PhD Studentship – Identification and analysis of speciation genes in island plants, UK

University of Southampton
Study in:UK
Deadline: 05 January 2018

PhD Studentship – Identification and analysis of speciation genes in island plants

Biological Sciences Research

Location:  Highfield Campus
Closing Date:   Friday 05 January 2018
Reference:  939717BJ

PhD Supervisor: Mark Chapman

Co supervisor: Lorraine Williams, Mark Carine (NHM)

Application Deadline: 5 January 2018
PhD Description:

In the current genomics revolution we are now in a position to investigate how mutation, selection, and gene flow contribute to phenotypic evolution and the origin of species. An excellent scenario in which to study this is the origin of species that are adapted to divergent altitudes, where steep ecological selection gradients vary over short geographic distance. By analysing genetic variation throughout related species’ genomes, we can pinpoint genes that correspond to reproductive isolation or ecological differentiation.

This project will analyse speciation genomics in Descurainia, a plant genus found throughout the Canary Islands. Several species are endemics, showing ecological speciation (the origin of species by adaptation to novel environments) within and between islands. A reference genome is being assembled and annotated in the lab and the SPITFIRE project will generate and analyse sequencing data from multiple individuals of all the endemic species.

Specific objectives:

1. Phylogenetic analyses of the dynamics of speciation, including the role of introgression in speciation.

2. Quantifying divergent adaptation between species through a reciprocal transplant experiment on Tenerife.

3. Identification of candidate ‘speciation genes’.

4. Determining the function of a subset of these candidate genes using transgenics.


The project will involve diverse techniques and approaches.

Initially fieldwork in the Canary Islands will be undertaken for seed and leaf collection as well as for testing local adaptation using a reciprocal transplant study.

Reduced-representation sequencing data are already available for the analysis of the phylogenetic relationships. Data analysis will use STACKS to call SNPs and population genetic analyses will infer bottlenecks and rates of gene flow between species.

The speciation genomics analysis will focus on the evolution of high altitude adaptation. Whole genome sequencing will be carried out for pooled populations of a high and low altitude species pair. To identify candidate adaptation/speciation genes the student will identify genomic regions of high divergence between species and increased linkage disequilibrium within species indicative of selective sweeps.

Functions of many candidate genes will be unknown; therefore a subset of those will be selected for functional analysis. Divergent alleles (i.e. the ‘high-adapted’ and ‘low-adapted’ alleles) will be cloned and transformed into the orthologous Arabidopsis knockout and into wild-type plants. The phenotypes of the knockout and transgenic lines will be compared as well as testing for differing freezing tolerance and fitness at reduced temperature.


The SPITFIRE DTP programme provides comprehensive personal and professional development training alongside extensive opportunities for students to expand their multi-disciplinary outlook through interactions with a wide network of academic, research and industrial/policy partners. The student will be registered at the University of Southampton and hosted at both the Natural History Museum and University of Southampton for periods of the project.

The student will carry out fieldwork (ca. two one-week trips) on Tenerife alongside local collaborators. This will include fieldwork and plant identification training and planning, setting-up and monitoring the reciprocal transplant experiment. The student will be trained in molecular biology and genetics, specifically DNA extraction and prep for sequencing, and gene cloning and transformation of Arabidopsis. Extended training in the bioinformatic analysis of large genome-scale datasets will be supplied, including a nationally run training course. The student will learn phylogenetics and analysis of patterns of variation throughout the genome.

For more information see

Funding Notes:

The project is funded for 3.5 years and welcomes applicants from the UK and EU who have or expect to obtain at least an upper second class degree in Biological Sciences or allied subjects. Funding will cover fees and a stipend at current research council rates of £ 14,553 per annum.

Due to funding restrictions this position is only open to UK/EU applicants

Information on how to apply:

Applications should be submitted online at:

Please place Mark Chapman’s name in the field for proposed supervisor.

General enquiries should be made to Mark Chapman ( Any queries on the application process should be made to

The University of Southampton and Biological Sciences both hold an Athena Swan Silver & Bronze Award, respectively, demonstrating their commitment to provide equal opportunities and to advance the representation of women in STEM/M subjects: science, technology, engineering, mathematics and medicine.   Due consideration will be given to applicants who have taken a career break.  University benefits include onsite childcare facilities, state-of-the-art on-campus sports, arts and culture facilities, a full programme of events and a range of staff discounts.

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