Identification of barriers to gene flow between Antirrhinum species

Richardson, Daniel (2022) Identification of barriers to gene flow between Antirrhinum species. Doctoral thesis, University of East Anglia.

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For natural diversity to persist, there must be mechanisms in place to protect it from the homogenising effects of gene flow. Studies at natural hybrid zones have shown that, where divergent populations meet and exchange genes, genetic loci involved in adaptive population characteristics can resist gene flow. This results in a homogeneous landscape of genomic divergence, with gene flow resistant regions showing elevated divergence compared to other loci. Identification of these divergent loci may inform about the genetic basis of population differentiation, and is therefore a major aim of speciation genomics. However, genomic divergence is inherently noisy, varying due to cryptic population histories and intrinsic genomic factors. Here I introduce the grouping tree scan as a method for summarising between-population diversity across groups of populations. By comparing between-population divergence across the whole genome for many populations simultaneously, this method reduces the noise associated with within-population effects, and provides increased power for detecting divergence signals that may not be detectable through conventional two-way genome scans. Furthermore, because relationships between populations are determined independently of a priori assumptions, the approach is resilient to ascertainment bias. I apply this approach to two sympatric subspecies of Antirrhinum majus with contrasting flower colours, demonstrating that colour genes alone may be sufficient to facilitate population divergence through epistatic reproductive barriers. I then expand the approach to look at more distantly related species with distinct growth habits, identifying a subset of genomic regions that may underlie reproductive barriers based on adaptation to different environments. Finally, I outline a bioinformatic approach for detecting sRNA-producing genomic inverted repeats, which may not otherwise be detectable through population comparisons. I propose the grouping tree scan as an extension of the genome scan toolkit, expanding the utility of pooled-sequence data for characterising genetic barriers.

Item Type: Thesis (Doctoral)
Faculty \ School: Faculty of Science > School of Biological Sciences
Depositing User: Chris White
Date Deposited: 05 Sep 2023 12:11
Last Modified: 05 Sep 2023 12:11

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