The generalized time variable reconstructed birth-death process

Journal of Theoretical Biology

Volumn 300, Issue , 2012, Pages 265-276

  Hallinan, Nathaniel ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Diversification; Lineage through time; Simulating trees

Indexed keywords

DISCRETE CHOICE ANALYSIS; MASS EXTINCTION; MAXIMUM LIKELIHOOD ANALYSIS; NUMERICAL MODEL; PHYLOGENY; TAXONOMY; TREE;

ANALYTIC METHOD; ARTICLE; BIODIVERSITY; BIRTH DEATH PROCESS; CALCULATION; GENETIC PARAMETERS; INTERMETHOD COMPARISON; LINEAGE; MASS EXTINCTION; MAXIMUM LIKELIHOOD METHOD; METHODOLOGY; MODEL; PALEONTOLOGY; PHYLOGENETIC TREE; PRIORITY JOURNAL; SAMPLING; SIMULATION; STATISTICAL CONCEPTS; STATISTICAL DISTRIBUTION; TIME;

ALGORITHMS; ANIMALS; BIRTH RATE; EXTINCTION, BIOLOGICAL; MARKOV CHAINS; MORTALITY; PALEONTOLOGY; PHYLOGENY;

EID: 84857001367     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2012.01.041     Document Type: Article

References (33)

1. Aldous D. Probability distributions on cladograms. Random Discrete Structures. IMA Volumes in Mathematics and its Applications 1996, vol. 76:1-18. Springer, New York.
2. Aldous D., Krikun M., Popovic L. Five statistical questions about the tree of life. Syst. Biol. 2011, 60(3):318-328.
3. Aldous D., Popovic L. A critical branching process model for biodiversity. Adv. Appl. Probab. 2005, 37(4):1094-1115.
4. Berger J. Statistical Decision Theory: Foundations, Concepts, and Methods. Springer Series in Statistics 1980, Springer, New York.
5. Crisp M., Cook L. Explosive radiation or cryptic mass extinction? Interpreting signatures in molecular phylogenies. Evolution 2009, 63(9):2257-2265.
6. Cusimano N., Renner S. Slowdowns in diversification rates from real phylogenies may not be real. Syst. Biol. 2010, 59(4):458-464.
7. Feller W. Die grundlagen der Volterraschen theorie des kampfes ums dasein in wahrscheinlichkeitstheoretischer behandlung. Acta Biotheor. 1939, 5(1):11-40.
8. Felsenstein J. Inferring Phylogenies 2004, Sinauer Associates, Sunderland, Massachusetts.
9. Foote M. Discordance and concordance between morphological and taxonomic diversity. Paleobiology 1993, 19(2):185-204.
10. Gernhard T. New analytic results for speciation times in neutral models. Bull. Math. Biol. 2008, 70(4):1082-1097.
11. Gernhard T. The conditioned reconstructed process. J. Theor. Biol. 2008, 253(4):769-778.
12. Hartmann K., Wong D., Stadler T. Sampling trees from evolutionary models. Syst. Biol. 2010, 59(4):465-476.
13. Kendall D.G. On the generalized "birth-and-death" process. Ann. Math. Statist. 1948, 19(1):1-15.
14. Morlon H., Parsons T., Plotkin J. Reconciling molecular phylogenies with the fossil record. Proc. Natl. Acad. Sci. USA 2011, 108(39):16327-16332.
15. Nee S., May R., Harvey P. The reconstructed evolutionary process. Philos. Trans. R. Soc. London Ser. B 1994, 344(1309):305-311.
16. Paradis E. Time-dependent speciation and extinction from phylogenies: a least squares approach. Evolution 2011, 65(3):661-672.
17. Rabosky D. LASER: a maximum likelihood toolkit for detecting temporal shifts in diversification rates from molecular phylogenies. Evol. Bioinform. Online 2006, 2(6):1152-1164.
18. Rabosky D. Likelihood methods for detecting temporal shifts in diversification rates. Evolution 2006, 60(6):1152-1164.
19. Rabosky D., Lovette I. Density-dependent diversification in North American wood warblers. Philos. Trans. R. Soc. London Ser. B 2008, 275(1649):2363-2371.
20. Rabosky D., Lovette I. Explosive evolutionary radiations: decreasing speciation or increasing extinction through time?. Evolution 2008, 62(8):1866-1875.
21. Rannala B. Gene genealogy in a population of variable size. Heredity 1997, 78(4):417-423.
22. Raup D., Gould S., Schopf T., Simberloff D. Stochastic models of phylogeny and the evolution of diversity. J. Geol. 1973, 81(5):525-542.
23. Sanderson M., Bharathan G. Does cladistic information affect inferences about branching rates?. Syst. Biol. 1993, 42(1):1-17.
24. Sepkoski J., Bambach R., Raup D., Valentine J. Phanerozoic marine diversity and the fossil record. Nature 1981, 293(5832):435-437.
25. Slatkin M., Hudson R. Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics 1991, 129(2):555-562.
26. Stadler T. Lineages-through-time plots of neutral models for speciation. Math. Biosci. 2008, 216(2):163-171.
27. Stadler T. Sampling-through-time in birth-death trees. J. Theor. Biol. 2010, 267(3):396-404.
28. Stadler T. Mammalian phylogeny reveals recent diversification rate shifts. Proc. Natl. Acad. Sci. USA 2011, 108(15):6187-6192.
29. Stadler T. Simulating trees with a fixed number of extant species. Syst. Biol. 2011, 60(5):676-684.
30. Thompson E. Human Evolutionary Trees 1975, Cambridge University Press, Cambridge.
31. Yang Z., Rannala B. Bayesian phylogenetic inference using DNA sequences: a Markov Chain Monte Carlo Method. Mol. Biol. Evol. 1997, 14(7):717-724.
32. YuanDong Z., RenBin Z., JunXuan F., JunFeng C., Xiao L. Principal aspects of the Ordovician biotic radiation. Sci. China Ser. D 2010, 53(3):382-394.
33. Yule G. A mathematical theory of evolution based on the conclusions of Dr. JC Willis, FRS. Philos. Trans. R. Soc. London Ser. B 1925, 213:21-87.