Oceanic island museomics: human impact and the natural laboratory paradigm

Trochetiopsis ebenus in Chelsea Physic Garden by Tim Waters licenced by CC BY-NC-ND 2.0

This project will investigate the assumption that islands are ideal model systems for studying evolution, given the scale and breadth of human impact on island habitats.

The studentship is part of the CENTA doctoral training partnership, funded by NERC and starts October 2019.

Apply for this course

Read the eligibility criteria and application guidance below, then apply through the University of Warwick's online application service.

Please submit your CENTA studentship application form as part of the application procedure.

Application deadline: 21 January 2019

Project Highlights

  • Testing the assumptions of the natural laboratory paradigm - the idea that islands are ideal model systems for studying evolution
  • Using archival collections in novel ways to address novel questions
  • Multidisciplinary training integrating a DNA work at University of Warwick with herbarium and field-based research at the Natural History Museum

Overview

Oceanic islands have long been recognised as ‘natural laboratories’, ideally suited for in-situ studies of evolution. They provide some of the most striking, text book examples of adaptive radiations and have played - and continue to play - a major role in the development of key concepts in biology.

At the same time, their biota, that are so rich in unique diversity, are also among the most globally endangered. In the Azores, for example, it is estimated that less than 10% of the native forest at the time of colonisation in 1439 survives. Whilst in the Canaries and in Easter island, palaeoecological data points to pre-historic, human-mediated extinction of dominant tree species.

More recent records of extinction - backed by specimens in museums and herbaria - are known from many oceanic islands worldwide.

Developments in molecular biology, notably the development of Next Generation Sequencing techniques (NGS) have the potential to greatly extend the scope of studies on ‘island laboratories’ to encompass fundamental questions relating to the genetic basis of island diversification events.

The acquisition of DNA sequence data at the genomic level is providing unprecedented opportunities to uncover the history of lineages in non-model organisms. It is allowing us to elucidate evolutionary relationships in rapidly evolving island lineages that were previously intractable and to start to understand the genomic basis of speciation events, to determine the number of loci involved in speciation, the nature of the genetic differences, and what those loci control.

However, the ‘natural laboratory’ paradigm assumes that diversity patterns on islands are the result of natural ecological and evolutionary processes. It assumes that the impact of humans is not significant for the interpretation of those patterns. Is that a valid assumption?

Given the scale and breadth of human impact on oceanic islands, this project aims to test this assumption of the natural laboratory paradigm across a spectrum of evolutionary questions.

Methodology

We propose to test the assumptions of the natural laboratory paradigm using the floras of St Helena. There are classic examples of evolutionary processes such as adaptive radiation; humans have had a profound impact on their biota and there is a history of botanical collecting spanning the last three hundred years, a period of profound change. We will focus the study on Trochetiopsis in St Helena.

Next generation sequencing coupled with ancient DNA techniques will be used to generate data from both living and herbarium material for these evolutionary radiations. We will contrast inferences based only on living material with those also incorporating archival samples. This will allow us to elucidate the impact of range reductions and extinctions on phylogenetic and phylogeographic questions at different scales – from broad scale sister taxon relationships of island clades to population-level analyses.

Training and Skills

This project is multidisciplinary in nature. At Warwick, the student will receive training in the generation of NGS data and the analysis of those data to address phylogenetic and phylogeographic questions. Integration of historic herbarium material in those analyses will be integral to the training provided. At the Natural History Museum, the student will develop expertise in island plant taxonomy, evolution and biogeography and will receive training in fieldwork and in herbarium-based research.

Timeline

Year 1: Sample acquisition of modern and herbarium samples, and de novo assembly of the Trochetiopsis genome wide sequence generation.

Year 2: Building on the Trochetiopsis genome we will sequence a number of modern and herbarium samples representing the breadth of the island over a period of time from the point of first contact.

Year 3: Genomic analyses of Trochetiopsis including phylogenomics, genetic diversity, signatures of selection and mutation load will be carried out to build a picture of how the species has changed since first human contact.

Partners and collaboration

This project is a collaboration between the University of Warwick and the Natural History Museum, London (NHM).

At Warwick Robin Allaby leads the plant ancient DNA group specializing in archaeogenomics and genome evolution.

At the NHM, Mark Carine is the lead curator for the botanical collections and a plant systematist with particular interests in island floras and biogeography. His research has been addressing taxonomic problems, biogeographic patterns and speciation processes in a number of taxa and island systems in the Atlantic.

Eligibility

CENTA studentships are available to UK and EU applicants only.

Residency rules apply. UK and EU students with qualifying residence in the UK are eligible for full-cost awards. Non-UK students from the EU who do not have qualifying residence are eligible for fees-only awards, which covers the tuition fees and Research Training Support Grant (RTSG), but not stipend. 

All applicants need to comply with the registered university's English-language requirements.

Applicants should have obtained or be about to obtain a First or Upper Second Class UK Honours degree, or equivalent qualifications gained outside the UK. Applicants with a Lower Second Class degree will be considered if they also have a master's degree. Applicants with a minimum Upper Second Class degree and significant relevant non-academic experience are encouraged to apply.

How to apply

Applications for the PhD are processed through the University of Warwick's online application service.

To apply:

  • Complete the online application form - choose PhD in Life Sciences and enter NERC studentship in the Finance section.
  • Please also complete the CENTA application form  and submit it as an attachment to your online application form.
  • Upload a transcript from your current or previous study, a CV and any other documents that you feel would support your application (within 24 hours of submitting your online applicaion you will receive a link allowing you to upload additional supporting documents).
  • Ask your referees to submit a reference for you by 28th January 2019 at the very latest. Note: when you submit your application, an email will automatically be sent to your referees requesting a reference for you. This email will contain a secure link for your referee to upload a reference for you.

The deadline for applications is 21 January 2019.

Any questions?

If you have any questions about the project please contact

Main supervisor: Prof Robin Allaby

Supervisors

University of Warwick

Main supervisor: Prof Robin Allaby

Natural History Museum

Co-supervisor: Dr Mark Carine

CENTA Doctoral Training Partnership

Joint PhD training partnerships involving the Universities of Birmingham, Leicester,  Warwick, Loughborough, Cranfield and The Open University and four NERC research organisations.

Funded by 

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