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NERC E4 Predicting adaptive potential from genomic data and its implications for conservation


   School of Biological Sciences

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  Dr J Hadfield, Dr S Johnston  No more applications being accepted  Competition Funded PhD Project (Students Worldwide)

About the Project

Interested individuals must follow the "how to apply" link on the Geosciences E4 Doctoral Training Partnership web page: http://www.ed.ac.uk/e4-dtp/how-to-apply

Summary

The adaptive potential of populations needs to be preserved if organisms are to cope with a changing world. This project will assess and develop methods for inferring adaptive potential from genetic sequencing data.

Project background

The environment is changing at an unprecedented rate, and many species will have to adapt to this change if they are to survive. The capacity of a species to adapt – adaptive potential – is often assessed by measuring the amount of genetic diversity at molecular markers, but empirical and theoretical studies have cast doubt on whether this approach is useful. Using a combination of theoretical, computational and empirical approaches this project will provide a comprehensive assessment of whether molecular markers are useful in the context of conservation biology. 

Research questions

1. Does genetic variation in adaptive traits have the same temporal dynamics as molecular genetic variation?

A sustained reduction in population size is usually accompanied by a loss of genetic diversity due to drift, but this can be replenished by mutation once the population starts to grow. Genetic variation at molecular markers is likely to be impacted by these processes differently than genetic variation for adaptive traits (henceforth quantitative genetic variation). The student will use theoretical and computational techniques to explore how molecular and quantitative genetic variation respond differently to changes in population size.

2. What is the best type of molecular marker (allozyme, microsatellite, nucleotide site) for predicting a species adaptive potential?

With the advent of cheap high-throughput sequencing technologies, molecular genetic diversity is now routinely assessed at the nucleotide level. However, the low mutation rate of nucleotide sites compared to other markers may make them poor predictors of quantitative genetic variation. This may be off-set, however, by the fact that they can be sequenced without ascertainment bias. Using results from Q1, coupled with new theoretical work, the student will assess the utility of different molecular markers for assessing adaptive potential. There will also be the potential to develop new methods for assessing adaptive potential based on multi-locus approaches.

3. Is there a relationship between nucleotide site diversity and genetic variation in adaptive traits?

The relationship between quantitative genetic variation and molecular genetic variation at allozyme and microsatellite loci has already been assessed systematically. However, the relationship between quantitative genetic variation and nucleotide diversity is unknown. Using the large amount of sequence data available in public repositories, the student will assess whether the relationship between nucleotide diversity and quantitative genetic variation is strong enough to be useful in a conservation context, and if not, the utility of the new multi-locus approach developed in Q2 will be tested.

Methodology

Each question will involve one year’s work and will be done sequentially. Q1 and Q2 will involve computer simulations and some analytical work and Q3 will involve handling and analysing sequence data obtained from public repositories. Complete training will be given for all aspects of the work.

Training

A comprehensive training programme will be provided comprising both specialist scientific training and generic transferable and professional skills.

Requirements

The successful applicant will have a previous degree with a 2:1 minimum and an interest and/or relevant experience in genetics, evolution or ecology.

jarrod.bio.ed.ac.uk/jarrod.html

[Email Address Removed]www.sejohnston.com

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Funding Notes

This project is eligible for the E4 Doctoral Training Partnership. The E4 projects are currently available for full NERC studentship funding which is competitive by interview to UK, EU and International applicants (The fee difference will be covered by the University of Edinburgh for successful international applicants.).
For application details see http://www.ed.ac.uk/e4-dtp/how-to-apply
Further details here - https://www.ed.ac.uk/e4-dtp/how-to-apply/e4-dtp-projects

References

Mittell, Elizabeth A., Shinichi Nakagawa, and Jarrod D. Hadfield. (2015) Are molecular markers useful predictors of adaptive potential?." Ecology letters 18(8) : 772-778.
de Villemereuil, P., Rutschmann, A., Lee, K. D., Ewen, J. G., Brekke, P., & Santure, A. W. (2019) Little adaptive potential in a threatened passerine bird. Current Biology 29(5): 889-894.
Teixeira, João C., and Christian D. Huber (2021) The inflated significance of neutral genetic diversity in conservation genetics. Proceedings of the National Academy of Sciences 118(10): e2015096118.
Kardos, Marty, et al. (2021) The crucial role of genome-wide genetic variation in conservation. Proceedings of the National Academy of Sciences 118(48): e2104642118.

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