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Using transcriptomics to understand adaptation and speciation in an island radiation


Biological Sciences

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Dr M Carine , Dr M Chapman No more applications being accepted Funded PhD Project (European/UK Students Only)

About the Project

The Natural History Museum is offering one joint PhD studentship with the University of Southampton, starting on 1 November 2014 or as soon as possible thereafter.

Applications are invited from suitably qualified graduates (first degree results at least 2:1) and the studentship is only open to those who qualify for ‘Home’ tuition fees (UK/EU residence).

Deadline for applications: 19 September 2014. See below for project details and application instructions.
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Studentship details:

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.

Full details can be found here: http://www.nhm.ac.uk/resources-rx/files/carine_chapman-project-132564.pdf

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