On incomplete sampling under birth–death models and connections to the sampling-based coalescent

Journal of Theoretical Biology - Tập 261 - Trang 58-66 - 2009
Tanja Stadler1
1Institut für Integrative Biologie, ETH Zürich, Universitätsstr. 16, 8092 Zürich, Switzerland

Tài liệu tham khảo

Aldous, 2005, A critical branching process model for biodiversity, Adv. Appl. Prob., 37, 1094, 10.1239/aap/1134587755 Aldous, 2001, Stochastic models and descriptive statistics for phylogenetic trees, from Yule to today, Statist. Sci., 16, 23, 10.1214/ss/998929474 Bronstein, I.N., Semendjajew, K.A., Musiol, G., Mühlig, H., 2001. Taschenbuch der Mathematik, expanded edition. Verlag Harri Deutsch, Thun. Colless, 1982, Phylogenetics: the theory and practice of phylogenetic systematics, Syst. Zool., 31, 100, 10.2307/2413420 Drummond, 2002, Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data, Genetics, 161, 1307, 10.1093/genetics/161.3.1307 Drummond, 2007, BEAST: Bayesian evolutionary analysis by sampling trees, BMC Evol. Biol., 7, 214, 10.1186/1471-2148-7-214 Edwards, 1970, Estimation of the branch points of a branching diffusion process (With discussion.), J. R. Stat. Soc. Ser. B, 32, 155 Feller, W., 1968. An Introduction to Probability Theory and its Applications, vol. I, third ed. Wiley, New York. Fisher, 1930 Ford, D., Matsen, E., Stadler, T., 2009. A method for investigating relative timing information on phylogenetic trees. Syst. Biol. 58 (2), 167–183. Gernhard, 2008, The conditioned reconstructed process, J. Theor. Biol., 253, 769, 10.1016/j.jtbi.2008.04.005 Gernhard, 2008, New analytic results for speciation times in neutral models, Bull. Math. Biol., 70, 1082, 10.1007/s11538-007-9291-0 Harvey, 1994, Phylogenies without fossils, Evolution, 48, 523, 10.2307/2410466 Kendall, 1948, On the generalized “birth-and-death” process, Ann. Math. Statist., 19, 1, 10.1214/aoms/1177730285 Kingman, 1982, The coalescent, Stochastic Process. Appl., 13, 235, 10.1016/0304-4149(82)90011-4 Kingman, 1982, Exchangeability and the evolution of large populations, Exchangeability Prob. Stat., 97 Kingman, 1982, On the genealogy of large populations, J. Appl. Prob., 19A, 27, 10.2307/3213548 Popovic, 2004, Asymptotic genealogy of a critical branching process, Ann. Appl. Prob., 14, 2120, 10.1214/105051604000000486 Pybus, 2000, Testing macro-evolutionary models using incomplete molecular phylogenies, Proc. R. Soc. London, 267, 2267, 10.1098/rspb.2000.1278 Ray, 2000, Genetic epidemiology of hepatitis C virus throughout Egypt, J. Infect. Dis., 182, 698, 10.1086/315786 Slowinski, 1990, Probabilities on n-trees under two models: a demonstration that asymmetrical interior nodes are not improbable, Syst. Zool., 39, 89, 10.2307/2992212 Stadler, T., 2006–2008. Cass 〈http://www.tb.ethz.ch/people/tstadler〉. Stadler, T., 2008a. Evolving trees—models for speciation and extinction in phylogenetics. Ph.D. Thesis, Technical University of Munich, 2008. Stadler, 2008, Lineages-through-time plots of neutral models for speciation, Math. Biosci., 216, 163, 10.1016/j.mbs.2008.09.006 Tanaka, 2006, Using approximate Bayesian computation to estimate tuberculosis transmission parameters from genotype data, Genetics, 173, 1511, 10.1534/genetics.106.055574 Thompson, 1975 Volkov, 2003, Neutral theory and relative species abundance in ecology, Nature, 424, 1035, 10.1038/nature01883 Wright, 1931, Evolution in mendelian populations, Genetics, 16, 97, 10.1093/genetics/16.2.97 Yang, 1997, Bayesian phylogenetic inference using DNA sequences: a Markov chain Monte Carlo method, Mol. Biol. Evol., 17, 717, 10.1093/oxfordjournals.molbev.a025811 Yule, 1924, A mathematical theory of evolution: based on the conclusions of Dr. J.C. Willis, Philos. Trans. R. Soc. London Ser. B, 213, 21, 10.1098/rstb.1925.0002