Biomedical subjects

Bastien Boussau

Publications and source records attributed to Bastien Boussau.

3 recordsLinked to original sources

PubMed2006

Efficient likelihood computations with nonreversible models of evolution.

Recent advances in heuristics have made maximum likelihood phylogenetic tree estimation tractable for hundreds of sequences. Noticeably, these algorithms are currently limited to reversible models of evolution, in which Felsenstein's pulley principle applies. In this paper we show that by reorganizing the way likelihood is computed, one can efficiently compute the likelihood of a tree from any of its nodes with a nonreversible model of DNA sequence evolution, and hence benefit from cutting-edge heuristics. This computational trick can be used with reversible models of evolution without any extra cost. We then introduce nhPhyML, the adaptation of the nonhomogeneous nonstationary model of Galtier and Gouy (1998; Mol. Biol. Evol. 15:871-879) to the structure of PhyML, as well as an approximation of the model in which the set of equilibrium frequencies is limited. This new version shows good results both in terms of exploration of the space of tree topologies and ancestral G+C content estimation. We eventually apply it to rRNA sequences slowly evolving sites and conclude that the model and a wider taxonomic sampling still do not plead for a hyperthermophilic last universal common ancestor.

Algorithms↗

PubMed2004

Computational inference of scenarios for alpha-proteobacterial genome evolution.

The alpha-proteobacteria, from which mitochondria are thought to have originated, display a 10-fold genome size variation and provide an excellent model system for studies of genome size evolution in bacteria. Here, we use computational approaches to infer ancestral gene sets and to quantify the flux of genes along the branches of the alpha-proteobacterial species tree. Our study reveals massive gene expansions at branches diversifying plant-associated bacteria and extreme losses at branches separating intracellular bacteria of animals and humans. Alterations in gene numbers have mostly affected functional categories associated with regulation, transport, and small-molecule metabolism, many of which are encoded by paralogous gene families located on auxiliary chromosomes. The results suggest that the alpha-proteobacterial ancestor contained 3,000-5,000 genes and was a free-living, aerobic, and motile bacterium with pili and surface proteins for host cell and environmental interactions. Approximately one third of the ancestral gene set has no homologs among the eukaryotes. More than 40% of the genes without eukaryotic counterparts encode proteins that are conserved among the alpha-proteobacteria but for which no function has yet been identified. These genes that never made it into the eukaryotes but are widely distributed in bacteria may represent bacterial drug targets and should be prime candidates for future functional characterization.

Alphaproteobacteria↗

PubMed2003

Phylogenetic dating and characterization of gene duplications in vertebrates: the cartilaginous fish reference.

Vertebrates originated in the lower Cambrian. Their diversification and morphological innovations have been attributed to large-scale gene or genome duplications at the origin of the group. These duplications are predicted to have occurred in two rounds, the "2R" hypothesis, or they may have occurred in one genome duplication plus many segmental duplications, although these hypotheses are disputed. Under such models, most genes that are duplicated in all vertebrates should have originated during the same period. Previous work has shown that indeed duplications started after the speciation between vertebrates and the closest invertebrate, amphioxus, but have not set a clear ending. Consideration of chordate phylogeny immediately shows the key position of cartilaginous vertebrates (Chondrichthyes) to answer this question. Did gene duplications occur as frequently during the 45 Myr between the cartilaginous/bony vertebrate split and the fish/tetrapode split as in the previous approximately 100 Myr? Although the time interval is relatively short, it is crucial to understanding the events at the origin of vertebrates. By a systematic appraisal of gene phylogenies, we show that significantly more duplications occurred before than after the cartilaginous/bony vertebrate split. Our results support rounds of gene or genome duplications during a limited period of early vertebrate evolution and allow a better characterization of these events.

Animals↗