Phylogenetic trees are appropriate models of "vertical" evolution. However, when horizontal transfer
of genetic material occurs, across or within species boundaries, trees fail to capture the whole story.
In this talk, I will describe our recent efforts in extending the coalescent to
enable simultaneous modeling of hybridization and deep coalescence. Using the new methods, I will
discuss identifiability of hybridization from gene tree topologies alone. Further, I will show the results
of a reanalysis of a yeast data set using the new methods.
If time permits, I will discuss our recent work on population genomics in bacteria to quantify the rate of
homologous recombination---a form of horizontal transfer that is ubiquitous in bacterial populations.
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