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Occam's razor in phylogenetic network reconstruction
Several parsimony-based methods aiming at reconstructing explicit phylogenetic networks have been developed in the last two decades. In the first part of this talk I will review several of these methods that share the same underlying approach: First, combinatorial objects such as phylogenetic trees, hierarchical clusters or trinets are constructed from the data of the species under study; Second, these combinatorial objects are combined into an explicit phylogenetic network. The way they are combined and the parameters to optimise (e.g. minimising the hybridisation number, i.e. the number of reticulations of the network, or the level, i.e. the maximum number of reticulations in each biconnected component) give a large range of different problems, each of biological interest. In the second part of the talk I will discuss different definitions of maximum parsimony for phylogenetic networks, as well as the pros and cons of each of them. Then I will introduce several algorithmic results to lay the foundations for new parsimony-based methods for 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.