2009/10/16 by Leo van Iersel, Steven Kelk, van Iersel, Leo +5
Agricultural and Biological Sciences · Biochemistry, Genetics and Molecular Biology · #FOS: Biological sciences #Genetic diversity and population structure #Genomics and Phylogenetic Studies #Plant Taxonomy and Phylogenetics #Populations and Evolution (q-bio.PE)
paper · pdf · doi:10.48550/arxiv.0910.3082
openalex publication_date 2009/10/16 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
Phylogenetic trees are widely used to display estimates of how groups of species evolved. Each phylogenetic tree can be seen as a collection of clusters, subgroups of the species that evolved from a common ancestor. When phylogenetic trees are obtained for several data sets (e.g. for different genes), then their clusters are often contradicting. Consequently, the set of all clusters of such a data set cannot be combined into a single phylogenetic tree. Phylogenetic networks are a generalization of phylogenetic trees that can be used to display more complex evolutionary histories, including reticulate events such as hybridizations, recombinations and horizontal gene transfers. Here we present the new CASS algorithm that can combine any set of clusters into a phylogenetic network. We show that the networks constructed by CASS are usually simpler than networks constructed by other available methods. Moreover, we show that CASS is guaranteed to produce a network with at most two reticulations per biconnected component, whenever such a network exists. We have implemented CASS and integrated it in the freely available Dendroscope software.