Exploring Evolutionary Relationships Across the Genome Using Topology Weighting.

S.H. Martin, S.M. Van Belleghem

Research output: Contribution to journalArticlepeer-review

Abstract

We introduce the concept of topology weighting, a method for quantifying relationships between taxa that are not necessarily monophyletic, and visualizing how these relationships change across the genome. A given set of taxa can be related in a limited number of ways, but if each taxon is represented by multiple sequences, the number of possible topologies becomes very large. Topology weighting reduces this complexity by quantifying the contribution of each taxon topology to the full tree. We describe our method for topology weighting by iterative sampling of subtrees (Twisst), and test it on both simulated and real genomic data. Overall, we show that this is an informative and versatile approach, suitable for exploring relationships in almost any genomic dataset. Scripts to implement the method described are available at http://github.com/simonhmartin/twisst.
Original languageEnglish
Pages (from-to)429-438
Number of pages10
JournalGenetics
Volume206
Issue number1
Early online date24 Mar 2017
DOIs
Publication statusPublished - 1 May 2017
Externally publishedYes

Keywords

  • incomplete lineage sorting
  • introgression
  • phylogenomics
  • population genomics
  • Evolution, Molecular
  • Genome
  • Genomics
  • Models, Genetic
  • Phylogeny

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