Evolutionary genomics of social insects.
Extensive theoretical work has explained how and why complex
societies evolve. However, only little is known about the genes
and molecular mechanisms responsible for social
phenotypes. We have been identifying genes and mechanisms
involved in the evolution of insect societies using modern
genomics tools (Illumina, RNAseq, RADseq...). For example we recently:
- sequenced and analyzed the genome of the invasive red fire ant Solenopsis invicta (PNAS 2011)
- discovered that a fundamental social trait in this species (how many queens
are accepted in the colony) is determined by
variants of a social chromosome (Nature 2013).
- described the gene expression changes that occur in a
virgin queen when she is given the opportunity of replacing her
mother (Mol Ecol 2010).
We are interested in themes including the genetics of behavior, the interplay between social evolution and genome evolution, and the molecular mechanisms responsible for differences between castes.
Genomics & Bioinformatics for emerging model organisms.
The recent 10,000-fold drop in the cost of DNA sequencing means
that any lab can sequence anything - and
lots of it. This brings exciting opportunities but also new
challenges. We develop innovative tools and approaches to
facilitate modern biological work on emerging model
organisms. For example:
- BLAST is the most commonly used bioinformatics tool. But setting it up for private data and using it is counter-intuitive. We're
developing SequenceServer to
make BLAST easy to use.
- Sequencing genomes has become straightforward. But you
quickly realize that most gene predictions need to be inspected
and many need to be manually fixed before performing analyses. This makes
multi-species, multi-gene analyses very challenging. We are developing infrastructure to obtain help for this using crowd-sourcing.
Moreover, to further help with the curation of newly sequenced genomes,
GeneValidator, a tool that helps with the identification of problematic
gene predictions. In order to make this more accessible to biologists, we
have also made GeneValidator available online at:
Genomic analyses require jumping back and forth between many
bioinformatics tools. The tools are young, often requiring frequent
updates, and can be challenging to install. Software updates can make
analyses difficult to reproduce and it is challenging to maintain
different versions of software for different projects. Realising that
isolated and reproducible bioinformatics software setup is possible
we are developing
- a docker wrapper to facilitate use of docker to run analyses and create