2007/09/03 by Stefan Grünewald, S. Grünewald, Katharina T. Huber +6
Biochemistry, Genetics and Molecular Biology · Earth and Planetary Sciences · Mathematics · #05C99 #92D15 #Combinatorics (math.CO) #Evolution and Paleontology Studies #FOS: Mathematics #Genetic diversity and population structure #Genomics and Phylogenetic Studies #math.CO #msc:05C99 #msc:92D15
paper · pdf · doi:10.48550/arxiv.0709.0283
25 pages
arxiv created 2007/09/03 · openalex publication_date 2007/09/03 · arxiv updated 2009/12/01 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/01
A contemporary and fundamental problem faced by many evolutionary biologists is how to puzzle together a collection \mathcal P of partial trees (leaf-labelled trees whose leaves are bijectively labelled by species or, more generally, taxa, each supported by e. g. a gene) into an overall parental structure that displays all trees in \mathcal P. This already difficult problem is complicated by the fact that the trees in \mathcal P regularly support conflicting phylogenetic relationships and are not on the same but only overlapping taxa sets. A desirable requirement on the sought after parental structure therefore is that it can accommodate the observed conflicts. Phylogenetic networks are a popular tool capable of doing precisely this. However, not much is known about how to construct such networks from partial trees, a notable exception being the Z-closure super-network approach and the recently introduced Q-imputation approach. Here, we propose the usage of closure rules to obtain such a network. In particular, we introduce the novel Y-closure rule and show that this rule on its own or in combination with one of Meacham's closure rules (which we call the M-rule) has some very desirable theoretical properties. In addition, we use the M- and Y-rule to explore the dependency of Rivera et al.'s ``ring of life'' on the fact that the underpinning phylogenetic trees are all on the same data set. Our analysis culminates in the presentation of a collection of induced subtrees from which this ring can be reconstructed.