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Archaea and Bacteria
Joint Bayesian inference of bacterial ancestral recombination graphs
Homologous recombination is a central feature of bacterial evolution, yet confounds traditional phylogenetic methods. In this seminar I will present a novel approach to inferring bacterial evolution based on the ClonalOrigin model (Didelot et al., Genetics, 2010). This method permits joint Bayesian inference of the entire bacterial recombination graph and associated model parameters. The method is implemented in the BEAST 2 phylogenetic inference package. It can be easily combined with a variety of substitution models accounting for site-to-site clock rate heterogeneity as well as parametric and non-parametric models of effective population size dynamics. I will also present work on summarizing posterior distributions over the space of tree-based recombination graphs which, together with the joint inference method, aims to bridge the technological gap between recombination-aware phylogenetic inference and traditional methods.
Talks in this series have largely focused on population genetic and phylogenetic methods for reconstructing micro- and macroevolutionary patterns consequent from microevolutionary processes. When natural selection is invoked, it is generally assumed to operate through the differential reproduction of favored variants among populations of physical entities, be they genes, cells, organisms or (rarely) species. The Gaia hypothesis of James Lovelock, co-developed and vigorously promoted by Lynn Margulis in the 1970s, has been very popular with the lay public. But most mainstream Darwinists scorned and still do not accept the notion. They cannot imagine global biospheric stability being selected for at any of the above levels, and do not see the Earth's biosphere as part of a population of comparable global entities engaged in reproductive competition. Most philosophers of biology would similarly argue that any global homeostatic systems (if they exist) can be only "fortuitous byproducts" of lower-level selection. I will suggest that we look at the biogeochemical cycles and other homeostatic processes that might confer stability â rather than the individual organisms or "species" (mostly microbial) that implement them â as the relevant units of selection. By thus focusing our attentions on the âsongâ, not the âsingersâ, a Darwinized Gaia might be developed. Our understanding of evolution by natural selection would however need to be stretched to accommodate differential persistence, and our definition of reproduction would need to be reworked.