Stickleback
Threespine stickleback population genetics
I received an NSERC postdoctoral fellowship (2009 -2011) to study population genetic of threespine stickleback fish populations from the Haida Gwaii Archipelago (off western Canada). These small freshwater populations evolved relatively recently from colonising marine stickleback fish (<15,000 years ago) and have been extensively studied over the past 40 years by Tom Reimchen and colleagues. Their work revealed extreme diversity in body form of these stickleback and documented the habitat specific selective pressures driving this radiation. With many genomic resources available for threespine stickleback when this was rare for non-model organisms (including a high-quality reference genome), these populations represented a fantastic system in which to study ecological and evolutionary genomics.
In my project I made use of a genome-wide SNP array (developed in David Kingsley's laboratory) to document patterns of genetic variation in stickleback collected from >100 population throughout Haida Gwaii. These data were used to provide a broad phylogeographic picture of the populations, to investigate drivers of genetic diversity, and to look at the geographic distribution of SNPs linked to some adaptive loci. We also carried out a focused analysis of the genetic adaptation occurring between stickleback living in adjacent stream-lake habitats.
Example publications:
Deagle BE, Jones FC, Absher DM, Kingsley DM, Reimchen TE (2013) Phylogeography and adaptation genetics of stickleback from the Haida Gwaii archipelago revealed using genome-wide single nucleotide polymorphism genotyping. Molecular Ecology 22: 1917-1932 (PDF)
Deagle BE, Jones FC, Chan YF, Absher DM, Kingsley DM, Reimchen TE (2012) Population genomics of parallel phenotypic evolution in stickleback across stream–lake ecological transitions. Proceedings of the Royal Society B: Biological Sciences 279: 1277-1286 (PDF)
The research continues...
The evolutionary genomic work in this incredible system has of course continued with some a newer publication coming out on whole genome sequencing of the Haida Gwaii stickleback samples: Adaptation of colour vision (PLoS Biology 2017); Rapid genomic adaptation to a new environment (Nature Ecology and Evolution 2018 - with nice background story to accompany the study here)
Collaborators
Tom Reimchen (University of Victoria, Canada)
David Kingsley (Stanford University, USA)
Felicity Jones (Max Planck Institute, Germany)
Tree constructed based on pairwise genetic distances between two stickleback from each of 115 Haida Gwaii localities. Colour indicates watershed (for details see Deagle et al. Mol. Ecol. 2013)
Typical threespine stickleback (Gasterosteus aculeatus) found in Mayer lake (Top) and a tributary stream (Bottom). Despite continuous habitat these fish have diverged across this ecological transition. Our work shows that there is relatively low genetic separation between these stream-lake ecotypes across most parts of the genome, but some regions are highly differentiated and presumably contain genetic code important for local adaptation.
Collecting stickleback in the lowland bogs of Northeast Haida Gwaii (top) and with Tom Reimchen at Stiu Lake on the west coast of Haida Gwaii (bottom).
