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Intertwining phylogenetic trees and networks
Author(s) -
Schliep Klaus,
Potts Alastair J.,
Morrison David A.,
Grimm Guido W.
Publication year - 2017
Publication title -
methods in ecology and evolution
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.425
H-Index - 105
ISSN - 2041-210X
DOI - 10.1111/2041-210x.12760
Subject(s) - phylogenetic tree , bootstrapping (finance) , phylogenetic network , tree (set theory) , inference , computer science , bayesian network , artificial intelligence , tree rearrangement , machine learning , data mining , theoretical computer science , mathematics , biology , combinatorics , econometrics , gene , biochemistry
Summary The fields of phylogenetic tree and network inference have dramatically advanced in the past decade, but independently with few attempts to bridge them. Here we provide a framework, implemented in the phangorn library in R, to transfer information between trees and networks. This includes: (i) identifying and labelling equivalent tree branches and network edges, (ii) transferring tree branch support to network edges, and (iii) mapping bipartition support from a sample of trees (e.g. from bootstrapping or Bayesian inference) onto network edges. The ability to readily combine tree and network information should lead to more comprehensive evolutionary comparisons and inferences.