PMID: 9541877May 16, 1998Paper

Duplication-based measures of difference between gene and species trees

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
Oliver EulensteinM Vingron

Abstract

In the framework of a duplication-based method for comparing gene and species trees, the concepts of "duplication" and "loss" are reformulated in set-theoretic terms. A number of related tree dissimilarity measures is suggested, and relations between them are analyzed. For any node in the species tree, the number of gene duplications for which it is a "non-child" loss coincides with the number of times when the node's parent is an intermediate between the mapping images of a gene node and its parent. This implies that the total number of losses is equal to the number of intermediate nodes plus the number of one-side duplications and, thus, provides an alternative proof for a conjecture made by Mirkin, Muchnik, and Smith (1995). Another formula proven involves crossings (incompatible gene-species node pairs): the number of losses equals the number of crossings plus the number of duplications.

References

Jan 1, 1988·Annual Review of Genetics·J Felsenstein
Jan 20, 1967·Science·W M Fitch, E Margoliash
Jan 1, 1995·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·B MirkinT F Smith
Oct 1, 1996·Molecular Phylogenetics and Evolution·R GuigóT F Smith
Jul 1, 1997·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·L Zhang

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Citations

Jul 11, 2006·Journal of Molecular Evolution·Ann-Charlotte Berglund-SonnhammerDavid A Liberles
Jul 13, 2000·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·V BafnaL Vawter
Dec 7, 2000·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·K ChenM Farach-Colton
Apr 7, 2006·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Dannie DurandBenjamin Vernot
Sep 24, 2008·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Benjamin VernotDannie Durand
Jan 24, 2007·Bioinformatics·Paweł Górecki, Jerzy Tiuryn
Nov 11, 2009·Molekuliarnaia biologiia·K Iu Gorbunov, V A Liubetskiĭ
Mar 28, 2013·BMC Bioinformatics·Thomas BigotGuy Perrière
Jun 11, 2010·BMC Evolutionary Biology·Jean-François FlotSharmishtha Dattagupta
Oct 13, 2010·BMC Evolutionary Biology·Liang LiuScott V Edwards
May 27, 2011·BMC Evolutionary Biology·Edward L BraunTamaki Yuri
Jun 28, 2011·BMC Evolutionary Biology·Juan S EscobarJacques David
Oct 4, 2011·BMC Evolutionary Biology·Francisca C AlmeidaNancy B Simmons
Jul 24, 2003·BMC Evolutionary Biology·Per G P EricsonJanette A Norman
Apr 29, 2008·BMC Evolutionary Biology·Gregory B EwingArndt von Haeseler
Nov 1, 2008·BMC Evolutionary Biology·Anja RautenbergBengt Oxelman
Jan 28, 2006·PLoS Genetics·K Kevin PfisterElizabeth M C Fisher
May 31, 2006·PLoS Genetics·James H Degnan, Noah A Rosenberg
Jan 9, 2007·PLoS Genetics·Sergey NikolaevStylianos E Antonarakis
Nov 26, 2009·PLoS Genetics·Michael A WhiteBret A Payseur
Jan 1, 2008·PloS One·Nicolas HubertLouis Bernatchez
Apr 3, 2010·PloS One·David W WeisrockAnne D Yoder
Jul 13, 2011·PloS One·Anne FischerSvante Pääbo

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