Comparative Genomics of Rapid Signal Evolution

Supervisors: Nathan W. Bailey, Mark Blaxter, Carolin Kosiol

Project Description:
This EASTBIO project examines the genomics of rapid signal evolution. The overarching question is: What are the genomic causes and patterns underlying animal signal diversity? The project addresses this question using a comparative approach focused on acoustic signalling in the insect genus Teleogryllus, a compelling field cricket system for interrogating and revealing genetic mechanisms of rapid signal evolution.

Animal signals are predicted to evolve rapidly and play an important role in promoting and maintaining species diversity, but it is challenging to test how genome organisation and genomic architecture contribute to signal variation. Understanding such genomic responses is important for predicting evolutionary potential and the origins and maintenance of biological diversity. The PhD student will work with researchers at the University of St Andrews and University of Edinburgh to address three goals: (1) characterise functional genomic features of QTL and candidate genes for interspecific song variation, (2) resequence genomes of multiple species and perform phylogenetic analysis of candidate gene and gene family evolution, and (3) develop new bioinformatics approaches to test theoretical predictions about genomic dynamics during rapid signal evolution.

The student will take advantage of ChirpBase, an open, web-based genome browser for singing insects developed by the Blaxter and Bailey labs. Novel annotation and gene prediction pipelines will be developed for the project and implemented in Teleogryllus oceanicus and allied species to facilitate comparative work. The student will gain wet-lab experience to produce next- and third-generation sequencing data. Training in bioinformatics will be oriented towards the goal of testing genome-wide patterns of linkage disequilibrium, recombination variation, and selection and introgression of regions implicated in signal diversity. Analyses will be performed to test hypotheses about rapid signal diversification in a comparative phylogenomics framework. The final goal will combine simulation models with empirical data to test predictions about the genomic architecture of acoustic signal traits. Each goal will lead to training in, and development of, novel bioinformatic and computational pipelines that will be broadly applicable to other systems and research questions.

The project is a collaboration involving lead supervisor Dr Nathan Bailey (St Andrews) and co-supervisors Prof Mark Blaxter (Edinburgh) and Dr Carolin Kosiol (St Andrews). In addition to EASTBIO induction and annual symposia, the student will participate in bioinformatics training modules at both universities, and undertake yearly secondments lasting between 1 - 2 months in the Blaxter lab. A key objective is for the student to become fluent in cutting-edge bioinformatics approaches, particularly as applied to non-model organisms. Both Bailey and Kosiol are members of the St Andrews Bioinformatics Unit, which will provide computing resources and infrastructure necessary for the project. Wet lab work will be undertaken at St Andrews, and next-generation sequencing will benefit from existing links between the Bailey lab and Edinburgh Genomics, of which Blaxter is Science Director. Bailey can be reached for further enquiries.

References:

  1. Pascoal S, Cezard T, Eik-Nes A, Gharbi K, Majewska J, Payne E, Ritchie MG, Zuk M, Bailey NW (2014) Rapid convergent evolution in wild crickets. Current Biology 24:1369-1374.
  2. Challis RJ, Kumar S, Dasmahapatra KKK, Jiggins CD, Blaxter M (2016) Lepbase: the Lepidopteran genome database. bioRxiv. http://dx.doi.org/10.1101/056994.
  3. Locke DP et al. (incl. Kosiol C) (2011) Comparative and demographic analysis of orang-utan genomes. Nature 469:529-533.
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