Best match graphs and reconciliation of gene trees with species trees.
Colored digraph
Horizontal gene transfer
Orthology
Phylogenetic combinatorics
Journal
Journal of mathematical biology
ISSN: 1432-1416
Titre abrégé: J Math Biol
Pays: Germany
ID NLM: 7502105
Informations de publication
Date de publication:
04 2020
04 2020
Historique:
received:
19
09
2019
revised:
08
01
2020
pubmed:
1
2
2020
medline:
29
5
2021
entrez:
1
2
2020
Statut:
ppublish
Résumé
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.
Identifiants
pubmed: 32002659
doi: 10.1007/s00285-020-01469-y
pii: 10.1007/s00285-020-01469-y
pmc: PMC7052050
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
1459-1495Références
Nat Methods. 2016 May;13(5):425-30
pubmed: 27043882
Front Genet. 2017 Oct 31;8:165
pubmed: 29163633
Algorithms Mol Biol. 2018 Feb 6;13:2
pubmed: 29441122
Nucleic Acids Res. 2009 Jul;37(Web Server issue):W84-9
pubmed: 19435885
J Math Biol. 2020 Feb;80(3):865-953
pubmed: 31691135
Biomed Res Int. 2014;2014:642089
pubmed: 24800245
Syst Zool. 1970 Jun;19(2):99-113
pubmed: 5449325
Bioinformatics. 2014 Nov 1;30(21):2993-8
pubmed: 25064571
J Comput Biol. 2009 Oct;16(10):1399-418
pubmed: 19754270
Algorithms Mol Biol. 2016 Apr 16;11:4
pubmed: 27087831
J Math Biol. 2018 Nov;77(5):1459-1491
pubmed: 29951855
Mol Phylogenet Evol. 1996 Oct;6(2):189-213
pubmed: 8899723
BMC Bioinformatics. 2008 Dec 04;9:518
pubmed: 19055798
Brief Bioinform. 2011 Sep;12(5):392-400
pubmed: 21949266
J Math Biol. 2019 Oct;79(5):1885-1925
pubmed: 31410552
Nat Rev Genet. 2010 Feb;11(2):97-108
pubmed: 20051986
Annu Rev Genet. 2005;39:309-38
pubmed: 16285863
Algorithms Mol Biol. 2017 Aug 29;12:23
pubmed: 28861118
Algorithms Mol Biol. 2020 Apr 9;15:5
pubmed: 32308731
Nucleic Acids Res. 2008 Jan;36(Database issue):D250-4
pubmed: 17942413
Genome Res. 2009 Feb;19(2):327-35
pubmed: 19029536
IEEE/ACM Trans Comput Biol Bioinform. 2011 Mar-Apr;8(2):517-35
pubmed: 21233529
Proc Natl Acad Sci U S A. 2015 Feb 17;112(7):2058-63
pubmed: 25646426
Nat Rev Genet. 2013 May;14(5):360-6
pubmed: 23552219
PLoS One. 2014 Aug 19;9(8):e105015
pubmed: 25137074
J Math Biol. 2019 Aug;79(3):969-986
pubmed: 31111195
Trends Genet. 2009 May;25(5):210-6
pubmed: 19368988
J Math Biol. 2017 Jul;75(1):199-237
pubmed: 27904954
Genes (Basel). 2018 Feb 28;9(3):
pubmed: 29495636
Science. 1997 Oct 24;278(5338):631-7
pubmed: 9381173
Trends Genet. 2000 May;16(5):227-31
pubmed: 10782117
Mol Biol Evol. 2012 Apr;29(4):1115-23
pubmed: 22160766
J Math Biol. 2019 Jun;78(7):2015-2057
pubmed: 30968198
BMC Genomics. 2014;15 Suppl 6:S12
pubmed: 25572629
J Math Biol. 2013 Jan;66(1-2):399-420
pubmed: 22456957
Genome Res. 2003 Sep;13(9):2178-89
pubmed: 12952885
J Comput Biol. 2008 Oct;15(8):981-1006
pubmed: 18808330
Bioinformatics. 2012 Jun 15;28(12):i283-91
pubmed: 22689773
Algorithms Mol Biol. 2017 Mar 11;12:4
pubmed: 28293276
Bioinformatics. 2005 Jun 1;21(11):2596-603
pubmed: 15713731
PLoS Comput Biol. 2012;8(5):e1002514
pubmed: 22615551
Bioinformatics. 2002 Jan;18(1):92-9
pubmed: 11836216
Life (Basel). 2016 Sep 08;6(3):
pubmed: 27618105