IAP2-22-414

Genetic differentiation and local adaptation of multivariate phenotype in a boreal sentinel species

The relative contributions of plasticity and genetic differentiation to phenotypic variation among populations is essential for understanding past evolutionary processes and how such histories may be relevant to managing species and their environments. Also, the relative contributions of genetic variation and other sources of individual differences are critical to understanding what current and future evolutionary trajectories populations may take, which is critical, for example, to our understanding of whether contemporary evolution can contribute to species persistence in the face of global change.

This project will investigate the genetic basis of variation in multivariate phenotype, including body size and morphology, thermal tolerance, and behaviours, in a common garden experiment in an iconic species, the lake trout, Salvelinus namaycush. As part of a large-scale long-term study being conducted by the PI and collaborators at the Experimental Lakes Area (IISD-ELA) in NW Ontario, a large common garden experiment was set up in October 2022 from five lakes. These lakes are well-characterised ecologically, and some progeny from the experiment will be reared at an experimental hatchery. This project will assess multivariate phenotype in these hatchery-reared common-garden fish to characterise the genetic basis of within- and among-population variation in traits that are relevant to local adaptation and the potential for evolutionary rescue in the face of ongoing global change.

Methodology

Existing resource – a common garden experiment was initiated in October 2022, and fish will be reared initially at a hatchery in Dorion, Ontario, to the eyed egg stage, at which time a sub-sample from families from each of 5 lakes will be transferred to an experimental fish culture facility in Codrington, Ontario. From commencement of the PhD in fall 2023, fish will be available for the collection of phenotypic data under the present project. The three key methodological areas for the student are as follows:

Pedigree reconstruction – the study involves a partial sires within dams design with offspring reared by maternal sibship. The student will collaborate with existing experienced staff to generate a marker panel to recover paternal sibship data such that the pedigree will be fully resolved.

Phenotyping – the student will collect multivariate phenotypic information on body size, morphology, temperature tolerance, and behavioural traits.

Statistical analysis – to assess the extent and nature genetic differentiation and within-population standing variation, and to test hypotheses about the relationship between genetic variation at these two levels, the student will estimate among- and within- population patterns of genetic variation in the phenotyped traits using linear mixed modelling frameworks.

Project Timeline

Year 1

The student will conduct several periods of phenotyping experimental fish at the experimental hatchery in Codrington, Ontario. On-site accommodation will facilitate logistics. The student will be supported by regular meetings with the supervisory team (including partners), and will prepare 4- and 9-month reports and participate in associated reviews. Initial stages of developing a molecular marker panel will begin (preparing samples for SNP discovery). Literature review material from the 4 month report will likely ultimately contribute to an introductory thesis chapter.

Year 2

Phenotyping will be completed during this year. A genotyping-in-thousands scale SNP panel will be developed to completely resolve the pedigree within the portion of the common garden fish subjected to multivariate phenotyping. Genotyping and pedigree resolution will begin in year 2. Thesis chapter(s) describing methodological development/ground-truthing to be prepared.. In addition to regular meetings with the advisory team, a 2 year review will be conducted.

Year 3

Genotyping will be completed and analyses of among- and within-population multivariate genotypic variation will be conducted. Preparation of manuscripts/thesis chapters (working from introductory and methodological materials previously compiled) to begin.

Year 3.5

Completion of thesis writing, manuscript preparation.

Training
& Skills

This project will provide a broad range of training opportunities, including:
– animal husbandry
– data collection and organisation
– taxon-specific but nonetheless widely-applicable practical skills
– field work experience through participation in large umbrella project
– foundational and advanced analytical techniques
– dissemination skills, including scientific writing, conference presentation, and interaction with non-academic stakeholders

References & further reading

Delph, L. 2018. The study of local adaptation: a thriving field of research. https://academic.oup.com/jhered/article/109/1/1/4605250

Houle, D. et al. 2017. Mutation predicts 40 million years of fly wing evolution. https://www.bio.fsu.edu/~dhoule/Publications/Houle@@17nature.pdf

Wilson, A.J. 2010. An ecologist’s guide to the animal model. https://besjournals.onlinelibrary.wiley.com/doi/10.1111/j.1365-2656.2009.01639.x

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