Improving Bayesian Population Dynamics Inference: a Coalescent-based Model for Multiple Loci

Overview

Journal Mol Biol Evol

Publisher Oxford University Press

Specialty Biology

Date 2012 Nov 28

PMID 23180580

Citations 317

Authors

Mandev S Gill

Philippe Lemey

Nuno R Faria

Andrew Rambaut

Beth Shapiro

Marc A Suchard

Affiliations

Soon will be listed here.

Abstract

Effective population size is fundamental in population genetics and characterizes genetic diversity. To infer past population dynamics from molecular sequence data, coalescent-based models have been developed for Bayesian nonparametric estimation of effective population size over time. Among the most successful is a Gaussian Markov random field (GMRF) model for a single gene locus. Here, we present a generalization of the GMRF model that allows for the analysis of multilocus sequence data. Using simulated data, we demonstrate the improved performance of our method to recover true population trajectories and the time to the most recent common ancestor (TMRCA). We analyze a multilocus alignment of HIV-1 CRF02_AG gene sequences sampled from Cameroon. Our results are consistent with HIV prevalence data and uncover some aspects of the population history that go undetected in Bayesian parametric estimation. Finally, we recover an older and more reconcilable TMRCA for a classic ancient DNA data set.

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References

Brennan C, Bodelle P, Coffey R, Devare S, Golden A, Hackett Jr J . The prevalence of diverse HIV-1 strains was stable in Cameroonian blood donors from 1996 to 2004. J Acquir Immune Defic Syndr. 2008; 49(4):432-9. DOI: 10.1097/QAI.0b013e31818a6561. View

Minin V, Bloomquist E, Suchard M . Smooth skyride through a rough skyline: Bayesian coalescent-based inference of population dynamics. Mol Biol Evol. 2008; 25(7):1459-71. PMC: 3302198. DOI: 10.1093/molbev/msn090. View

Rambaut A, Pybus O, Nelson M, Viboud C, Taubenberger J, Holmes E . The genomic and epidemiological dynamics of human influenza A virus. Nature. 2008; 453(7195):615-9. PMC: 2441973. DOI: 10.1038/nature06945. View

Heled J, Drummond A . Bayesian inference of population size history from multiple loci. BMC Evol Biol. 2008; 8:289. PMC: 2636790. DOI: 10.1186/1471-2148-8-289. View

Opgen-Rhein R, Fahrmeir L, Strimmer K . Inference of demographic history from genealogical trees using reversible jump Markov chain Monte Carlo. BMC Evol Biol. 2005; 5:6. PMC: 548300. DOI: 10.1186/1471-2148-5-6. View

Donnelly P, Tavare S . Coalescents and genealogical structure under neutrality. Annu Rev Genet. 1995; 29:401-21. DOI: 10.1146/annurev.ge.29.120195.002153. View

Hemelaar J, Gouws E, Ghys P, Osmanov S . Global trends in molecular epidemiology of HIV-1 during 2000-2007. AIDS. 2011; 25(5):679-89. PMC: 3755761. DOI: 10.1097/QAD.0b013e328342ff93. View

Drummond A, Nicholls G, Rodrigo A, Solomon W . Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data. Genetics. 2002; 161(3):1307-20. PMC: 1462188. DOI: 10.1093/genetics/161.3.1307. View

Pybus O, Rambaut A, Harvey P . An integrated framework for the inference of viral population history from reconstructed genealogies. Genetics. 2000; 155(3):1429-37. PMC: 1461136. DOI: 10.1093/genetics/155.3.1429. View

10.

Drummond A, Rambaut A, Shapiro B, Pybus O . Bayesian coalescent inference of past population dynamics from molecular sequences. Mol Biol Evol. 2005; 22(5):1185-92. DOI: 10.1093/molbev/msi103. View

11.

Edo-Matas D, Lemey P, Tom J, Serna-Bolea C, van den Blink A, van t Wout A . Impact of CCR5delta32 host genetic background and disease progression on HIV-1 intrahost evolutionary processes: efficient hypothesis testing through hierarchical phylogenetic models. Mol Biol Evol. 2010; 28(5):1605-16. PMC: 3080134. DOI: 10.1093/molbev/msq326. View

12.

Hasegawa M, Kishino H, Yano T . Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol. 1985; 22(2):160-74. DOI: 10.1007/BF02101694. View

13.

Campos P, Willerslev E, Sher A, Orlando L, Axelsson E, Tikhonov A . Ancient DNA analyses exclude humans as the driving force behind late Pleistocene musk ox (Ovibos moschatus) population dynamics. Proc Natl Acad Sci U S A. 2010; 107(12):5675-80. PMC: 2851807. DOI: 10.1073/pnas.0907189107. View

14.

Kuhner M, Yamato J, Felsenstein J . Maximum likelihood estimation of population growth rates based on the coalescent. Genetics. 1998; 149(1):429-34. PMC: 1460154. DOI: 10.1093/genetics/149.1.429. View

15.

Faria N, Suchard M, Abecasis A, Sousa J, Ndembi N, Bonfim I . Phylodynamics of the HIV-1 CRF02_AG clade in Cameroon. Infect Genet Evol. 2011; 12(2):453-60. PMC: 4677783. DOI: 10.1016/j.meegid.2011.04.028. View

16.

Shapiro B, Drummond A, Rambaut A, Wilson M, Matheus P, Sher A . Rise and fall of the Beringian steppe bison. Science. 2004; 306(5701):1561-5. DOI: 10.1126/science.1101074. View

17.

Drummond A, Suchard M, Xie D, Rambaut A . Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol. 2012; 29(8):1969-73. PMC: 3408070. DOI: 10.1093/molbev/mss075. View

18.

Griffiths R, Tavare S . Sampling theory for neutral alleles in a varying environment. Philos Trans R Soc Lond B Biol Sci. 1994; 344(1310):403-10. DOI: 10.1098/rstb.1994.0079. View

19.

Felsenstein J . Accuracy of coalescent likelihood estimates: do we need more sites, more sequences, or more loci?. Mol Biol Evol. 2005; 23(3):691-700. DOI: 10.1093/molbev/msj079. View

20.

Strimmer K, Pybus O . Exploring the demographic history of DNA sequences using the generalized skyline plot. Mol Biol Evol. 2001; 18(12):2298-305. DOI: 10.1093/oxfordjournals.molbev.a003776. View