book.bib

@book{darwin1859,
  title={The origin of species by means of natural selection: or, the preservation of favored races in the struggle for life},
  author={Darwin, Charles},
  year={1859}
}

@article{joy2016ancestral,
  title={Ancestral reconstruction},
  author={Joy, Jeffrey B and Liang, Richard H and McCloskey, Rosemary M and Nguyen, T and Poon, Art FY},
  journal={PLoS computational biology},
  volume={12},
  number={7},
  pages={e1004763},
  year={2016},
  doi={10.1371/journal.pcbi.1004763},
  publisher={Public Library of Science San Francisco, CA USA}
}

@article{heath2014calibration,
  title={The fossilized birth–death process for coherent calibration of divergence-time estimates},
  author={Heath, Tracy A and Huelsenbeck, John P and Stadler, Tanja},
  journal={PNAS},
  volume={111},
  number={29},
  pages={E2957-E2966},
  year={2014},
  doi={10.1073/pnas.1319091111}
}




@incollection{symonds2014primer,
  title={A primer on phylogenetic generalised least squares},
  author={Symonds, Matthew RE and Blomberg, Simon P},
  booktitle={Modern phylogenetic comparative methods and their application in evolutionary biology},
  pages={105--130},
  year={2014},
  publisher={Springer}
}

@article{harmon2018phylogenetic,
  title={Phylogenetic comparative methods: learning from trees},
  author={Harmon, Luke},
  year={2018},
  url={https://lukejharmon.github.io/pcm/},
  publisher={EcoEvoRxiv}
}

@article{houle2011measurement,
  title={Measurement and meaning in biology},
  author={Houle, David and P{\'e}labon, Christophe and Wagner, G{\"u}nter P and Hansen, Thomas F},
  journal={The quarterly review of biology},
  volume={86},
  number={1},
  pages={3--34},
  year={2011},
  doi={10.1086/658408},
  publisher={The University of Chicago Press}
}

@article{holder2003,
  title={Phylogeny estimation: traditional and Bayesian approaches},
  author={Holder, Mark and Lewis, Paul O},
  journal={Nature reviews genetics},
  volume={4},
  number={4},
  pages={275--284},
  year={2003},
  doi={10.1038/nrg1044},
  publisher={Nature Publishing Group}
}

@article{huelsenbeck2001mrbayes,
  title={MRBAYES: Bayesian inference of phylogenetic trees},
  author={Huelsenbeck, John P and Ronquist, Fredrik},
  journal={Bioinformatics},
  volume={17},
  number={8},
  pages={754--755},
  year={2001},
  doi={10.1093/bioinformatics/17.8.754},
  publisher={Oxford University Press}
}

@article{larget1999markov,
  title={Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees},
  author={Larget, Bret and Simon, Donald L},
  journal={Molecular biology and evolution},
  volume={16},
  number={6},
  pages={750--759},
  year={1999},
  doi={10.1093/oxfordjournals.molbev.a026160},
  publisher={Chicago, Ill.: University of Chicago Press, c1983-}
}

@article{metropolis1953,
  title={Equation of state calculations by fast computing machines},
  author={Metropolis, Nicholas and Rosenbluth, Arianna W and Rosenbluth, Marshall N and Teller, Augusta H and Teller, Edward},
  journal={The journal of chemical physics},
  volume={21},
  number={6},
  pages={1087--1092},
  year={1953},
  doi={10.1063/1.1699114},
  publisher={American Institute of Physics}
}


@book{Burnham2002,
  title={Model Selection and Multimodel Inference: A Practical Information-Theoretic Approach},
  author={Burnham, KP and Anderson, DR},
  edition={2},
  publisher={Springer},
  doi={10.1007/b97636},
  year={2002}
}

@article{10.1093/molbev/msx055,
    author = {Czech, Lucas and Huerta-Cepas, Jaime and Stamatakis, Alexandros},
    title = "{A Critical Review on the Use of Support Values in Tree Viewers and Bioinformatics Toolkits}",
    journal = {Molecular Biology and Evolution},
    volume = {34},
    number = {6},
    pages = {1535-1542},
    year = {2017},
    month = {03},
    abstract = "{Phylogenetic trees are routinely visualized to present and interpret the evolutionary relationships of species. Most empirical evolutionary data studies contain a visualization of the inferred tree with branch support values. Ambiguous semantics in tree file formats can lead to erroneous tree visualizations and therefore to incorrect interpretations of phylogenetic analyses. Here, we discuss problems that arise when displaying branch values on trees after rerooting. Branch values are typically stored as node labels in the widely-used Newick tree format. However, such values are attributes of branches. Storing them as node labels can therefore yield errors when rerooting trees. This depends on the mostly implicit semantics that tools deploy to interpret node labels. We reviewed ten tree viewers and ten bioinformatics toolkits that can display and reroot trees. We found that 14 out of 20 of these tools do not permit users to select the semantics of node labels. Thus, unaware users might obtain incorrect results when rooting trees. We illustrate such incorrect mappings for several test cases and real examples taken from the literature. This review has already led to improvements in eight tools. We suggest tools should provide options that explicitly force users to define the semantics of node labels.}",
    issn = {0737-4038},
    doi = {10.1093/molbev/msx055},
    url = {https://doi.org/10.1093/molbev/msx055},
    eprint = {https://academic.oup.com/mbe/article-pdf/34/6/1535/17942399/msx055.pdf},
}


@article{felsenstein1985confidence,
  title={Confidence limits on phylogenies: an approach using the bootstrap},
  author={Felsenstein, Joseph},
  journal={evolution},
  volume={39},
  number={4},
  pages={783--791},
  year={1985},
  DOI = {10.1111/j.1558-5646.1985.tb00420.x},
  publisher={Wiley Online Library}
}


@article{zhang1999performance,
  title={Performance of likelihood ratio tests of evolutionary hypotheses under inadequate substitution models.},
  author={Zhang, Jianzhi},
  journal={Molecular biology and evolution},
  volume={16},
  number={6},
  pages={868--875},
  year={1999},
  DOI = {10.1093/oxfordjournals.molbev.a026171},
  publisher={Oxford University Press}
}

@article{yang1994maximum,
  title={Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods},
  author={Yang, Ziheng},
  journal={Journal of Molecular evolution},
  volume={39},
  number={3},
  pages={306--314},
  year={1994},
  DOI = {10.1007/BF00160154},
  publisher={Springer}
}

@article{posada2004model,
  title={Model selection and model averaging in phylogenetics: advantages of Akaike information criterion and Bayesian approaches over likelihood ratio tests},
  author={Posada, David and Buckley, Thomas R},
  journal={Systematic biology},
  volume={53},
  number={5},
  pages={793--808},
  year={2004},
  DOI = {10.1080/10635150490522304},
  publisher={Society of Systematic Zoology}
}


@article{maddison1997gene,
  title={Gene trees in species trees},
  author={Maddison, Wayne P},
  journal={Systematic biology},
  volume={46},
  number={3},
  pages={523--536},
  year={1997},
  DOI = {10.1093/sysbio/46.3.523},
  publisher={Oxford University Press}
}

@article{box1976science,
  title={Science and statistics},
  author={Box, George EP},
  journal={Journal of the American Statistical Association},
  volume={71},
  number={356},
  pages={791--799},
  year={1976},
  DOI = {10.1080/01621459.1976.10480949},
  publisher={Taylor \& Francis}
}

@book{godfrey2016philosophy,
  title={Philosophy of biology},
  author={Godfrey-Smith, Peter},
  year={2013},
  publisher={Princeton University Press}
}

@book{jc1969,
  booktitle={Mammalian Protein Metabolism},
  title={Evolution of Protein Molecules},
  author={Jukes, TH and Cantor, CR},
  year={1969},
  DOI={10.1016/B978-1-4832-3211-9.50009-7},
  pages = {21--132},
  publisher={Academic Press New York, NY}
}

@article{rosenberg2003,
    author = {Rosenberg, Michael S. and Subramanian, Sankar and Kumar, Sudhir},
    title = "{Patterns of Transitional Mutation Biases Within and Among Mammalian Genomes}",
    journal = {Molecular Biology and Evolution},
    volume = {20},
    number = {6},
    pages = {988-993},
    year = {2003},
    month = {06},
    abstract = "{Significant transition/transversion mutation bias is a well-appreciated aspect of mammalian nuclear genomes; however, patterns of bias among genes within a genome and among species remain largely uncharacterized. Understanding these patterns is important for understanding similarities and differences in mutational patterns among genomes and genomic regions. Therefore, we have conducted an analysis of 7,587 pairs of sequences of 4,347 mammalian protein-coding genes from seven species (human, mouse, rat, cow, sheep, pig, and macaque) and from the introns of 51 gene pairs and multiple intergenic regions (37 kbp, 52 kbp and 65 kbp) from the human, chimpanzee, and baboon genomes. Our analyses show that genes and regions with widely varying base composition exhibit uniformity of transition mutation rate both within and among mammalian lineages, as long as the transitional mutations caused by CpG hypermutability are excluded. The estimates show no relationship to potential intrachromosomal or interchromosomal effects. This uniformity points to similarity in point mutation processes in genomic regions with substantially different GC-content biases.}",
    issn = {0737-4038},
    doi = {10.1093/molbev/msg113},
    url = {https://doi.org/10.1093/molbev/msg113},
    eprint = {https://academic.oup.com/mbe/article-pdf/20/6/988/3052276/msg113.pdf},
}


@book{swofford1996molecular,
  booktitle={Molecular systematics},
  editor={Hillis, David M and Moritz, Craig and Mable, Barbara K and Olmstead, Richard G},
  title={Phylogenetic Inference},
  author={Swofford, DL and Olsen, GJ and Waddell, PJ and Hillis, DM},
  year={1996},
  publisher={Sinauer Associates Sunderland, MA}
}

@article{steel2000parsimony,
  title={Parsimony, likelihood, and the role of models in molecular phylogenetics},
  author={Steel, Mike and Penny, David},
  journal={Molecular biology and evolution},
  volume={17},
  number={6},
  pages={839--850},
  year={2000},
  DOI = {10.1093/oxfordjournals.molbev.a026364},
  publisher={Society for Molecular Biology and Evolution}
}


@article{breiman2001statistical,
  title={Statistical modeling: The two cultures (with comments and a rejoinder by the author)},
  author={Breiman, Leo and others},
  journal={Statistical science},
  volume={16},
  number={3},
  pages={199--231},
  year={2001},
  url = {https://projecteuclid.org/euclid.ss/1009213726},
  publisher={Institute of Mathematical Statistics}
}

@article{Felsenstein:1981vk,
author = {Felsenstein, J.},
title = {{Evolutionary trees from DNA sequences: a maximum likelihood approach.}},
journal = {Journal of Molecular Evolution},
year = {1981},
volume = {17},
number = {6},
pages = {368--376},
pmid = {7288891},
language = {English},
read = {Yes},
rating = {0},
date-added = {2018-10-16T15:34:12GMT},
date-modified = {2018-10-16T15:35:05GMT},
abstract = {The application of maximum likelihood techniques to the estimation of evolutionary trees from nucleic acid sequence data is discussed. A computationally feasible method for finding such maximum likelihood estimates is developed, and a computer program is available. This method has advantages over the traditional parsimony algorithms, which can give misleading results if rates of evolution differ in different lineages. It also allows the testing of hypotheses about the constancy of evolutionary rates by likelihood ratio tests, and gives rough indication of the error of ;the estimate of the tree.},
url = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=7288891&retmode=ref&cmd=prlinks},
local-url = {file://localhost/Users/cdunn/Dropbox/articles/Library.papers3/Files/D7/D7C6E6E8-AA6E-4D17-822C-E383AE558B4C.pdf},
file = {{D7C6E6E8-AA6E-4D17-822C-E383AE558B4C.pdf:/Users/cdunn/Dropbox/articles/Library.papers3/Files/D7/D7C6E6E8-AA6E-4D17-822C-E383AE558B4C.pdf:application/pdf}},
uri = {\url{papers3://publication/uuid/85009339-08F2-4648-81A3-A0827CE1E30C}}
}


@book{hennig1966,
  title={Phylogenetic Systematics},
  author={Hennig, Willi},
  year={1966},
  publisher={University of Illionois Press}
}

@book{deQueiroz2020,
  title={International Code of Phylogenetic Nomenclature (PhyloCode): A Phylogenetic Code of Biological Nomenclature},
  author={deQueiroz, Kevin and Cantino, Philip D},
  year={2020},
  publisher={CRC Press}
}

@article{upham2019,
  title={Inferring the mammal tree: Species-level sets of phylogenies for questions in ecology, evolution, and conservation},
  author={Upham, Nathan S and Esselstyn, Jacob A and Jetz, Walter},
  journal={PLoS biology},
  volume={17},
  number={12},
  pages={e3000494},
  year={2019},
  DOI = {10.1371/journal.pbio.3000494},
  publisher={Public Library of Science San Francisco, CA USA}
}

@book{haeckel1897,
  title={The evolution of man},
  author={Haeckel, Ernst},
  volume={1},
  year={1897},
  publisher={D. Appleton}
}

@Book{xie2015,
  title = {Dynamic Documents with {R} and knitr},
  author = {Yihui Xie},
  publisher = {Chapman and Hall/CRC},
  address = {Boca Raton, Florida},
  year = {2015},
  edition = {2nd},
  note = {ISBN 978-1498716963},
  url = {http://yihui.org/knitr/},
}


@Book{wagner2014,
  title = {Homology, Genes, and Evolutionary Innovation},
  author = {Gunter Wagner},
  publisher = {Princeton},
  year = {2014}
}

@article{hadfield2018nextstrain,
  title={Nextstrain: real-time tracking of pathogen evolution},
  author={Hadfield, James and Megill, Colin and Bell, Sidney M and Huddleston, John and Potter, Barney and Callender, Charlton and Sagulenko, Pavel and Bedford, Trevor and Neher, Richard A},
  journal={Bioinformatics},
  volume={34},
  number={23},
  pages={4121--4123},
  year={2018},
  DOI = {10.1093/bioinformatics/bty407},
  publisher={Oxford University Press}
}

@article{chang2015genomic,
  title={Genomic insights into the evolutionary origin of Myxozoa within Cnidaria},
  author={Chang, E Sally and Neuhof, Moran and Rubinstein, Nimrod D and Diamant, Arik and Philippe, Herv{\'e} and Huchon, Doroth{\'e}e and Cartwright, Paulyn},
  journal={Proceedings of the National Academy of Sciences},
  volume={112},
  number={48},
  pages={14912--14917},
  year={2015},
  DOI = {10.1073/pnas.1511468112},
  publisher={National Acad Sciences}
}

@article{dunn2018pairwise,
  title={Pairwise comparisons across species are problematic when analyzing functional genomic data},
  author={Dunn, Casey W and Zapata, Felipe and Munro, Catriona and Siebert, Stefan and Hejnol, Andreas},
  journal={Proceedings of the National Academy of Sciences},
  volume={115},
  number={3},
  pages={E409--E417},
  year={2018},
  DOI = {10.1073/pnas.1707515115},
  publisher={National Acad Sciences}
}

@article{landis2020joint,
  title={Joint phylogenetic estimation of geographic movements and biome shifts during the global diversification of Viburnum},
  author={Landis, Michael J and Eaton, Deren AR and Clement, Wendy L and Park, Brian and Spriggs, Elizabeth L and Sweeney, Patrick W and Edwards, Erika J and Donoghue, Michael J},
  journal={Systematic Biology},
  DOI = {10.1093/sysbio/syaa027},
  year={2020}
}


@article{Hohna2014,
   author = {Hohna, S. and Heath, T. A. and Boussau, B. and Landis, M. J. and Ronquist, F. and Huelsenbeck, J. P.},
   title = {Probabilistic graphical model representation in phylogenetics},
   journal = {Syst Biol},
   volume = {63},
   number = {5},
   pages = {753-71},
   ISSN = {1076-836X (Electronic)
1063-5157 (Linking)},
   DOI = {10.1093/sysbio/syu039},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/24951559},
   year = {2014},
   type = {Journal Article}
}

@article{zapata2015,
  title={Phylogenomic analyses support traditional relationships within Cnidaria},
  author={Zapata, Felipe and Goetz, Freya E and Smith, Stephen A and Howison, Mark and Siebert, Stefan and Church, Samuel H and Sanders, Steven M and Ames, Cheryl Lewis and McFadden, Catherine S and France, Scott C and others},
  journal={PloS one},
  volume={10},
  number={10},
  pages={e0139068},
  year={2015},
  publisher={Public Library of Science}
}

@book{chen2014bayesian,
  title={Bayesian Phylogenetics: Methods, Algorithms, and Applications},
  author={Chen, Ming-Hui and Kuo, Lynn and Lewis, Paul O},
  year={2014},
  publisher={CRC Press}
}