The trees in the peaks

David Sankoff, Chunfang Zheng, Eric Lyons, Haibao Tang

Research output: Chapter in Book/Report/Conference proceedingConference contribution

4 Scopus citations


We suggest a gene-tree/species-tree approach to speciation and whole genome duplication (WGD) to resolve the occurrence of these events in phylogenetic analysis. We propose a more principled way of estimating the parameters of gene divergence and fractionation than the standard mixture of normals analysis. We formulate an algorithm for resolving data on local peaks in the distributions of duplicate gene similarities for a number of related genomes. Illustrating with a comprehensive analysis of WGD-origin duplicate gene data from six members of the family Brassicaceae, we discuss the effects of variable evolutionary rates and data degradation due to fractionation. We introduce the notion of peak tree, as a template for all gene trees evolving by speciation, WGD and fractionation.

Original languageEnglish (US)
Title of host publicationAlgorithms for Computational Biology - 3rd International Conference, AlCoB 2016, Proceedings
EditorsMiguel A. Vega-Rodríguez, Sergio Santander-Jiménez, María Botón-Fernández, Carlos Martín-Vide
Number of pages12
ISBN (Print)9783319388267
StatePublished - 2016
Event3rd International Conference on Algorithms for Computational Biology, AlCoB 2016 - Trujillo, Spain
Duration: Jun 21 2016Jun 22 2016

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349


Other3rd International Conference on Algorithms for Computational Biology, AlCoB 2016


  • Algorithms
  • Brassicaceae
  • Gene tree
  • Mixture of distributions
  • Species tree
  • Whole genome duplication

ASJC Scopus subject areas

  • Theoretical Computer Science
  • General Computer Science


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