An inordinate fondness for beetles, or an arms race with plants?
Channel: SIB - Swiss Institute of Bioinformatics
Date: 2019-10-28

What you will discover: a behind-the-scenes look at how the authors retrieved the genomic signatures accompanying the dietary shift to phytophagy in beetles – and the bioinformatics pipeline and resources associated

Target audience: Evolutionary biologists working with genomics data

Speaker: Robert M. Waterhouse, Group Leader, Evolutionary-Functional Genomics Group, University of Lausanne and SIB Swiss Institute of Bioinformatics

Click to access specific sections of the talk:
• The hypothesis: coevolution with the plants they feed on are key drivers of beetles’ diversification 01:54
• Input data: genomes and transcriptomes 04:36
• Assessing the gene set completeness (BUSCO) 05:21
• Delineating ortholog groups (OrthoDB) 06:30
• Creating a robust species phylogeny 07:09
• Inferring gene gain and loss (CAFE) 07:49
• Testing whether the changes are adaptive (OUwie in R) 10:01
• Example of adaptive lineage specific expansion 11:10
• Conclusion 11:56

Reference paper
Seppey et al. Genomic signatures accompanying the dietary shift to phytophagy in polyphagan beetles. Genome Biology 2019, https://doi.org/10.1186/s13059-019-1704-5

Bioinformatics resources mentioned in this talk
https://busco.ezlab.org/
https://www.orthodb.org/
https://github.com/hahnlab/CAFE
https://cran.r-project.org/web/packages/OUwie/index.html

Any question about this talk? Contact Robert: robert.waterhouse@unil.ch or find him on Twitter @rmwaterhouse

More about the speaker: 
Robert Waterhouse is an assistant professor at the Department of Ecology and Evolution of the University of Lausanne and a Group Leader at the SIB Swiss Institute of Bioinformatics. His research is focused on elucidating interactions between gene evolution and gene function through developing computational approaches to interrogate evolutionary and functional genomics data. His group works on insects and other arthropods as their countless adaptations to exploit ecological niches mean that they are ideal for investigating how conservation or divergence of functional genomic elements give rise to the splendour of animal biology.

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