Population Genomics in Stream-Lake Stickleback
I am examining a large-scale population genomics dataset to determine how predictable patterns of genomic divergence are and what genetic and/or ecological factors affect predictability.
Natural Selection in the Wild
Over the last few years we have sampled cohorts of benthic and limnetic stickleback in the wild. We are now using genotyping-by-sequencing methods to identify regions of the genome underlying divergent adaptation and contributing to reproductive isolation.
Visual Adaptation to Sulphur Streams
In collaboration with Michi Tobler, I am continuing my work examining how opsin genes and spectral sensitivity evolve under divergent spectral conditions. Of interest to us are Poecilia species (P. sulphuraria, P. thermalis and P. mexicana), which reside in the streams of eastern Mexico. This work focuses on determining how visual sensitivity differs among populations inhabiting divergent spectral environments and how this corresponds to the local light environment.
Gut Microbiome and Adaptation
Another project I have investigates how species interactions at the microbial level may influence adaptation to novel environments. To investigate this I have used next-generation sequencing technology to determine how microbial communities associated with stickleback (in their gut) differ between populations inhabiting divergent environments.
Ecological & Evolutionary Genetics of Threespine Stickleback
My PhD work aimed to characterize the genetic basis of adaptation in the threespine stickleback (Gasterosteus aculeatus) to predation and other sources of divergent selection. My projects included both field studies and multi-generation selection experiments in semi-natural ponds (pictured below). The purpose of this work was to further understand the general mechanisms that underlie genetic variation, adaptation in novel or changing environments and speciation.
The stickleback that I used in my PhD research (pictured below), were sympatric benthic and limnetic species pairs that are found in five coastal freshwater lakes in southern British Columbia. Benthic and limnetic stickleback have diverged in many aspects of their morphology, behaviour and ecology. These species pairs have formed independently within the last 12,000 years and are therefore a phenomenal example of rapid speciation and adaptation.
The presence or absence of certain fish predators appears to be a good predictor of whether or not benthic and limnetic species pairs will be found in a given lake. Thus, we believe that predation has played an important role in the divergence of these stickleback. To test this hypothesis we conducted a large scale experimental evolution study at the UBC experimental ponds facility. This manipulative experiment examines whether cutthroat trout (Oncorhynchus clarkii) are an important source of divergent selection on sympatric stickleback.
Over the course of the experiment we monitored changes in allele frequency genome-wide to determine the genetic basis of adaptation to predation. We have also estimated natural selection on boney armour (lateral plates and spines) and trophic traits (e.g. Gill rakers). Other aspects of this experiment included determining the ecological consequences and behavioural changes associated with predation; papers associated with these aspects have now been published and PDFs can be found using the tabs above.
Visual Adaptation in Threespine stickleback
Spectral sensitivity is thought to evolve to match features of the local light environment. Marine and freshwater threespine stickleback inhabit divergent light environments and therefore provided an opportunity to test the hypothesis of spectral matching. I surveyed the opsin gene expression and spectral sensitivity of multiple marine and freshwater populations to test this hypothesis. This paper has now been published and PDFs can be found using the tabs above.
Reproducibility and Data Archiving in Science
This work was conducted as part of a working group based at the University of British Columbia and led by Tim Vines. Our studies focused on providing empirical data to evaluate reproducibility and data availability in biology. The purpose of this work was to convince the scientific community that data sharing is both important and necessary.
Visual Ecology and Gene Duplication
Colouration influences mate choice in many species and often has been shown to be a reliable proxy for male quality. However, the molecular basis of female preferences for colour traits and indeed most male secondary traits in many species is poorly understood.
In the guppy (Poecilia reticulata), a model species for the study of sexual selection, females often prefer the most colourful males. Therefore color vision is thought to be fundamental to mate preference in this species. My M.Sc work exploited the technique of in situ hybridization to characterize the expression patterns of cone opsins (the genes responsible for colour vision) across the surface of the retina in this species, to give further insight into the visual capacity and mate preference of guppies. I also used phylogenetic methods to investigate patterns of gene duplication and divergence across the phylogeny of teleost fish. These studies are published and the corresponding PDFs can be found using the ‘publications’ tab above.