The evolutionary genomics of life-history adaptations in pinnipeds

Pinnipeds (seals, sea lions, fur seals and walrus) are keystone marine predators, and sentinels for marine ecosystem health. Advances in genomics technologies are opening up the possibility to identify and dissect the genetics and molecular evolution underlying the adaptions of pinnipeds to the marine environment and the startling variation in ecology and life history present within the family. Understanding these mechanisms not only provides fundamental insights into the process of evolution, but is also important for assessing species vulnerability and responses to potential future environmental change. Some of the unique adaptions of pinnipeds may also be of relevance to human health and therapeutics, such as adaptations in fat metabolism.

This project will build on rapidly growing genomic resources for pinnipeds, including de novo seal genome assemblies generated by the Goodman/O’Connell labs and other colleagues in the Pinniped Genome Consortium. These provide an opportunity to use comparative genomics to examine key aspects of pinniped ecology and evolution including physiological adaptations underpinning different life-history strategies and among species variation in disease susceptibility.

Among the 33 extant species of pinnipeds there are a diverse array of adaptations to varying ecological conditions and life histories. One of the most striking aspects of pinnipeds is the variation exhibited in foraging and reproductive strategies, which are associated with among species body size variation, and the habitats they exploit. For example, adult body size can range from less than 100kg in Caspian seals to more than 2000kg for male elephant seals, while weaning times vary from 4-12 days in hooded and harp seals up to 18 months in some sea lions, and 2 years in the walrus. Pinnipeds have also evolved lipid rich milk, with fat content for some species exceeding 60%. The ecological drivers of these differences appear to be related to breeding substrates and ecological feeding niche exploited by species. In previous work we have identified 100s of genes that show signatures of adaptive evolution unique to different pinniped lineages and species which may underpin these adaptations. Many of these genes are associated with key elements of lipid metabolism and milk properties.

Our next aim is to understand how these genes have evolved across the pinniped lineage, and how past environmental changes created selection pressures shaping their evolution, and the evolution of pinnipeds overall. To do this we will use a variety of genomic approaches including de novo sequencing of seal genomes, molecular evolution and phylogenomic analyses, and population genetic studies at the genomic level.

Secondly, we will also use multiomic approaches to understand the functional significance of amino acid substitutions between species in subsets of genes strongly associated with our traits of interest, and will evaluate how changes in gene expression might also contribute to evolution of traits such high fat content in pinniped milk, and tolerance of rapid fluxes of lipid in and out of blubber.

Resolving the genomic basis of such adaptations is important for understanding many aspects of pinniped biology, but may also contribute to predicting adaptive responses of pinniped species to future climate change and loss of sea ice.

Further information about the project can be found at: https://yes-dtn.ac.uk/research/the-evolutionary-genomics-of-life-history-adaptations-in-pinnipeds/

Research context and partners

The student will join the Ecology and Evolution group in the School of Biology, and will be integrated with the LIDA and Leeds Omics virtual institutes which encompass a large group of researchers working on genomics and bioinformatics related projects. The work will be conducted within the framework of our Pinniped Genomes Consortium, which is a collaboration of researchers from the UK, Europe, China and USA, including:

• Dr Ian Carr, University of Leeds
• Prof Mary O’Connell, University of Nottingham
• Dr Kimberley Bennett, Abertay University

Eligibility

The minimum entry requirements for PhD study is a 2.1 honours degree, or equivalent, in a subject relating to your proposed area of research, or a good performance in a Masters level course in a relevant subject. A first class honours degree (or equivalent) is usually required to be competitive for scholarship funding and a Masters degree is also a valuable asset.

If English is not your first language, you’ll need to provide evidence of a language qualification. The minimum English language entry requirement for postgraduate research study in the Faculty of Biological Sciences is an IELTS of 6.0 overall with at least 5.5 in each component (reading, writing, listening and speaking) or equivalent. The test must be dated within two years of the start date of the course in order to be valid.

How to Apply

1) Complete the University of Leeds online application form

Select ‘NERC YES DTN Yorkshire Environmental Sciences’ as the Planned Course of Study.

The supporting documents needed to process your application are:

• certificates and transcripts of any academic qualifications
• English language qualification certificates
• visa and immigration documents

All documents should be in English or be accompanied by a certified translation into English. 

They can be sent via the online research degree application or can be emailed to ENV-PGR@leeds.ac.uk after you have submitted your application. Your email should include your student ID number (emailed to you on submission of your application), full name and your intended course of study. Please do not send original documents at the application stage and only provide documents via email.

2) Complete the YES.DTN application form. This is available on the YES•DTN website