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The University of Southampton
Biological SciencesPostgraduate study

Title of project - Using transcriptomics to understand adaptation and speciation in an island radiation

Name and department of supervisors

Mark Chapman (Centre for Biological Sciences, University of Southampton); Mark Carine (Department of Life Sciences, Natural History Museum)

Rationale for the study

The evolutionary outcomes of hybridisation can range from being of little consequence to the origin of entirely new species. In some cases, hybridisation is rare, but if the hybrids exhibit adaptation to a novel habitat they can be maintained as a new species. These scenarios are ideal for understanding the intersection between adaptation, migration, hybridisation and speciation.

Of particular value to these studies is using Next Generation Sequencing (NGS) to assay the expressed portion of the genome (the transcriptome), simultaneously providing gene expression and sequence polymorphism data for thousands of genes. Firstly, this allows detection of differentially expressed loci that underlie adaptive divergence between differentially adapted or independently evolved taxa. Secondly, the genetic signatures of sequence-based adaptive divergence can be investigated by assaying polymorphism and divergence between species, identifying loci with non- neutral patterns of sequence polymorphism. In the past, such analyses were only possible for model organisms; however one can now study non-model organisms, in prime ecological and evolutionary scenarios, to investigate the genetic control of these phenomena.

Isolated oceanic archipelagos are natural laboratories of evolution, ideally suited for in situ studies of speciation. The volcanic oceanic archipelagos of Macaronesia (the Azores, Madeira, Canaries and Cape Verde Islands) are a notable example, demonstrating a high degree of endemism, and spectacular examples of evolutionary radiations with geographic isolation, habitat shifts and hybridisation all contributing to the rapid diversification of endemic lineages. The endemic genus Argyranthemum (Compositae) provides an excellent example of a Macaronesian radiation, comprising twenty-four species that have evolved following a single colonisation of the region. As with many Macaronesian endemic lineages, phylogenetic relationships are not fully resolved and hence any efforts to study speciation processes will require an accurate phylogenetic and population genetic understanding of the species involved. Argyranthemum also provides a rare, well-documented case of homoploid hybrid speciation with the hybrid species A. sundingii derived on multiple occasions from A. frutescens and A. broussonetii. This makes Argyranthemum an ideal biological scenario to understand multiple evolutionary phenomena in concert.

 

Aims and objectives

This studentship will use the homoploid hybrid A. sundingii as an exemplary scenario with which to investigate the genomics of adaptation, reproductive isolation and hybrid speciation. Multi-locus phylogenetic analyses will be carried out and used to understand genus-wide patterns and processes of evolution. The project will specifically address three questions:

(1) How has hybrid speciation modulated gene expression? Hybrid species exhibit an amalgam of genomic segments from the parental species; however the extent to which gene expression is inherited and/or modified is poorly understood. This investigation will (A) detect loci with a novel expression phenotype (relative to the parents), an exciting route to explaining evolutionary novelty, (B) identify genes and pathways that play a role in speciation and adaptation to a novel environment, and (C) identify networks of co-expressed genes to determine if networks of co-expression are co-inherited from one parent. This has never before been studied in hybrid species.

(2) What is the relative contribution of the parental species to the genome of the hybrid  species A. sundingii? In a hybrid species, selection for co-adapted gene complexes and removal of unfit allelic combinations will take place early in its establishment. Comparisons of transcriptome sequences for the hybrid species and A. frutescens and A. broussonetii will (A) determine the parental contributions to the hybrid genome of A. sundingii, and (B) detective selective sweeps and adaptive divergence, hallmarks of Darwinian selection. Further, investigating the degree to which two lineages of the hybrid species have converged on a similar genomic composition will reveal how selection versus stochastic loss of parental loci occurs. This is an exciting and important question in speciation genomics, but can only be answered in a handful of biological situations such as Argyranthemum.

(3) How have geographical isolation, habitat shifts and hybridisation contributed to the diversification of Argyranthemum? Current phylogenetic data, based primarily on just two loci, indicates patterns of diversification consistent with geographical isolation, habitat shifts and hybridisation during the evolution of Argyranthemum. To fully clarify these patterns, phylogenetic and population genetic analyses of all Argyranthemum species sequenced across multiple loci will take place. This study will leverage Targeted Amplicon Sequencing, a method to simultaneously sequence dozens of loci from hundreds of individuals using NGS. Around 20 suitably variable loci from the thousands sequenced in investigations 1-2 above will be identified and amplified from approximately 200 individuals, an unprecedented depth for this type of investigation. Phylogenetic relationships and divergence times will be established and used to investigate the processes driving the diversification of the genus. A monograph of Argyranthemum was produced at NHM and the herbarium consequently includes extensive collections and a wealth of data for this task.

Training elements of the project

The student will receive a broad training in systematics, evolutionary biology and bioinformatics. The student will receive training in the processing of transcriptomics data using software already in use in the Chapman lab. Fieldwork will give the student the opportunity to develop field collecting skills. A range of phylogenetic techniques will be used. Training will be provided both through direct training and participation in short courses.

Essential requirements

Desirable requirements

For more information please contact Dr Mark Carine at M.Carine@nhm.ac.uk

Information

For more information please contact Dr Mark Carine at M.Carine@nhm.ac.uk

Applications

Please send the following documents to Dr Eileen J. Cox (postgradoffice@nhm.ac.uk) by 19th September 2014.

Interview date: Mid October at The Natural History Museum

Start date: 1 November 2014 or as soon as possible thereafter

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