Tangled trees: The challenge of inferring species trees from coalescent and noncoalescent genes

Christian N.K. Anderson, Liang Liu, Dennis Pearl, Scott V. Edwards

Research output: Chapter in Book/Report/Conference proceedingChapter

17 Scopus citations

Abstract

Phylogenies based on different genes can produce conflicting phylogenies; methods that resolve such ambiguities are becoming more popular, and offer a number of advantages for phylogenetic analysis. We review so-called species tree methods and the biological forces that can undermine them by violating important aspects of the underlying models. Such forces include horizontal gene transfer, gene duplication, and natural selection. We review ways of detecting loci influenced by such forces and offer suggestions for identifying or accommodating them. The way forward involves identifying outlier loci, as is done in population genetic analysis of neutral and selected loci, and removing them from further analysis, or developing more complex species tree models that can accommodate such loci.

Original languageEnglish (US)
Title of host publicationEvolutionary Genomics
Subtitle of host publicationStatistical and Computational Methods, Volume 2
EditorsMaria Anisimova, Maria Anisimova
Pages3-28
Number of pages26
DOIs
StatePublished - 2012

Publication series

NameMethods in Molecular Biology
Volume856
ISSN (Print)1064-3745

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Genetics

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