*EASTBIO* Evolution of chromosome organisation in holocentric genomes

Evolutionary genomics is beginning to describe genetic changes that underlie biodiversity at both micro- and macro-evolutionary scales. However, the role of structural changes - those that alter the order and organisation of chromosomes, remains poorly understood1. This knowledge gap is particularly relevant for holocentric organisms - those that lack defined centromeres - in which genome reorganisation is hypothesised to be less constrained2.

Lepidoptera provide a perfect model system to study the causes and consequences of genome reorganisation in holocentric taxa, thanks to the fine scale sampling of genomes across the lepidopteran phylogeny. While chromosome structure and number is largely conserved in Lepidoptera at a macro-level, there are a number of radiations that have undergone spectacular and rapid changes in genome organisation and deviate widely from the ancestral state of n=31 chromosomes. A recent study in wood whites (Leptidea) has shown a possible link between transposable element (TE) content and the explosion in chromosome number (up to n=106) in this group3. However, it is unclear whether TE proliferation has triggered chromosomal fissions or vice versa. In general, the factors that drive and constrain the number of chromosomes in holocentric groups remain largely unknown. We also lack understanding of the micro-evolutionary consequences of chromosomal reorganisation, such as its role in generating reproductive barriers between species.

This project will investigate the evolution of chromosome organisation over both macro and micro-evolutionary scales in Lepidoptera. The student will make use of the rapidly growing number of publicly available reference genomes (lepbase.org) including assemblies that are currently being generated by the Martin and the Lohse labs. The specific aims of this project are to:

1. Characterize and reconstruct genome structural evolution across the Lepidopteran phylogeny.

2. Investigate the drivers and constraints to chromosome reorganisation, including transposable elements, chromosome features such as telomeres and gene families.

3. Develop bioinformatic tools for inferring, visualising and modeling structural evolution.

4. Investigate the population genomic consequences of chromosomal fusion and fission events and their potential role in speciation, focusing on selected taxa: Danaus, Heliconius, Leptidea and Lycaenids.

The lead supervisor, Simon Martin, brings extensive experience in butterfly speciation genomics and bioinformatics. Co-supervisor 1, Konrad Lohse has extensive experience in population genomics and as part of an ERC funded project is generating genome assemblies and whole genome re-sequence data for several sister species pairs of European butterflies. Co-supervisor 2, Mark Blaxter has extensive experience in genome evolution and bioinformatics. 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 (http://genomics.ed.ac.uk). This project is mainly computational/quantitative with ample scope for developing theoretical models of speciation and/or new inference approaches. The project may also include some fieldwork and/or a short spell in the wet-lab to generate RNASeq data.