Genetic differentiation and local adaptation

Overview

The genetic basis of ecologically important differences among individuals populations is critical for interpreting patterns of adaptive differentiation. However, it is frequently difficult to characterise such genetic variation. Additionally, important differences among individuals and populations are often characterised on a trait-by-trait basis, whereas co-ordinated patterns of variation among multivariate phenotypes are likely to be most important for fitness.

This project will take advantage of an ongoing, large-scale, common garden experiment where lake trout (Salvelinus namaycush) are being raised from five ecologically well-characterised source lakes in the IISD-ELA (Experimental Lakes Area) in Northwestern Ontario. Pedigreed individuals will be avialble for life history, morphological, and behavioural phenotyping. Phenotypic data can feed into a range of ecologically-motivated quantitative genetic studies. The student will have substantial latitude to build a PhD project based on this basic resource.

Methodology

The PhD project will be focused on fish reared in an experimental hatchery (in Codrington, Ontario). Fish will be communally reared, and lake of origin and pedigree will be recovered genetically. The project will be focused on multivariate phenotyping, especially once experimental fish become large enough to tag and track individually (from approximately late 2022). Standard methods for morphological, behavioural, and life history phenotyping will be employed. Pedigree and lake of origin determination will be via a GT-Seq SNP panel. Statistical analyses will, depending on the direction of the PhD project, involve mixed model-based quantitative genetic analysis of multivariate phenotypes and association/QTL analysis.

Project Timeline

Year 1

Background reading, development of thesis plan, trip 1 to Ontario to undertake phenotyping. Additional training (e.g., International Summer Institute in Statistical Genetics courses).

Year 2

Trip 2 to Ontario for phenotyping, quantitative genetic analyses.

Year 3

Quantitative genetic analyses, thesis chapter/manuscript writing.

Year 3.5

Thesis completion

Training
& Skills

Literature survey, organisation.
Statistical analysis, especially mixed-model analysis.
Genotyping methodology
Animal husbandry and fish biology
Writing and editing

References & further reading

https://www.nature.com/articles/hdy2010158

Further Information

For further information, please contact Michael Morrissey mbm5@st-andrews.ac.uk

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