PhD Supervisor: Hugues ROEST CROLLIUS
Host Laboratory: Dynamique et Organisation des Génomes (DYOGEN), Institut de Biologie de l’ENS (IBENS), UMR 8197, 46 rue d’Ulm, 75005 Paris
Doctoral School: ED657 – Science du Vivant, Université PSL
ATLASea Targeted Project involved in the project: BYTE-Sea
Resources available in the laboratory for the PhD: The PhD student will be hosted at the Institut de Biologie de l’ENS (IBENS) in central Paris. IBENS is composed of 30 research teams covering a wide range of fields, several high-level technical platforms including a computer cluster (4000 CPU and 13 GPU). IBENS hosts a great diversity of nationalities and includes a dynamic student and post-doc association.
Skills requirements: Bioinformatics (programming), comparative genomics, knowledge in evolution.
Summary
One of the major challenges of modern genomics is to understand genome evolution in order to link genotype to phenotype through the lens of species evolution and adaptation. Comparative genomics is currently benefiting from an unprecedented influx of new data, driven by large-scale biodiversity sequencing initiatives under the umbrella of the Earth BioGenome Project, of which ATLASea is a part. These large datasets provide an ideal resource for identifying genotype–phenotype relationships using both “forward” and “reverse” genomics approaches, which associate genomic signatures with phenotypic changes.
For several years, the DYOGEN team has focused in particular on teleost fish genomes, which underwent a whole-genome duplication prior to the major radiation of teleosts, giving rise to approximately 30,000 extant species. This PhD project will build on the team’s expertise in bioinformatics and comparative genomics of fish to develop and apply these strategies to well-documented cases of convergent evolution in teleosts. Convergent evolution — where the same phenotype independently appears or disappears in multiple lineages — provides a particularly powerful framework for identifying genotype–phenotype relationships, as it relies on naturally replicated evolutionary events. Numerous examples have been described in fish, including:
- The emergence of amphibious traits,
- The evolution of viviparity,
- Adaptations in osmoregulation,
- The emergence of endothermy,
- Extremely short or long lifespans,
- The loss of the swim bladder, stomach, scales, or fins.
A more exploratory approach to the convergent evolution of life-history traits or morphological characters will also be investigated using data compiled from databases such as FishBase and the Encyclopedia of Life (EOL).
The approach will involve constructing reference datasets including:
- Phylogenies of protein-coding genes,
- Families of conserved non-coding elements (CNEs).
More than 600 high-quality fish genomes are currently available and will provide the basis for defining relevant subsets (gene families, multiple genome alignments, etc.).
When no specific genomic element (gene or CNE) can be directly associated with a phenotype of interest through discrete patterns of presence or absence, two complementary strategies will be implemented to broaden the range of genetic determinants considered:
- Extension of the biological context.Functional annotations (Gene Ontology, metabolic pathways,paralogy relationships) will be used to place genes within an extended functional framework.
- Analysis of continuous variation in molecular evolutionary rates. Rather than relying solely on binary presence/absence patterns, continuous signals of variation in evolutionary rates will be measured along phylogenies in order to detect accelerations or constraints associated with the phenotypes under study.
This project offers a unique opportunity to leverage the rapidly growing collection of high-quality teleost genomes generated by ATLASea and other biodiversity sequencing initiatives, in order to explore, in an integrated manner, the genetic basis of phenotypic innovation in fishes.
Keywords: Evolution, Comparative genomics, Bioinformatics, Phenotypes, Teleostean fishes, Marine biology