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Abstract:
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Biologists and statisticians have introduced numerous statistical approaches to explore non-vertical evolution, such as horizontal gene transfer, recombination, and genomic reassortment, through collections of Markov-dependent gene-trees. These tree collections allow for inference of non-vertical evolution, but only indirectly, making findings difficult to interpret and models difficult to generalize. Recently, we have begun to correct these limitations by developing a model a stochastic model for reassortment and transfer events (SMARTIE) drawing upon ancestral recombination graphs (ARGs). ARGs are directed graphs that jointly model vertical speciation events and non-vertical evolutionary events, thus alleviating issues plaguing previous methods. To demonstrate SMARTIE, we tackle three separate phylogenetic applications.
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