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These papers were cited in the Spring 2024 version of the course.

Ané, C., B. Larget, D. A. Baum, S. D. Smith, and A. Rokas. 2007. Bayesian estimation of concordance among gene trees. Molecular Biology and Evolution 24:412-426. (Describes the DPP model behind BUCKy) (Apr 9)

Beaulieu, J. M., and B. C. O’Meara. 2016. Detecting hidden diversification shifts in models of trait-dependent speciation and extinction. Systematic Biology 65:583-601. (Apr 23)

Bergthorsson U., Adams K. L., Thomason B., Palmer J. D. 2003. Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature 424:197–201. (Apr 2)

Blomberg, S. P., T. Garland Jr., and A. R. Ives. 2003. Testing for phylogenetic signal in comparative data: behavioral traits are more labile. Evolution 57(4):717-745. (Apr 4)

Blomberg, S. P., J. G. Lefevre, J. A. Wells, and M. Waterhouse. 2012. Independent contrasts and PGLS regression estimators are equivalent. Systematic Biology 61:382–391. (Apr 2)

Brown, W., E. Prager, A. Wang, and A. Wilson. 1982. Mitochondrial DNA sequences of primates, tempo and mode of evolution. Journal of Molecular Evolution 18:225-239. (Jan 25)

Buneman, M. 1971. The recovery of trees from measurements of dissimilarity. Pp. 387-395 in Mathematics in the Archeological and Historical Sciences (Hodson, F. R., Kendall, D. G., and Tautu, P., eds.), Edinburgh Univ. Press, Edinburgh. (Jan 25)

Cavalli-Sforza, L. L., and A. W. F. Edwards. 1967. Evolution 32:550-570. (Jan 25)

Chifman, J., and Kubatko, L. S. 2014. Quartet Inference from SNP Data Under the Coalescent Model. Bioinformatics 30(23):3317-3324. (Mar 21)

Darwin, C. R. 1859. Origin of species by means of natural selection (or the preservation of favoured races in the struggle for life). Originally published by John Murray. This figure from pp. 160-161 in Penguin Classics edition published 1985 by Penguin Books, London. (Jan 16)

Dayhoff, M.O., Schwartz, R.M., Orcutt, B.C. 1978. A model for evolutionary change in proteins. Atlas of Protein Sequence and Structure, 5, 345–352. (PAM amino acid model) (Apr 11)

Degnan, J. H., and N. A. Rosenberg. 2006. Discordance of species trees with their most likely gene trees. PLoS Genetics 2:e68. (The anomaly zone) (Mar 19)

Drummond A.J., Suchard M.A. 2010. Bayesian random local clocks, or one rate to rule them all. BMC Biol. 8:114. (Random local clocks)

Fan, Y., Wu, R., Chen, M.-H., Kuo, L., and Lewis, P. O. 2011. Molecular Biology and Evolution 28(1):523-532. (Generalized stepping-stone marginal likelihood estimation) (Feb 29)

Farris, J. S. 1974. Formal definitions of paraphyly and polyphyly. Systematic Zoology 23: 548-554. (Jan-16)

Felsenstein, J. 1978. Cases in which parsimony or compatibility methods will be positively misleading. Systematic Biology 27:401-410. (Characterized the long branch attraction problem) (Feb 15)

Felsenstein, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of Molecular Evolution 17:368-376. (F81 model, pruning algorithm, origin of likelihood-based phylogenetics) (Feb 1, Feb 8)

Felsenstein, J. 1985a. Confidence intervals on phylogenies: an approach using the bootstrap. Evolution 39:783-791. (nonparametric bootstrapping) (Feb 15)

Felsenstein, J. 1985b. Phylogenies and the comparative method. American Naturalist 125:1-15. (independent contrasts) (Apr 2)

Felsenstein, J. 1992. Phylogenies from restriction sites: a maximum-likelihood approach. Evolution 46:159-173. (conditioning on variability in discrete trait likelihood calculations) (Mar 21)

Fitch, W. M., and E. Margoliash. 1967. Science 155:279-284. (Jan 25)

Fitch, W. M., and E. Markowitz. 1970. An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution. Biochemical Genetics 4: 579–593.

Fitch, W. 1971. Toward defining the course of evolution: minimum change for a specific tree topology. Systematic Zoology 20:406-416. (Jan 23)

FitzJohn, R. G. 2010. Quantitative traits and diversification. Systematic Biology 59:619–633. (Apr 23)

Fitzjohn, R. G. 2012. Diversitree: comparative phylogenetic analyses of diversification in R. Methods in Ecology and Evolution 3:1084-1092. (Apr 23)

Fowler, D. M., C. L. Araya, S. J. Fleishman, E. H. Kellogg, J. J. Stephany, D. Baker. and S. Fields. 2010. High-resolution mapping of protein sequence-function relationships. Nature Methods 7:741-746. (Apr 11)

Geyer, C. J. 1991. Markov chain Monte Carlo maximum likelihood for dependent data. Pages 156-163 in Computing Science and Statistics (E. Keramidas, ed.). (Metropolis-coupled MCMC a.k.a. heated chains) (Feb 22)

Goldberg, E. E., L. T. Lancaster, and R. H. Ree. 2011. Phylogenetic inference of reciprocal effects between geographic range evolution and diversification. Systematic Biology 60:451–465. (Apr 23)

Goldman, N., and Z. Yang. 1994. A codon-based model of nucleotide substitution for protein-coding DNA sequences. Molecular Biology and Evolution, 11, 725-736. (Goldman-Yang codon model) (Apr-11)

Gould, S. J. 1977. Ontogeny and phylogeny. Harvard University Press, Cambridge, Massachusetts. (Jan-16)

Green, P. J. 1995. Reversible jump Markov chain Monte Carlo computation and Bayesian model determination. Biometrika 82:711-732. (Mar 26)

Harvey, P. H., R. M. May, and S. Nee. 1994. Phylogenies without fossils. Evolution 48:523-529. (Apr 23)

Hasegawa, M., H. Kishino, and T. Yano. 1985. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. Journal of Molecular Evolution 21:160-174. (HKY85 model) (Feb 1)

Hastings, W. K. 1970. Monte Carlo sampling methods using Markov chains and their applications. Biometrika 57:97-109. (Hastings ratio) (Feb 22)

Heath, T. A., Huelsenbeck, J. P., & Stadler, T. 2014. The fossilized birth–death process for coherent calibration of divergence-time estimates. PNAS 111(29):E2957–E2966. (Fossilized birth-death process dating method)

Huelsenbeck, J. P., and D. M. Hillis. 1993. Success of phylogenetic methods in the four taxon case. Systematic Biology 42:247-264. (coined the term Felsenstein Zone) (Feb 15)

Huelsenbeck, J. P., R. Nielsen, and J. P. Bollback. 2003. Stochastic mapping of morphological characters. Systematic Biology 52(2): 131-158. (Mar 28)

Huelsenbeck, J. P., Jain, S., Frost, S., and Pond, S. 2006. A Dirichlet process model for detecting positive selection in protein-coding DNA sequences. Proceedings of the National Academy USA 103:6263–6268. (DP mixture model for omega) (Apr 9)

Huelsenbeck, J. P., and Suchard, M. A. 2007. A nonparametric method for accommodating and testing across-site rate variation. Systematic Biology 56:975–987. (DP model for among site rate heterogeneity) (Apr 9)

Heled, J., and Drummond, A. J. 2010. Bayesian inference of species trees from multilocus data. Molecular Biology and Evolution 27:570-580. (Bayesian species tree estimation) (Mar 19)

Huson, D. H., and D. Bryant. 2006. Application of phylogenetic networks in evolutionary studies. Mol. Biol. Evol. 23:254-267. (SplitsTree) (jan 25)

Jones, D. T., Taylor, W. R., and Thornton, J. M. 1992. The rapid generation of mutation data matrices from protein sequences. Comput Applic Biosci, 8, 275–282. (JTT amino acid model) (Apr 11)

Jones, C. S., F. T. Bakker, C. D. Schlichting, and A. B. Nicotra. 2009. Leaf shape evolution in the South African genus Pelargonium L’Hér. (Geraniaceae). International Journal of Organic Evolution 63:479-497. (Mar 28)

Jukes, T. H., and C. R. Cantor. 1969. Evolution of protein molecules. Pages 21-132 in H. N. Munro (ed.), Mammalian Protein Metabolism. Academic Press, New York. (JC69 model) (Jan 30)

Kidd, K. K., and Sgaramella-Zonta, L. A. 1971. Phylogenetic analysis: concepts and methods. American Journal of Human Genetics 23: 235-252. (Jan 25)

Kimura, M. 1980. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution 16:111-120. (K80/K2P model) (Feb 1)

Kishino, H., and M. Hasegawa. 1989. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea. Journal of Molecular Evolution 29: 170-179. (F84 model, KH test) (Feb 1)

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

Kolaczkowski, B., and J. W. Thornton. 2004. Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous. Nature 431:980-984.

Kolaczkowski, B., and J. W. Thornton. 2008. A mixed branch length model of heterotachy improves phylogenetic accuracy. Molecular Biology and Evolution 25:1054–1066. (mixture of edge length sets heterotachy model)

Kuhner, M. K. 2009. Coalescent genealogy samplers: windows into population history. Trends Ecol. Evol. 24:86-93. (Mar 7)

Lanave, C., G. Preparata, C. Saccone, and G. Serio. 1984. A new method for calculating evolutionary substitution rates. Journal of Molecular Evolution 20:86-93. (GTR model) (Feb 1)

Larget, B., and D. L. Simon. 1999. Markov chain monte carlo algorithms for the Bayesian analysis of phylogenetic trees. Molecular Biology and Evolution 16: 750-759. (see also Holder et al. 2005) (Feb 27)

Lartillot, N., and Philippe, H. 2004. A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. Molecular Biology and Evolution, 21:1095–1109. (DP mixture model for amino acid spectra) (Apr 9)

Lartillot, N., and H. Philippe. 2006. Computing bayes factors using thermodynamic integration. Systematic Biology 55(2): 195-207. (Thermodynamic integration (a.k.a. path sampling) marginal likelihood estimation) (Feb 29)

Le, S. Q., and Gascuel, O. 2008. An improved general amino acid replacement matrix. Molecular Biology and Evolution, 25(7):1307-1320. (LG amino acid model) (Apr 11)

Lewis, L. A., B. D. Mishler, and R. Vilgalys. 1997. Phylogenetic relationships of the liverworts (Hepaticae), a basal embryophyte lineage, inferred from nucleotide sequence data of the chloroplast gene _rbc_L Molecular Phylogenetics and Evolution 7:377-393.

Lewis, P. O. 2001a. A likelihood approach to estimating phylogeny from discrete morphological character data. Systematic Biology 50:913-925. (Mar 21)

Lewis, P. O. 2001b. Phylogenetic systematics turns over a new leaf. Trends in Ecology and Evolution 16:30-37. (Apr 11)

Lewis, P. O., M. T. Holder, and K. E. Holsinger. 2005. Polytomies and Bayesian phylogenetic inference. Systematic Biology 54:241–253. (Mar 26)

Lewis, P. O., M.-H. Chen, L. Kuo, L. A. Lewis, K. Fučíková, S. Neupane, Y.-B. Wang, and D. Shi. 2016. Estimating Bayesian phylogenetic information content. Systematic Biology 65(6):1009-1023. (Apr 2, Apr 25)

Lovette, I. J., and E. Bermingham. 1999. Explosive speciation in the New World Dendroica warblers. Proc. R. Soc. Lond. B 266:1629-1636.

Maddison W. P., Midford P. E., Otto S. P. 2007. Estimating a binary character’s effect on speciation and extinction. Systematic Biology 56:701–710. (Apr 23)

Martins, E. P., and T. F. Hansen. 1997. Phylogenies and the comparative method: a general approach to incorporating phylogenetic information into the analysis of interspecific data. The American Naturalist 149:646-667. (PGLS) (Apr 2)

Metropolis, N., A. W. Rosenbluth, M. N. Rosenbluth, A. H. Teller, and E. Teller. 1953. Equation of state calculations by fast computing machines. J. Chem. Phys. 21:1087-1092. (The Metropolis algorithm used in MCMC) (Feb 22)

Mirarab, S., and T. Warnow. 2015. ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes. Bioinformatics 31(12):i44–52. (Mar 19)

Moore, B. R., S. Hohna, M. R. May, B. Rannala, and J. P. Huelsenbeck. 2016. Critically evaluating the theory and performance of Bayesian analysis of macroevolutionary mixtures. PNAS 113:9569-9574. (Apr 23)

Muse, S. V., and B. S. Gaut. 1994. A likelihood approach for comparing synonymous and nonsynonymous substitution rates, with application to the chloroplast genome. Molecular Biology and Evolution, 11, 715-724. (Apr 11)

Neupane, S., P. O. Lewis, S. Dessein, H. Shanks, S. Paudyal, and F. Lens. 2017. Evolution of woody life form on tropical mountains in the tribe Spermacoceae (Rubiaceae). American Journal of Botany 104(3):419-438. (Apr 23)

Newton, M. A., and A. E. Raftery. 1994. Approximate Bayesian inference with the weighted likelihood bootstrap (with discussion). J. Roy. Statist. Soc. B 56:3-48. [Harmonic mean method for estimating marginal likelihood] (Feb 29)

Nielsen, R. 2002. Mapping mutations on phylogenies. Systematic Biology 51(5): 729-739. (Mar 28)

Pagel, M. 1994. Detecting correlated evolution on phylogenies: a general method for the comparative analysis of discrete characters. Proceedings of the Royal Society of London B 255:37-45. (assessing evolutionary correlation between two discrete traits) (Mar 21)

Pagel, M. 1999. Inferring the historical patterns of biological evolution. Nature 401:877–884. (introduced the delta and lambda scaling factors used in comparative analyses) (Apr 4)

Pagel, M., and A. Meade. 2004. A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or character-state data. Systematic Biology 53:571-581. (mixture of Q-matrices model)

Pagel, M., and A. Meade. 2006. Bayesian anaysis of correlated evolution of discrete characters by reversible-jump Markov chain Monte Carlo. American Naturalist 167:808-825. (rjMCMC for discrete character correlation) (Mar 26)

Pagel, M., and A. Meade. 2008. Modelling heterotachy in phylogenetic inference by reversible-jump Markov chain Monte Carlo. Phil. Trans. R. Soc. B 363:3955-3964. (rjMCMC heterotachy model)

Pettigrew, J. D. 1991. Wings or brain? convergent evolution in the origins of bats. Systematic Zoology, 40(2):199-216. (Feb 15)

Pybus, O. G., and P. H. Harvey. 2000. Testing macro-evolutionary models using incomplete molecular phylogenies. Proc. R. Soc. Lond. B 267:2267-2272. (Apr 23)

Rabosky, D. L., F. Santini, J. Eastman, S. A. Smith, B. Sidlauskas, J, Chang, and M. E. Alfaro. 2013. Rates of speciation and morphological evolution are correlated across the largest vertebrate radiation. Nature Communications 4:1958. (Apr 23)

Rabosky, D. L. 2014. Automatic detection of key innovations, rate shifts, and diversity-dependence on phylogenetic trees. PLoS One 9(2):e89543. (Apr 23)

Rabosky, D. L., S. C. Donnellan, M. Grundler, and I. J. Lovette. 2014. Analysis and visualization of complex macroevolutionary dynamics: an example from Australian scincid lizards. Systematic Biology 63:610-627. (Apr 23)

Rabosky, D. L., J. S. Mitchell, and J. Chang. 2017. Is BAMM flawed? Theoretical and practical concerns in the analysis of multi-rate diversification models. Systematic Biology 66:477-498. (Apr 23)

Rannala B., Zhu T., Yang Z. 2012. Tail paradox, partial identifiability, and influential priors in Bayesian branch length inference. Molecular Biology and Evolution. 29:325–335. (Gamma-Dirichlet multivariate edge length prior) (Mar 5)

Ree, R. R. 2005. Detecting the historical signature of key innovations using stochastic models of character evolution and cladogenesis. Evolution 59(2):257–265. (Apr 23)

Reeves, J. H. 1992. Heterogeneity in the substitution process of amino acid sites of proteins coded for by mitochondrial DNA. Journal of Molecular Evolution 35:17-31. (+I among-site rate heterogeneity model) (Feb 8)

Ricklefs, R. E. 2007. Estimating diversification rates from phylogenetic information. TREE 22:601-610. (Apr 23)

Ronquist, F., Klopfstein, S., Vilhelmsen, L., Schulmeister, S., Murray, D. L., and Rasnitsyn, A. P. 2012. A total-evidence approach to dating with fossils, applied to the early radiation of the Hymenoptera. Systematic Biology 61(6):973–999. (Tip dating)

Rzhetsky, A., and Nei, M. 1992. Statistical properties of the ordinary least-squares, generalized least-squares, and minimum-evolution methods of phylogenetic inference. Journal of Molecular Evolution 35: 367-375. (Jan 25)

Saitou, N., and M. Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4: 406-425. (Neighbor joining method) (Jan 25)

Sankoff, D. 1975. Minimal mutation trees of sequences. SIAM Journal on Applied Mathematics 28:35-42. (generalized parsimony, step matrices) (Jan 23)

Schluter, D., T. Price, A. Ø. Mooers, and D. Ludwig. 1997. Likelihood of ancestor states in adaptive radiation. Evolution 51:1699-1711. (Mar 21)

Shi, J. J., and D. L. Rabosky. 2015. Speciation dynamics during the global radiation of extant bats. Evolution 69:1528-1545. (Apr 23)

Si Quang, L., O. Gascuel, and N. Lartillot. 2008. Empirical profile mixture models for phylogenetic reconstruction. Bioinformatics 24(20): 2317-2323. (Apr 11)

Suchard, M. A., R. E. Weiss, and J. S. Sinsheimer. 2001. Bayesian selection of continuous-time Markov chain evolutionary models. Molecular Biology and Evolution 18:1001-1013. (Mar 5)

Sytsma, K. J., and L. D. Gottlieb. 1986. Chloroplast DNA evidence for the origin of the genus Heterogaura from a species of Clarkia (Onagraceae). PNAS 83: 5554-5557. (Outgroup may be part of ingroup) (Jan-16)

Thorne, J. L., H. Kishino, and I. S. Painter. 1998. Estimating the rate of evolution of the rate of molecular evolution. Molecular Biology and Evolution 15: 1647-1657. (Correlated relaxed clocks)

Tuffley C, Steel M. 1998. Modeling the covarion hypothesis of nucleotide substitution. Math Biosci. 147:63–91. (covarion model)

Van Den Bussche, R., Baker, R., Huelsenbeck, J. P., and Hillis, D. M. 1998. Base compositional bias and phylogenetic analyses: A test of the “flying DNA” hypothesis. Molecular Phylogenetics and Evolution, 10(3), 408–416. (Feb 15)

Whelan, S., and N. Goldman. 2001. A general empirical model of protein evolution derived from multiple protein families using a maximum likelihood approach. Molecular Biology and Evolution, 18, 691-699. (WAG amino acid model) (Apr 11)

Wright, A. M., Lloyd, G. T., & Hillis, D. M. (2016). Modeling character change heterogeneity in phylogenetic analyses of morphology through the use of priors. Systematic Biology 65:602–611. (Mar 21)

Xie, W.G., P. O. Lewis, Y. Fan, L. Kuo and M.-H. Chen. 2011. Improving Marginal Likelihood Estimation for Bayesian Phylogenetic Model Selection. Systematic Biology 60(2):150-160. (Stepping-stone marginal likelihood estimation) (Feb 29)

Yang, Z. 1993. Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. Molecular Biology and Evolution 10:1396-1401. (Feb 8)

Yang, Z. 1994. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. Journal of Molecular Evolution 39:306-314. (+G among-site rate heterogeneity model) (Feb 8)

Yang, Z., and B. Rannala. 2010. Bayesian species delimitation using multilocus sequence data. PNAS 107(20):9264-9269. (Apr 25)

Zhang, C., Stadler, T., Klopfstein, S., Heath, T. A., and Ronquist, F. 2016. Total-evidence dating under the fossilized birth–death process. Systematic Biology 65:228–249.

Zhou, Y., H. Brinkmann, N. Rodrigue, N. Lartillot, and H. Philippe. 2010. A Dirichlet Process covarion mixture model and its assessments using posterior predictive discrepency tests. Molecular Biology and Evolution 27:371-384.

Zwickl, D., and M. T. Holder. 2004. Model parameterization, prior distributions, and the general time-reversible model in Bayesian phylogenetics. Systematic Biology 53: 877-888. (Mar 5)