The multifurcating skyline plot.
coalescent
maximum likelihood
multifurcating
phylodynamics
phylogenetics
Journal
Virus evolution
ISSN: 2057-1577
Titre abrégé: Virus Evol
Pays: England
ID NLM: 101664675
Informations de publication
Date de publication:
Jul 2019
Jul 2019
Historique:
entrez:
19
9
2019
pubmed:
19
9
2019
medline:
19
9
2019
Statut:
epublish
Résumé
A variety of methods based on coalescent theory have been developed to infer demographic history from gene sequences sampled from natural populations. The 'skyline plot' and related approaches are commonly employed as flexible prior distributions for phylogenetic trees in the Bayesian analysis of pathogen gene sequences. In this work we extend the classic and generalized skyline plot methods to phylogenies that contain one or more multifurcations (i.e. hard polytomies). We use the theory of Λ-coalescents (specifically,
Identifiants
pubmed: 31528357
doi: 10.1093/ve/vez031
pii: vez031
pmc: PMC6736156
doi:
Types de publication
Journal Article
Langues
eng
Pagination
vez031Commentaires et corrections
Type : ErratumIn
Références
Trends Ecol Evol. 2015 Jun;30(6):306-13
pubmed: 25887947
Mol Biol Evol. 2017 Nov 1;34(11):2982-2995
pubmed: 28981709
Genetics. 2013 Nov;195(3):1037-53
pubmed: 24026094
J Math Biol. 2020 Apr;80(5):1497-1521
pubmed: 32008102
Proc Natl Acad Sci U S A. 2014 Feb 11;111(6):2385-90
pubmed: 24469801
Genetics. 2019 Mar;211(3):1019-1028
pubmed: 30651284
Virus Evol. 2016 Mar 02;2(1):vew003
pubmed: 27774296
Philos Trans R Soc Lond B Biol Sci. 1994 Jun 29;344(1310):403-10
pubmed: 7800710
Mol Biol Evol. 2005 May;22(5):1185-92
pubmed: 15703244
Genetics. 2012 Jan;190(1):187-201
pubmed: 22042576
Genetics. 2018 Nov;210(3):1053-1073
pubmed: 30171032
Proc Natl Acad Sci U S A. 2018 Apr 17;115(16):4200-4205
pubmed: 29610334
Philos Trans R Soc Lond B Biol Sci. 2010 Jun 27;365(1548):1879-90
pubmed: 20478883
Theor Popul Biol. 2004 Sep;66(2):129-38
pubmed: 15302222
Genetics. 2016 Apr;202(4):1549-61
pubmed: 26883445
Genetics. 2015 Mar;199(3):841-56
pubmed: 25575536
Mol Biol Evol. 2008 Jul;25(7):1459-71
pubmed: 18408232
Genetics. 1988 Nov;120(3):819-29
pubmed: 3066685
Proc Natl Acad Sci U S A. 1999 Mar 2;96(5):2187-91
pubmed: 10051616
Theor Popul Biol. 2008 Aug;74(1):104-14
pubmed: 18554676
Mol Biol Evol. 2013 Mar;30(3):713-24
pubmed: 23180580
Nature. 2005 Nov 17;438(7066):355-9
pubmed: 16292310
Genet Res. 1988 Dec;52(3):213-22
pubmed: 3243426
BMC Evol Biol. 2007 Nov 08;7:214
pubmed: 17996036
Stat Appl Genet Mol Biol. 2018 Jun 13;17(3):
pubmed: 29897888
Genetics. 2005 Feb;169(2):1061-70
pubmed: 15489538
Genetics. 2000 Jul;155(3):1429-37
pubmed: 10880500
Proc Natl Acad Sci U S A. 2013 Jan 8;110(2):437-42
pubmed: 23269838
Genetics. 1988 Nov;120(3):831-40
pubmed: 3147214
Nat Rev Genet. 2009 Aug;10(8):540-50
pubmed: 19564871
Mol Biol Evol. 2001 Dec;18(12):2298-305
pubmed: 11719579
Proc Natl Acad Sci U S A. 2017 Feb 28;114(9):2337-2342
pubmed: 28193880
Mol Ecol Resour. 2011 May;11(3):423-34
pubmed: 21481200