Split probabilities and species tree inference under the multispecies coalescent model

2017/04/13 by Elizabeth S. Allman, Allman, Elizabeth S., James H. Degnan +3
Biochemistry, Genetics and Molecular Biology · #92D15 #FOS: Biological sciences #Populations and Evolution (q-bio.PE) #msc:92D15 #q-bio.PE

paper · pdf · doi:10.48550/arxiv.1704.04268

43 pages

arxiv created 2017/04/13 · arxiv updated 2017/04/17

Abstract

Using topological summaries of gene trees as a basis for species tree inference is a promising approach to obtain acceptable speed on genomic-scale datasets, and to avoid some undesirable modeling assumptions. Here we study the probabilities of splits on gene trees under the multispecies coalescent model, and how their features might inform species tree inference. After investigating the behavior of split consensus methods, we investigate split invariants --- that is, polynomial relationships between split probabilities. These invariants are then used to show that, even though a split is an unrooted notion, split probabilities retain enough information to identify the rooted species tree topology for trees of more than 5 taxa, with one possible 6-taxon exception.

Related

• Determining species tree topologies from clade probabilities under the coalescent
• Species tree inference from gene splits by Unrooted STAR methods
• Identifying the Rooted Species Tree from the Distribution of Unrooted Gene Trees under the Coalescent
• Computing the probability of gene trees concordant with the species tree in the multispecies coalescent
• Species tree inference by the STAR method, and generalizations