Speciation and sex-biased gene expression in butterflies

Supervisors: Konrad Lohse, Michael Ritchie

Project description:

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. 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 (Huylmans et al 2017). 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.

ii) Compare the evolutionary dynamics during species divergence between sex biased genes and unbiased genes by fitting explicit models of the speciation process (Lohse et al. 2016).

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 and bioinformatics and has developed inference methods to model divergence and gene flow from genomic data. In collaboration with LepBase and Alex Hayward (Exeter University), the Lohse lab is generating reference assemblies genome-wide polymorphism data for several sister species pairs of European butterflies. Co-supervisor Mike Ritchie has extensive experience with designing RNASeq experiments and speciation research. 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 Genomics. This project is mainly computational/quantitative but also includes some fieldwork and/or a short spell in the wet-lab to generate RNASeq data.

Contact details: Dr. Konrad Lohse konrad.lohse@ed.ac.uk

Background reading:

Ellegren H & Parsch J. 2007. The evolution of sex-biased genes and sex biased gene expression. Nature Reviews Genetics (8): 689-698.

Huylmans AK, Macon A, Vicoso B; 2017. Global Dosage Compensation Is Ubiquitous in Lepidoptera, but Counteracted by the Masculinization of the Z Chromosome, MBE, https://doi.org/10.1093/molbev/msx190

Lohse K, Chmelik M. Martin, & SH Barton NH. 2016. Efficient Strategies for Calculating Blockwise Likelihoods Under the Coalescent, 202 (2), 775-786.