Evolution in action: using museum DNA to understand disease resistance in island birds

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We lack fundamental knowledge of (i) the rate of immunogenetic change over time within natural vertebrate populations, (ii) how different mutational processes facilitate it, and (iii) the role of specific pathogen-mediated mechanisms (heterozygote advantage, frequency-dependent and fluctuating selection) in this1,2. In the post-genomics era numerous immune genes have been identified3 and methods exist to screen such loci using museum samples7. Consequently, it is now possible to investigate temporal immunogenetic change in wild populations if sufficient temporal samples are available4. The 13 discrete island populations of Berthelot's pipit across Macaronesia make it an excellent system for studying evolutionary processes in the wild, and the supervisors have in-depth understanding of this species' ecology and demography1,5-7. Pathogen faunas differ across these populations in line with biogeographical expectations5 thus generating consistently differing selection regimes. The force of genetic drift also differs because of contrasting effective population sizes6.The student will use 13 pipit genomes - recently sequenced as part of another project - to quantify genomic divergence between populations and identify highly divergent immune loci that are candidates for being under pathogen-mediated selection. They will then develop sequence capture probes (myBaits) to screen 25 samples from each of the four most divergent populations at each time point. Sequence capture allows for the sequencing of large numbers of genes across multiple individuals at low cost8. Importantly, it works well using small amounts of degraded DNA (i.e. museum samples)7. The student will use the 1820 (museum) and 2006 samples already available, but collect the 2020 samples themselves. They will undertake all the molecular work and bioinformatics work to address the objectives, including pathogen screening to quantify pathogen regimes across populations5 using the 2020 samples. The defined objectives provide a firm conceptual framework to produce high quality, novel work, but allow scope for independent development. For example, developing and testing hypotheses on how pathogen-mediated selection mechanisms will affect temporal immunogenetic variation, or following up additional questions arising from the work - such as how specific pathogens may be associated with genomic variation.The initial genomes already exist, as do the majority of temporal samples and pathogen data, plus the supervisors have considerable experience with the required genomic and bioinformatics tools, and expertise in the conceptual area1,2,5-7,9. This is therefore an exceptional opportunity to investigate cutting-edge questions around a fundamental concept in a low-risk manner. The data generated will be sufficiently powerful and focused enough to provide clear results, but modest enough to be manageable. Thus the project is ideally suited to a PhD studentship.The UEA supervisors will provide expert molecular, bioinformatics and data analysis training. All supervisors will help develop the student's conceptual understanding and scientific communication skills. Fieldwork and animal handling skills will be taught by DSR. The time spent in Tenerife will provide an excellent opportunity to experiencing a different academic environment thus promoting overall personal development, The overall collaborative nature of the project will facilitate teamwork, communication and networking.