The effects of partitioning on phylogenetic inference

David Kainer, Robert Lanfear

Research output: Contribution to journalArticle

57 Citations (Scopus)

Abstract

Partitioning is a commonly used method in phylogenetics that aims to accommodate variation in substitution patterns among sites. Despite its popularity, there have been few systematic studies of its effects on phylogenetic inference, and there have been no studies that compare the effects of different approaches to partitioning across many empirical data sets. In this study, we applied four commonly used approaches to partitioning to each of 34 empirical data sets, and then compared the resulting tree topologies, branch-lengths, and bootstrap support estimated using each approach. We find that the choice of partitioning scheme often affects tree topology, particularly when partitioning is omitted. Most notably, we find occasional instances where the use of a suboptimal partitioning scheme produces highly supported but incorrect nodes in the tree. Branch-lengths and bootstrap support are also affected by the choice of partitioning scheme, sometimes dramatically so. We discuss the reasons for these effects and make some suggestions for best practice.
Original languageEnglish
Pages (from-to)1611-1627
Number of pages17
JournalMolecular Biology and Evolution
Volume32
Issue number6
DOIs
Publication statusPublished - Jun 2015

Keywords

  • partitioning
  • tree topology
  • tree inference
  • molecular evolution

Fingerprint Dive into the research topics of 'The effects of partitioning on phylogenetic inference'. Together they form a unique fingerprint.

Cite this