatlandi) using long-read and whole-genome resequencing data. The evolutionary strata were defined at a high resolution, and several chromosomal inversions were identified between the X and Y chromosomes of G. wheatlandi. By comparing Y assemblies between G. aculeatus and G. wheatlandi, I discovered that G. wheatlandi exhibits a faster rate of gene loss and higher levels of deleterious mutation accumulation, even in the homologous region on the Y chromosome. My findings in these two chapters highlight the role of evolutionary forces, such as drift and sexually-antagonistic selection, in driving sex chromosome evolution and turnover. Through an examination of the observed patterns of chromosomal rearrangements in stickleback species, my thesis work has expanded our understanding of how large structural variation contributes to genomic evolution and adaptation.
| Item Type: | Thesis |
|---|---|
| Dissertation Type: | Cumulative |
| Date of Defense: | 22 June 2023 |
| Subjects: | 500 Science > 570 Life sciences; biology |
| Institute / Center: | 08 Faculty of Science > Department of Biology > Institute of Ecology and Evolution (IEE) |
| Depositing User: | Sarah Stalder |
| Date Deposited: | 03 Jul 2024 13:33 |
| Last Modified: | 04 Jul 2024 12:36 |
| URI: | https://boristheses.unibe.ch/id/eprint/4420 |
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