Graph hierarchies for phylogeography

Philosophical Transactions of the Royal Society B: Biological Sciences

Volumn 368, Issue 1614, 2013, Pages

  Cybis, Gabriela B ^a   Sinsheimer, Janet S ^a,b   Lemey, Philippe ^c   Suchard, Marc A ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITY OF LEUVEN   (Belgium)

Author keywords

Bayesian statistics; Dengue; HIV; Phylodynamics; Phylogenetics; Random graphs

Indexed keywords

BAYESIAN ANALYSIS; DATA SET; DENGUE FEVER; DISPERSION; EVOLUTIONARY THEORY; HIERARCHICAL SYSTEM; HUMAN IMMUNODEFICIENCY VIRUS; PHYLOGENETICS; PHYLOGEOGRAPHY;

ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; DENGUE VIRUS; GENETICS; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; METHODOLOGY; PHYLOGENY; PHYLOGEOGRAPHY; WESTERN HEMISPHERE;

AMERICAS; BAYES THEOREM; DENGUE VIRUS; HIV-1; HUMANS; MODELS, GENETIC; PHYLOGENY; PHYLOGEOGRAPHY;

MLCS; MLOWN;

EID: 84880467251     PISSN: 09628436     EISSN: 14712970     Source Type: Journal    
DOI: 10.1098/rstb.2012.0206     Document Type: Article

References (32)

1. UNAIDS. 2010 Global Report: UNAIDS report on the global AIDS epidemic. See http://www.unaids.org/ globalreport/Global_report.htm (accessed 10 December 2012).
2. Wallace RG, HoDac H, Lathrop RH, Fitch WM. 2007 A statistical phylogeography of influenza A H5N1. Proc. Natl Acad. Sci. USA 104, 4473-4478. (doi:10.1073/pnas.0700435104)
3. Biek R, Henderson JC, Waller LA, Rupprecht CE, Real LA. 2007 A high-resolution genetic signature of demographic and spatial expansion in epizootic rabies virus. Proc. Natl Acad. Sci. USA 104, 7993-7998. (doi:0.1073/pnas.0700741104)
4. Paraskevis D et al. 2009 Tracing the HIV-1 serotype B mobility in Europe: a phylogeographic approach. Retrovirology 6, 49. (doi:10.1186/1742-4690-6-49)
5. Fagundes NJR, Ray N, Beaumont M, Neuenschwander S, Salzano FM, Bonatto SL, Excoffier L. 2007 Statistical evaluation of alternative models of human evolution. Proc. Natl Acad. Sci. USA 104, 17614-17619. (doi:10.1073/pnas.0708280104)
6. vonHoldt BM et al. 2010 Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication. Nature 464, 898-902. (doi:10.1038/nature08837)
7. Bloomquist EW, Lemey P, Suchard MA. 2010 Three roads diverged? Routes to phylogeographic inference. Trends Ecol. Evol. 25, 625-632. (doi:10.1016/j.tree.2010.08.010)
8. Lemey P, Rambaut A, Drummond AJ, Suchard MA. 2009 Bayesian phylogeography finds its roots. PLoS Comput. Biol. 5, e1000520. (doi:10.1371/journal. pcbi.1000520)
9. Lemey P, Rambaut A, Welch J, Suchard M. 2010 Phylogeography takes a relaxed random walk in continuous space and time. Mol. Biol. Evol. 27, 1877-1885. (doi:10.1093/molbev/msq067)
10. Faria NR, Suchard MA, Rambaut A, Lemey P. 2011 Toward a quantitative understanding of viral phylogeography. Curr. Opin. Virol. 1, 423-429. (doi:10.1016/j.coviro.2011.10.003)
11. Halstead SB. 2008 Dengue virus-mosquito interactions. Annu. Rev. Entomol. 53, 273-291. (doi:10.1146/annurev.ento.53.103106.093326)
12. Allicock OM et al. 2012 Pylogeography and population dynamics of dengue viruses in the Americas. Mol. Biol. Evol. 29, 1533-1543. (doi:10.1093/molbev/msr320)
13. Sanmartín I, van der Mark P, Ronquist F. 2008 Inferring dispersal: a Bayesian approach to phylogeny-based island biogeography, with special reference to the Canary Islands. J. Biogeogr. 35, 428-449. (doi:10.1111/j.1365-2699.2008.01885.x)
14. Suchard MA, Kitchen CMR, Sinsheimer JS, Weiss RE. 2003 Hierarchical phylogenetic models for analyzing multipartite sequence data. Syst. Biol. 52, 649-664. (doi:10.1080/10635150390238879)
15. Edo-Matas D, Lemey P, Tom JA, Serna-Bolea C, van den Blink AE, van't Wout AB, Schuitemaker H, Suchard MA. Impact of CCR5D 32 host genetic background and disease progression on HIV-1 intra-host evolutionary processes: efficient hypothesis testing through hierarchical phylogenetic models. Mol. Biol. Evol. 28, 1605-1616. (doi:10.1093/molbev/ msq326)
16. Tom J, Sinsheimer JS, Suchard MA. 2012 Reuse, recycle, reweigh: combating influenza through efficient sequential Bayesian computation for massive data. Ann. Appl. Stat. 4, 1722-1748. (doi:10.1214/10-AOAS349)
17. Drummond A, Nicholls G, Rodrigo A, Solomon W. 2002 Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data. Genetics 161, 1307-1320.
18. Drummond AJ, Suchard MA, Xie D, Rambaut A. 2012 Bayesian phylogenetics with BEAUti and the BEAST v. 1.7. Mol. Biol. Evol. 29, 1969-1973. (doi:10.1093/molbev/mss075)
19. Grey RM. 2009 Entropy and information theory. New York, NY: Springer.
20. Guzman MG et al. 2010 Dengue: a continuing global threat. Nat. Rev. Microbiol. 8(Suppl. 12), S7-S16. (doi:10.1038/nrmicro2460)
21. San Martín JL, Brathwaite O, Zambrano B, Solorzano JO, Bouckenooghe A, Dayan GH, Guzmán MG. 2010 The epidemiology of dengue in the Americas over the last three decades: a worrisome reality. Am. J. Trop. Med. Hyg. 82, 128-135. (doi:10.4269/ajtmh.2010. 09-0346)
22. Bielejec F, Rambaut A, Suchard MA, Lemey P. 2011 SPREAD: spatial phylogenetic reconstruction of evolutionary dynamics. Bioinformatics 27, 2910-2912. (doi:10.1093/bioinformatics/btr481)
23. Potter SJ, Lemey P, Dyer WB, Sullivan JS, Chew CB, Vandamme A, Dwyer DE, Saksena NK. 2006 Genetic analyses reveal structured HIV-1 populations in serially sampled T lymphocytes of patients receiving HAART. Virology 348, 35-46. (doi:10.1016/j.virol.2005.12.031)
24. Nelson MI et al. 2011 Spatial dynamics of humanorigin H1 influenza A virus in North American swine. PLoS Pathog. 7, e1002077. (doi:10.1371/ journal.ppat.1002077)
25. Auguste AJ et al. 2010 Yellow fever virus maintenance in trinidad and its dispersal throughout the Americas. J. Virol. 84, 9967-9977. (doi:10.1128/JVI.00588-10)
26. Liang L-J, Weiss RE. 2007 A hierarchical semiparametric regression model for combining HIV-1 phylogenetic analyses using iterative reweighting algorithms. Biometrics 63, 733-741. (doi:10.1111/j.1541-0420.2007.00753.x)
27. Brown PJ, Vannucci M. 1998 Multivariate Bayesian model selection and prediction. J. Roy. Stat. Soc. B 60, 627-641. (doi:10.1111/1467-9868.00144)
28. Dobra A, Hans C, Jones B, Yao G, West M. 2004 Sparse graphical models for exploring gene expression data. J. Multivariate Anal. 90, 196-212. (doi:10.1016/j.jmva.2004.02.009)
29. Carvalho CM, Scott JG. 2009 Objective Bayesian model selection in Gaussian graphical models. Biometrika 96, 497-512. (doi:10.1093/biomet/ asp017)
30. Telesca D, Müller P, Parmigiani G, Freedman RS. 2012 Modeling dependent gene expression. Ann. Appl. Stat. 6, 542-560. (doi:10.1214/11-AOAS525)
31. Minin VN, Bloomquist EW, Suchard MA. 2008 Smooth skyride through a rough skyline: Bayesian coalescent-based inference of population dynamics. Mol. Biol. Evol. 25, 1459-1471. (doi:10.1093/ molbev/msn090)
32. Drummond AJ, Ho SYW, Phillips MJ, Rambaut A. 2006 Relaxed phylogenetics and dating with confidence. PLoS Biol. 4, e88. (doi:10.1371/journal. pbio.0040088)