@Article{MCMCglmm,
  title = {MCMC Methods for Multi-Response Generalized Linear Mixed Models: The {MCMCglmm} {R} Package},
  author = {Jarrod D Hadfield},
  journal = {Journal of Statistical Software},
  year = {2010},
  volume = {33},
  number = {2},
  pages = {1--22},
  url = {https://www.jstatsoft.org/v33/i02/},
}

@software{mulTree,
  author       = {Thomas Guillerme and
                  Kevin Healy},
  title        = {{mulTree: a package for running MCMCglmm analysis 
                   on multiple trees}},
  month        = nov,
  year         = 2014,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.12902},
  url          = {https://doi.org/10.5281/zenodo.12902}
}

@article{cooney2017,
  title={Mega-evolutionary dynamics of the adaptive radiation of birds},
  author={Cooney, Christopher R and Bright, Jen A and Capp, Elliot JR and Chira, Angela M and Hughes, Emma C and Moody, Christopher JA and Nouri, Lara O and Varley, Zo{\"e} K and Thomas, Gavin H},
  journal={Nature},
  volume={542},
  number={7641},
  pages={344--347},
  year={2017},
  publisher={Nature Publishing Group}
}


@article{hadfield2010,
  title = {MCMC Methods for Multi-Response Generalized Linear Mixed Models: The {MCMCglmm} {R} Package},
  author = {Jarrod D Hadfield},
  journal = {Journal of Statistical Software},
  year = {2010},
  volume = {33},
  number = {2},
  pages = {1--22},
  url = {https://www.jstatsoft.org/v33/i02/}
}



@article{beckancient2014,
  title={Ancient dates or accelerated rates? {M}orphological clocks and the antiquity of placental mammals.},
  author={Beck, Robin M and Lee, Michael S},
  journal={Proceedings of the Royal Society B: Biological Sciences},
  volume={281},
  number={20141278},
  year={2014},
  pages={1-10},
  doi={10.1098/rspb.2014.1278},
  url={http://dx.doi.org/10.1098/rspb.2014.1278}
}

@article{GuillermeSTD,
  title={Mammalian morphological diversity does not increase in response to the Cretaceous-Paleogene mass extinction and the extinction of the (non-avian) dinosaurs.},
  author={Guillerme, Thomas and Cooper, Natalie},
  year={in prep.},
  url={https://github.com/TGuillerme/SpatioTemporal_Disparity/raw/master/Writing/STD_draft.pdf}
}

@article{Wills1994,
    Author = {Wills, Matthew A. and Briggs, Derek E. G. and Fortey, Richard A.},
    Cr = {Copyright \copyright  1994 Paleontological Society},
    Date = {1994/04/01},
    Date-Added = {2014-08-25 13:32:46 +0000},
    Date-Modified = {2014-08-25 13:32:46 +0000},
    Doi = {10.2307/2401014},
    Isbn = {00948373},
    Journal = {Paleobiology},
    M1 = {ArticleType: research-article / Full publication date: Spring, 1994 / Copyright {\copyright}1994 Paleontological Society},
    Month = {04},
    Number = {2},
    Pages = {93-130},
    Publisher = {Paleontological Society},
    Title = {Disparity as an Evolutionary Index: A Comparison of {C}ambrian and Recent Arthropods},
    Ty = {JOUR},
    Url = {http://www.jstor.org/stable/2401014},
    Volume = {20},
    Year = {1994},
    Bdsk-Url-1 = {http://www.jstor.org/stable/2401014},
    Bdsk-Url-2 = {http://dx.doi.org/10.2307/2401014}
}

@article{DonohueDim,
	Author = {Donohue, Ian and Petchey, Owen L. and Montoya, Jos{\'e} M. and Jackson, Andrew L. and McNally, Luke and Viana, Mafalda and Healy, Kevin and Lurgi, Miguel and O'Connor, Nessa E. and Emmerson, Mark C.},
	Doi = {10.1111/ele.12086},
	Issn = {1461-0248},
	Journal = {Ecology Letters},
	Keywords = {Ecosystem function, ellipsoid, extinction, invasion, multidimensional stability, persistence, resilience, resistance, robustness, variability},
	Number = {4},
	Pages = {421-429},
	Title = {On the dimensionality of ecological stability},
	Url = {http://dx.doi.org/10.1111/ele.12086},
	Volume = {16},
	Year = {2013},
	Bdsk-Url-1 = {http://dx.doi.org/10.1111/ele.12086}
}

@article{finlay2015morphological,
  title={Morphological diversity in tenrecs ({A}frosoricida, {T}enrecidae): comparing tenrec skull diversity to their closest relatives},
  author={Finlay, Sive and Cooper, Natalie},
  journal={PeerJ},
  volume={3},
  pages={e927},
  year={2015},
  publisher={PeerJ Inc.},
  url={http://dx.doi.org/10.7717/peerj.927}
}



@article {GuillermeCooper,
title = "Effects of missing data on topological inference using a {T}otal {E}vidence approach ",
journal = "Molecular Phylogenetics and Evolution ",
volume = "94, Part A",
number = "",
pages = "146-158",
year = "2016",
note = "",
issn = "1055-7903",
doi = "http://dx.doi.org/10.1016/j.ympev.2015.08.023",
url = "http://dx.doi.org/10.1016/j.ympev.2015.08.023",
author = "Thomas Guillerme and Natalie Cooper"
}

@article {OReilly2016,
	author = {O{\textquoteright}Reilly, Joseph E. and Puttick, Mark N. and Parry, Luke and Tanner, Alastair R. and Tarver, James E. and Fleming, James and Pisani, Davide and Donoghue, Philip C. J.},
	title = {Bayesian methods outperform parsimony but at the expense of precision in the estimation of phylogeny from discrete morphological data},
	volume = {12},
	number = {4},
	year = {2016},
	doi = {10.1098/rsbl.2016.0081},
	publisher = {The Royal Society},
	abstract = {Different analytical methods can yield competing interpretations of evolutionary history and, currently, there is no definitive method for phylogenetic reconstruction using morphological data. Parsimony has been the primary method for analysing morphological data, but there has been a resurgence of interest in the likelihood-based Mk-model. Here, we test the performance of the Bayesian implementation of the Mk-model relative to both equal and implied-weight implementations of parsimony. Using simulated morphological data, we demonstrate that the Mk-model outperforms equal-weights parsimony in terms of topological accuracy, and implied-weights performs the most poorly. However, the Mk-model produces phylogenies that have less resolution than parsimony methods. This difference in the accuracy and precision of parsimony and Bayesian approaches to topology estimation needs to be considered when selecting a method for phylogeny reconstruction.},
	issn = {1744-9561},
	URL = {http://dx.doi.org/10.1098/rsbl.2016.0081},
	eprint = {http://rsbl.royalsocietypublishing.org/content/12/4/20160081.full.pdf},
	journal = {Biology Letters}
}

@article{puttick2017uncertain,
  title={Uncertain-tree: discriminating among competing approaches to the phylogenetic analysis of phenotype data},
  author={Puttick, Mark N and O'Reilly, Joseph E and Tanner, Alastair R and Fleming, James F and Clark, James and Holloway, Lucy and Lozano-Fernandez, Jesus and Parry, Luke A and Tarver, James E and Pisani, Davide and others},
  journal={Proceedings of the Royal Society B},
  volume={284},
  number={1846},
  pages={20162290},
  year={2017},
  organization={The Royal Society},
  url={http://dx.doi.org/10.1098/rspb.2016.2290}
}

@article{OReilly2017,
author = {O{\textquoteright}Reilly Joseph E. and Puttick Mark N. and Pisani Davide and Donoghue Philip C. J.},
title = {Probabilistic methods surpass parsimony when assessing clade support in phylogenetic analyses of discrete morphological data},
journal = {Palaeontology},
volume = {61},
number = {1},
pages = {105-118},
keywords = {phylogenetic analysis, morphology, parsimony, Maximum Likelihood, Bayesian, Mk model},
doi = {10.1111/pala.12330},
url = {http://dx.doi.org/10.1111/pala.12330},
eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1111/pala.12330}
}

@article{diaz2016global,
  title={The global spectrum of plant form and function},
  author={D{\'\i}az, Sandra and Kattge, Jens and Cornelissen, Johannes HC and Wright, Ian J and Lavorel, Sandra and Dray, St{\'e}phane and Reu, Bj{\"o}rn and Kleyer, Michael and Wirth, Christian and Prentice, I Colin and others},
  journal={Nature},
  volume={529},
  number={7585},
  pages={167},
  year={2016},
  publisher={Nature Publishing Group},
  url={http://dx.doi.org/10.1038/nature16489}
}

@article{paradisape2004,
  title={{APE:} Analyses of Phylogenetics and Evolution in {R} language.},
  author={Paradis, Emmanuel and Claude, Julien and Strimmer, Korbinian},
  journal={Bioinformatics},
  volume={20},
  number={2},
  pages={289-290},
  year={2004},
  url={http://bioinformatics.oxfordjournals.org/content/20/2/289.short}
}

@article{fitzjohndiversitree2012,
  author={FitzJohn, Richard G.},
  title={Diversitree: comparative phylogenetic analyses of diversification in {R}},
  journal={Methods in Ecology and Evolution},
  volume={3},
  number={6},
  publisher={Blackwell Publishing Ltd},
  issn={2041-210X},
  url={http://dx.doi.org/10.1111/j.2041-210X.2012.00234.x},
  doi={10.1111/j.2041-210X.2012.00234.x},
  pages={1084-1092},
  keywords={birth–death process, comparative methods, extinction, macroevolution, speciation},
  year={2012}
}

@article{HKY85,
   author={Hasegawa, M. and Kishino, H. and Yano, T. A.},
   title={Dating of the Human Ape Splitting by a Molecular Clock of Mitochondrial-{D}{N}{A}},
   journal={Journal of Molecular Evolution},
   volume={22},
   number={2},
   pages={160-174},
   year={1985}
}

@article{lewisa2001,
	Author = {Lewis, P.},
	Doi = {10.1080/106351501753462876},
	Journal = {Systematic Biology},
	Number = {6},
	Pages = {913-925},
	Title = {A likelihood approach to estimating phylogeny from discrete morphological character data.},
	Url = {http://dx.doi.org/10.1080/106351501753462876},
	Volume = {50},
	Year = {2001},
	Bdsk-Url-1 = {http://dx.doi.org/10.1080/106351501753462876}
}

@article{time-slice,
   author={Guillerme, T. and Cooper, N.},
   title={Time for a rethink: time sub-sampling methods in disparity-through-time analyses},
   journal={Palaeontology},
   volume = {61},
   number = {4},
   pages = {481-493},
   year={2018},
   doi={10.1111/pala.12364},
   url={http://dx.doi.org/10.1111/pala.12364}
}

@article{hunt2006fitting,
  title={Fitting and comparing models of phyletic evolution: random walks and beyond},
  author={Hunt, Gene},
  journal={Paleobiology},
  volume={32},
  number={4},
  pages={578--601},
  year={2006},
  publisher={Cambridge University Press},
  url={https://doi.org/10.1666/05070.1}
}

@article{hunt2012measuring,
  title={Measuring rates of phenotypic evolution and the inseparability of tempo and mode},
  author={Hunt, Gene},
  journal={Paleobiology},
  volume={38},
  number={3},
  pages={351--373},
  year={2012},
  publisher={GeoScienceWorld},
  url={https://doi.org/10.1666/11047.1}
}

@article{hunt2015simple,
  title={Simple versus complex models of trait evolution and stasis as a response to environmental change},
  author={Hunt, Gene and Hopkins, Melanie J and Lidgard, Scott},
  journal={Proceedings of the National Academy of Sciences},
  pages={201403662},
  year={2015},
  publisher={National Acad Sciences},
  url={https://doi.org/10.1073/pnas.1403662111}
}

@article{guillermedisprity,
  title={{dispRity}: a modular {R} package for measuring disparity},
  author={Guillerme, Thomas},
  year={2018},
  volume = {9},
  number = {7},
  pages = {1755-1763},
  journal={Methods in Ecology and Evolution},
  publisher={Wiley Online Library},
  url={https://doi.org/10.1111/2041-210X.13022}
}

@article{murrell2018global,
  title={A global envelope test to detect non-random bursts of trait evolution},
  author={Murrell, David J},
  journal={Methods in Ecology and Evolution},
  year={2018},
  volume = {9},
  number = {7},
  pages = {1739-1748},
  publisher={Wiley Online Library},
  url={https://doi.org/10.1111/2041-210X.13006}
}

@article{Cooper2016,
	author = {Cooper, Natalie and Thomas, Gavin H. and Venditti, Chris and Meade, Andrew and Freckleton, Rob P.},
	title = {A cautionary note on the use of Ornstein Uhlenbeck models in macroevolutionary studies},
	journal = {Biological Journal of the Linnean Society},
	volume = {118},
	number = {1},
	pages = {64-77},
	year = {2016},
	doi = {10.1111/bij.12701},
	URL = {http://dx.doi.org/10.1111/bij.12701},
	eprint = {/oup/backfile/content_public/journal/biolinnean/118/1/10.1111_bij.12701/1/bij12701.pdf}
}
@article{brazeau2018,
    author = {Brazeau, Martin D and Guillerme, Thomas and Smith, Martin R},
    title = "{An algorithm for Morphological Phylogenetic Analysis with Inapplicable Data}",
    journal = {Systematic Biology},
    volume = {68},
    number = {4},
    pages = {619-631},
    year = {2018},
    month = {12},
    abstract = "{Morphological data play a key role in the inference of biological relationships and evolutionary history and are essential for the interpretation of the fossil record. The hierarchical interdependence of many morphological characters, however, complicates phylogenetic analysis. In particular, many characters only apply to a subset of terminal taxa. The widely used “reductive coding” approach treats taxa in which a character is inapplicable as though the character’s state is simply missing (unknown). This approach has long been known to create spurious tree length estimates on certain topologies, potentially leading to erroneous results in phylogenetic searches—but pratical solutions have yet to be proposed and implemented. Here, we present a single-character algorithm for reconstructing ancestral states in reductively coded data sets, following the theoretical guideline of minimizing homoplasy over all characters. Our algorithm uses up to three traversals to score a tree, and a fourth to fully resolve final states at each node within the tree. We use explicit criteria to resolve ambiguity in applicable/inapplicable dichotomies, and to optimize missing data. So that it can be applied to single characters, the algorithm employs local optimization; as such, the method provides a fast but approximate inference of ancestral states and tree score. The application of our method to published morphological data sets indicates that, compared to traditional methods, it identifies different trees as “optimal.” As such, the use of our algorithm to handle inapplicable data may significantly alter the outcome of tree searches, modifying the inferred placement of living and fossil taxa and potentially leading to major differences in reconstructions of evolutionary history.}",
    issn = {1063-5157},
    doi = {10.1093/sysbio/syy083},
    url = {https://doi.org/10.1093/sysbio/syy083},
    eprint = {https://academic.oup.com/sysbio/article-pdf/68/4/619/28824698/syy083.pdf},
}



@article{Guillerme2020,
author = {Guillerme, Thomas  and Cooper, Natalie  and Brusatte, Stephen L.  and Davis, Katie E.  and Jackson, Andrew L.  and Gerber, Sylvain  and Goswami, Anjali  and Healy, Kevin  and Hopkins, Melanie J.  and Jones, Marc E. H.  and Lloyd, Graeme T.  and O'Reilly, Joseph E.  and Pate, Abi  and Puttick, Mark N.  and Rayfield, Emily J.  and Saupe, Erin E.  and Sherratt, Emma  and Slater, Graham J.  and Weisbecker, Vera  and Thomas, Gavin H.  and Donoghue, Philip C. J. },
title = {Disparities in the analysis of morphological disparity},
journal = {Biology Letters},
volume = {16},
number = {7},
pages = {20200199},
year = {2020},
doi = {10.1098/rsbl.2020.0199},
URL = {https://royalsocietypublishing.org/doi/abs/10.1098/rsbl.2020.0199},
eprint = {https://royalsocietypublishing.org/doi/pdf/10.1098/rsbl.2020.0199}
}


@article{moms,
  title={Shifting spaces: Which disparity or dissimilarity measurement best summarize occupancy in multidimensional spaces?},
  author={Guillerme, Thomas and Puttick, Mark N and Marcy, Ariel E and Weisbecker, Vera},
  journal={Ecology and Evolution},
  year={2020},
  publisher={Wiley Online Library}
}


@article{endler2005,
  title={Animal visual systems and the evolution of color patterns: sensory processing illuminates signal evolution},
  author={Endler, John A and Westcott, David A and Madden, Joah R and Robson, Tim},
  journal={Evolution},
  volume={59},
  number={8},
  pages={1795--1818},
  year={2005},
  publisher={Wiley Online Library}
}


@article{aguilera2004,
  title={General n-dimensional rotations},
  author={Aguilera, Antonio and P{\'e}rez-Aguila, Ricardo},
  year={2004},
  publisher={V{\'a}clav Skala-UNION Agency},
  URL = {http://wscg.zcu.cz/wscg2004/Papers_2004_Short/N29.pdf}
}


@article{guillerme2023innovation,
  title={Innovation and elaboration on the avian tree of life},
  author={Guillerme, Thomas and Bright, Jen A and Cooney, Christopher R and Hughes, Emma C and Varley, Zo{\"e} K and Cooper, Natalie and Beckerman, Andrew P and Thomas, Gavin H},
  journal={Science Advances},
  volume={9},
  number={43},
  pages={eadg1641},
  year={2023},
  publisher={American Association for the Advancement of Science}
}
