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Genomic basis of convergent evolution in the Trinidadian Guppy

Periodic Reporting for period 3 - GUPPYCon (Genomic basis of convergent evolution in the Trinidadian Guppy)

Reporting period: 2020-04-01 to 2021-09-30

Many species have independently evolved similar phenotypes in response to similar environmental challenges. This phenomenon, termed convergent evolution, reflects both the power and the limits of adaptation. However, we often do not know the genetic basis of convergent evolution. This is because, until recently, it has not been possible to investigate the genomic basis of evolution in most systems, limiting our understanding of the factors that facilitate or inhibit convergence and adaptation. To fully understand convergent evolution we need to query the genomic response to selection and determine genotype-phenotype links in systems where convergent adaptation is well established. The Trinidadian guppy (Poecilia reticulata) is a system that offers the opportunity to test the roles of multiple factors in convergent evolution: this species includes multiple natural and experimentally established populations that have repeatedly evolved similar phenotypes under similar predation environments. The aim of this project is to fully characterise the genomic-basis of repeated adaptive evolution in guppies. Aim 1 will identify regions that repeatedly show signatures of selection, and will contrast the nature of selection in natural and experimental populations that differ in age and levels of founding genetic diversity. Aim 2 will identify genomic regions associated with phenotypes that are known to play a significant role in local adaptation in the guppy using quantitative genetics approaches. We will then directly test the effects of candidate genes using novel functional genomic approaches, in Aim 3. Overall, this project will test whether repeated selection led to convergence at the genomic level, determine the genetic basis of convergent adaptations, and ultimately understand how convergent evolution has occurred in an important wild system.
We are making good progress on GUPPYCon. We have completed a new assembled reference genome that will be an important resource for all three aims. We have completed all sampling and the majority of sequencing to complete aim 1. Through this, we have identified regions of the genome that show evidence of both rapid evolution and repeated independent selection in different rivers. We have completed a pilot experiment for aim 2, that has provided preliminary results, identifying genomic regions associated with adaptive phenotypes. Now, using these results we have refined our experimental design and have begun animal breeding for a larger experiment, which we predict will further narrow these regions to candidate genes. Finally, aim 3 requires both aim 1 and aim 2 to be completed to identify candidate genes and their resulting phenotypes and therefore is the focus of the later portion of the project.
GUPPYCon is cross disciplinary; combing population, quantitative, and functional genetics to fully understand convergent evolution. To do so, we use an evolutionary biology and ecology model system, the Trinidadian guppy. We expect that we will be able to identify genes under selection and how they relate to the phenotype. Additionally, using experimental populations we will be able to track these genes in real time.
Overall, GuppyCon has the potential to have broad impact on how we understand selection in natural populations and the level at which evolution is repeatable.