The evolutionary genomics of life-history adaptations and disease susceptibility in pinnipeds

Project summary

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 lab 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. We will use a variety of genomic approaches including de novo sequencing of seal genomes, and population genetic studies at the genomic level using methods such as ddRAD. The student can expect to gain experience in cutting edge DNA sequencing and genomics methods, together with developing skills in bioinformatics, comparative genomics, molecular evolution and population genetics analysis. There will opportunities to visit collaborators from the Pinniped Genomes consortium in Denmark and Finland.

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. The ecological drivers of this difference appear to be related to breeding substrates and ecological feeding niche exploited by species. We will use comparative genomics to identify adaptive genetic changes among species in candidate genes which may underpin these adaptations, and map them on to the time line of the pinniped phylogeny to understand how such adaptations may have driven pinniped evolution. Resolving the genomic basis of such adaptations may also contribute to predicting potential responses of pinniped species to climate change and loss of sea ice.

The harbour seal (Phoca vitulina) is the world’s most widely distributed pinniped species, and in Europe has a range extending from Svarlbard to Northern France, and from the Baltic to the west coast of Ireland. Within this distribution the species exploits a wide variety of habitats and experiences a large range of environmental conditions. The species has also experienced 2 mass mortalities from phocine distemper virus (PDV; a member of the morbillivirus family), which killed more than 50% of the European population in 1988 and 2002, and an outbreak of influenza A in 2014 which killed 10-20% of the population around Danish, Swedish and German coasts. Levels of PDV mortality varied substantially among populations, and intriguingly, grey seals (Halichoreus grypus), which are sympatric with harbour seals in much of Europe, were exposed to PDV during the epizootics but did not suffer extensive mortality. The species is therefore is a good model for examining how environmental and ecological conditions influence population structure in marine mammals and for evaluating how genetic variation might contribute to within and among species susceptibility to viruses.

In addition to whole genome comparisons we will also use ddRAD, and PacBio Sequel 2 sequencing of immune related candidate genes to examine population structure, demographic history, and associations between virus mortality and genetic variation.

Expected outcomes: New knowledge on the molecular adaptions underpinning variation in pinniped life-history strategies; a detailed understanding of the way environmental factors influence population structure in a long-lived, marine mammal; insights into the population demographic history of harbour seals over long and short timescales in relation to past environmental change; potential identification of adaptations and functional genetic variation in harbour seals from across their geographic range and their genomic basis; identification of genetic variation contributing to within and among species variability in susceptibility to viruses; generation of data relevant to the conservation management of seal populations.

Requirements

Hons degree and/or Masters in a topic relating to Biology, Zoology, Ecology, Genetics, Biodiversity, Evolution, Bioinformatics, Maths & Biology etc. An interest in working at the interface of ecology, biodiversity and population/evolutionary genomics is desirable. Prior experience of bioinformatics is helpful but not essential. However interest in developing skills in bioinformatics and computing is important.

Training

Training will be provided in population and evolutionary genetics/genomics, phylogenetics, bioniformatics, statistical modeling in R, GIS-based spatial analysis and mapping. There may be some opportunities to participate in fieldwork alongside seal ecologists. In addition the student will also benefit from wider general skills training provided within the framework of the Leeds-York-Hull DTP.

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, Denmark, Finland and USA, including:

Further reading

Baldwin MW, Toda Y, Nakagita T, O’Connell MJ, Klasing KC, Misaka T, Edwards SV, Liberles SD (2014) Evolution of sweet taste perception in hummingbirds by transformation of the ancestral umami receptor. Science 345 929-933.

Foote AD, Liu Y, Thomas GWC, Vinař T, Alföldi J, Deng J, … Gibbs R. A. (2015) Convergent evolution of the genomes of marine mammals. Nature Genetics 47 272–275.

McCarthy AJ, Shaw MA, Goodman SJ (2007) Pathogen evolution and disease emergence in carnivores P R SOC B 274 3165-3174.

McCarthy AJ, Shaw MA, Jepson PD, Brasseur SM, Reijnders PJ, Goodman SJ (2011) Variation in European harbour seal immune response genes and susceptibility to phocine distemper virus (PDV). Infect Genet Evol 11 1616-1623.

Morgan CC, Mc Cartney AM, Donoghue MTA, Loughran NB, Spillane C, Teeling EC, O’Connell MJ (2013) Molecular adaptation of telomere associated genes in mammals BMC Evolutionary Biology 13

Webb AE, Gerek ZN, Morgan CC, Walsh TA, Loscher CE, Edwards SV, O’Connell MJ (2015) Adaptive evolution as a predictor of species-specific innate immune response Molecular Biology and Evolution 32 1717-1729.

Keane M, Semeiks J, Webb AE, Li YI, Quesada V, Craig T, Madsen LB, van Dam S, Brawand D, Marques PI, Michalak P, Kang L, Bhak J, Yim HS, Grishin NV, Nielsen NH, Heide-Jørgensen MP, Oziolor EM, Matson CW, Church GM, Stuart GW, Patton JC, George JC, Suydam R, Larsen K, López-Otín C, O’Connell MJ, Bickham JW, Thomsen B, deMagalhães JP (2015) Insights into the evolution of longevity from the bowhead whale genome. Cell Reports 10 112-122.

Liu S, Lorenzen ED, Fumagalli M, Li B, Harris K, Xiong Z, Zhou L, Korneliussen TS, Somel M, Babbitt C, Wray G, Li J, He W, Wang Z, Fu W, Xiang X, Morgan CC, Doherty A, O’Connell MJ, McInerney JO, Born EW, Dalén L, Dietz R, Orlando L, Sonne C, Zhang G, Nielsen R, Willerslev E, Wang J (2014) Population genomics reveal recent speciation and rapid evolutionary adaptation in polar bears Cell 157 785-794.