University of Cambridge
The Genomics of Divergence and Adaptation in Sister Reef Fishes Separated by the Isthmus of Panamá
Abstract
dc:description.abstractUnderstanding the genetic basis of adaptation to changing environmental conditions is challenging. This is especially true in marine systems where connectivity between populations may be high and past conditions difficult to reconstruct. The emergence of the Isthmus of Panamá provides a unique, natural experiment where multiple populations of marine species have been divided and exposed to radically different environmental conditions. This event provides the ideal setting to explore adaptive divergence in multiple marine species in different contexts of evolutionary time, gene flow and environmental pressures. By combining comparative, population and functional genomics approaches, my thesis leverages this system to understand the evolutionary processes underlying adaptation and resilience across two distinct lineages of reef fish: the Pomacentridae and Serranidae. Firstly, I explored in-depth the molecular basis of adaptation in the visual system to the contrasting visual environments of the Tropical Eastern Pacific (TEP) and Caribbean. I compiled de novo transcriptomes of the retina and investigated expression and coding sequence changes in opsin genes and expression changes in other key visual pathways. I use microspectrophotometry readings of visual sensitivity within the retina to compare overall shifts in visual sensitivity between species. I found parallel shifts in visual phenotype consistent with the different light environments and showed how these shifts were underlied by distinct molecular changes between the two families. Next, I took a broader approach to assess genome-wide changes. I utilised whole genome assemblies and comparative methods to identify signals of selection in protein coding genes and instances of gene family expansion and contraction between the lineages in the TEP and Caribbean. Whilst both families exhibited evidence of adaptations to their environments with pathways involved in responses to fluctuating nutrient levels and osmotic and thermal stress under selection between the two oceans, the specific genes and pathways involved predominantly varied between the families. Finally, I determined the extent to which the processes underlying adaptation between species were similar to the ones underlying local adaptation within species using populations of Pomacentridae distributed along a steep environmental gradient in the TEP and the more environmentally homogeneous Caribbean coast. As part of this analysis I developed an R package to streamline the use of genetic clustering approaches in R. I found minimal population structuring and yet multiple signals of local adaptation between populations on both sides of the Isthmus. Overall, both genome-wide comparative analysis and in-depth analyses of the visual system revealed consistent patterns of distinct molecular targets and mechanisms underlying adaptive divergence in the Pomacentridae and Serranidae families. Notably, these distinct molecular adaptations often resulted in shifts in similar functional groups and, in the case of the visual system, strong phenotypic parallelism. Within species, despite low population structure, I found evidence of potential ongoing environmental filtering driving signals of local adaptation between populations.
Degree
thesis:*- Name dc:type.qualificationname
- Doctor of Philosophy (PhD)
- Level dc:type.qualificationlevel
- Doctoral
- Grantor dc:publisher.institution
- University of Cambridge
- Year dc:date.issued
- 2024
Author and committee
dc:creator, dc:contributor.*- Author dc:creator
-
- Tysall, Eirlys Elizabeth
- Advisors dc:contributor.advisor
-
- Manica, Andrea
- McMillan, Owen
Subjects
dc:subject × 6Rights
dc:rightsIdentifiers
dc:identifier.*- DOI dc:identifier.doi
- https://doi.org/10.17863/CAM.118805
- OAI identifier oai:identifier
- oai:www.repository.cam.ac.uk:1810/385000