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Deciphering the genetics of adaptation to the environment in wild and domesticated bovids


College of Medicine and Veterinary Medicine

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Dr P Wiener , Dr J Prendergast , Dr L Morrison No more applications being accepted Competition Funded PhD Project (Students Worldwide)

About the Project

Project summary: Population genetics and bioinformatics techniques will be used to characterize the genetic structure of African cattle and buffalo populations and to identify common genomic signatures of environmental adaptation.

Background: A better understanding of animal adaptation to the natural environment can inform both conservation of wild species and management of domesticated breeds without excessive reliance on external inputs. In particular, as climate change continues to impact global conditions, it will become increasingly important to promote those genotypes that can tolerate new environmental challenges.

Despite their lower productivity in comparison to European breeds, native African cattle (Bos taurus) display better survival rates as a result of thousands of years of both natural and human-imposed selection and admixture with Asian breeds. The closely related wild species, African buffalo (Syncerus caffer), inhabits many of the same ecological regions as cattle and thus has been subjected to many of the same selection pressures. Because buffalo (unlike cattle) have only been under natural selection, shared selection signatures between the two species are likely to be associated with environmental factors rather than human-imposed pressures. In this project, the student will analyse whole-genome sequence data from hundreds of cattle and buffalo sampled across Africa, using a variety of statistical tools to identify the most important environmental selection pressures on the two species and the genes and gene networks that have been under common selection.

Project description: The student will have access to unique cattle and buffalo whole genome sequencing datasets spanning hundreds of animals for both species, and they will first conduct bioinformatics analyses of these data to identify genetic variants segregating in different breeds and sub-species. Subsequent population genetic analyses will address several goals: evaluate structure of cattle and buffalo genomes and test for evidence of admixture; map genomic regions associated with environmental adaptation traits; perform a functional analysis of genomic regions associated with adaptation; and compare the genomic basis of environmental adaptation across species.

Training: A comprehensive training programme will be provided, comprising both specialist scientific training and generic transferable and professional skills. Specialised skills include techniques in quantitative and population genetics, statistics, bioinformatics and genomics.

Funding Notes

All applicants, regardless of nationality, are eligible. The ideal student will have strong quantitative and computational skills and interests in genetics. Applicants should have at least an upper 2.1 degree. An MSc in bioinformatics, computational biology, genetics or a related field will be an advantage.

Please see this website for instructions on how to apply: http://www.ed.ac.uk/e4-dtp/how-to-apply

References

Friedrich & Wiener. 2020. Selection signatures for high-altitude adaptation in ruminants. Animal Genetics, 51(2), 157-165. https://onlinelibrary-wiley-com.ezproxy.is.ed.ac.uk/doi/full/10.1111/age.12900

Flori et al. 2019. A genomic map of climate adaptation in Mediterranean cattle breeds. Molecular Ecology 28(5), 1009-1029. https://onlinelibrary-wiley-com.ezproxy.is.ed.ac.uk/doi/full/10.1111/mec.15004

Meadows & Lindblad-Toh, 2017. Dissecting evolution and disease using comparative vertebrate genomics. Nature Reviews Genetics, 18(10), 624-636. https://www-nature-com.ezproxy.is.ed.ac.uk/articles/nrg.2017.51
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