genomics; evolution; bioinformatics; selection; development; database
Roux J., Liu J., Robinson-Rechavi M. (2017), Selective Constraints on Coding Sequences of Nervous System Genes Are a Major Determinant of Duplicate Gene Retention in Vertebrates, in Molecular Biology and Evolution
, 34, 2773-2791.
Kryuchkova-Mostacci N., Robinson-Rechavi M. (2016), A benchmark of gene expression tissue-specificity metrics, in Briefings in Bioinformatics
, 18, 205-214.
Kryuchkova-Mostacci N., Robinson-Rechavi M. (2016), Tissue-Specificity of Gene Expression Diverges Slowly between Orthologs, and Rapidly between Paralogs, in PLOS Computational Biology
, 12, e1005274.
Robinson-Rechavi Marc (2015), Genomics is changing Evo-Devo, in Journal of Experimental Zoology Part B: Molecular and Developmental Evolution
, 324(4), 315-315.
Bastian F.B., Chibucos M.C., Gaudet P., Giglio M., Holliday G..L., Huang H., Lewis S.E., Niknejad A., Orchard S., Poux S., Skunka N., Robinson-Rechavi M. (2015), The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations, in Database
, 2015, bav043.
Kryuchkova-Mostacci N., Robinson-Rechavi M. (2015), Tissue-Specific Evolution of Protein Coding Genes in Human and Mouse, in PLOS One
, 10, e0131673.
Roux J., Rosikiewicz M., Robinson-Rechavi M. (2015), What to compare and how: Comparative transcriptomics for Evo‐Devo, in Journal of Experimental Zoology Part B: Molecular and Developmental Evolution
, 324B, 372-382.
Morphological and developmental innovations must be encoded in genomes, and thus their evolution must be understandable at least in part in terms of genome evolution. Among these innovations, at least some are expected to be adaptive. The proportion of adaptive changes in developmental evolution, and the proportion of developmental changes in adaptation, are both poorly known, the two topics having been studied separately since the neo-Darwinian synthesis. Functional genomics and population genomics, together with increasingly powerful and specific bioinformatics tools, provide us for the first time with a framework to integrate Evo-Devo with the study of adaptation. In this project, we intend to investigate this question using publicly available data and bioinformatics tools developed in our group, with a focus on two aspects: the role of gene and genome duplication in adaptation and in development; and the role of adaptation and neutral processes in the high inter-species divergence of genes expressed in late development, when divergent morphologies are established. The main challenge that we will address is distinguishing high evolutionary rates due to adaptation from high evolutionary rates due to neutral processes, for protein coding sequences, regulatory non coding sequences, and expression patterns.