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A genomic perspective on the origins, evolution and adaptation of Galapagos Iguanas

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  • Full or part time
    Dr S Goodman
    Dr G Gentile
  • Application Deadline
    No more applications being accepted
  • Competition Funded PhD Project (European/UK Students Only)
    Competition Funded PhD Project (European/UK Students Only)

Project Description

The revolution in sequencing technology and genomic science in recent years is now allowing evolutionary biologists to dissect the genetic basis of adaptation and population histories of non-model organisms in unprecedented detail. Key questions related to adaptation include, the type and number of genetic changes which underpin the evolution of new phenotypes, the strength and time scales for selection, the extent of parallel and convergent evolution among different taxa, and the nature of environmental and ecological factors which drive natural selection. 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.
This project provides a unique opportunity to examine adaptation and evolutionary history in an iconic set of species for evolutionary biologists, the marine (Amblyrhynchus cristatus) and land iguanas (Conolophus sp) of the Galapagos archipelago. Both genera of Galapagos iguanas originate from the same common ancestor, diverging around 4.5-10.5 million years ago, with both groups subsequently spreading across the archipelago. Land iguanas diversified to form 3 species - Conolophus subcristatus, native to six islands, and Conolophus pallidus, which is restricted to Santa Fe. The third species Conolophus marthae, known as the pink iguana, is only found on Volcan Wolf at the northern end of Isabela. It was only recently recognised as forming a genetically and ecologically distinct species and is now considered endangered due to its small population size and restricted distribution.
The process of divergence and diversification among these iguanas has generated many novel adaptations over relatively short evolutionary timescales – most strikingly adaptation to diving and the marine environment in Amblyrhynchus cristatus, which is the world’s only fully marine lizard. Land iguanas have their own adaptations to the harsh terrestrial environment in the Galapagos, including diet, tolerance of arid conditions and fluctuating resources, as well as various differences in morphology and pigmentation. This provides an amazing natural model system for evolutionary biologists to characterise the genomic basis of adaptation and novel phenotypes; the process of speciation, including mechanisms that prevent hybridization and genetic introgression; as well as characterising the origins and history of iguana populations. These can be linked with palao- and present environmental data to yield a better understanding of the environmental and ecological conditions which drove the evolution of these species.
The project is a part of a collaborative iguana genome and evolution consortium led by Dr Gabriele Gentile at the University of Rome Tor Vergata. Dr Gentile has been pioneering the study and conservation of pink iguanas for many years. The student will spend time working in both Leeds and Rome.
Multiple genome sequences for all land and marine iguana species are currently being generated, as a result of a collaboration between the University of Rome Tor Vergata and the Universiti Kebangsaan Malaysia (Prof. Mohd Firdaus Raih) and will be completed shortly.

Methodologies
This is essentially a bioinformatics/computation project, but there may be opportunities to gain hands on laboratory experience of associated DNA sequencing techniques. The project will use data from a range of Next Generation Sequencing (NGS) approaches including de novo sequencing on Illumina and other platforms to build and annotate de novo assemblies of iguana genomes. Data will be then be analysed with a range of bioinformatics, population genomics and molecular evolution tools in high performance computing environments, as appropriate to the research questions.
Requirements
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.
Research context and partners
This project is part of a consortium involving researchers from the University of Leeds, University of Rome, Tor Vergata, and Universiti Kebangsaan, Malaysia. The student will join the Ecology and Evolution group in the School of Biology, Leeds, 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 student will also spend significant time working with Dr Gentile in Rome, and visiting other collaborating institutions across Europe and further afield.

Funding Notes

The Faculty of Biological Sciences is pleased to announce a number of fully-funded PhD studentships to start in Oct 2019, covering academic fees at UK/EU level and providing a stipend at research council rate (£15,009 for 2019-20) for 4 years. Candidates should have, or be expecting, a 2.1 or above at undergraduate level in a relevant subject. A range of projects, spanning the research areas of the faculty, are eligible for funding. Please apply online, clearly stating which project/supervisor you are interested in and including a CV and transcripts.

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