Ant genomics and social evolution

Målgruppe:Bioinformatics, Biology
Niveau:Masters, Bachelor

The ants have evolved a stunning global diversity with more than 15,000 extant species belonging to over 330 genera. Over their history, these colonial insects have been impressive innovators, evolving a huge diversity of advanced traits such as an advanced division of labor with specialized, morphologically distinct castes (queens, workers and even soldiers). The GAGA project was launched in 2017 to generate and study high-resolution genomes for up to 200 ant species, covering most of the genomic and phenotypic diversity of the ants. Since then, 551 samples of 266 species from 130 genera were collected during the first phase of the project, resulting in the generation of 135 new genome assemblies. This dataset, together with the current publicly available genome data for ants, represent a total of ~150 ant genome assemblies, which sets an unprecedent number of available genomes in ants, and even for any invertebrate family. Based on the comparative analysis of these data, we will be able to understand global trends of ant evolution and narrow down the genetic features that have been particularly relevant for the diversification and astonishing evolutionary success of ants.

In particular, the offered master project is flexible and allows the student to work on a particular topic of interest, and familiarize with common bioinformatics tools used in genomics in a research group with demonstrated expertise in this field. Among the possible topics, the hundred high-quality genome assemblies will allow to reconstruct the ant Tree of Life, untangling the relationships across the major genus and allowing to map comparative data to test hypothesis about social evolution at an unprecedent scale. Specifically, you will learn about phylogenomic methods using large-scale genome data with the objective of reconstructing the best supported ant phylogeny.

In addition, there are a number of genes and gene families hypothesized to play an important role in the development of physically differentiated castes, as well as in life-history adaptation of several ant species. However, the genomic basis and the overlap of convergently evolved pathways are still unknown. Here, you can study particular genes or gene families in the surveyed genomes and test evolutionary hypothesis by using popular bioinformatic tools in comparative genomics analyses. The gene families that can be studied with specific interest in social evolution are: chemosensory-related gene families, immune system, developmental genes (Hox, sex determination genes, major royal jelly proteins…), among many others.

Anvendte metoder:State-of-the-art bioinformatic tools to analyse large-scale genome data, including: Gene annotation, phylogenetic inference, detecting positive selection, gene gain and loss. Familiarity with Unix and any programming language (R, Python, Perl) would be beneficial.
Keywords:Bioinformatics, Comparative genomics, Genome annotation, Gene family evolution, Phylogenomics
Vejleder(e): Guojie Zhang and Joel Vizueta