Approximate Bayesian Computation of diversification rates from molecular phylogenies: Introducing a new efficient summary statistic, the nLTT

Methods in Ecology and Evolution

Volumn 6, Issue 5, 2015, Pages 566-575

  Janzen, Thijs ^a   Höhna, Sebastian ^b   Etienne, Rampal S ^a  

^a UNIVERSITY OF GRONINGEN   (Netherlands)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Approximate Bayesian Computation; Lineages Through Time; Phylogenetics; Summary statistic

Indexed keywords

EID: 84929509741     PISSN: None     EISSN: 2041210X     Source Type: Journal    
DOI: 10.1111/2041-210X.12350     Document Type: Article

References (54)

1. Barnes, C.P., Silk, D. & Stumpf, M.P.H. (2011) Bayesian design strategies for synthetic biology. Interface Focus, 1, 895-908.
2. Bazin, E., Dawson, K.J. & Beaumont, M.A. (2010) Likelihood-free inference of population structure and local adaptation in a Bayesian hierarchical model. Genetics, 185, 587-602.
3. Beaumont, M.A. (2010) Approximate Bayesian computation in evolution and ecology. Annual Review of Ecology, Evolution, and Systematics, 41, 379-406.
4. Beaumont, M.A., Zhang, W. & Balding, D.J. (2002) Approximate Bayesian computation in population genetics. Genetics, 162, 2025-35.
5. Blum, M. & François, O. (2006) Which random processes describe the tree of life? A large-scale study of phylogenetic tree imbalance. Systematic Biology, 55, 685-691.
6. Blum, M.G.B. & François, O. (2009) Non-linear regression models for approximate Bayesian computation. Statistics and Computing, 20, 63-73.
7. Blum, M.G.B. & Tran, V.C. (2010) HIV with contact tracing: a case study in approximate Bayesian computation. Biostatistics, 11, 644-60.
8. Bokma, F. (2010) Time, species, and separating their effects on trait variance in clades. Systematic Biology, 59, 602-7.
9. Clarke, K. & Warwick, R. (2001) A further biodiversity index applicable to species lists: variation in taxonomic distinctness. Marine Ecology Progress Series, 216, 265-278.
10. Colless, D. (1982) Review of phylogenetics: the theory and practice of phylogenetic systematics. Systematic Zoology, 31, 100-104.
11. Coyne, J. & Orr, H. (2004) Speciation. Sinauer Associates, Sunderland, Massachusetts.
12. Csilléry, K., Blum, M.G.B., Gaggiotti, O.E. & François, O. (2010) Approximate Bayesian Computation (ABC) in practice. Trends in Ecology and Evolution, 25, 410-8.
13. Davies, T.J., Allen, A.P., Borda-de-Água, L., Regetz, J. & Melián, C.J. (2011) Neutral biodiversity theory can explain the imbalance of phylogenetic trees but not the tempo of their diversification. Evolution, 65, 1841-1850.
14. Del Moral, P., Doucet, A., Jasra, A. & Moral, P. (2012) An adaptive sequential Monte Carlo method for approximate Bayesian computation. Statistics and Computing, 22, 1009-1020.
15. Drovandi, C. & Pettitt, A. (2011) Estimation of parameters for macroparasite population evolution using approximate Bayesian computation. Biometrics, 67, 225-33.
16. Etienne, R.S. & Rosindell, J. (2012) Prolonging the past counteracts the pull of the present: protracted speciation can explain observed slowdowns in diversification. Systematic Biology, 61, 204-13.
17. Etienne, R.S., Haegeman, B., Stadler, T., Aze, T., Pearson, P.N., Purvis, A. & Phillimore, A.B. (2012) Diversity-dependence brings molecular phylogenies closer to agreement with the fossil record. Proceedings of the Royal Society B: Biological Sciences, 279, 1300-1309.
18. Faith, D.P. (1992) Conservation evaluation and phylogenetic diversity. Biological Conservation, 61, 1-10.
19. FitzJohn, R.G., Maddison, W.P. & Otto, S.P. (2009) Estimating trait-dependent speciation and extinction rates from incompletely resolved phylogenies. Systematic Biology, 58, 595-611.
20. Fordyce, J.A. (2010) Interpreting the γ statistic in phylogenetic diversification rate studies: a rate decrease does not necessarily indicate an early burst. PLoS ONE, 5, e11781.
21. Goldberg, E.E., Lancaster, L.T. & Ree, R.H. (2011) Phylogenetic inference of reciprocal effects between geographic range evolution and diversification. Systematic Biology, 60, 451-65.
22. Gould, S. & Eldredge, N. (1977) Punctuated equilibria: the tempo and mode of evolution reconsidered. Paleobiology, 3, 115-151.
23. Harmon, L.J., Schulte, J.A., Larson, A. & Losos, J.B. (2003) Tempo and mode of evolutionary radiation in iguanian lizards. Science, 301, 961-4.
24. Hastings, W. (1970) Monte Carlo sampling methods using Markov chains and their applications. Biometrika, 57, 97-109.
25. Höhna, S. (2013) Fast simulation of reconstructed phylogenies under global time-dependent birth-death processes. Bioinformatics, 29, 1367-74.
26. Höhna, S. (2014) Likelihood inference of non-constant diversification rates with incomplete taxon sampling. PLoS ONE, 9, 17-20.
27. Jabot, F. & Chave, J. (2009) Inferring the parameters of the neutral theory of biodiversity using phylogenetic information and implications for tropical forests. Ecology letters, 12, 239-48.
28. Kutsukake, N. & Innan, H. (2013) Simulation-based likelihood approach for evolutionary models of phenotypic traits on phylogeny. Evolution; International Journal of Organic Evolution, 67, 355-67.
29. Lambert, A. & Stadler, T. (2013) Birth-death models and coalescent point processes: the shape and probability of reconstructed phylogenies. Theoretical Population Biology, 90, 113-28.
30. Lenormand, M., Jabot, F. & Deffuant, G. (2013) Adaptive approximate Bayesian computation for complex models. Computational Statistics, 28, 2777-2796.
31. Maddison, W.P., Midford, P.E. & Otto, S.P. (2007) Estimating a binary character's effect on speciation and extinction. Systematic Biology, 56, 701-10.
32. Marjoram, P., Molitor, J., Plagnol, V. & Tavare, S. (2003) Markov chain Monte Carlo without likelihoods. Proceedings of the National Academy of Sciences, USA, 100, 15324-8.
33. Metropolis, N., Rosenbluth, A.W., Rosenbluth, M.N., Teller, A.H. & Teller, E. (1953) Equation of state calculations by fast computing machines. Journal of Chemical Physics, 21, 1087.
34. Morlon, H. (2014) Phylogenetic approaches for studying diversification. Ecology Letters, 17, 508-25.
35. Morlon, H., Parsons, T.L. & Plotkin, J.B. (2011) Reconciling molecular phylogenies with the fossil record. Proceedings of the National Academy of Sciences, USA, 108, 16327-32.
36. Nee, S., May, R.M. & Harvey, P.H. (1994) The reconstructed evolutionary process. Philosophical Transactions of the Royal Society of London Series B, Biological Sciences, 344, 305-11.
37. Paradis, E. (2011) Time-dependent speciation and extinction from phylogenies: a least squares approach. Evolution, 65, 661-72.
38. Paradis, E., Claude, J. & Strimmer, K. (2004) APE: Analyses of phylogenetics and evolution in R language. Bioinformatics, 20, 289-290.
39. Peters, S. & Foote, M. (2002) Determinants of extinction in the fossil record. Nature, 416, 420-424.
40. Pigot, A.L., Phillimore, A.B., Owens, I.P.F. & Orme, C.D.L. (2010) The shape and temporal dynamics of phylogenetic trees arising from geographic speciation. Systematic Biology, 59, 660-73.
41. Pybus, O. & Harvey, P. (2000) Testing macro-evolutionary models using incomplete molecular phylogenies. Proceedings of the Royal Society B: Biological Sciences, 267, 2267-72.
42. R Core Team (2014) R: A Language and Environment for Statistical Computing. Vienna, Austria. http://www.R-project.org
43. Rabosky, D.L. (2009) Heritability of extinction rates links diversification patterns in molecular phylogenies and fossils. Systematic Biology, 58, 629-40.
44. Rabosky, D.L. & Lovette, I.J. (2008a) Density-dependent diversification in North American wood warblers. Proceedings of the Royal Society B: Biological Sciences, 275, 2363-71.
45. Rabosky, D.L. & Lovette, I.J. (2008b) Explosive evolutionary radiations: decreasing speciation or increasing extinction through time? Evolution, 62, 1866-1875.
46. Raup, D. & Sepkoski, J.J. Jr (1982) Mass extinctions in the marine fossil record. Science, 215, 1501-1503.
47. Robert, C.P., Cornuet, J.-M., Marin, J.-M. & Pillai, N.S. (2011) Lack of confidence in approximate Bayesian computation model choice. Proceedings of the National Academy of Sciences of the United States of America, 108, 15112-7.
48. Sackin, M. (1972) "Good" and "bad" phenograms. Systematic Biology, 21, 225-226.
49. Slater, G.J., Harmon, L.J., Wegmann, D., Joyce, P., Revell, L.J. & Alfaro, M.E. (2012) Fitting models of continuous trait evolution to incompletely sampled comparative data using approximate Bayesian computation. Evolution; International Journal of Organic Evolution, 66, 752-62.
50. Stadler, T. (2011) Mammalian phylogeny reveals recent diversification rate shifts. Proceedings of the National Academy of Sciences, 108, 6187-92.
51. Stadler, T. (2013) Recovering speciation and extinction dynamics based on phylogenies. Journal of Evolutionary Biology, 26, 1203-19.
52. Sunnåker, M., Busetto, A.G., Numminen, E., Corander, J., Foll, M. & Dessimoz, C. (2013) Approximate Bayesian computation. PLoS Computational Biology, 9, e1002803.
53. Tavaré, S., Balding, D., Griffiths, R. & Donnelly, P. (1997) Inferring coalescence times from DNA sequence data. Genetics, 145, 505-518.
54. Toni, T., Welch, D., Strelkowa, N., Ipsen, A. & Stumpf, M.P.H. (2009) Approximate Bayesian computation scheme for parameter inference and model selection in dynamical systems. Journal of the Royal Society Interface, 6, 187-202.