Measuring Asymmetry in Time-Stamped Phylogenies

PLoS Computational Biology

Volumn 11, Issue 7, 2015, Pages

  Dearlove, Bethany L ^a   Frost, Simon D W ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGY;

COALESCENCE TIME; CURRENT TEST; FALSE NEGATIVES; FALSE POSITIVE; HIV INFECTION; LOCALISED; PHYLOGENETICS; POPULATION STRUCTURES; SAMPLING TIME; SIMPLE++;

PHYLOGENETIC;

ARTICLE; ASYMMETRY; CALCULATION; CHEMICAL DATABASE; CONTROLLED STUDY; EBOLAVIRUS; HUMAN IMMUNODEFICIENCY VIRUS; INFLUENZA VIRUS A H5N1; MEASUREMENT; NONHUMAN; PHYLOGENY; BIOLOGICAL MODEL; COMPUTER SIMULATION; EVOLUTION; GENETIC VARIATION; GENETICS; MUTATION; PEDIGREE; POPULATION GENETICS; SPECIES DIFFERENTIATION; STATISTICAL MODEL; VIRUS;

BIOLOGICAL EVOLUTION; COMPUTER SIMULATION; GENETIC SPECIATION; GENETIC VARIATION; GENETICS, POPULATION; MODELS, GENETIC; MODELS, STATISTICAL; MUTATION; PEDIGREE; PHYLOGENY; VIRUSES;

EID: 84938675286     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1004312     Document Type: Article

References (56)

1. Pybus OG, Rambaut A, (2009) Evolutionary analysis of the dynamics of viral infectious disease. Nat Rev Genet 10: 540–50. 19564871
2. Grenfell BT, Pybus OG, Gog JR, Wood JLN, Daly JM, et al. (2004) Unifying the epidemiological and evolutionary dynamics of pathogens. Science 303: 327–32. doi: 10.1126/science.1090727 14726583
3. Frost SDW, Volz EM, (2010) Viral phylodynamics and the search for an ‘effective number of infections’. Phil Trans R Soc B 365: 1879–90. doi: 10.1098/rstb.2010.0060 20478883
4. Dearlove B, Wilson DJ, (2013) Coalescent inference for infectious disease: meta-analysis of hepatitis C. Phil Trans R Soc B 368: 20120314. doi: 10.1098/rstb.2012.0314 23382432
5. Frost SDW, Volz EM, (2013) Modelling tree shape and structure in viral phylodynamics. Phil Trans R Soc B 368: 20120208. doi: 10.1098/rstb.2012.0208 23382430
6. Mooers AO, Heard SB, (1997) Inferring evolutionary process from phylogenetic tree shape. Q Rev Biol 72: 31–54. doi: 10.1086/419657
7. Leventhal GE, Kouyos R, Stadler T, Wyl VV, Yerly S, et al. (2012) Inferring epidemic contact structure from phylogenetic trees. PLoS Comput Biol 8: e1002413. doi: 10.1371/journal.pcbi.1002413 22412361
8. Pompei S, Loreto V, Tria F, (2012) Phylogenetic properties of RNA viruses. PLoS One 7: e44849. doi: 10.1371/journal.pone.0044849 23028645
9. Blum MGB, François O, (2005) On statistical tests of phylogenetic tree imbalance: the Sackin and other indices revisited. Math Biosci 195: 141–53. doi: 10.1016/j.mbs.2005.03.003 15893336
10. Colless DH, (1982) Phylogenetics: the theory and practice of phylogenetic systematics. Syst Zool 31: 100–104. doi: 10.2307/2413420
11. Sackin MJ, (1972) “Good” and “bad” phenograms. Syst Zool 21: 225–226. doi: 10.2307/2412292
12. McKenzie A, Steel M, (2000) Distributions of cherries for two models of trees. Math Biosci 164: 81–92. doi: 10.1016/S0025-5564(99)00060-7 10704639
13. Kirkpatrick M, Slatkin M, (1993) Searching for evolutionary patterns in the shape of a phylogenetic tree. Evolution 47: 1171–1181. doi: 10.2307/2409983
14. Bortolussi N, Durand E, Blum M, François O, (2006) apTreeshape: statistical analysis of phylogenetic tree shape. Bioinformatics 22: 363–364. doi: 10.1093/bioinformatics/bti798 16322049
15. R Core Team (2013). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL http://www.r-project.org/.
16. Rogers JS, (1996) Central moments and probability distributions of three measures of phylogenetic tree imbalance. Syst Biol 45: 99–110. doi: 10.1093/sysbio/45.1.99
17. Blum MGB, François O, Janson S, (2006) The mean, variance and limiting distribution of two statistics sensitive to phylogenetic tree balance. Ann Appl Probab 16: 2195–2214. doi: 10.1214/105051606000000547
18. Maechler M, Rousseeuw P, Struyf A, Hubert M, Hornik K (2014). cluster: Cluster analysis basics and extensions. R package version 1.15.2.
19. Ernst MD, (2004) Permutation methods: a basis for exact inference. Stat Sci 19: 676–685. doi: 10.1214/088342304000000396
20. Holm S, (1979) A simple sequentially rejective multiple test procedure. Scand J Stat 6: 65–70.
21. Hochberg Y, (1988) A sharper Bonferroni procedure for multiple tests of significance. Biometrika 75: 800–802. doi: 10.1093/biomet/75.4.800
22. Hommel G, (1988) A stagewise rejective multiple text procedure based on a modified Bonferroni test. Biometrika 75: 383–6. doi: 10.1093/biomet/75.2.383
23. Benjamini Y, Hochberg Y, (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc B 57: 289–300.
24. Benjamini Y, Yekutieli D, (2001) The control of the false discovery rate in multiple testing under depencency. Ann Stat 29: 1165–1188.
25. Storey JD, (2002) A direct approach to false discovery rates. J R Stat Soc B 64: 479–498. doi: 10.1111/1467-9868.00346
26. Storey JD, Tibshirani R, (2003) Statistical significance for genomewide studies. Proc Natl Acad Sci USA 100: 9440–9445. doi: 10.1073/pnas.1530509100 12883005
27. Storey JD, (2003) The positive false discovery rate: a Bayesian interpretation and the q-value. Ann Stat 31: 2013–2035. doi: 10.1214/aos/1074290335
28. Anderson CNK, Ramakrishnan U, Chan YL, Hadly EA, (2005) Serial SimCoal: a population genetics model for data from multiple populations and points in time. Bioinformatics 21: 1733–4. doi: 10.1093/bioinformatics/bti154 15564305
29. Drummond AJ, Suchard MA, Xie D, Rambaut A, (2012) Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol 29: 1969–73. doi: 10.1093/molbev/mss075 22367748
30. Gire SK, Goba A, Andersen KG, Sealfon RSG, Park DJ, et al. (2014) Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak. Science 345: 1369–1372. doi: 10.1126/science.1259657 25214632
31. 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 17360548
32. Frost SDW, Wrin T, Smith DM, Kosakovsky Pond SL, Liu Y, et al. (2005) Neutralizing antibody responses drive the evolution of human immunodeficiency virus type 1 envelope during recent HIV infection. Proc Natl Acad Sci USA 102: 18514–9. doi: 10.1073/pnas.0504658102 16339909
33. Edgar RC, (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792–7. doi: 10.1093/nar/gkh340 15034147
34. Tavaré S, (1986) Some probabilistc and statistical problems in the analysis of DNA sequences. Lectures Math Life Sci 17: 57–86.
35. 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 16683862
36. Palacios JA, Minin VN (2012) Integrated nested Laplace approximation for Bayesian nonparametric phylodynamics. In: Proceedings of the Twenty-Eighth Conference on Uncertainty in Artificial Intelligence (UAI-12), Corvallis, Oregon: AUAI Press. pp. 726–735.
37. WHO (2015). Ebola data and statistics: Situation summary. Data published on 15 April 2015. URL http://apps.who.int/gho/data/view.ebola-sitrep.ebola-summary-20150415?lang=en.
38. Volz E, Kosakovsky Pond S, (2014) Phylodynamic analysis of Ebola virus in the 2014 Sierra Leone epidemic. PLoS Curr outbreaks. doi: 10.1371/currents.outbreaks.6f7025f1271821d4c815385b08f5f80e
39. Stadler T, Kühnert D, Rasmussen DA, du Plessis L, (2014) Insights into the early epidemic spread of Ebola in Sierra Leone provided by viral sequence data. PLoS Curr outbreaks. doi: 10.1371/currents.outbreaks.02bc6d927ecee7bbd33532ec8ba6a25f
40. Łuksza M, Bedford T, Lässig M (2014) Epidemiological and evolutionary analysis of the 2014 Ebola virus outbreak. ArXiv e-prints:http://arxiv.org/abs/1411.1722.
41. Ferguson NM, Galvani AP, Bush RM, (2003) Ecological and immunological determinants of influenza evolution. Nature 422: 428–433. doi: 10.1038/nature01509 12660783
42. Poon AFY, Walker LW, Murray H, McCloskey RM, Harrigan PR, et al. (2013) Mapping the shapes of phylogenetic trees from human and zoonotic RNA viruses. PLoS One 8: e78122. doi: 10.1371/journal.pone.0078122 24223766
43. Gray RR, Pybus OG, Salemi M, (2011) Measuring the Temporal Structure in Serially-Sampled Phylogenies. Methods Ecol Evol 2: 437–445. doi: 10.1111/j.2041-210X.2011.00102.x 22121470
44. Shao KT, Sokal RR, (1990) Tree balance. Syst Zool 39: 266–276. doi: 10.2307/2992186
45. Agapow PM, Purvis A, (2002) Power of eight tree shape statistics to detect nonrandom diversification: a comparison by simulation of two models of cladogenesis. Syst Biol 51: 866–872. doi: 10.1080/10635150290102564 12554452
46. Purvis A, Katzourakis A, Agapow PM, (2002) Evaluating phylogenetic tree shape: two modifications to Fusco & Cronk’s method. J Theor Biol 214: 99–103. doi: 10.1006/jtbi.2001.2443 11786035
47. Romero-Severson E, Skar H, Bulla I, Albert J, Leitner T, (2014) Timing and order of transmission events is not directly reflected in a pathogen phylogeny. Mol Biol Evol 31: 2472–2482. doi: 10.1093/molbev/msu179 24874208
48. Steel M, (2005) Should phylogenetic models be trying to ‘fit an elephant’? Trends Genet 21: 307–9. doi: 10.1016/j.tig.2005.04.001 15922824
49. Huelsenbeck JP, Ronquist F, Nielsen R, Bollback JP, (2001) Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294: 2310–4. doi: 10.1126/science.1065889 11743192
50. Bollback JP, (2002) Bayesian model adequacy and choice in phylogenetics. Mol Biol Evol 19: 1171–80. doi: 10.1093/oxfordjournals.molbev.a004175 12082136
51. Bollback JP, Nielsen R, (2005) Posterior mapping and posterior predictive distributions. In: Statistical Methods in Molecular Evolution, New York: Springer. pp. 439–462.
52. Brown JM, ElDabaje R, (2009) PuMA: Bayesian analysis of partitioned (and unpartitioned) model adequacy. Bioinformatics 25: 537–8. doi: 10.1093/bioinformatics/btn651 19098028
53. Drummond AJ, Suchard MA, (2008) Fully Bayesian tests of neutrality using genealogical summary statistics. BMC Genet 9: 68. doi: 10.1186/1471-2156-9-68 18976476
54. 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 19779555
55. Hudson RR, (1991) Gene genealogies and the coalescent process. Oxford Surv Evol Biol 7: 1–44.
56. Notohara M, (1990) The coalescent and the genealogical process in geographically structured population. J Math Biol 29: 59–75. doi: 10.1007/BF00173909 2277236