*EASTBIO* Speciation and sex-biased gene expression in butterflies

Although males and females share most of their genome, their biology differs in fundamental ways. Sexually dimorphic traits are under intense natural and sexual selection favouring opposing optima in males and females. Studies in model systems like Drosophila have shown that over 50% of genes show sex biased or sex limited expression and it is thought that sex-biased expression has evolved to resolve sexually antagonistic selection (Ellegren & Parsch 2007).

Recent empirical work has shown that sex-biased genes evolve at faster rates and - as predicted by theoretical models - are concentrated on the sex-chromosomes in a number of organisms (Ellegren & Parsch 2007). However, we still know very little about how quickly sex-biased gene expression evolves as species diverge and what knock-on effects the distinct evolutionary dynamics of sex-biased genes have on the speciation process. For example, an intriguing possibility is that sex-specific genes, by virtue of their faster rates of evolution, potential involvement in sexual selection and linkage to sex chromosomes may disproportionately trigger reproductive isolation in the early stages of speciation. Comparative studies suggest that rates of speciation may indeed be correlated with levels of sexually antagonistic evolution. There is also recent evidence that in mammals male-biased genes on the X-chromosome have undergone repeated bouts of strong positive selection, and, as a result, show increased divergence between species. However, genome-wide data on gene-expression are limited to a small number of model systems and we currently lack any direct comparison between sex-specific and unbiased genes in terms of the relevant forces that act during the speciation process. Studies on female heterogametic systems (e.g. birds and butterflies) are particularly valuable, because contrasting them with male heterogametic organisms allows us to find out what mechanisms cause sex-biased genes to accumulate on the sex-chromosomes.

The aim of the project is to use sister-species of European butterflies as a model to quantify both sex-biased and species specific gene expression and investigate the interplay between gene expression, selection and gene-flow during speciation. The specific aims are to:

i) Measure the turn-over in sex-specific expression during species divergence to ask whether sex-biased genes also show disproportional levels of specific-specific expression?

ii) Compare the evolutionary dynamics during species divergence between sex biased genes and unbiased genes. Fitting explicit models of the speciation process (Lohse et al. 2016) and selective sweeps will allow to test whether sex biased genes show reduced levels of post-divergence gene flow and/or and increased rate of selective sweeps.

iii) Test whether butterfly Z chromosomes are enriched for male-biased genes as expected if positive selection at sex-biased genes is driven by dominant mutations.

The lead supervisor, Konrad Lohse, brings extensive experience in population genetics, insect speciation genomics and bioinformatics and has developed inference methods to model divergence and gene flow between young species from genomic data. In collaboration with LepBase and Alex Hayward (Exeter University), the Lohse lab is generating genome assemblies and genome-wide polymorphism data for several sister species pairs of European butterflies. Co-supervisor 1, Laura Ross, brings experience in analysing RNASeq data and has been studying paternal genome elimination and dosage compensation in a variety of insect systems. Co-supervisor 2 Mark Blaxter has extensive experience with designing RNASeq experiments and is leading LepBase (http://lepbase.org/), a BBSRC-funded database for Lepidopteran genomes. All supervisors will advise and help the student to design RNASeq experiments and to analyse transcriptomic and genomic data.

The student will obtain state of the art training in genomics, bioinformatics and advanced evolutionary genetics and statistics. This will also involve basic training through EastBio workshops as well as tailored bioinformatics and coding workshops offered by Edinburgh Genomic. This project is mainly computational/quantitative with ample scope for developing theoretical models of speciation and/or new inference approaches. The project also includes some fieldwork and/or a short spell in the wet-lab to generate RNASeq data.

Lab web site url: http://lohse.bio.ed.ac.uk/

Lab web site url: http://lauraross.bio.ed.ac.uk

Lab web site url http://www.nematodes.org//