Evolutionary Genomics pp 3-28

Part of the Methods in Molecular Biology book series (MIMB, volume 856) | Cite as

Tangled Trees: The Challenge of Inferring Species Trees from Coalescent and Noncoalescent Genes

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

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.

Key words

Species tree Gene tree discordance Non-coalescent genes Outlier analysis 

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Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  • Christian N. K. Anderson
    • 1
  • Liang Liu
    • 2
  • Dennis Pearl
    • 3
  • Scott V. Edwards
    • 1
  1. 1.Department of Organismic and Evolutionary Biology & Museum of Comparative ZoologyHarvard UniversityCambridgeUSA
  2. 2.Department of Agriculture and Natural ResourcesDelaware State UniversityDoverUSA
  3. 3.Department of StatisticsThe Ohio State UniversityColumbusUSA

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