Best match graphs and reconciliation of gene trees with species trees.

Autor: Geiß M; Bioinformatics Group, Department of Computer Science, Interdisciplinary Center of Bioinformatics, University of Leipzig, Härtelstraße 16-18, 04107, Leipzig, Germany., Laffitte MEG; CONACYT-Instituto de Matemáticas, UNAM Juriquilla, Blvd. Juriquilla 3001, 76230, Juriquilla, Querétaro, QRO, Mexico., Sánchez AL; CONACYT-Instituto de Matemáticas, UNAM Juriquilla, Blvd. Juriquilla 3001, 76230, Juriquilla, Querétaro, QRO, Mexico., Valdivia DI; Centro de Ciencias Básicas, Universidad Autónoma de Aguascalientes, Av. Universidad 940, 20131, Aguascalientes, AGS, México.; Instituto de Matemáticas, UNAM Juriquilla, Blvd. Juriquilla 3001, 76230, Juriquilla, Querétaro, QRO, Mexico., Hellmuth M; Institute of Mathematics and Computer Science, University of Greifswald, Walther-Rathenau-Straße 47, 17487, Greifswald, Germany.; Center for Bioinformatics, Saarland University, Building E 2.1, P.O. Box 151150, 66041, Saarbrücken, Germany., Rosales MH; CONACYT-Instituto de Matemáticas, UNAM Juriquilla, Blvd. Juriquilla 3001, 76230, Juriquilla, Querétaro, QRO, Mexico., Stadler PF; Bioinformatics Group, Department of Computer Science, Interdisciplinary Center of Bioinformatics, University of Leipzig, Härtelstraße 16-18, 04107, Leipzig, Germany. studla@bioinf.uni-leipzig.de.; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany. studla@bioinf.uni-leipzig.de.; Competence Center for Scalable Data Services and Solutions, Leipzig Research Center for Civilization Diseases, Leipzig University, Härtelstraße 16-18, 04107, Leipzig, Germany. studla@bioinf.uni-leipzig.de.; Max-Planck-Institute for Mathematics in the Sciences, Inselstraße 22, 04103, Leipzig, Germany. studla@bioinf.uni-leipzig.de.; Inst. f. Theoretical Chemistry, University of Vienna, Währingerstraße 17, 1090, Wien, Austria. studla@bioinf.uni-leipzig.de.; Facultad de Ciencias, Universidad National de Colombia, Bogotá, Colombia. studla@bioinf.uni-leipzig.de.; Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM, 87501, USA. studla@bioinf.uni-leipzig.de.
Jazyk: angličtina
Zdroj: Journal of mathematical biology [J Math Biol] 2020 Apr; Vol. 80 (5), pp. 1459-1495. Date of Electronic Publication: 2020 Jan 30.
DOI: 10.1007/s00285-020-01469-y
Abstrakt: A wide variety of problems in computational biology, most notably the assessment of orthology, are solved with the help of reciprocal best matches. Using an evolutionary definition of best matches that captures the intuition behind the concept we clarify rigorously the relationships between reciprocal best matches, orthology, and evolutionary events under the assumption of duplication/loss scenarios. We show that the orthology graph is a subgraph of the reciprocal best match graph (RBMG). We furthermore give conditions under which an RBMG that is a cograph identifies the correct orthlogy relation. Using computer simulations we find that most false positive orthology assignments can be identified as so-called good quartets-and thus corrected-in the absence of horizontal transfer. Horizontal transfer, however, may introduce also false-negative orthology assignments.
Databáze: MEDLINE
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