Novel Metrics for the Comparison of Phylogenetic Networks

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For the last two centuries, biologists have modeled species evolution with phylogenetic trees, which assume that genetic material is exclusively transmitted through direct descent. However, there is an abundance of organisms whose evolution cannot be represented as a tree, including plants, bacteria, and viruses. For such species, a network is needed to represent non-treelike events such as hybridization and gene transfer. Several methods build a network from genomic data, but developers lack the tools to evaluate their algorithms against reference or simulated networks.In this proposal, we will develop novel approaches for the comparison of phylogenetic networks. For tree comparison, the Robinson-Foulds (RF) distance is the de facto standard, but in phylogenetic networks, there appears to be no metric that is as strongly established. This is mainly because unlike the RF distance, all current network measures impose a trade-off between desirable properties such as biological relevance, low computational requirements, and interpretability.We introduce new operational distances between networks with these advantages in mind. First, we will build the theoretical foundations of our novel metrics by establishing their mathematical and algorithmic properties. Second, the developed algorithms will be implemented in an open-source software package. Third, we will validate and compare our metrics on real and simulated biological datasets. Our multidisciplinary team is composed of experts in mathematical modeling, high-quality software development, and biology. Our research will lead to clearer comparison metric options for evolutionary biologists and provide a more accurate picture of evolution. The proposal is also an excellent opportunity to establish long-term collaborations between early career professors from different provinces. Furthermore, Québec and Canada are known for their leadership in comparative genomics, and the research in this proposal will reinforce it even further.