Genomic signatures of speciation in Drosophila

Supervisors: Michael Ritchie, Konrad Lohse

Project Description:

Genetic adaptation, gene flow and population history are key processes to understand how species cope with challenges and how both contemporary and historical environmental change has influenced their divergence, distribution and abundance. Advances in the availability and methods for the analysis of complete genomes allow us to reconstruct species evolution with unprecedented resolution. Much new data is emerging on patterns of genomic divergence both within and between species, and debates over the causes of genomic divergence are a major issue in comparative genomics. This project will examine patterns of genomic divergence in one of the best understood of all organisms, the fruit fly Drosophila. Genome scale data will be compiled in combination with data on the extent of evolutionary divergence (in terms of pre- and post-mating reproductive isolation) between species and their distribution and ecological specialisations, and mating system variation. The data will come from both published and novel genome sequences and detailed compilations of the strength of different types of reproductive isolation and ecology exist. The student will integrate this database and use novel analytical techniques to determine genetic divergence and gene flow (inferred as migration rate across different genomic regions). New approaches to outstanding questions in evolutionary divergence can be asked such as; do similar patterns of genomic divergence correlate with sexual or post-mating isolation? Do both influence sex-chromosomes versus autosomes similarly? Do ecological generalists show different patterns of genomic divergence from specialists? Do patterns of divergence differ between sympatry and allopatry, and how often do we detect gene flow in sympatric species? The lead supervisor brings extensive experience of speciation in Drosophila and the co-supervisor is developing new statistical approaches to the analysis of genome scale data. The student will receive advanced training in evolutionary biology, genomics, bioinformatics and biostatistics. Enquiries to Mike Ritchie.

Background reading:

Lohse et al. 2015. Genome-wide tests for introgression between cactophilic Drosophila implicate a role of inversions during speciation. Evolution. 69: 1178-90.

Ravinet, M., et al. 2017. Interpreting the genomic landscape of speciation: a road map for finding barriers to gene flow. J. Evol. Biol., 30: 1450–1477.

Yukilevich, R. 2014. The rate test of speciation: estimating the likelihood of non-allopatric speciation from reproductive isolation rates in Drosophila. Evolution 64: 1150-1162.