The origin of maize (Zea mays ssp. mays) in the US Southwest remains contentious, with conflicting archaeological data supporting either coastal or highland routes of diffusion of maize into the US.Furthermore, the genetics of adaptation to the new environmental and cultural context of the Southwest is largely uncharacterized. To address these issues, we compared nuclear DNA from 32 archaeological maizesamples spanning 6000 years of evolution to modern landraces from across Mexico. We found that the initial diffusion of maize into the Southwest at about 4000 years ago likely occurred along a highland route, followedby gene flow from a lowland coastal maize beginning at least 2000 years ago. Our population genetic analysis also enabled us to differentiate selection during domestication for adaptation to the novel climatic andcultural environment of the Southwest, identifying adaptation loci relevant to drought tolerance and sugar content. 

Neuroendocrine axes, composed by brain neurohormones, pituitary hormones and peripheral gland hormones, regulate major physiological functions and key-steps of life cycles in Vertebrates. We investigate how whole genome duplication events (WGD) that occurred at the basis of the vertebrate lineage (“1R and 2R” for 1rst and 2nd Rounds of WGD) and at the basis of the teleost lineage (“3R” for 3rd Round of WGD) have impacted the molecular and functional evolution of neuroendocrine axes and their roles in the control of life cycles. Model fish species investigated are chosen for their phylogenetical, ecological, socio-economical relevance and the complexity of their life cycle. 

Je présenterai les transformations actuelles des structures en faveur de l’intégrité scientifique en France et dans le monde et je passerai en revue différentes facettes de l’intégrité scientifique, de la réflexion méthodologique aux règles de promotion et de recrutement, en passant par le soin que l’on doit porter collectivement aux données et l’incitation à la science ouverte.

How did evolution emerge in physical-chemical systems during the origin of life? Reproduction requires autocatalysis, but evolution further requires a diversity of autocatalytic systems. In a first study, we found universal stoichiometric criteria to recognize autocatalysis in reaction networks. This analysis unifies our view of self-reproductionin already known systems and indicates that there may exist many others. In a second study, we experimentally measured the dynamics of thousands of autocatalytic RNA reaction networks. The resulting landscape reveals trade-offs between the Darwinian properties of variation and selection in self-reproducing systems. Finally, I will discuss how Darwinian evolution may ultimately be implemented in RNA recombination networks. Bibliography [1] Ameta, S., Arsène, S., Foulon, S., Saudemont, B., Clifton, B. E., Griffiths, A. D., & Nghe, P. (2021). Darwinian properties and theirtrade-offs in autocatalytic RNA reaction networks, Nature Communications (2021, in press) [2] Blokhuis, A., Lacoste, D., & Nghe, P., Universal motifs and the diversity of autocatalytic systems. Proceedings of the National Academyof Sciences, 117(41), 25230-25236…

Comparative genomics studies are central in identifying the coding and non-coding elements associated with complex traits, and the functional annotation of genomes is a critical step to decipher the genotype-to-phenotype relationships in livestock animals. As part of the Functional Annotation of Animal Genomes (FAANG) action, the FR-AgENCODE project aimed to create reference functional maps of domesticated animals by profiling the landscape of transcription (RNA-seq), chromatin accessibility (ATAC-seq) and conformation (Hi-C) in species representing ruminants (cattle, goat), monogastrics (pig) and birds (chicken), using three target samples related to metabolism (liver) and immunity (CD4+ and CD8+ T cells). RNA-seq assays considerably extended the available catalog of annotated transcripts and identified differentially expressed genes with unknown function, including new syntenic lncRNAs. ATAC-seq highlighted an enrichment for transcription factor binding sites in differentially accessible regions of the chromatin. Comparative analyses revealed a core set of conserved regulatory regions across species. Topologically associating domains (TADs) and epigenetic…

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I will describe two projects going on in my lab: 1) CACTUS: integrating clonal architecture with genomic clustering and transcriptome profiling of single tumor cells and 2) Interpretable deep recommender system model for prediction of kinase inhibitor efficacy across cancer cell lines. Below I provide a short summary for both of them.1) CACTUS: integrating clonal architecture with genomic clustering and transcriptome profiling of single tumor cells  Drawing genotype-to-phenotype maps in tumors is of paramount importance for understanding tumor heterogeneity. Assignment of single cells to their tumor clones of origin can be approached by matching the genotypes of the clones to the mutations found in RNA sequencing of the cells. CACTUS is a probabilistic model that leverages the information from an independent genomic clustering of cells and exploits the scarce single cell RNA sequencing data to map single cells to given imperfect genotypes of tumor clones. We apply CACTUS to two follicular lymphoma patient samples, integrating three…