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Phylogenetic Networks: From Displayed Trees to a Distribution of Gene Trees
Phylogenetic networks are leaf-labeled, rooted, directed acyclic graphs that are used to represent and model reticulate, or non-treelike, evolutionary histories. Phylogenetic networks have received significant attention in the last two or three decades and the computational phylogenetics community has developed a wide array of mathematical results and algorithmic techniques for their inference. A fundamental observation that guided much of these developments was that a network is a summary of a set of trees. This observation gave rise to the parsimonious formulation of inferring a network with the smallest number of non-tree events that displays a given set of trees.
More recently, though, efforts have been dedicated to statistical inference of these networks from data of multiple, unlinked loci. This formulation is based on extending the multi-species coalescent to species phylogenies whose topologies are networks. With this extension, inferences simultaneously account for reticulation events, such as hybridization, in the presence of incomplete lineage sorting, thus not interpreting all heterogeneity in the data as caused solely by reticulation.
In this seminar, I will introduce the phylogenetic network model, and give a brief survey of the results based on the parsimonious formulation. I will then introduce the multispecies network coalescent and describe recent results on statistical inference of phylogenetic networks from multi-locus data under this model.
Occam's razor in phylogenetic network reconstruction
From reconstructing to using phylogenetic networks
I will first highlight why network reconstruction is worth the effort, and then explain some of the challenges of network reconstruction and network intepretation. These challenges include identifiability issues, difficulties to summarize network uncertainty, and interpretation issues related to network-thinking. Finally, I will describe new phylogenetic comparative methods that can be applied to phylogenetic networks, and are implemented in the PhyloNetworks Julia package.