References

Box, George EP. 1976. “Science and Statistics.” Journal of the American Statistical Association 71 (356): 791–99. https://doi.org/10.1080/01621459.1976.10480949.
Breiman, Leo et al. 2001. “Statistical Modeling: The Two Cultures (with Comments and a Rejoinder by the Author).” Statistical Science 16 (3): 199–231. https://projecteuclid.org/euclid.ss/1009213726.
Burnham, KP, and DR Anderson. 2002. Model Selection and Multimodel Inference: A Practical Information-Theoretic Approach. 2nd ed. Springer. https://doi.org/10.1007/b97636.
Chang, E Sally, Moran Neuhof, Nimrod D Rubinstein, Arik Diamant, Hervé Philippe, Dorothée Huchon, and Paulyn Cartwright. 2015. “Genomic Insights into the Evolutionary Origin of Myxozoa Within Cnidaria.” Proceedings of the National Academy of Sciences 112 (48): 14912–17. https://doi.org/10.1073/pnas.1511468112.
Czech, Lucas, Jaime Huerta-Cepas, and Alexandros Stamatakis. 2017. A Critical Review on the Use of Support Values in Tree Viewers and Bioinformatics Toolkits.” Molecular Biology and Evolution 34 (6): 1535–42. https://doi.org/10.1093/molbev/msx055.
Darwin, Charles. 1859. The Origin of Species by Means of Natural Selection: Or, the Preservation of Favored Races in the Struggle for Life.
deQueiroz, Kevin, and Philip D Cantino. 2020. International Code of Phylogenetic Nomenclature (PhyloCode): A Phylogenetic Code of Biological Nomenclature. CRC Press.
Dunn, Casey W, Felipe Zapata, Catriona Munro, Stefan Siebert, and Andreas Hejnol. 2018. “Pairwise Comparisons Across Species Are Problematic When Analyzing Functional Genomic Data.” Proceedings of the National Academy of Sciences 115 (3): E409–17. https://doi.org/10.1073/pnas.1707515115.
Felsenstein, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of Molecular Evolution 17 (6): 368–76. http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=7288891&retmode=ref&cmd=prlinks.
Felsenstein, Joseph. 1985. “Confidence Limits on Phylogenies: An Approach Using the Bootstrap.” Evolution 39 (4): 783–91. https://doi.org/10.1111/j.1558-5646.1985.tb00420.x.
Godfrey-Smith, Peter. 2013. Philosophy of Biology. Princeton University Press.
Hadfield, James, Colin Megill, Sidney M Bell, John Huddleston, Barney Potter, Charlton Callender, Pavel Sagulenko, Trevor Bedford, and Richard A Neher. 2018. “Nextstrain: Real-Time Tracking of Pathogen Evolution.” Bioinformatics 34 (23): 4121–23. https://doi.org/10.1093/bioinformatics/bty407.
Haeckel, Ernst. 1897. The Evolution of Man. Vol. 1. D. Appleton.
Harmon, Luke. 2018. “Phylogenetic Comparative Methods: Learning from Trees.” https://lukejharmon.github.io/pcm/.
Hennig, Willi. 1966. Phylogenetic Systematics. University of Illionois Press.
Hohna, S., T. A. Heath, B. Boussau, M. J. Landis, F. Ronquist, and J. P. Huelsenbeck. 2014. “Probabilistic Graphical Model Representation in Phylogenetics.” Journal Article. Syst Biol 63 (5): 753–71. https://doi.org/10.1093/sysbio/syu039.
Holder, Mark, and Paul O Lewis. 2003. “Phylogeny Estimation: Traditional and Bayesian Approaches.” Nature Reviews Genetics 4 (4): 275–84. https://doi.org/10.1038/nrg1044.
Houle, David, Christophe Pélabon, Günter P Wagner, and Thomas F Hansen. 2011. “Measurement and Meaning in Biology.” The Quarterly Review of Biology 86 (1): 3–34. https://doi.org/10.1086/658408.
Huelsenbeck, John P, and Fredrik Ronquist. 2001. “MRBAYES: Bayesian Inference of Phylogenetic Trees.” Bioinformatics 17 (8): 754–55. https://doi.org/10.1093/bioinformatics/17.8.754.
Joy, Jeffrey B, Richard H Liang, Rosemary M McCloskey, T Nguyen, and Art FY Poon. 2016. “Ancestral Reconstruction.” PLoS Computational Biology 12 (7): e1004763. https://doi.org/10.1371/journal.pcbi.1004763.
Jukes, TH, and CR Cantor. 1969. Evolution of Protein Molecules. Academic Press New York, NY. https://doi.org/10.1016/B978-1-4832-3211-9.50009-7.
Landis, Michael J, Deren AR Eaton, Wendy L Clement, Brian Park, Elizabeth L Spriggs, Patrick W Sweeney, Erika J Edwards, and Michael J Donoghue. 2020. “Joint Phylogenetic Estimation of Geographic Movements and Biome Shifts During the Global Diversification of Viburnum.” Systematic Biology. https://doi.org/10.1093/sysbio/syaa027.
Larget, Bret, and Donald L Simon. 1999. “Markov Chain Monte Carlo Algorithms for the Bayesian Analysis of Phylogenetic Trees.” Molecular Biology and Evolution 16 (6): 750–59. https://doi.org/10.1093/oxfordjournals.molbev.a026160.
Maddison, Wayne P. 1997. “Gene Trees in Species Trees.” Systematic Biology 46 (3): 523–36. https://doi.org/10.1093/sysbio/46.3.523.
Metropolis, Nicholas, Arianna W Rosenbluth, Marshall N Rosenbluth, Augusta H Teller, and Edward Teller. 1953. “Equation of State Calculations by Fast Computing Machines.” The Journal of Chemical Physics 21 (6): 1087–92. https://doi.org/10.1063/1.1699114.
Paradis, Emmanuel, Simon Blomberg, Ben Bolker, Joseph Brown, Santiago Claramunt, Julien Claude, Hoa Sien Cuong, et al. 2023. Ape: Analyses of Phylogenetics and Evolution.
Posada, David, and Thomas R Buckley. 2004. “Model Selection and Model Averaging in Phylogenetics: Advantages of Akaike Information Criterion and Bayesian Approaches over Likelihood Ratio Tests.” Systematic Biology 53 (5): 793–808. https://doi.org/10.1080/10635150490522304.
Rosenberg, Michael S., Sankar Subramanian, and Sudhir Kumar. 2003. Patterns of Transitional Mutation Biases Within and Among Mammalian Genomes.” Molecular Biology and Evolution 20 (6): 988–93. https://doi.org/10.1093/molbev/msg113.
Steel, Mike, and David Penny. 2000. “Parsimony, Likelihood, and the Role of Models in Molecular Phylogenetics.” Molecular Biology and Evolution 17 (6): 839–50. https://doi.org/10.1093/oxfordjournals.molbev.a026364.
Swofford, DL, GJ Olsen, PJ Waddell, and DM Hillis. 1996. Phylogenetic Inference. Edited by David M Hillis, Craig Moritz, Barbara K Mable, and Richard G Olmstead. Sinauer Associates Sunderland, MA.
Symonds, Matthew RE, and Simon P Blomberg. 2014. “A Primer on Phylogenetic Generalised Least Squares.” In Modern Phylogenetic Comparative Methods and Their Application in Evolutionary Biology, 105–30. Springer.
Upham, Nathan S, Jacob A Esselstyn, and Walter Jetz. 2019. “Inferring the Mammal Tree: Species-Level Sets of Phylogenies for Questions in Ecology, Evolution, and Conservation.” PLoS Biology 17 (12): e3000494. https://doi.org/10.1371/journal.pbio.3000494.
Wagner, Gunter. 2014. Homology, Genes, and Evolutionary Innovation. Princeton.
Xie, Yihui. 2016. Bookdown: Authoring Books and Technical Documents with R Markdown. Boca Raton, Florida: Chapman; Hall/CRC. https://bookdown.org/yihui/bookdown.
Yang, Ziheng. 1994. “Maximum Likelihood Phylogenetic Estimation from DNA Sequences with Variable Rates over Sites: Approximate Methods.” Journal of Molecular Evolution 39 (3): 306–14. https://doi.org/10.1007/BF00160154.
Yu, Guangchuang, Tommy Tsan-Yuk Lam, and Shuangbin Xu. 2022. Ggtree: An r Package for Visualization of Tree and Annotation Data.
Zapata, Felipe, Freya E Goetz, Stephen A Smith, Mark Howison, Stefan Siebert, Samuel H Church, Steven M Sanders, et al. 2015. “Phylogenomic Analyses Support Traditional Relationships Within Cnidaria.” PloS One 10 (10): e0139068.
Zhang, Jianzhi. 1999. “Performance of Likelihood Ratio Tests of Evolutionary Hypotheses Under Inadequate Substitution Models.” Molecular Biology and Evolution 16 (6): 868–75. https://doi.org/10.1093/oxfordjournals.molbev.a026171.