Divergence dating using mixed effects clock modelling: An application to HIV-1

被引:21
作者
Bletsa, Magda [1 ]
Suchard, Marc A. [2 ,3 ,4 ]
Ji, Xiang [2 ]
Gryseels, Sophie [1 ,5 ]
Vrancken, Bram [1 ]
Baele, Guy [1 ]
Worobey, Michael [5 ]
Lemey, Philippe [1 ]
机构
[1] Univ Leuven, KU Leuven, Rega Inst, Dept Microbiol Immunol & Transplantat, Leuven, Belgium
[2] Univ Calif Los Angeles, David Geffen Sch Med, Dept Biomath, Los Angeles, CA 90095 USA
[3] Univ Calif Los Angeles, David Geffen Sch Med, Dept Human Genet, Los Angeles, CA 90095 USA
[4] Univ Calif Los Angeles, Fielding Sch Publ Hlth, Dept Biostat, Los Angeles, CA USA
[5] Univ Arizona, Dept Ecol & Evolutionary Biol, Tucson, AZ USA
基金
比利时弗兰德研究基金会; 英国惠康基金; 欧洲研究理事会;
关键词
molecular clock; HIV; divergence time; Bayesian inference; mixed effects; HUMAN-IMMUNODEFICIENCY-VIRUS; DISEASE PROGRESSION; SUBSTITUTION RATES; ORIGIN; EVOLUTION; SEQUENCES; EPIDEMIC; DYNAMICS; HISTORY; TYPE-1;
D O I
10.1093/ve/vez036
中图分类号
Q93 [微生物学];
学科分类号
071005 ; 100705 ;
摘要
The need to estimate divergence times in evolutionary histories in the presence of various sources of substitution rate variation has stimulated a rich development of relaxed molecular clock models. Viral evolutionary studies frequently adopt an uncorrelated clock model as a generic relaxed molecular clock process, but this may impose considerable estimation bias if discrete rate variation exists among clades or lineages. For HIV-1 group M, rate variation among subtypes has been shown to result in inconsistencies in time to the most recent common ancestor estimation. Although this calls into question the adequacy of available molecular dating methods, no solution to this problem has been offered so far. Here, we investigate the use of mixed effects molecular clock models, which combine both fixed and random effects in the evolutionary rate, to estimate divergence times. Using simulation, we demonstrate that this model outperforms existing molecular clock models in a Bayesian framework for estimating time-measured phylogenies in the presence of mixed sources of rate variation, while also maintaining good performance in simpler scenarios. By analysing a comprehensive HIV-1 group M complete genome data set we confirm considerable rate variation among subtypes that is not adequately modelled by uncorrelated relaxed clock models. The mixed effects clock model can accommodate this rate variation and results in a time to the most recent common ancestor of HIV-1 group M of 1920 (1915-25), which is only slightly earlier than the uncorrelated relaxed clock estimate for the same data set. The use of complete genome data appears to have a more profound impact than the molecular clock model because it reduces the credible intervals by 50 per cent relative to similar estimates based on short envelope gene sequences.
引用
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页数:11
相关论文
共 47 条
[1]   Recombination confounds the early evolutionary history of human immunodeficiency virus type 1: Subtype G is a circulating recombinant form [J].
Abecasis, Ana B. ;
Lemey, Philippe ;
Vidal, Nicole ;
de Oliveira, Tulio ;
Peeters, Martine ;
Camacho, Ricardo ;
Shapiro, Beth ;
Rambaut, Andrew ;
Vandamme, Anne-Mieke .
JOURNAL OF VIROLOGY, 2007, 81 (16) :8543-8551
[2]   The substitution rate of HIV-1 subtypes: a genomic approach [J].
Angel Patino-Galindo, Juana ;
Gonzalez-Candelas, Fernando .
VIRUS EVOLUTION, 2017, 3 (02)
[3]  
Ayres DL, 2012, SYST BIOL, V61, P170, DOI [10.1093/sysbio/syr100, 10.1093/sysbio/sys029]
[4]   Bayesian codon substitution modelling to identify sources of pathogen evolutionary rate variation [J].
Baele, Guy ;
Suchard, Marc A. ;
Bielejec, Filip ;
Lemey, Philippe .
MICROBIAL GENOMICS, 2016, 2 (06)
[5]   Unequal evolutionary rates in the human immunodeficiency virus type I (HIV-1) pandemic: The evolutionary rate of HIV-1 slows down when the epidemic rate increases [J].
Berry, Irina Maljkovic ;
Ribeiro, Ruy ;
Kothari, Moulik ;
Athreya, Gayathri ;
Daniels, Marcus ;
Lee, Ha Youn ;
Bruno, William ;
Leitner, Thomas .
JOURNAL OF VIROLOGY, 2007, 81 (19) :10625-10635
[6]   πBUSS: a parallel BEAST/BEAGLE utility for sequence simulation under complex evolutionary scenarios [J].
Bielejec, Filip ;
Lemey, Philippe ;
Carvalho, Luiz Max ;
Baele, Guy ;
Rambaut, Andrew ;
Suchard, Marc A. .
BMC BIOINFORMATICS, 2014, 15
[7]   BEAST 2: A Software Platform for Bayesian Evolutionary Analysis [J].
Bouckaert, Remco ;
Heled, Joseph ;
Kuehnert, Denise ;
Vaughan, Tim ;
Wu, Chieh-Hsi ;
Xie, Dong ;
Suchard, Marc A. ;
Rambaut, Andrew ;
Drummond, Alexei J. .
PLOS COMPUTATIONAL BIOLOGY, 2014, 10 (04)
[8]   Relaxed phylogenetics and dating with confidence [J].
Drummond, Alexei J. ;
Ho, Simon Y. W. ;
Phillips, Matthew J. ;
Rambaut, Andrew .
PLOS BIOLOGY, 2006, 4 (05) :699-710
[9]   Bayesian random local clocks, or one rate to rule them all [J].
Drummond, Alexei J. ;
Suchard, Marc A. .
BMC BIOLOGY, 2010, 8
[10]   The early spread and epidemic ignition of HIV-1 in human populations [J].
Faria, Nuno R. ;
Rambaut, Andrew ;
Suchard, Marc A. ;
Baele, Guy ;
Bedford, Trevor ;
Ward, Melissa J. ;
Tatem, Andrew J. ;
Sousa, Joao D. ;
Arinaminpathy, Nimalan ;
Pepin, Jacques ;
Posada, David ;
Peeters, Martine ;
Pybus, Oliver G. ;
Lemey, Philippe .
SCIENCE, 2014, 346 (6205) :56-61