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Adaptive Radiation and Molecular Studies

The Salmon Forest Project

Molecular Studies

Members of the lab



 Bruce  Deagle, Post-Doc
email: bdeagle@uvic.ca

The focus of my research has been using information in DNA to address ecological and evolutionary questions. I am currently working on a stickleback population genomics project in Tom Reimchen’s laboratory; we are working in close collaboration with David Kingsley’s group at Stanford University. During my PhD, I looked at methods to study the diet of large marine predators by analysing prey DNA in their faeces.


Postdoctoral work: SNP variation in Haida Gwaii threespine stickleback   

Studies of Haida Gwaii stickleback over the last 35 years have revealed a remarkable level of phenotypic variation within and among freshwater populations, providing a classic example of adaptive radiation (see Reimchen publications). With recent completion of a high-quality reference genome sequence, the threespine stickleback is also quickly becoming an important model in the field of evolutionary genomics (see Kingsley publications). In this postdoctoral project we are obtaining a genomic perspective of the genetic structure and history of Haida Gwaii stickleback using a genome-wide SNP (single nucleotide polymorphisms) genotyping system (Illumina® GoldenGate) developed at Stanford (Figure 1).  Particular areas of interest include:

                       (A) Phylogeography of the Haida Gwaii freshwater populations

                       (B) The population genomics of parapatric stream/lake pairs of stickleback

                      (C) Associations between genetic markers and particular morphological traits



(A) Phylogeography

 Since phylogenetic hypotheses underlie most conclusions in studies of adaptive evolution, a robust phylogeographic study in this model system would be invaluable. Initial analysis shows that populations from within a watershed cluster together and separate watersheds are generally independent. A few cases of genetic linkages between separate watersheds in adjoining geographical areas may reflect past watershed connections, or possibly ongoing gene flow. Populations that do not group with others are either: a single sampling site within a watershed, close to a river mouth (continued marine gene flow), or are isolated lakes with low heterozygosity which obscures historical relationships.


(B) Parapatric stream/lake pairs of stickleback

Parapatric lake and stream populations of stickleback are a classic example of ecological speciation. Two watersheds on Haida Gwaii (Drizzle and Mayer) contain previously described stream/lake pairs (Moodie 1972 Can. J. Zool. 50: 721-732; Reimchen et al. 1985 Can. J. Zool. 63:294-2951). To investigate the genetics underlying stream/lake divergence we SNP genotyped fish from (1) Drizzle Lake and Drizzle Outlet, and (2) Mayer Lake and two inlet streams (Gold and Woodpile).

Data confirm independent origin of these stream/lake pairs in the separate watersheds (Figure 2 ). Within the Mayer watershed, fish from two inlet creeks are closer to each other than to Mayer Lake fish. At the Gold Creek sampling site, both lake and stream forms were collected and these samples are genetically distinct in sympatry.



Genomic divergence between stream and lake forms within a watershed was highly heterogeneous: most loci show moderate levels of divergence but some loci (outliers) were highly differentiated and are likely linked to genes under strong divergent selection (Figure 3).



(C) Associations between SNPs and morphological traits

Populations of Haida Gwaii stickleback exhibit a range of phenotypes defined by the location-specific selective landscapes (Moodie and Reimchen 1976 Systematic Zoology 25: 49-61). With morphological data from over 100 populations (Reimchen et al. In prep) and SNP data that characterizes individuals from these populations, it may be possible to identify loci linked to particular morphological traits (Figure 4).




PhD work at the University of Tasmania: DNA-based methods to study diet

Studying animal diet is a difficult undertaking especially in the marine environment where it is rarely possible to observe feeding activity. Some prey remains survive digestion and morphological analysis of remains in faecal material can provide an indication of what predators are eating. In my PhD I looked at the potential for use of DNA-based identification methods in dietary studies of marine predators. When I started it was clear that prey DNA was present in animal faeces but how useful it would be for dietary studies was an open question. So, in collaboration with researchers from the Marine Mammal Unit at UBC, I started by looking at samples collected from captive Steller sea lions to address some basic questions:

·       Can prey DNA be reliably detected in the soft matrix of faecal samples?

·       Can DNA from prey items fed as a small proportion of the diet be detected?

·       Are the relative amounts of DNA recovered from prey species proportional to their mass in the diet?

·       What is the quality of the prey DNA recovered?


These questions are the focus of three papers from my thesis:


Deagle BE, Tollit DJ, Jarman SN, Hindell MA, Trites AW, Gales NJ (2005) Molecular scatology as a tool to study diet: analysis of prey DNA in scats from captive Steller sea lions. Molecular Ecology 14: 1831–1842. (pdf)


Deagle BE, Eveson JP, Jarman SN (2006) Quantification of damage in DNA recovered from highly degraded samples — a case study on DNA in faeces. Frontiers in Zoology e3:11. (pdf)


Deagle BE, Tollit DJ (2007) Quantitative analysis of prey DNA in pinniped faeces: potential to estimate diet composition? Conservation Genetics 8: 743–747. (pdf)




The methods were further evaluated in a field-based study looking at the diet of macaroni penguins at Heard Island. Most recently I have been involved in projects using high-throughput sequencing to look at diet of Australian fur seals and little penguins:


Deagle BE, Gales NJ, Evans K, Jarman SN, Robinson S, Trebilco R, Hindell MA (2007) Studying seabird diet through genetic analysis of faeces: a case study on macaroni penguins (Eudyptes chrysolophus). PLoS ONE 2: e831. (pdf)


Deagle BE, Kirkwood R, Jarman SN (2009) Analysis of Australian fur seal diet by pyrosequencing prey DNA in faeces. Molecular Ecology 18: 2022–2038.


Deagle BE, Chiaradia A, McInnes J, Jarman SN (2010) Pyrosequencing faecal DNA to determine diet of little penguins: is what goes in what comes out? Conservation Genetics 11: 2039–2048.






For my other papers, please see publication list.