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Detecting Diversification Rate Variation in Supertrees

  • Chapter
Phylogenetic Supertrees

Part of the book series: Computational Biology ((COBO,volume 4))

Abstract

Although they typically do not provide reliable information on divergence times, supertrees are nevertheless attractive candidates for the study of diversification rates: by combining a collection of less inclusive source trees, they promise to increase both the number and density of taxa included in the composite phylogeny. The relatively large size and possibly more dense taxonomic sampling of supertrees have the potential to increase the statistical power and decrease the bias, respectively, of methods for studying diversification rates that are robust to uncertainty regarding the timing of diversification events. These considerations motivate the development of atemporal methods that can take advantage of recent and anticipated advances in supertree estimation. Herein, we describe a set of whole-tree, topologybased methods intended to address two questions pertaining to the study of diversification rates. First, has a given (super)tree experienced significant variation in diversification rates among its branches? Second, if so, where have significant shifts in diversification rate occurred? We present results of simulation studies that characterize the statistical behavior of these methods, illustrating their increased power and decreased bias. We also applied the methods to a published supertree of primates, demonstrating their ability to contend with relatively large, incompletely resolved (super)trees. All the methods described in this chapter have been implemented in the freely available program, SymmeTREE.

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References

  • Agapow, P.-M. and Purvis, A. 2002. Power of eight tree shape statistics to detect nonrandom diversification: A comparison of two models of cladogenesis. Systematic Biology 51:866–872.

    Article  PubMed  Google Scholar 

  • Arnason, U., Gullberg, A., and Janke, A. 1998. Molecular timing of primate divergences as estimated by two non-primate calibration points. Journal of Molecular Evolution 47:718–727.

    Article  PubMed  CAS  Google Scholar 

  • Baldwin B. G. and Sanderson, M. J. 1998. Age and rate of diversification of the Hawaiian silversword alliance (Compositae). Proceedings of the National Academy of Sciences of the United States ofAmerica 95:9402–9406.

    Article  CAS  Google Scholar 

  • Barraclough, T. G., Harvey, P. H., and Nee, S. 1996. Rate of rbcL gene sequence evolution and species diversification in flowering plants (angiosperms). Proceedings of the Royal Society ofLondon B 263:589–591.

    Article  Google Scholar 

  • Barraclough, T. G., Nee, S., and Harvey, P. H. 1998. Sister-group analysis in identifying correlates of diversification: comment. Evolutionary Ecology 12:751–754.

    Article  Google Scholar 

  • Barraclough, T. G. and Nee, S. 2001. Phylogenetics and speciation. Trends in Ecology and Evolution 16:391–399.

    Article  PubMed  Google Scholar 

  • Barraclough, T. G. and Savolainen, V. 2001. Evolutionary rates and species diversity in flowering plants. Evolution 55:677–683.

    Article  PubMed  CAS  Google Scholar 

  • Bininda-Emonds, O. R. P., Gittleman, J. L., and Purvis, A. 1999. Building large trees by combining phylogenetic information: a complete phylogeny of the extant Carnivora (Mammalia). Biological Reviews 74:143–175.

    Article  PubMed  CAS  Google Scholar 

  • Bremer, B. and Eriksson, O. 1992. Evolution of fruit characters and dispersal modes in the tropical family Rubiaceae. Biological Journal of the Linnean Society 47:79–95.

    Article  Google Scholar 

  • Bryant, D., Semple, C., and Steel, M. 2004. Supertree methods for ancestral divergence dates and other applications. In O. R. P. Bininda-Emonds (ed). Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life, pp. 129–150. Kluwer Academic, Dordrecht, the Netherlands.

    Google Scholar 

  • Chan, K. M. A. and Moore, B. R. 1999. Accounting for mode of speciation increases power and realism of tests of phylogenetic asymmetry. American Naturalist 153:332–346.

    Article  Google Scholar 

  • Chan, K. M. A. and Moore, B. R. 2002. Whole-tree methods for detecting differential diversification rates. Systematic Biology 51:855–865.

    Article  PubMed  Google Scholar 

  • Colless, D. H. 1982. Review of Phylogenetics: The Theory and Practice of Phylogenetic Systematics, by E. O. Wiley. Systematic Zoology 31:100–104.

    Article  Google Scholar 

  • Dodd, M. E., Silvertown, J., and C Hase, M. W. 1999. Phylogenetic analysis of trait evolution and species diversity variation among angiosperm families. Evolution 53:732–744.

    Article  Google Scholar 

  • Donoghue, M. J. and Ackerly, D. D. 1996. Phylogenetic uncertainties and sensitivity analyses in comparative biology. Philosophical Transactions of the Royal Society of London B 351:1241–1249.

    Article  Google Scholar 

  • Doyle, J. A. and Donoghue, M. J. 1993. Phylogenies and angiosperm diversification. Paleobiology 19:141–167.

    Google Scholar 

  • Edgington, E. S. 1972a. An additive method for combining probability values from independent experiments. Journal of Psychology 80:351–363.

    Article  Google Scholar 

  • Edgington, E. S. 1972b. A normal curve method for combining probability values from independent experiments. Journal ofPsychology 82:85–89.

    Article  Google Scholar 

  • Edgington, E. S. and Haller, O. 1984. Combining probabilities from discrete probability distributions. Educational and Psychological Measurement 44: 265–274.

    Article  Google Scholar 

  • Eriksson, O. and Bremer, B. 1991. Fruit characteristics, life forms, and species richness in the plant family Rubiaceae. American Naturalist 138:751–761.

    Article  Google Scholar 

  • Eriksson, O. and Bremer, B. 1992. Pollination systems, dispersal modes, life forms, and diversification rates in angiosperm families. Evolution 46:258–256.

    Article  Google Scholar 

  • Farrell, B. D. 1998. “Inordinate fondness” explained: why are there so many beetles? Science 281:555–559.

    Article  PubMed  CAS  Google Scholar 

  • Farrell, B. D. and Mitter, C. 1998. The timing of insect/plant diversification: might Tetraopes (Coleoptera: Cerambycidae) and Asclepias (Asclepiadaceae) have co-evolved? Biological Journal of the Linnean Society 63:553–577.

    Google Scholar 

  • Felsenstein, J. 1988. Phylogenies from molecular sequences: Inference and reliability. Annual Review of Genetics 22:521–565.

    Article  PubMed  CAS  Google Scholar 

  • Felsenstein, J. 1989. Phylip — Phylogeny Inference Package (Version 3.2). Cladistics 5:164–166. (http://evolution.genetics.washington.edu/phylip.html)

    Google Scholar 

  • Fisher, R. A. 1932. Statistical Methods for Research Workers. 4th edition. Oliver and Boyd, Edinburgh.

    Google Scholar 

  • Furnas, G. W. 1984. The generation of random, binary unordered trees. Journal of Classification 1:187–233.

    Article  Google Scholar 

  • Fusco, G. and Cronk, Q. C. B. 1995. A new method for evaluating the shape of large phylogenies. Journal of Theoretical Biology 175:235–243.

    Article  Google Scholar 

  • Goudet, J. 1999. An improved procedure for testing the effects of key innovations on rate of speciation. American Naturalist 153:549–555.

    Article  Google Scholar 

  • Gould, S. J., Raup, D. M., Sepowski, J. J., Schopf, T. J. M., and Simberloff, D. S. 1977. The shape of evolution: a comparison of real and random clades. Paleobiology 3:23–40.

    Google Scholar 

  • Guyer, C. and Slowinski, J. B. 1991. Comparisons of observed phylogenetic topologies with null expectations among three monophyletic lineages. Evolution 45:340–350.

    Article  Google Scholar 

  • Guyer, C. and Slowinski, J. B. 1993. Adaptive radiations and the topology of large phylogenies. Evolution 47:253–263.

    Article  Google Scholar 

  • Harris, T. E. 1964. The Theory ofBranching Processes. Springer-Verlag, Berlin.

    Google Scholar 

  • Harvey, P. H., Nee, S., Mooers, A. Ø., and Partridge, L. 1991. These hierarchical views of life: phylogenies and metapopulations. In R. J. Berry, T. J. Cranford, and G. M. Hewitt (eds), Genes in Ecology, pp. 123–137. Blackwell Scientific, Oxford.

    Google Scholar 

  • Harvey, P. H. and Nee, S. 1993. New uses for new phylogenies. European Review 1:11–19.

    Article  Google Scholar 

  • Harvey, P. H. and Nee, S. 1994. Comparing real with expected patterns from molecular phylogenies. In P. Eggleton and R. I. Vane-Wright (eds), Phylogenetics and Ecology, pp. 219–231. Academic Press, London.

    Google Scholar 

  • Harvey, P. H., Holmes, E. C., Mooers, A. Ø., and Nee, S. 1994a. Inferring evolutionary processes from molecular phylogenies. In R. W. Scotland, D. J. Siebert, and D. M. Williams (eds), Models in Phylogeny Reconstruction, pp. 313–333. Clarendon Press, Oxford.

    Google Scholar 

  • Harvey, P. H., May, R. M., and Nee, S. 1994b. Phylogenies without fossils. Evolution 48:523–529.

    Article  Google Scholar 

  • Harvey, P. H., Rambaut, A., and Nee, S. 1996. New computer packages for analysing phylogenetic tree structure. In J. Colbert and R. Barbault (eds), Aspects of the Genesis and Maintenance of Biological Diversity, pp. 60–68. Oxford University Press, Oxford.

    Google Scholar 

  • Harding, E. F. 1971. The probabilities of rooted tree-shapes generated by random bifurcation. Advances in Applied Probability 3:44–77.

    Article  Google Scholar 

  • Heard, S. B. 1992. Patterns in tree balance among cladistic, phenetic, and randomly generated phylogenetic trees. Evolution 46:1818–1826.

    Article  Google Scholar 

  • Hennig, W. 1966. Phylogenetic Systematics. University of Illinois Press, Urbana, Illinois.

    Google Scholar 

  • Hey, J. 1992. Using phylogenetic trees to study speciation and extinction. Evolution 46:627–640.

    Article  Google Scholar 

  • Huelsenbeck, J. P., Larget, B., and Swofford, D. 2000a. A compound Poisson process for relaxing the molecular clock. Genetics 154:1879–1892.

    PubMed  CAS  Google Scholar 

  • Huelsenbeck, J. P., Rannala, B., and Masly, J. P. 2000b. Accommodating phylogenetic uncertainty in evolutionary studies. Science 288:2349–2350.

    Article  CAS  Google Scholar 

  • Hulbert, R. C. 1993. Taxonomic evolution in North American Neogene horses (subfamily Equinae): the rise and fall of an adaptive radiation. Paleobiology 19:216–234.

    Google Scholar 

  • Jensen, J. S. 1990. Plausibility and testability: Assessing the consequences of evolutionary innovation. In M. H. Nitecki (ed.), Evolutionary Innovations, pp. 171–190. University of Chicago Press, Chicago.

    Google Scholar 

  • Jobson, R. W. and Albert, V. A. 2002. Molecular rates parallel diversification contrasts between carnivorous plant sister lineages. Cladistics 18:127–136.

    Google Scholar 

  • Jones, K. E., Purvis, A., Maclarnon, A., Bininda-Emonds, O. R. P., and Simmons, N. B. 2002. A phylogenetic supertree of the bats (Mammalia: Chiroptera). Biological Reviews 77:223–259.

    Article  PubMed  Google Scholar 

  • Judd, W. S., Sanders, R. W., and Donoghue, M. J. 1994. Angiosperm family pairs: preliminary phylogenetic analyses. Harvard Papers in Botany 1:1–51.

    Google Scholar 

  • Kelley S. T. and Farrell, B. D. 1998. Is specialization a dead end? The phylogeny of host use in Dendroctonus bark beetles (Scolytidae). Evolution 52:1731–1743.

    Article  CAS  Google Scholar 

  • Kendall, D. G. 1948. On the generalized birth-and-death process. Annals of Mathematical Statistics 19:1–15.

    Article  Google Scholar 

  • Kennedy, M. and Page, R. D. M. 2002. Seabird supertrees: combining partial estimates of procellariiform phylogeny. The Auk 119:88–108.

    Google Scholar 

  • Kirkpatrick, M. and Slatkin, M. 1993. Searching for evolutionary patterns in the shape of a phylogenetic tree. Evolution 47:1171–1181.

    Article  Google Scholar 

  • Kishino, H., Thorne, J. L., and Bruno, W. J. 2001. Performance of divergence time estimation methods under a probabilistic model of rate evolution. Molecular Biology and Evolution 18: 352–361.

    Article  PubMed  CAS  Google Scholar 

  • Kubo, T. and Iwasa, Y. 1995. Inferring rates of branching and extinction from molecular phylogenies. Evolution 49:694–704.

    Article  Google Scholar 

  • Lapointe, F.-J. and Cucumel, G. 1997. The average consensus procedure: combination of weighted trees containing identical or overlapping sets of taxa. Systematic Biology 46:306–312.

    Article  Google Scholar 

  • Lapointe, F.-J. and Levasseur, C. 2004. Everything you always wanted to know about the average consensus, and more. In O. R. P. Bininda-Emonds (ed.), Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life, pp. 87–105. Kluwer Academic, Dordrecht, the Netherlands.

    Google Scholar 

  • Lee, M. S. Y. 1999. Molecular clock calibrations and Metazoan divergence dates. Journal of Molecular Evolution 49:385–391.

    Article  PubMed  CAS  Google Scholar 

  • Losos, J. B. and Adler, F. R. 1995. Stumped by trees? A generalized null model for patterns of organismal diversity. American Naturalist 145:329–342.

    Article  Google Scholar 

  • Maddison, W. P. 1989. Reconstructing character evolution on polytomous cladograms. Cladistics 5:365–377.

    Article  Google Scholar 

  • Magallon, S. and Sanderson, M. J. 2001. Absolute diversification rates in angiosperm clades. Evolution 55:1762–1780.

    PubMed  CAS  Google Scholar 

  • Mckenzie, A. and Steel, M. 2000. Distributions of cherries for two models of trees. Mathematical Biosciences 164:81–92.

    Article  PubMed  CAS  Google Scholar 

  • Mindell, D. P., Sites, J. W., Jr., and Graur, D. 1989. Speciational evolution: a phylogenetic test with allozymes in Sceloporus (Reptilia). Cladistics 5:49–61.

    Article  Google Scholar 

  • Mooers, A. O. 1995. Tree balance and tree completeness. Evolution 49:379–384.

    Article  Google Scholar 

  • Mooers, A. O. and Heard, S. B. 1997. Inferring evolutionary process from phylogenetic tree shape. Quarterly Review ofBiology 72:31–54.

    Article  Google Scholar 

  • Nee, S. 2001. Inferring speciation rates from phylogenies. Evolution 55:661–668.

    Article  PubMed  CAS  Google Scholar 

  • Nee, S., Mooers, A. O., and Harvey, P. H. 1992. Tempo and mode of evolution revealed from molecular phylogenies. Proceedings of the National Academy of Sciences of the United States ofAmerica 89:8322–8326.

    Article  CAS  Google Scholar 

  • Nee, S. R. and Harvey, P. H. 1994. Getting to the root of flowering plant diversity. Science 264:1549–1550.

    Article  PubMed  CAS  Google Scholar 

  • Nee, S., Holmes, E. C., May, R. M., and Harvey, P. H. 1994a. Extinction rates can be estimated from molecular phylogenies. Philosophical Transactions of the Royal Society of London B 344:77–82.

    Article  CAS  Google Scholar 

  • Nee, S., May, R. M., and Harvey, P. H. 1994b. The reconstructed evolutionary process. Philosophical Transactions of the Royal Society of London B 344:305–311.

    Article  CAS  Google Scholar 

  • Nee, S., Holmes, E. C., May, R. M., and Harvey, P. H. 1995. Estimating extinction from molecular phylogenies. In J. H. Lawton and R. M. May (eds), Extinction Rates, pp. 164–182. Oxford University Press, Oxford.

    Google Scholar 

  • Nee, S., Barraclough, T. G., and Harvey, P. H. 1996. Temporal changes in biodiversity: detecting patterns and identifying causes. In K. J. Gaston (ed.), Biodiversity: a Biology of Numbers and Differences, pp. 230–252. Blackwell Science, Oxford.

    Google Scholar 

  • Page, R. D. M. 1993. On describing the shape of rooted and unrooted trees. Cladistics 9:93–99.

    Article  Google Scholar 

  • Paradis, E. 1997. Assessing temporal variations in diversification rates from phylogenies: Estimation and hypothesis testing. Proceedings of the Royal Society of London B 264:1141–1147.

    Article  Google Scholar 

  • Paradis, E. 1998a. Detecting shifts in diversification rates without fossils. American Naturalist 152:176–187.

    Article  CAS  Google Scholar 

  • Paradis, E. 1998b. Testing for constant diversification rates using molecular phylogenies: a general approach based on statistical tests for goodness of fit. Molecular Biology and Evolution 15:476–479.

    Article  CAS  Google Scholar 

  • Purvis, A. 1995. A composite estimate of primate phylogeny. Philosophical Transactions of the Royal Society ofLondon B 348:405–421.

    Article  CAS  Google Scholar 

  • Purvis, A. 1996. Using interspecies phylogenies to test macroevolutionary hypotheses. In K. J. Gaston (ed.), Biodiversity: a Biology of Numbers and Differences, pp. 151–168. Blackwell Science, Oxford.

    Google Scholar 

  • Purvis, A., Nee, S., and Harvey, P. H. 1995. Macroevolutionary inferences from primate phylogeny. Proceedings of the Royal Society ofLondon B 260:329–333.

    Article  CAS  Google Scholar 

  • Purvis, A., Katzourakis, A, and Agapow, P.-M. 2002. Evaluating phylogenetic tree shape: two modifications to Fusco and Cronk’s method. Journal of Theoretical Biology 214:99–103.

    Article  PubMed  Google Scholar 

  • Pybus, O. G. and Harvey, P. H. 2000. Testing macro-evolutionary models using incomplete molecular phylogenies. Proceedings of the Royal Society ofLondon B 267:2267–2272.

    Article  CAS  Google Scholar 

  • Pybus, O. G., Rambaut, A, Holmes, E. C., and Harvey, P. H. 2002. New inferences from tree shape: numbers of missing taxa and population growth rates. Systematic Biology 51:881–888.

    Article  PubMed  CAS  Google Scholar 

  • Rambaut, A., Harvey, P. H., and Nee, S. 1997. End-Epi: an application for inferring phylogenetic and population dynamical processes from molecular sequences. Computer Applications in the Biosciences 13:303–306.

    PubMed  CAS  Google Scholar 

  • Rambaut, A. and B Romham, L. 1998. Estimating divergence dates from molecular sequences. Molecular Biology and Evolution 15:442–448.

    Article  PubMed  CAS  Google Scholar 

  • Raup, D. M., Gould, S. J, Schopf, T. J. M., and Simberloff, D. S. 1973. Stochastic models of phylogeny and the evolution of diversity. Journal of Geology 81:525–542.

    Article  Google Scholar 

  • Ricklefs, R. E. and Renner, S. S. 1994. Species richness within families of flowering plants. Evolution 48:1619–1636.

    Article  Google Scholar 

  • Rogers, J. S. 1993. Response of Colless’s tree imbalance to number of terminal taxa. Systematic Biology 42:102–105.

    Google Scholar 

  • Rogers, J. S. 1994. Central moments and probability distribution of Colless’ coefficient of tree imbalance. Evolution 48:2026–2036.

    Article  Google Scholar 

  • Rogers, J. S. 1996. Central moments and probability distributions of three measures of phylogenetic tree imbalance. Systematic Biology 45:99–110.

    Article  Google Scholar 

  • Ronquist, F., Huelsenbeck, J. P., and Britton, T. 2004. Bayesian supertrees. In O. R. P. Bininda-Emonds (ed.), Phylogenetic Supertrees: Combining Information to Reveal the Tree ofLife, pp. 193–224. Kluwer Academic, Dordrecht, the Netherlands.

    Google Scholar 

  • Salamin, N., Hodkinson, T. R., and Savolainen, V. 2002. Building supertrees: an empirical assessment using the grass family (Poaceae). Systematic Biology 51:136–150.

    Article  PubMed  Google Scholar 

  • Sanderson, M. J. 1994. Reconstructing the history of evolutionary processes using maximum likelihood. In D. M. Fambrough (ed.), Molecular Evolution of Physiological Processes, Society of General Physiologists Series 49:13–26. Rockefeller University Press, New York.

    Google Scholar 

  • Sanderson, M. J. 1997. A non-parametric approach to estimating divergence times in the absence of rate constancy. Molecular Biology and Evolution 14:1218–1231.

    Article  CAS  Google Scholar 

  • Sanderson, M. J. 2002. Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. Molecular Biology and Evolution 19:101–109.

    Article  PubMed  CAS  Google Scholar 

  • Sanderson, M. J. and Bharathan, G. 1993. Does cladistic information affect inferences about branching rates? Systematic Biology 42:1–17.

    Google Scholar 

  • Sanderson, M. J. and Donoghue, M. J. 1994. Shifts in diversification rate with the origin of angiosperms. Science 264:1590–1593.

    Article  PubMed  CAS  Google Scholar 

  • Sanderson, M. J. and Donoghue, M. J. 1996. Reconstructing shifts in diversification rates on phylogenetic trees. Trends in Ecology and Evolution 11:15–20.

    Article  PubMed  CAS  Google Scholar 

  • Sanderson, M. J. and Wojciechowski, M. F. 1996. Diversification rates in a temperate legume clade: are there “so many species” of Astragalus (Fabaceae)? American Journal of Botany 83:1488–1502.

    Article  Google Scholar 

  • Sanmartín, I., Enghof, H., and Ronquist, F. 2001. Patterns of animal dispersal, vicariance and diversification in the Holarctic. Biological Journal of the Linnean Society 73:345–390.

    Google Scholar 

  • Sarich, V. and Wilson, A. C. 1967. Rates of albumin evolution in primates. Proceedings of the National Academy of Sciences of the United States ofAmerica 58:142–148.

    Article  CAS  Google Scholar 

  • Savolainen, V. and Goudet, J. 1998. Rate of gene sequence evolution and species diversification in flowering plants: a re-evaluation. Proceedings of the Royal Society of London B 265:603–607.

    Article  Google Scholar 

  • Shao, K.-T. and Sokal, R. R. 1990. Tree balance. Systematic Zoology 39:266–276.

    Article  Google Scholar 

  • Simms, H. J. and McConway, K. J. 2003. Nonstochastic variation of species-level diversification rates within angiosperms. Evolution 57:460–479.

    Google Scholar 

  • Slowinski, J. B. 1990. Probabilities of n-trees under two models: Demonstration that asymmetrical interior nodes are not improbable. Systematic Zoology 39:89–94.

    Article  Google Scholar 

  • Slowinski, J. B. and Guyer, C. 1989a. Testing the stochasticity of patterns of organismal diversity: an improved null model. American Naturalist 134:907–921.

    Article  Google Scholar 

  • Slowinski, J. B. and Guyer, C. 1989b. Testing null models in questions of evolutionary success. Systematic Zoology 38:189–191.

    Article  Google Scholar 

  • Slowinski, J. B. and Guyer, C. 1993. Testing whether certain traits have caused amplified diversification: an improved method based on a model of random speciation and extinction. American Naturalist 142:1019–1024.

    Article  PubMed  CAS  Google Scholar 

  • Stanley, S. M. 1979. Macroevolution: Pattern and Process. W. H. Freeman, San Francisco.

    Google Scholar 

  • Stone, J. and Repka, J. 1998. Using a nonrecursive formula to determine cladogram probabilities. Systematic Biology 47:617–624.

    Article  PubMed  CAS  Google Scholar 

  • Stoner, C. J., Bininda-Emonds, O. R. P, and Caro, T. 2003. The adaptive significance of coloration in lagomorphs. Biological Journal of the Linnean Society 79:309–328.

    Article  Google Scholar 

  • Takezaki, N., Rzhetsky, A, and Nei, M. 1995. Phylogenetic test of the molecular clock and linearized trees. Molecular Biology and Evolution 12:823–833.

    PubMed  CAS  Google Scholar 

  • Thorne, J. L., Kishino, H, and Painter, I. S. 1998. Estimating the rate of evolution of the rate of molecular evolution. Molecular Biology and Evolution 15:1647–1657.

    Article  PubMed  CAS  Google Scholar 

  • Thorne, J. L. and Kishino, H. 2002. Divergence time and evolutionary rate estimation with multilocus data. Systematic Biology 51:689–702.

    Article  PubMed  Google Scholar 

  • Tiffney, B. H. and Mazer, S. J. 1995. Angiosperm growth habit, dispersal and diversification reconsidered. Evolutionary Ecology 9:93–117.

    Article  Google Scholar 

  • Vos, R. A. and Mooers, A. O. 2004. Reconstructing divergence times for Supertrees. In O. R. P. Bininda-Emonds (ed.), Phylogenetic Supertrees: Combining Information to Reveal the Tree ofLife, pp. 281–299. Kluwer Academic, Dordrecht, the Netherlands.

    Google Scholar 

  • Wallis, W. A. 1942. Compounding probabilities from independent significance tests. Econometrica 10:229–248.

    Article  Google Scholar 

  • Wiley, E. O. 1981. Phylogenetics: the Theory and Practice of Phylogenetic Systematics. Wiley and Sons, New York.

    Google Scholar 

  • Wojciechowski, M. F., Sanderson, M. J., Steel, K. P., and Liston, A. 2000. Molecular phylogeny of the “temperate herbaceous tribes” of papilionoid legumes: a supertree approach. In P. Herendeen and A. Bruneau (eds), Advances in Legume Systematics 9:277–298. Royal Botanic Garden, Kew.

    Google Scholar 

  • Wu, C.-I. and Li, W.-H. 1985. Evidence for higher rates of nucleotide substitution in rodents than in man. Proceedings of the National Academy of Sciences of the United States ofAmerica 82:1741–1745.

    Article  CAS  Google Scholar 

  • Yoder, A. D. and Yang, Z. H. 2000. Estimation of speciation dates using local molecular clocks. Molecular Biology and Evolution 17:1081–1090.

    Article  PubMed  CAS  Google Scholar 

  • Yoder, A. D. and Yang, Z. H. In press. Divergence dates for Malagasy lemurs estimated from multiple gene loci: fit with climatological events and speciation models. Molecular Ecology

    Google Scholar 

  • Yule, G. U. 1924. A mathematical theory of evolution, based on the conclusions of Dr. J. C. Willis. Philosophical Transactions of the Royal Society of London B 213:21–87.

    Article  Google Scholar 

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Authors
  1. Brian R. Moore
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  2. Kai M. A. Chan
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  3. Michael J. Donoghue
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Editors and Affiliations

  1. Lehrstuhl für Tierzucht, Technische Universität München, Freising- Weihenstephan, Germany

    Olaf R. P. Bininda-Emonds

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Moore, B.R., Chan, K.M.A., Donoghue, M.J. (2004). Detecting Diversification Rate Variation in Supertrees. In: Bininda-Emonds, O.R.P. (eds) Phylogenetic Supertrees. Computational Biology, vol 4. Springer, Dordrecht. https://doi.org/10.1007/978-1-4020-2330-9_23

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