Calibrated birth-death phylogenetic time-tree priors for Bayesian inference

Systematic Biology

Volumn 64, Issue 3, 2015, Pages 369-383

  Heled, Joseph ^a,b   Drummond, Alexei J ^a,b  

^a Allan Wilson Centre for Molecular Ecology & Evolution   (New Zealand)

^b UNIVERSITY OF AUCKLAND   (New Zealand)

Author keywords

Bayesian inference; BEAST; birth death tree prior; fossil calibrations; multiple calibrations; Yule prior

Indexed keywords

ALGORITHM; ANIMAL; ANURA; BAYES THEOREM; CALIBRATION; CLASSIFICATION; COMPUTER SIMULATION; PHYLOGENY; PROCEDURES; TIME; TYPHACEAE;

ALGORITHMS; ANIMALS; ANURA; BAYES THEOREM; CALIBRATION; CLASSIFICATION; COMPUTER SIMULATION; PHYLOGENY; TIME; TYPHACEAE;

EID: 84929584290     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1093/sysbio/syu089     Document Type: Article

References (30)

1. Adam J.B., Frédéric J.J.C., Joseph H., Ben J.E. 2012. The pipid root. Syst. Biol. 61(6):913-926.
2. Remco R.B., Joseph H., Denise K., Tim V., Chieh-Hsi W., Dong X., Marc A.S., Andrew R., Alexei J.D. 2014 Apr. Beast 2: A software platform for bayesian evolutionary analysis. PLoS Comput. Biol. 10:e1003537. doi:10.1371/journal.pcbi.1003537.
3. Drummond A.J., Rambaut A. 2007. Beast: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7:214. doi:10.1186/1471-2148-7-214.
4. Drummond A.J., Ho S.Y.W., Phillips M.J., Rambaut A. 2006. Relaxed phylogenetics and dating with confidence. PLoS Biol. 4(5):e88.
5. Felsenstein J. 1981. Evolutionary trees from DNA sequences: A maximum likelihood approach. J. Mol. Evol. 17(6):368-376.
6. Alexandra G., David W., Alexei J.D. 2013. Recursive algorithms for phylogenetic tree counting. Algorithms for Mol. Biol. 8(1):26.
7. GernhardT. 2008. The conditioned reconstructed process. J. Theor. Biol. 253(4):769-778.
8. Joseph H., Remco R.B. 2013. Looking for trees in the forest: summary tree from posterior samples. BMC Evol. Biol. 13(1):221.
9. Joseph H., Alexei J.D. 2010. Bayesian inference of species trees from multilocus data. Mol. Biol. Evol. 27(3):570-580.
10. Joseph H., Alexei J.D. 2012. Calibrated tree priors for relaxed phylogenetics and divergence time estimation. Syst. Biol. 61(1):138-149.
11. Sebastian H., Tanja S., Fredrik R., TomB. 2011 Sep. Inferring speciation and extinction rates under different sampling schemes. Mol. Biol. Evol. 28(9):2577-89.
12. Huelsenbeck J.P., Ronquist F. 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17(8):754-755.
13. David G.K. 1948. On the generalized "birth-and-death" process. Ann. Math. Stat. 19(1):1-15.
14. Kingman J.F.C. 1982. The coalescent. Stoch. Proc. Appl. 13(3): 235-248.
15. Hirohisa K., Jeffrey L.T.,William J.B. 2001. Performance of a divergence time estimation method under a probabilistic model of rate evolution. Mol. Biol. Evol. 18(3):352-361.
16. Nee S., Holmes E.C.,May R.M., Harvey P.H. 1994a Apr. Extinction rates can be estimated from molecular phylogenies. Philos. Trans. R. Soc. Lond. B. Biol. Sci. 344(1307):77-82.
17. Nee S., May R.M., Harvey P.H. 1994b May. The reconstructed evolutionary process. Philos. Trans. R. Soc. Lond. B. Biol. Sci. 344(1309):305-311.
18. Pabijan M., Wandycz A., Hofman S., Wecek K., Piwczynski M., Szymura J.M. 2013. Complete mitochondrial genomes resolve phylogenetic relationships within bombina (anura: Bombinatoridae). Mol. Phylogenet. Evol. 69(1):63-74.
19. Rannala B., Yang Z. 1996 Sep. Probability distribution of molecular evolutionary trees: A new method of phylogenetic inference. J. Mol. Evol. 43(3):304-11.
20. Rannala B., ZihengY. 2007. Inferring speciation times under an episodic molecular clock. Syst. Biol. 56(3):453-466.
21. Renzo S. 2006. An introduction to mathematical methods in combinatorics. Dipartimento di Sistemi e Informatica Viale Morgagni.
22. Tanja S. 2009aNov.Onincomplete sampling under birth-deathmodels and connections to the sampling-based coalescent. J. Theor. Biol. 261(1):58-66.
23. Tanja S. 2009b. On incomplete sampling under birth-death models and connections to the sampling-based coalescent. J. Theor. Biol. 261(1):58-66.
24. Mike S., Arne M. 2010. The expected length of pendant and interior edges of a yule tree. Appl. Math. Lett. 23:1315-1319.
25. Joshua D.S., Bryan T.D., Chloe D., Eisuke H., Kenneth J.S. 2013. Systematics, biogeography, and character evolution of sparganium (typhaceae): Diversification of a widespread, aquatic lineage. Am. J. Bot. 100(10):2023-2039.
26. Jeffrey L.T., Hirohisa K. 2002. Divergence time and evolutionary rate estimation with multilocus data. Syst. Biol. 51(5):689-702.
27. Thorne J.L., Kishino H., Painter I.S. 1998. Estimating the rate of evolution of the rate of molecular evolution. Mol. Biol. Evol. 15:1647-1657.
28. Yang Z., Rannala B. 1997 Jul. Bayesian phylogenetic inference using dna sequences: A markov chain monte carlo method. Mol. Biol. Evol. 14(7):717-24.
29. Yang Z., Rannala B. 2006. Bayesian estimation of species divergence times under amolecular clock using multiple fossil calibrations with soft bounds. Mol. Biol. Evol. 23(1):212-226.
30. Yule G.U. 1924. A mathematical theory of evolution based on the conclusions of dr. j.c. willis. Philos. T. Roy. Soc. B. 213:21-87.