Section: New Results

Inference of evolutionary molecular events at different scales

We have progressed in the integration of several evolutionary events at different scales of genomes in a single model used for inference of ancient events from the observation of extant genomes. We handle nucleotide substitutions, gene duplications, losses, lateral transfers and rearrangements. We have tested the framework on 36 cyanobacteria species, reconstructing up to 80% of ancestral chromosomes in some clades [8] . The inference algorithm is still mainly sequencial, in the sense that it first accounts for nucleotide substitutions, gene duplications, losses, lateral transfers [29] , and then for rearrangements. But we also developed a way to provide a feedback of the result on rearrangements to the inference of substitutions by correcting gene trees [22] , [38] . We have used these methods to reconstruct a nucleotide-scale sequence of the genome of the medieval black death agent [9] ,[44] . It includes a chromosome and three plasmids, and is different in structure from any extant strain. We follow the first ancient bacterial genome sequencing in 2011 and complete and order the genome with computational predictions. We then dispose of a complete view of the molecular evolution in the Yersinia pestis clade.

This work was part of Murray Patterson's post-doctoral fellowship. It also involved collaborations with L. Gueguen and V. Daubin from the Laboratoire de Biométrie et Biologie Evolutive (UMR CNRS 5558, Lyon), with Nadia El-Mabrouk from the Département d'Informatique et de Recherche Opérationnelle in Montréal (Canada), with Cédric Chauve from the Department of Mathematics of Simon Fraser University (Burnaby, Canada), and with G. Szollosi from the Biophysics Research Group in Budapest (Hungary).