The trees in the peaks

David Sankoff, Chunfang Zheng, Eric H Lyons, Haibao Tang

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

3 Citations (Scopus)

Abstract

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
PublisherSpringer Verlag
Pages3-14
Number of pages12
Volume9702
ISBN (Print)9783319388267
DOIs
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)
Volume9702
ISSN (Print)03029743
ISSN (Electronic)16113349

Other

Other3rd International Conference on Algorithms for Computational Biology, AlCoB 2016
CountrySpain
CityTrujillo
Period6/21/166/22/16

Fingerprint

Genes
Gene
Genome
Duplication
Speciation
Fractionation
Phylogenetic Analysis
Template
Resolve
Divergence
Degradation

Keywords

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

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)

Cite this

Sankoff, D., Zheng, C., Lyons, E. H., & Tang, H. (2016). The trees in the peaks. In Algorithms for Computational Biology - 3rd International Conference, AlCoB 2016, Proceedings (Vol. 9702, pp. 3-14). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 9702). Springer Verlag. https://doi.org/10.1007/978-3-319-38827-4_1

The trees in the peaks. / Sankoff, David; Zheng, Chunfang; Lyons, Eric H; Tang, Haibao.

Algorithms for Computational Biology - 3rd International Conference, AlCoB 2016, Proceedings. Vol. 9702 Springer Verlag, 2016. p. 3-14 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 9702).

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

Sankoff, D, Zheng, C, Lyons, EH & Tang, H 2016, The trees in the peaks. in Algorithms for Computational Biology - 3rd International Conference, AlCoB 2016, Proceedings. vol. 9702, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 9702, Springer Verlag, pp. 3-14, 3rd International Conference on Algorithms for Computational Biology, AlCoB 2016, Trujillo, Spain, 6/21/16. https://doi.org/10.1007/978-3-319-38827-4_1
Sankoff D, Zheng C, Lyons EH, Tang H. The trees in the peaks. In Algorithms for Computational Biology - 3rd International Conference, AlCoB 2016, Proceedings. Vol. 9702. Springer Verlag. 2016. p. 3-14. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). https://doi.org/10.1007/978-3-319-38827-4_1
Sankoff, David ; Zheng, Chunfang ; Lyons, Eric H ; Tang, Haibao. / The trees in the peaks. Algorithms for Computational Biology - 3rd International Conference, AlCoB 2016, Proceedings. Vol. 9702 Springer Verlag, 2016. pp. 3-14 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).
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