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Comparative and Integrative Genomics of Organ Development

Disciplines evolutionary developpemental biology and evolutionary genomics
Research fields  
Supporting Organisms ENS Lyon
Geographical location Lyon, ENS
Team Leader Sophie Pantalacci/Marie Sémon

Studying the temporal dynamics of development is key to understand adult phenotypes. Hence, we mostly study embryos to understand their developmental history. Biological systems are also the product of more long term history, evolution. Comparing organs in different species is a way to delineate general rules, for instance by distinguishing similarities due to heritage (conservation) and to independent acquisition (convergence). Our main model is the rodent molar, which we study through approaches at the interface of evolutionary developpemental biology and evolutionary genomics. For this, we became specialized in handling transcriptome data in different species and in a developmental context.

1) Comparing organ development with transcriptomes

During development, the expression of thousands of genes is regulated, which modulates the behavior and fate of complex cell populations. By comparing the transcriptomes of different molar germs (lower/upper molar), we are studying how organ identity arises during development and results into different final phenotypes. This is made possible by a combination of transcriptomes at the level of whole organs -which record the relative proportions of tissue types-, at the level of intra-organ compartments, up to the level of single cells.

2) Repeated evolution by developmental facilitation

Convergent evolution is often interpreted as a consequence of a strong selective pressure, such as the adaptation to a new ecological niche. Here we wish to test a complementary interpretation, where repeated phenotypic evolution is facilitated by developmental biases. In mouse the elongation of the first upper molar evolved repeteadly in lab strains and in wild populations. By studying the developmental dynamics in several mouse lab strains and wild populations, we suggest that repeated molar elongation in mouse is facilitated by developmental biases. We also observe that sharp early developmental differences may result in very small final variations.

Collaboration : LBBE, Lyon ; Renata Peterkova, Institute of Experimental medecine, Czech Republic

3) Multispecies detection of convergent genomic evolution.

Convergent evolution is widespread in the history of animals, yet the genomic origins of phenotypic convergence are poorly understood. For instance, we don’t know how much of the evolution of convergent phenotypes is due to the appearance of genomic changes that are convergent themselves. We are involved in a collaborative project for an integrative study of convergent genomic evolution across three animal groups. In this context, we notably develop methods to integrate RNA-seq data in phylogenies and to measure convergent evolution at the level of expression.

Collaboration : LBBE, IGFL, LEHNA

4) Does convergent evolution imply convergent development ?

There are little examples in the litterature documenting the mechanisms underlying the repeated acquitision of a complex morphology. One such case is the independent acquisition of the murine dental plan in mouse and Acomys lineages, where two supplementary cusps develop lingually at the surface of the molar crown. What makes the lingual side special in the upper molar ? Is the development convergent in mouse and Acomys ? By tracking whole genome expression in transcriptome timeseries, combined with fine-resolution description of morphogenesis and patterning, we compare the development of molars in several rodent species.