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@ARTICLE{Lieberman2010111,
	author = {Bruce S. Lieberman and Talia S. Karim},
	title = {Tracing the trilobite tree from the root to the tips: A model marriage
	of fossils and phylogeny },
	journal = {Arthropod Structure \& Development},
	year = {2010},
	volume = {39},
	pages = {111 - 123},
	number = {2–3},
	note = {<ce:title>Fossil Record and Phylogeny of the Arthropoda</ce:title>
	},
	doi = {10.1016/j.asd.2009.10.004},
	issn = {1467-8039},
	keywords = {Trilobites},
	url = {http://trilobites.lifedesks.org/files/trilobites/liebermankarim.pdf}
	}
%% This BibTeX bibliography file was created using BibDesk.
%% http://www.cs.ucsd.edu/~mmccrack/bibdesk.html
%% Created for Mark Holder at 2012-07-30 15:25:03 -0400
%% Saved with string encoding Unicode (UTF-8)
@article{Congreve2012,
	Author = {Curtis R. Congreve},
	Journal = {Paleontology},
	Pages = {{\em in review}},
	Title = {{Quantifying catastrophe during the end Ordovician mass extinction}},
	Year = {2012}}
@article{Stigall2010,
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	Volume = {5},
	Year = {2010}}
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	Title = {{Punctuated equilibria: an alternative to phyletic gradualism}},
	Year = {1972}}
@article{HolderS2011,
	Author = {Mark T. Holder and Mike Steel},
	Journal = {Journal of Theoretical Biology},
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	Volume = {280},
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	}
@article{LiuWHNYSL2011,
	Author = {Kevin Liu and Tandy J. Warnow and Mark T. Holder and Serita Nelesen and Jiaye Yu and Alexandros Stamatakis and C. Randal Linder},
	Doi = {10.1093/sysbio/syr095},
	Journal = {Systematic Biology},
	Number = {1},
	Pages = {90-106},
	Title = {{SAT{\'e}-II}: Very Fast and Accurate Simultaneous Estimation of Multiple Sequence Alignments and Phylogenetic Trees},
	Url = {http://sysbio.oxfordjournals.org/content/61/1/90.abstract?sid=58895a54-2686-4b58-a676-3cc4d73a3b76},
	Volume = {61},
	Year = {2012}
	}
@article{HolderLS2010,
	Author = {Mark T. Holder and Paul O. Lewis and David L. Swofford},
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	Journal = {Systematic Biology},
	Month = {Jul},
	Number = {4},
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	Volume = {59},
	Year = {2010}
	}
@article{HolderSL2008,
	Author = {Mark T. Holder and Jeet Sukumaran and Paul O. Lewis},
	Doi = {10.1080/10635150802422308},
	Journal = {Systematic Biology},
	Number = {5},
	Pages = {814-821},
	Title = {A justification for reporting majority-rule consensus tree in {B}ayesian phylogenetics},
	Url = {http://sysbio.oxfordjournals.org/cgi/content/full/57/5/814},
	Volume = {57},
	Year = {2008}
	}
@article{HolderZD2008,
	Author = {Mark T. Holder and Derrick J. Zwickl and Christophe Dessimoz},
	Doi = {10.1098/rstb.2008.0162},
	Journal = {Philosophical Transactions of the Royal Society B: Biological Sciences},
	Pages = {4013-4012},
	Title = {Evaluating the Robustness of Phylogenetic Methods to Among-Site Variability in Substitution Processes},
	Url = {http://rstb.royalsocietypublishing.org/content/363/1512/4013},
	Volume = {363},
	Year = {2008}
	}
@article{NEXML,
	Author = {Rutger A. Vos and James P. Balhoff and Jason Caravas and Mark T. Holder and Hilmar Lapp and Peter Midford and Anurag Priyam and Jeet Sukumaran and Xuhua Xia and Arlin Stoltzfus},
	Doi = {10.1093/sysbio/sys025},
	Journal = {Systematic Biology},
	Number = {4},
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	Title = {{NeXML:} rich, extensible, and verifiable representation of comparative data and metadata},
	Url = {http://sysbio.oxfordjournals.org/content/early/2012/02/12/sysbio.sys025},
	Volume = {61},
	Year = {2012}
	}
@article{AyresEtAl2012,
	Author = {Daniel L. Ayres and Aaron Darling and Derrick J. Zwickl and Peter Beerli and Mark T. Holder and Paul O. Lewis and John P. Huelsenbeck and Fredrik Ronquist and David L. Swofford and Michael P. Cummings and Andrew Rambaut and Marc A. Suchard},
	Doi = {10.1093/sysbio/syr100},
	Journal = {Systematic Biology},
	Number = {1},
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	Title = {{BEAGLE}: an Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics},
	Url = {http://sysbio.oxfordjournals.org/content/61/1/170.full.pdf+html},
	Volume = {61},
	Year = {2012}
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@article{HeathHH2012,
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	Journal = {Molecular Biology and Evolution},
	Number = {3},
	Pages = {939-955},
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	Year = {2012}
	}
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@book{LiebermanKaesler2010,
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	Year = {2010}}
@article{PollittEtAl2005,
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	Volume = {3},
	Year = {2005}}
@article{Lieberman2012b,
	Author = {Bruce S. Lieberman},
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	Title = {The geography of evolution and the evolution of geography},
	Volume = {DOI:10.1007/s12052-012-0414-1},
	Year = {2012}}
@article{Lieberman2012a,
	Author = {Bruce S. Lieberman},
	Journal = {Evolutionary Biology},
	Pages = {181-191},
	Title = {Adaptive radiations in the context of macroevolutionary theory: a paleontological perspective},
	Volume = {39},
	Year = {2012}}
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	Year = {1994}}
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	Volume = {43},
	Year = {2003}}
@article{Lieberman2001a,
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	Year = {2001}}
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	Year = {2011}}
@article{MyersLieberman2011,
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	Title = {{Sharks that pass in the night: Using GIS to investigate competition in the Cretaceous Western Interior Seaway}},
	Volume = {278},
	Year = {2011}
	}
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	Year = {2012}}
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	Url = {http://gsa.confex.com/gsa/2011AM/finalprogram/abstract_195121.htm},
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	Year = {2004}}
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	Year = {2008}}
@article{LiebermanKarim2010,
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	Title = {Tracing the trilobite tree from the root to the tips: a model marriage of fossils and phylogeny},
	Volume = {39},
	Year = {2010}}
@article{RodeLieberman2005,
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	Year = {2005}}
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	Volume = {24},
	Year = {2008}}
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	Year = {2005}}
@article{RodriguePL2006,
	Abstract = {In recent works, methods have been proposed for applying phylogenetic models that allow for a general interdependence between the amino acid positions of a protein. As of yet, such models have focused on site interdependencies resulting from sequence-structure compatibility constraints, using simplified structural representations in combination with a set of statistical potentials. This structural compatibility criterion is meant as a proxy for sequence fitness, and the methods developed thus far can incorporate different site-interdependent fitness proxies based on other measurements. However, no methods have been proposed for comparing and evaluating the adequacy of alternative fitness proxies in this context, or for more general comparisons with canonical models of protein evolution. In the present work, we apply Bayesian methods of model selection-based on numerical calculations of marginal likelihoods and posterior predictive checks-to evaluate models encompassing the site-interdependent framework. Our application of these methods indicates that considering site-interdependencies, as done here, leads to an improved model fit for all data sets studied. Yet, we find that the use of pairwise contact potentials alone does not suitably account for across-site rate heterogeneity or amino acid exchange propensities; for such complexities, site-independent treatments are still called for. The most favored models combine the use of statistical potentials with a suitably rich site-independent model. Altogether, the methodology employed here should allow for a more rigorous and systematic exploration of different ways of modeling explicit structural constraints, or any other site-interdependent criterion, while best exploiting the richness of previously proposed models.},
	Affiliation = {Canadian Institute for Advanced Research, D{\'e}partement de Biochimie, Universit{\'e} de Montr{\'e}al, Montr{\'e}al, Qu{\'e}bec, Canada. nicolas.rodrigue@umontreal.ca},
	Author = {Nicolas Rodrigue and Herv\'e Philippe and Nicolas Lartillot},
	Doi = {10.1093/molbev/msl041},
	Issue = {9},
	Journal = {MBE},
	Keywords = {Protein Structure, Tertiary, Likelihood Functions, Computational Biology, Models, Statistical, Genetic Heterogeneity, Proteins, Phylogeny, Bayes Theorem, Forecasting, Selection (Genetics), Evolution, Molecular, Models, Genetic},
	Month = {Aug},
	Number = {9},
	Pages = {1762--75},
	Pii = {msl041},
	Title = {Assessing site-interdependent phylogenetic models of sequence evolution},
	Url = {http://mbe.oxfordjournals.org/cgi/content/abstract/23/9/1762},
	Volume = {23},
	Year = {2006}
	}
@article{RobinsonJKGT2003,
	Author = {Douglas M. Robinson and David T. Jones and Hirohisa Kishino and Nick Goldman and Jeffrey L. Thorne},
	Issue = {10},
	Journal = {Molecular Biology and Evolution},
	Pages = {1692--1704},
	Title = {Protein Evolution with Dependence Among Codons Due to Tertiary Structure},
	Volume = {20},
	Year = {2003}}
@article{PagelMB2004,
	Author = {Mark Pagel and Andrew Meade and Daniel Barker},
	Journal = {Systematic Biology},
	Number = {5},
	Pages = {673-684},
	Title = {{B}ayesian Estimation of Ancestral Character States on Phylogenies},
	Volume = {53},
	Year = {2004}}
@article{PagelM2006,
	Author = {Pagel, Mark and Meade, Andrew},
	Journal = {The American Naturalist},
	Month = may,
	Number = {6},
	Pages = {808--825},
	Title = {{Bayesian Analysis of Correlated Evolution of Discrete Characters by Reversible-Jump Markov Chain Monte Carlo.}},
	Volume = {167},
	Year = {2006}}
@article{RosenblumEtAl2012,
	Author = {Rosenblum, Erica Bree and Sarver, Brice A J and Brown, Joseph W and Des Roches, Simone and Hardwick, Kayla M and Hether, Tyler D and Eastman, Jonathan M and Pennell, Matthew W and Harmon, Luke J},
	Journal = {Evolutionary Biology},
	Month = jun,
	Number = {2},
	Pages = {255--261},
	Title = {{Goldilocks Meets Santa Rosalia: An Ephemeral Speciation Model Explains Patterns of Diversification Across Time Scales.}},
	Volume = {39},
	Year = {2012}}
@article{SmithLieberman1999,
	Author = {L. H. Smith and Bruce S. Lieberman},
	Journal = {Paleobiology},
	Pages = {459-470},
	Title = {Disparity and constraint in olenelloid trilobites and the {Cambrian} radiation},
	Volume = {25},
	Year = {1999}}
@article{ParhamI2008,
	Abstract = {We reassess a study on a fossil-calibrated molecular clock that provides a new method for evaluating the accuracy of calibration points. We address several pitfalls that molecular systematists should be aware of when calculating rates of molecular evolution based on fossil calibrations. These caveats involve the substantiation and accurate use of geologic dates, the inappropriate use of fixed calibration points, and the explicit and objective phylogenetic placement of fossil taxa. Paleontological data, like molecular data, should be treated with the utmost rigor.},
	Author = {Parham, James F and Irmis, Randall B},
	File = {:Users/mholder/Library/Application Support/Mendeley Desktop/Downloaded/Parham, Irmis - 2008 - Caveats on the use of fossil calibrations for molecular dating a comment on Near et al.pdf:pdf},
	Institution = {Department of Herpetology, California Academy of Sciences, San Francisco, California 94103, USA. jparham@calacademy.org},
	Journal = {The American Naturalist},
	Keywords = {animals,fossils,phylogeny,time factors,turtles},
	Number = {1},
	Pages = {132--136},
	Publisher = {JSTOR},
	Title = {Caveats on the use of fossil calibrations for molecular dating: a comment on {Near et al.}},
	Url = {http://www.ncbi.nlm.nih.gov/pubmed/18171158},
	Volume = {171},
	Year = {2008}
	}
@article{Rabosky2009,
	Author = {Rabosky, Daniel L},
	Journal = {Evolution},
	Number = {6},
	Pages = {1816--1824},
	Title = {EXTINCTION RATES SHOULD NOT BE ESTIMATED FROM MOLECULAR PHYLOGENIES},
	Volume = {64},
	Year = {2009}}
@article{EldredgeEtAl2005,
	Abstract = {The fossil record displays remarkable stasis in many species over long time periods, yet studies of extant populations often reveal rapid phenotypic evolution and genetic differentiation among populations. Recent advances in our understanding of the fossil record and in population genetics and evolutionary ecology point to the complex geographic structure of species being fundamental to resolution of how taxa can commonly exhibit both short-term evolutionary dynamics and long-term stasis.},
	Author = {Eldredge, Niles and Thompson, John N and Brakefield, Paul M and Gavrilets, Sergey and Jablonski, David and Jackson, Jeremy B C and Lenski, Richard E and Lieberman, Bruce S and McPeek, Mark A and Miller, William},
	Doi = {10.1666/0094-8373(2005)031[0133:TDOES]2.0.CO;2},
	Issn = {00948373},
	Journal = {Paleobiology},
	Number = {sp5},
	Pages = {133--145},
	Publisher = {Paleontological Soc},
	Title = {{The dynamics of evolutionary stasis}},
	Url = {http://www.bioone.org/doi/abs/10.1666/0094-8373\%282005\%29031\%5B0133\%3ATDOES\%5D2.0.CO\%3B2},
	Volume = {31},
	Year = {2005}
	}
@article{PagelVM2006,
	Abstract = {A long-standing debate in evolutionary biology concerns whether species diverge gradually through time or by punctuational episodes at the time of speciation. We found that approximately 22\% of substitutional changes at the DNA level can be attributed to punctuational evolution, and the remainder accumulates from background gradual divergence. Punctuational effects occur at more than twice the rate in plants and fungi than in animals, but the proportion of total divergence attributable to punctuational change does not vary among these groups. Punctuational changes cause departures from a clock-like tempo of evolution, suggesting that they should be accounted for in deriving dates from phylogenies. Punctuational episodes of evolution may play a larger role in promoting evolutionary divergence than has previously been appreciated.},
	Author = {Pagel, Mark and Venditti, Chris and Meade, Andrew},
	Doi = {10.1029/2005GL023216},
	Isbn = {3145796119},
	Issn = {00948276},
	Journal = {Science},
	Number = {5796},
	Pages = {2005--2007},
	Publisher = {American Association for the Advancement of Science},
	Title = {{Large Punctuational Contribution of Speciation to Evolutionary Divergence at the Molecular Level}},
	Url = {http://www.agu.org/pubs/crossref/2005/2005GL023216.shtml},
	Volume = {314},
	Year = {2006}
	}
@article{Adrain1998,
	Abstract = {Cladistic analysis of the trilobite subfamily Acanthoparyphinae Whittington and Evitt, 1954, yields an explicit hypothesis of relationship for the group. All Silurian species together form a robustly supported monophylum including the genera Hyrokybe Lane, 1972, Parayoungia Chatterton and Perry, 1984, and Youngia Lindstrom, 1885. Sister to this is the Ordovician type species of Acanthoparypha Whittington and Evitt, 1954. Remaining species that have historically been assigned to either Acanthoparypha or Pandaspinapyga Esker and Levin, 1964, form a rather labile paraphylum. Nevertheless, the entire group thus identified is definitely monophyletic, and supported by several prominent synapomorphic character-states. The basal structure and basal node of the subfamily are more difficult to assess. The relationships of the genera Hammannopyge Pribyl, Vanek, and Pek, 1985, Holia Bradley, 1930, and Nieszkowskia Schmidt, 1881, need to be addressed within the wider context of the family as a whole. The traditional assignment of Holia to the acanthoparyphines is followed. Wenlock acanthoparyphines from the Cape Phillips Formation of the central Canadian Arctic islands include several species of Hyrokybe and Parayoungia. They are similar to, and in one case conspecific with, coeval forms to the southwest in the southern Mackenzie Mountains. Five species are new: Holia glabra, Hyrokybe lightfooti, Hyrokybe youngi, Hyrokybe mitchellae, and Parayoungia mclaughlini. At least four other potentially new species are reported in open nomenclature.},
	Author = {Adrain, Jonathan M},
	Doi = {10.2307/1306696},
	Issn = {00223360},
	Journal = {Journal of Paleontology},
	Keywords = {acanthoparypha,arctic,canada,holia glabra,hyrokybe lightfooti,hyrokybe mitchellae,hyrokybe youngi,northwest territories,pandaspinapyga,parayoungia mclaughlini,silurian,taxonomy,trilobita,youngia},
	Number = {4},
	Pages = {698--718},
	Publisher = {Paleontological Society},
	Title = {Systematics of the {Acanthoparyphinae (Trilobita)}, with species from the {Silurian of Arctic Canada}},
	Url = {http://www.scopus.com/scopus/inward/record.url?eid=2-s2.0-0031878538\&partnerID=40\&rel=R7.0.0},
	Volume = {72},
	Year = {1998}
	}
@article{Pyron2011,
	Author = {R Alexander Pyron},
	Journal = {Systematic Biology},
	Number = {4},
	Pages = {466--481},
	Title = {Divergence time estimation using fossils as terminal taxa and the origins of {Lissamphibia}},
	Volume = {60},
	Year = {2011}}
@unpublished{CongreveL2011a,
	Author = {Curtis R. Congreve and Bruce S. Lieberman},
	Note = {Geol. Soc. Amer. Ann. Meet., Minneapolis, MN, Abstracts with Programs},
	Title = {Quantifying Catastrophe: Estimating Speciation Rates and Extinction Rates in Trilobites during the End {Ordovician} Mass Extinction Event},
	Year = {2011}}
@article{GappLPD2011,
	Author = {Gapp, I Wesley and Lieberman, Bruce S and Pope, Michael C and Dilliard, Kelly A},
	Issn = {11755326},
	Journal = {Zootaxa},
	Pages = {15--28},
	Title = {New olenelline trilobites from the {Northwest Territories, Canada}, and the phylogenetic placement of {{\em {J}udomia absita}} {Fritz}, 1973},
	Url = {http://www.mapress.com/zootaxa/2011/f/z02918p028f.pdf},
	Volume = {2918},
	Year = {2011}
	}
@unpublished{GappHL2011,
	Author = {I. W. Gapp and Mark T. Holder and Bruce S. Lieberman},
	Note = {Geol. Soc. Amer. Ann. Meeting, Minneapolis, MN, Abstracts with Programs},
	Title = {Building phylogenetic trees for trilobites using maximum likelihood.},
	Year = {2011}}
@book{Stanley1979,
	Address = {San Francisco, CA.},
	Author = {S. M. Stanley},
	Publisher = {W. H. Freeman and Company},
	Title = {Macroevolution: Pattern and process},
	Year = {1979}}
@article{Lieberman1998,
	Author = {Bruce S. Lieberman},
	Journal = {Journal of Paleontology},
	Number = {1},
	Pages = {59--5978},
	Title = {Cladistic analysis of the {Early Cambrian} olenelloid trilobites},
	Volume = {72},
	Year = {1998}}
@article{Lieberman2001b,
	Author = {Bruce S. Lieberman},
	Journal = {Proceedings of the Royal Society of London, Series B: Biological Sciences},
	Number = {1477},
	Pages = {1707--1714},
	Title = {A test of whether rates of speciation were unusually high during the {C}ambrian radiation},
	Volume = {268},
	Year = {2001}}
@article{Green1995,
	Author = {Peter J. Green},
	Journal = {Biometrika},
	Number = {4},
	Pages = {711--732},
	Title = {Reversible jump {M}arkov chain {M}onte {C}arlo computation and {B}ayesian model determination},
	Volume = {82},
	Year = {1995}}
@article{Sanderson2002,
	Author = {M. J. Sanderson},
	Journal = {Molecular Biology and Evolution},
	Pages = {101-109},
	Title = {Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach},
	Volume = {19},
	Year = {2002}}
@article{HuelsenbeckR2001,
	Author = {John P. Huelsenbeck and F. R. Ronquist},
	Journal = {Bioinformatics},
	Number = {8},
	Pages = {754--755},
	Title = {{MRBAYES}: Bayesian inference of phylogenetic trees},
	Volume = {17},
	Year = {2001}}
@article{DrummondR2007,
	Author = {Drummond, A. and Rambaut, A.},
	Journal = {BMC Evolutionary Biology},
	Pages = {214},
	Title = {{BEAST}: {B}ayesian evolutionary analysis by sampling tree},
	Volume = {7},
	Year = {2007}}
@article{GilinskyG1991,
	Abstract = {In this paper we model the process of taxonomic evolution as a Galton-Watson branching process in discrete time and, using maximum likelihood, develop methods to estimate the probabilities of origination, persistence, and extinction of fossil taxa. We use the methods to estimate the probabilities of origination, persistence, and extinction of families (1) within 135 orders of marine invertebrate organisms, (2) within 12 phyla, and (3) within all marine invertebrate life (independently of the suprafamilial classification). Most orders, including the arcoid bivalves, the dentaloid scaphopods, the orders of chitins, and many others, have relatively low probabilities of familial origination and extinction. The various ammonoid and trilobite orders, and some others, have high probabilities of origination and extinction. Among the phyla, the Archaeocyatha have the highest probabilities of familial origination and extinction, and the Annelida the lowest, with the more typical phyla of shelly organisms clustering near the high end of the probability scale. The Porifera and Protozoa also have low probabilities but not as low as the Annelida. The estimated origination and extinction probabilities for families within all marine invertebrate life are 0.470 and 0.452 per stage, respectively, values that are at the high end of the probability scale. We have also estimated the probabilities of ultimate extinction (extinction of all families) of the supertaxa. By analyzing the changes of the diversity during each stratigraphic stage separately, we have also determined the trajectories of the estimated origination and extinction probabilities for families also determined the trajectories of the estimated origination and extinction probabilities for families within all marine invertebrate life. The estimated origination probability is relatively high in association with the expansion of the Cambrian and Paleozoic evolutionary faunas and declines to more normal levels for the remainder of the Phanerozoic. The trajectory of the estimated extinction probability is from nearly zero early in the Phanerozoic to more normal levels later, showing clearly defined peaks in association with the five Phanerozoic mass-extinction events. The terminal Cretaceous mass extinction is the only one of the five that was not preceded by a monotonic decline of origination probability or by a series of stages with low origination probability. It appears to have been a unique, singular event. Because the mathematical theory we employ as a model corresponds so closely to the processes of taxonomic evolution as we understand them, we believe that the theory provides a reasonable model of biological reality.},
	Author = {Gilinsky, N L and Good, I J},
	Doi = {10.2307/2400742},
	Issn = {00948373},
	Journal = {Paleobiology},
	Number = {2},
	Pages = {145--166},
	Title = {Probabilities of origination, persistence, and extinction of families of marine invertebrate life},
	Url = {http://www.jstor.org/stable/2400742},
	Volume = {17},
	Year = {1991}
	}
@article{Stadler2010,
	Author = {Stadler, Tanja},
	Journal = {Journal of Theoretical Biology},
	Number = {3},
	Pages = {396--404},
	Title = {Sampling-through-time in birth-death trees},
	Volume = {267},
	Year = {2010}}
@article{FitzJohnMO2009,
	Abstract = {Species traits may influence rates of speciation and extinction, affecting both the patterns of diversification among lineages and the distribution of traits among species. Existing likelihood approaches for detecting differential diversification require complete phylogenies; that is, every extant species must be present in a well-resolved phylogeny. We developed 2 likelihood methods that can be used to infer the effect of a trait on speciation and extinction without complete phylogenetic information, generalizing the recent binary-state speciation and extinction method. Our approaches can be used where a phylogeny can be reasonably assumed to be a random sample of extant species or where all extant species are included but some are assigned only to terminal unresolved clades. We explored the effects of decreasing phylogenetic resolution on the ability of our approach to detect differential diversification within a Bayesian framework using simulated phylogenies. Differential diversification caused by an asymmetry in speciation rates was nearly as well detected with only 50\% of extant species phylogenetically resolved as with complete phylogenetic knowledge. We demonstrate our unresolved clade method with an analysis of sexual dimorphism and diversification in shorebirds (Charadriiformes). Our methods allow for the direct estimation of the effect of a trait on speciation and extinction rates using incompletely resolved phylogenies.},
	Author = {FitzJohn, Richard G and Maddison, Wayne P and Otto, Sarah P},
	Institution = {Department of Zoology, University of British Columbia, Vancouver, BC, V6T 1Z4 Canada. fitzjohn@zoology.ubc.ca},
	Journal = {Systematic Biology},
	Number = {6},
	Pages = {595--611},
	Publisher = {Oxford University Press},
	Title = {Estimating trait-dependent speciation and extinction rates from incompletely resolved phylogenies},
	Url = {http://www.ncbi.nlm.nih.gov/pubmed/20525612},
	Volume = {58},
	Year = {2009}
	}
@article{MaddisonMO2007,
	Author = {Wayne Maddison and Peter E. Midford and S. E Otto},
	Journal = {Systematic Biology},
	Number = {5},
	Pages = {701--710},
	Rating = {0},
	Read = {Yes},
	Title = {Estimating a binary character's effect on speciation and extinction},
	Url = {http://www.informaworld.com.www2.lib.ku.edu:2048/10.1080/10635150701607033},
	Volume = {56},
	Year = {2007}
	}
@article{Pagel1994,
	Author = {Mark Pagel},
	Journal = {Proceedings of the Royal Society of London, Series B: Biological Sciences},
	Number = {1342},
	Pages = {37-45},
	Title = {Detecting Correlated Evolution on Phylogenies: A General Method for the Comparative Analysis of Discrete Characters},
	Volume = {255},
	Year = {1994}}
@article{TuffleyS1997Covarion,
	Author = {Chris Tuffley and Mike Steel},
	Journal = {Mathematical Biosciences},
	Pages = {63-91},
	Title = {Modelling the covarion hypothesis of nucleotide substitution},
	Volume = {147},
	Year = {1997}}
@phdthesis{GARLI,
	Author = {Derrick J. Zwickl},
	School = {The University of Texas at Austin.},
	Title = {Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion},
	Url = {www.bio.utexas.edu/faculty/antisense/garli/Garli.html},
	Year = {2006}
	}
@article{AllmanHR2010,
	Author = {Elizabeth S. Allman and Mark T. Holder and John A. Rhodes},
	Doi = {DOI: 10.1016/j.jtbi.2009.12.001},
	Issn = {0022-5193},
	Journal = {Journal of Theoretical Biology},
	Keywords = {Mkv model},
	Number = {1},
	Pages = {108-119},
	Title = {Estimating trees from filtered data: Identifiability of models for morphological phylogenetics},
	Url = {http://www.sciencedirect.com/science/article/B6WMD-4XX160T-2/2/5adf8b8af77dd551890d7cb5b0e62dba},
	Volume = {263},
	Year = {2010}
	}
@article{Lewis2001,
	Author = {P. O. Lewis},
	Journal = {Systematic Biology},
	Number = {6},
	Pages = {913--925},
	Title = {A likelihood approach to estimating phylogeny from discrete morphological character data},
	Volume = {50},
	Year = {2001}}
@article{Felsenstein1981a,
	Author = {Joseph Felsenstein},
	Journal = {Journal of Molecular Evolution},
	Pages = {368-376},
	Title = {Evolutionary trees from {DNA} sequences: a maximum likelihood approach},
	Volume = {17},
	Year = {1981}}
@incollection{Neyman1971,
	Address = {New York},
	Author = {J. Neyman},
	Booktitle = {Statistical decision theory and related topics},
	Editor = {S. S. Gupta and J. Yackel},
	Pages = {1--27},
	Publisher = {Academic Press},
	Title = {Molecular studies of evolution: a source of novel statistical problems},
	Year = {1971}}
@article{Wagner1998,
	Abstract = {Estimates of phylogenetic relationships among fossil taxa implicitly provide hypotheses about the quality of the fossil record. Phylogenetic inferences also provide hypotheses about character evolution. The likelihood of any hypothesis that makes predictions about two data sets is simply the likelihood of the hypothesis given the first data set times the likelihood of the same hypothesis given the second data set. In this case, data set 1 represents stratigraphy and data set 2 represents morphology. Statistical methods exist for determining the likelihood of hypothesized levels of sampling. The likelihood of a hypothesized amount of character change yielding a particular most-parsimonious solution (i.e, Lhypothesized length parsimony length can be evaluated with simulations. A reanalysis of hyaenid phylogeny based on published character and stratigraphic data is presented here, using the maximum likelihood method. Two trees are found, depending on assumptions about ambiguous species, which are 11 and 10 steps longer than the most parsimonious tree (61 or 60 vs. 50 steps). However, the trees invoke far less stratigraphic debt (9 or 12 units vs. 47 units as measured in Mammal Zones). An important feature of the results is that the most likely tree length given hyaenid character data is estimated to be 56 to 62 steps (depending on the model of character evolution) rather than 50 steps. The likelihood tree suggests stronger trends toward bone-crushing specializations than does the parsimony tree and further suggests that high levels of homoplasy caused parsimony to underestimate the true extent of those trends. Simulations based on the character data and fossil record of hyaenids suggest that the maximum likelihood method is better able to estimate correct trees than is parsimony and somewhat better able to do so than previously proposed phylogenetic methods incorporating stratigraphy.},
	Author = {Wagner, P J},
	Journal = {Paleobiology},
	Number = {4},
	Pages = {430--449},
	Title = {A likelihood approach for evaluating estimates of phylogenetic relationships among fossil taxa},
	Url = {http://www.scopus.com/scopus/inward/record.url?eid=2-s2.0-0032408552\&partnerID=40},
	Volume = {24},
	Year = {1998}
	}
@article{WilkinsonPCC2005,
	Author = {Wilkinson, Mark and Pisani, Davide and Cotton, James A and Corfe, Ian},
	Institution = {Department of Zoology, The Natural History Museum, London SW7 5BD, UK. marw@nhm.ac.uk},
	Journal = {Systematic Biology},
	Keywords = {classification,classification methods,phylogeny,reproducibility results},
	Number = {5},
	Pages = {823--831},
	Title = {Measuring support and finding unsupported relationships in supertrees},
	Url = {http://www.ncbi.nlm.nih.gov/pubmed/16243766},
	Volume = {54},
	Year = {2005}
	}
@article{Lieberman2001,
	Abstract = {Phylogenetic analysis was used to evaluate evolutionary relationships within the Cambrian suborder Olenellina Walcott, 1890; special emphasis was placed on those taxa outside of the Olenelloidea. Fifty-seven exoskeletal characters were coded for 24 taxa within the Olenellina and two outgroups referable to the "fallotaspidoid" grade. The Olenelloidea, along with the genus Gabriellus Fritz, 1992, are the sister group of the Judomioidea Repina, 1979. The "Nevadioidea" Hupe, 1953 are a paraphyletic grade group. Four new genera are recognized, Plesionevadia, Cambroinyoella, Callavalonia, and Sdzuyomia, and three new species are described, Nevadia fritzi, Cirquella nelsoni, and Cambroinyoella wallacei. Phylogenetic parsimony analysis is also used to make predictions about the ancestral morphology of the Olenellina. This morphology most resembles the morphology found in Plesionevadia and Pseudojudomia Egorova in Goryanskii and Egorova, 1964.},
	Author = {Bruce S. Lieberman},
	Issn = {00223360},
	Journal = {Journal of Paleontology},
	Number = {1},
	Pages = {96--115},
	Publisher = {Paleontological Soc},
	Title = {Phylogenetic analysis of the {Olenellina Walcott}, 1890 {(Trilobita, Cambrian)}},
	Url = {http://jpaleontol.geoscienceworld.org/cgi/content/abstract/75/1/96},
	Volume = {75},
	Year = {2001}
	}
@article{Lieberman1999,
	Author = {Bruce S. Lieberman},
	Journal = {Peabody Museum of Natural History Yale University Bulletin},
	Pages = {1--150},
	Title = {Systematic revision of the {Olenelloidea (Trilobota, Cambrian)}},
	Volume = {45},
	Year = {1999}}
@article{HeardM2000,
	Abstract = {If we are to plan conservation strategies that minimize the loss of evolutionary history through human-caused extinctions, we must understand how this loss is related to phylogenetic patterns in current extinction risks and past speciation rates. Nee \& May (1997, Science 278, 692-694) showed that for a randomly evolving clade (i) a single round of random extinction removed relatively little evolutionary history, and (ii) extinction management (choosing which taxa to sacrifice) offered only marginal improvement. However, both speciation rates and extinction risks vary across lineages within real clades. We simulated evolutionary trees with phylogenetically patterned speciation rates and extinction risks (closely related lineages having similar rates and risks) and then subjected them to several biologically informed models of extinction. Increasing speciation rate variation increases the extinction-management pay-off. When extinction risks vary among lineages but are uncorrelated with speciation rates, extinction removes more history (compared with random trees), but the difference is small. When extinction risks vary and are correlated with speciation rates, history loss can dramatically increase (negative correlation) or decrease (positive correlation) with speciation rate variation. The loss of evolutionary history via human-caused extinctions may therefore be more severe, yet more manageable, than first suggested.},
	Author = {Heard, S B and Mooers, A \O},
	Institution = {Department of Biological Sciences, University of Iowa, Iowa City 52242, USA. stephen-heard@uiowa.edu},
	Journal = {Proceedings of the Royal Society B Biological Sciences},
	Keywords = {biological,computer simulation,evolution,models,phylogeny},
	Number = {1443},
	Pages = {613--620},
	Title = {Phylogenetically patterned speciation rates and extinction risks change the loss of evolutionary history during extinctions},
	Url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1690578\&tool=pmcentrez\&rendertype=abstract},
	Volume = {267},
	Year = {2000}
	}
@article{Fortey2001,
	Abstract = {The progress achieved in trilobite systematics over the last 75 years is briefly reviewed. Different approaches to phylogenetics have influenced the way trilobites have been classified. Classical evolutionary taxonomy, the stratigraphical approach, and cladistics have all contributed in different ways to the current classification, which has evolved piecemeal, and is still unsatisfactory is some ways. Nonetheless, progress towards a phylogenetic classification has been made, especially as the result of information from ontogenies provided by well-preserved silificified material. Trilobites are a well-defined clade within a larger arachnomorph group. Agnostida have been excluded from Trilobita, but are perhaps best considered as specialised trilobites, at least until limbs of eodiscids are described. The outstanding problems in classification of each trilobite order are reviewed. Most are concerned with the recognition of the appropriate Cambrian sister taxa, and the discovery of the relevant ontogenies. It is very likely that post-Cambrian clades "root" deeply into the Cambrian. The coherence, or otherwise, of Proetida, Asaphida, Corynexochida and the lichid/odontopleurid groups will be resolved by such studies. The problems of paraphyly in Ptychopariida and Redlichiina may prove more obdurate. The temporal brevity of certain Cambrian family ranges may be partly a taxonomic artefact. The possibility of a late Cambrian gap in the record on some clades should be considered.},
	Author = {Fortey, Richard A},
	Doi = {10.1666/0022-3360(2001)075<1141:TSTLY>2.0.CO;2},
	Issn = {00223360},
	Journal = {Journal of Paleontology},
	Number = {6},
	Pages = {1141--1151},
	Publisher = {Paleontological Soc},
	Title = {Trilobite Systematics: the Last 75 Years},
	Url = {http://jpaleontol.geoscienceworld.org/cgi/content/abstract/75/6/1141},
	Volume = {75},
	Year = {2001}
	}
@article{Foote2000,
	Abstract = {Changes in genus diversity within higher taxa of marine animals on the temporal scale of a few million years are more strongly correlated with changes in extinction rate than with changes in origination rate during the Paleozoic. After the Paleozoic the relative roles of origination and extinction in diversity dynamics are reversed. Metazoa as well as individual higher taxa shift from one mode of diversity dynamics to the other. The magnitude of taxonomic rates, the relative variance of origination and extinction rates, and the presence or absence of a long-term secular increase in diversity all fail to account for the shift in importance of origination and extinction in diversity changes. Origination and extinction rates both tend to be diversity-dependent, but different modes of diversity-dependence may contribute to the change in diversity dynamics from the Paleozoic to the post-Paleozoic. During the Paleozoic, there is a weak tendency for extinction rates to be more diversity-dependent than origination rates, whereas after the Paleozoic the two rates are about equally diversity-dependent on average.},
	Author = {Foote, Mike},
	Doi = {10.1666/0094-8373(2000)026<0578:OAECOT>2.0.CO;2},
	Issn = {00948373},
	Journal = {Paleobiology},
	Number = {4},
	Pages = {578--605},
	Publisher = {Paleobiology},
	Title = {Origination and extinction components of taxonomic diversity: {Paleozoic} and {post-Paleozoic} dynamics},
	Url = {http://www.bioone.org/doi/abs/10.1666/0094-8373(2000)026<0578:OAECOT>2.0.CO;2},
	Volume = {26},
	Year = {2000}
	}
@article{CowmanB2011,
	Abstract = {Diversification rates within four conspicuous coral reef fish families (Labridae, Chaetodontidae, Pomacentridae and Apogonidae) were estimated using Bayesian inference. Lineage through time plots revealed a possible late Eocene/early Oligocene cryptic extinction event coinciding with the collapse of the ancestral Tethyan/Arabian hotspot. Rates of diversification analysis revealed elevated cladogenesis in all families in the Oligocene/Miocene. Throughout the Miocene, lineages with a high percentage of coral reef-associated taxa display significantly higher net diversification rates than expected. The development of a complex mosaic of reef habitats in the Indo-Australian Archipelago (IAA) during the Oligocene/Miocene appears to have been a significant driver of cladogenesis. Patterns of diversification suggest that coral reefs acted as a refuge from high extinction, as reef taxa are able to sustain diversification at high extinction rates. The IAA appears to support both cladogenesis and survival in associated lineages, laying the foundation for the recent IAA marine biodiversity hotspot.},
	Author = {Cowman, P F and Bellwood, D R},
	Doi = {10.1111/j.1420-9101.2011.02391.x},
	File = {:Users/mholder/Library/Application Support/Mendeley Desktop/Downloaded/Cowman, Bellwood - 2011 - Coral reefs as drivers of cladogenesis expanding coral reefs, cryptic extinction events, and the development of biodiversity hotspots.pdf:pdf},
	Issn = {14209101},
	Journal = {Journal of Evolutionary Biology},
	Number = {12},
	Pages = {1--20},
	Title = {Coral reefs as drivers of cladogenesis: expanding coral reefs, cryptic extinction events, and the development of biodiversity hotspots},
	Url = {http://www.ncbi.nlm.nih.gov/pubmed/21985176},
	Volume = {24},
	Year = {2011}
	}
@article{CongreveL2011b,
	Abstract = {Background: Sphaerexochinae is a speciose and widely distributed group of cheirurid trilobites. Their temporal range extends from the earliest Ordovician through the Silurian, and they survived the end Ordovician mass extinction event (the second largest mass extinction in Earth history). Prior to this study, the individual evolutionary relationships within the group had yet to be determined utilizing rigorous phylogenetic methods. Understanding these evolutionary relationships is important for producing a stable classification of the group, and will be useful in elucidating the effects the end Ordovician mass extinction had on the evolutionary and biogeographic history of the group. Methodology/Principal Findings: Cladistic parsimony analysis of cheirurid trilobites assigned to the subfamily Sphaerexochinae was conducted to evaluate phylogenetic patterns and produce a hypothesis of relationship for the group. This study utilized the program TNT, and the analysis included thirty-one taxa and thirty-nine characters. The results of this analysis were then used in a Lieberman-modified Brooks Parsimony Analysis to analyze biogeographic patterns during the Ordovician-Silurian. Conclusions/Significance: The genus Sphaerexochus was found to be monophyletic, consisting of two smaller clades (one composed entirely of Ordovician species and another composed of Silurian and Ordovician species). By contrast, the genus Kawina was found to be paraphyletic. It is a basal grade that also contains taxa formerly assigned to Cydonocephalus. Phylogenetic patterns suggest Sphaerexochinae is a relatively distinctive trilobite clade because it appears to have been largely unaffected by the end Ordovician mass extinction. Finally, the biogeographic analysis yields two major conclusions about Sphaerexochus biogeography: Bohemia and Avalonia were close enough during the Silurian to exchange taxa; and during the Ordovician there was dispersal between Eastern Laurentia and the Yangtze block (South China) and between Eastern Laurentia and Avalonia.},
	Author = {Curtis R. Congreve and Bruce S. Lieberman},
	Editor = {Moreau, Corrie S},
	Institution = {Department of Geology and Biodiversity Institute, University of Kansas, Lawrence, Kansas, United States of America. oldjack327@yahoo.com},
	Journal = {PLoS ONE},
	Number = {6},
	Pages = {11},
	Publisher = {Public Library of Science},
	Title = {Phylogenetic and Biogeographic Analysis of {Sphaerexochine} Trilobites},
	Volume = {6},
	Year = {2011}}
@article{CongreveL2010,
	Abstract = {Cladistic parsimony analysis of the subfamily Deiphoninae Raymond, 1913 was conducted to produce a hypothesis of relationship for the group. The genera Deiphon Barrande, 1850 and Onycopyge Woodward, 1880 are found to be monophyletic, while the genus Sphaerocoryphe Angelin, 1854, as it was previously defined, is paraphyletic. A modified Brooks Parsimony Analysis using the phylogenetic hypothesis reveals patterns of biogeography, in particular, vicariance and geodispersal, during the Ordovician-Silurian. The analysis yields three major conclusions about deiphonine biogeography: Eastern Laurentia and Baltica were close enough during the late Ordovician to exchange taxa via sea level rise and fall; chance dispersal occurred between Northwestern Laurentia and Australia; and deiphonine trilobites likely originated in Baltica or Eastern Laurentia. 2010 The Paleontological Society.},
	Author = {Congreve, Curtis R and Bruce S. Lieberman},
	Doi = {10.1666/09-026.1},
	Issn = {00223360},
	Journal = {Journal of Paleontology},
	Number = {1},
	Pages = {128--136},
	Publisher = {The Paleontological Society},
	Title = {Phylogenetic and Biogeographic Analysis of {Deiphonine} Trilobites},
	Url = {http://www.bioone.org/doi/abs/10.1666/09-026.1},
	Volume = {84},
	Year = {2010}
	}
@article{BinindaEmondsGS2002,
	Abstract = {Supertree construction is a new, rigorous approach for combining phylogenetic information to produce more inclusive phylogenies. It has been used to provide some of the largest, most complete phylogenies for diverse groups (e.g., mammals, flowering plants, and dinosaurs) at a variety of taxonomic levels. We critically review methods for assembling supertrees, discuss some of their more interesting mathematical properties, and describe the strengths and limitations of the supertree approach. To document the need for supertrees in biology, we identify how supertrees have already been used beyond the systematic information they provide to examine models of evolution, test rates of cladogenesis, detect patterns of trait evolution, and extend phylogenetic information to biodiversity conservation.},
	Author = {Bininda-Emonds, Olaf R P and Gittleman, John L and Steel, Mike A},
	Doi = {10.1146/annurev.ecolsys.33.010802.150511},
	Issn = {00664162},
	Journal = {Annual Review of Ecology and Systematics},
	Keywords = {a new,algorithms,biodiversity,consensus techniques,has been used,logenetic information produce,macroevolution,matrix representation,more inclusive phylogenies,phy,pro,rigorous approach combining,s abstract supertree construction,total evidence,trees},
	Number = {1},
	Pages = {265--289},
	Publisher = {JSTOR},
	Title = {The {(Super)Tree} of Life: Procedures, Problems, and Prospects},
	Url = {http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.ecolsys.33.010802.150511},
	Volume = {33},
	Year = {2002}
	}
@article{AlfaroEtAl2009,
	Abstract = {The uneven distribution of species richness is a fundamental and unexplained pattern of vertebrate biodiversity. Although species richness in groups like mammals, birds, or teleost fishes is often attributed to accelerated cladogenesis, we lack a quantitative conceptual framework for identifying and comparing the exceptional changes of tempo in vertebrate evolutionary history. We develop MEDUSA, a stepwise approach based upon the Akaike information criterion for detecting multiple shifts in birth and death rates on an incompletely resolved phylogeny. We apply MEDUSA incompletely to a diversity tree summarizing both evolutionary relationships and species richness of 44 major clades of jawed vertebrates. We identify 9 major changes in the tempo of gnathostome diversification; the most significant of these lies at the base of a clade that includes most of the coral-reef associated fishes as well as cichlids and perches. Rate increases also underlie several well recognized tetrapod radiations, including most modern birds, lizards and snakes, ostariophysan fishes, and most eutherian mammals. In addition, we find that large sections of the vertebrate tree exhibit nearly equal rates of origination and extinction, providing some of the first evidence from molecular data for the importance of faunal turnover in shaping biodiversity. Together, these results reveal living vertebrate biodiversity to be the product of volatile turnover punctuated by 6 accelerations responsible for >85\% of all species as well as 3 slowdowns that have produced "living fossils." In addition, by revealing the timing of the exceptional pulses of vertebrate diversification as well as the clades that experience them, our diversity tree provides a framework for evaluating particular causal hypotheses of vertebrate radiations.},
	Author = {Alfaro, Michael E and Santini, Francesco and Brock, Chad and Alamillo, Hugo and Dornburg, Alex and Rabosky, Daniel L and Carnevale, Giorgio and Harmon, Luke J},
	Chapter = {13410},
	Institution = {Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA. michaelalfaro@ucla.edu},
	Journal = {Proceedings of the National Academy of Sciences of the United States of America},
	Keywords = {animals,biodiversity,biological evolution,jaw,jaw anatomy \& histology,likelihood functions,phylogeny,vertebrates,vertebrates genetics},
	Number = {32},
	Pages = {13410--13414},
	Publisher = {National Acad Sciences},
	Title = {Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates.},
	Url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2715324\&tool=pmcentrez\&rendertype=abstract},
	Volume = {106},
	Year = {2009}
	}
@article{AbeL2009,
	Abstract = {Evolutionary radiations, times of profound diversification of species against a broader background of more muted evolutionary change, have long been considered one of the fundamental patterns in the fossil record. Further, given the important role geological, environmental, and climatic processes play in causing speciation, analyzing the biogeographic context of radiations can yield important insight into their evolutionary mechanisms. In this study we examine biogeographic patterns and quantify rates of speciation in a diverse group of Devonian trilobites, the calmoniids, that has been hailed as a classic paleontological example of an evolutionary radiation. In particular, a phylogenetic biogeographic analysismodified Brooks Parsimony Analysiswas used to examine the processes and geographic setting of speciation within the group. Results indicate that the Malvinokaffric Realm was a geographically complex area, and this geographic complexity created various opportunities for speciation via geodispersal and vicariance that created the fuel that fed the speciation in these taxa. Part of the geographic complexity was created not only by the inherent geologic backdrop of the region, but the overlying changes of sea level rise and fall. Rates of speciation were highest when sea level was lowest. Low sea level encouraged isolation of faunas in different tectonic basins. By contrast, sea level rise facilitated range expansion and geodispersal to other distinct tectonic basins, and speciation rates concomitantly fell; however, the taxa with the expanded ranges were later fodder for diversification when sea level fell again. Here we present a view of evolutionary radiations driven fundamentally by external abiotic factorsgeology and climatethat cause range expansion and opportunities for geographic isolation with resultant rapid speciation.},
	Author = {Abe, Francine R and Bruce S. Lieberman},
	Doi = {10.1007/s11692-009-9060-0},
	Isbn = {1169200990},
	Issn = {00713260},
	Journal = {Evolutionary Biology},
	Keywords = {evolutionary radiations \'{a} macroevolution,speciation rates \'{a} devonian,trilobites \'{a} biogeography \'{a},\'{a}},
	Number = {2},
	Pages = {225--234},
	Title = {The Nature of Evolutionary Radiations: A Case Study Involving {Devonian} Trilobites},
	Url = {http://www.springerlink.com/index/10.1007/s11692-009-9060-0},
	Volume = {36},
	Year = {2009}
	}
@article{Wagner2000,
	Abstract = {Frequencies of new character state derivations are analyzed for 56 fossil taxa. The hypothesis that new character states are added continuously throughout clade history can be rejected for 48 of these clades. Two alternative explanations are considered: finite states and ordered states. The former hypothesizes a limited number of states available to each character and is tested using rarefaction equations. The latter hypothesizes that there are limited possible descendant morphologies for any state, even if the character has infinite potential states. This is tested using power functions. The finite states hypothesis explains states: steps relationships significantly better than does the ordered states hypothesis in 14 cases; the converse is true for 14 other cases. Under either hypothesis, trilobite clades show appreciably more homoplasty after the same numbers of steps than do molluscs, echinoderms, or vertebrates. The prevalence of the exhaustion pattern among different taxonomic groups implies that worker biases are not to blame and instead implicates biological explanations such as intrinsic constraints or persistent selective trends. Regardless of the source of increased homoplasy, clades appear to exhaust their available character spaces. Nearly all examined taxa show significant increases in proportions of incompatible character pairs (i.e., those necessarily implying homoplasy) as progressively younger taxa are added to character matrices. Thus, a deterioration of hierarchical structure accompanies character state exhaustion. Exhaustion has several implications: (1) the basic premise of cladistic analyses (i.e., that maximum congruence reflects homology rather than homoplasy) becomes increasingly less sound as clades age; (2) sampling high proportions of taxa probably is needed for congruence to discern homoplasy from homology; (3) stratigraphic data might be necessary to discern congruent homoplasy from congruent homology; and (4) in many cases, character states appear to have evolved in ordered patterns.},
	Author = {Wagner, P J},
	Doi = {10.1554/0014-3820(2000)054},
	Issn = {00143820},
	Journal = {Evolution: International Journal of Organic Evolution},
	Number = {2},
	Pages = {365--386},
	Publisher = {John Wiley \& Sons},
	Title = {Exhaustion of morphologic character states among fossil taxa},
	Url = {http://www.ncbi.nlm.nih.gov/pubmed/10937214},
	Volume = {54},
	Year = {2000}
	}
@article{Wagner1995,
	Abstract = {Cladograms predict the order in which fossil taxa appeared and, thus, make predictions about general patterns in the stratigraphic record. Inconsistencies between cladistic predictions and the observed stratigraphic record reflect either inadequate sampling of a clade's species, incomplete estimates of stratigraphic ranges, or homoplasy producing an incorrect phylogenetic hypothesis. A method presented in this paper attempts to separate the effects of homoplasy from the effects of inadequate sampling. Sampling densities of individual species are used to calculate confidence intervals on their stratigraphic ranges. The method uses these confidence intervals to test the order of branching predicted by a cladogram. The Lophospiridae ("Archaeogastropoda") of the Ordovician provide a useful test group because the clade has a good fossil record and it produced species over a long time. Confidence intervals reject several cladistic hypotheses that postulate improbable "ghost lineages." Other hypotheses are acceptable only with explicit ancestor-descendant relationships. The accepted cladogram is the shortest one that stratigraphic data cannot reject. The results caution against evaluating phylogenetic hypotheses of fossil taxa without considering both stratigraphic data and the possible presence of ancestral species, as both factors can affect interpretations of a clade's evolutionary dynamics and its patterns of morphologic evolution.},
	Author = {Wagner, Peter J},
	Doi = {10.2307/2401074},
	Issn = {00948373},
	Journal = {Paleobiology},
	Number = {2},
	Pages = {153--178},
	Publisher = {JSTOR},
	Title = {Stratigraphic tests of cladistic hypotheses},
	Url = {http://www.jstor.org/stable/2401074},
	Volume = {21},
	Year = {1995}
	}
@article{SandersonPH1998,
	Abstract = {Systematists and comparative biologists commonly want to make statements about relationships among taxa that have never been collectively included in any single phylogenetic analysis. Construction of phylogenetic 'supertrees' provides one solution. Supertrees are estimates of phylogeny assembled from sets of smaller estimates (source trees) sharing some but not necessarily all their taxa in common. If certain conditions are met, supertrees can retain all or most of the information from the source trees and also make novel statements about relationships of taxa that do not co-occur on any one source tree. Supertrees have commonly been constructed using subjective and informal approaches, but several explicit approaches have recently been proposed.},
	Author = {Sanderson, M J and Purvis, A and Henze, C},
	Institution = {Section of Evolution and Ecology, University of California, Davis, CA 95616, USA.},
	Journal = {Trends in Ecology and Evolution},
	Number = {3},
	Pages = {105--109},
	Publisher = {Elsevier},
	Title = {Phylogenetic supertrees: Assembling the trees of life},
	Url = {http://linkinghub.elsevier.com/retrieve/pii/S0169534797012421},
	Volume = {13},
	Year = {1998}
	}
@article{SandersonD1996,
	Abstract = {Few issues in evolutionary biology have received as much attention over the years or have generated as much controversy as those involving evolutionary rates. One unresolved issue is whether or not shifts in speciation and/or extinction rates are closely tied to the origin of 'key' innovations in evolution, This discussion has long been dominated by 'time-based' methods using data from the fossil record. Recently, however, attention has shifted to 'tree-based' methods, in which time, if it plays any role at all, is incorporated secondarily, usually based on molecular data, Tests of hypotheses about key innovations do require information about phylogenetic relationships, and some of these tests can be implemented without any information about time. However, every effort should be made to obtain information about time, which greatly increases the power of such tests.},
	Author = {Sanderson, Michael and Donoghue, Michael J},
	Doi = {10.1016/0169-5347(96)81059-7},
	Issn = {01695347},
	Journal = {Trends in Ecology and Evolution},
	Number = {1},
	Pages = {10153--10157},
	Publisher = {Elsevier},
	Title = {Reconstructing shifts in diversification rates on phylogenetic trees},
	Url = {http://linkinghub.elsevier.com/retrieve/pii/0169534796810597},
	Volume = {11},
	Year = {1996}
	}
@article{RodeL2005,
	Abstract = {The integration of Geographic Information System (GIS) methodology within a phylogenetic and statistical framework provides a background against which to evaluate the relationship between biogeographic changes and evolution in the fossil record. A case study based on patterns in Middle and Late Devonian phyllocarids (Crustacea) illustrates the usefulness of this integrated approach. Using a combined approach enhances determination of rates of biodiversity change and the relationship between biogeographic and evolutionary changes. Because the interaction between speciation and extinction rates fundamentally determines biodiversity dynamics, and speciation and extinction rates are influenced by the geographic ranges of component taxa, the relationship between biogeography and evolution is important. Furthermore, GIS makes it possible to quantify paleobiogeographic ranges. Phylogenetic biogeography resolved patterns of both vicariance and geodispersal and revealed that range expansions were more abundant than range contractions in Devonian phyllocarids. In addition, statistical tests on GIS-constrained species ranges and evolutionary-rate data revealed a relationship between increasing species' ranges and increases in both speciation and extinction rates. Extinction rate, however, increased more rapidly than speciation rate in the phyllocarids. The pattern of extinction rate increasing faster than speciation rate in the phyllocarids may illuminate aspects of the Late Devonian biodiversity crisis in particular, and protracted biodiversity crises in general.},
	Author = {Rode, Alycia L and Bruce S Lieberman},
	Doi = {10.1666/0022-3360(2005)079<0267:IEABAC>2.0.CO;2},
	Isbn = {1111111111},
	Issn = {00223360},
	Journal = {Journal of Paleontology},
	Number = {2},
	Pages = {267--276},
	Title = {Integrating Evolution and Biogeography: a Case Study Involving {Devonian} Crustaceans},
	Url = {http://www.bioone.org/doi/abs/10.1666/0022-3360(2005)079<0267:IEABAC>2.0.CO;2},
	Volume = {79},
	Year = {2005}
	}
@article{Raup1985,
	Abstract = {The evolutionary pattern of speciation and extinction in any biologic group may be described by a variety of mathematical models. These models provide a framework for describing the history of taxonomic diversity (clade shape) and other aspects of larger evolutionary patterns. The simplest model assumes time homogeneity: that is, speciation and extinction probabilities are constant through time and within taxonomic groups. In some cases the homogeneous model provides a good fit to real world paleontological data, but in other cases the model serves only as a null hypothesis that must be rejected before more complex models can be applied. In cases where the homogeneous model does not fit the data, time-inhomogeneous models can be formulated that specify change, regular or episodic, in speciation and extinction probabilities. An appendix provides a list of the most useful equations based on the homogeneous model.},
	Author = {Raup, David M},
	Doi = {10.2307/2400422},
	Issn = {00948373},
	Journal = {Paleobiology},
	Number = {1},
	Pages = {42--52},
	Publisher = {JSTOR},
	Title = {Mathematical models of cladogenesis},
	Url = {http://www.jstor.org/stable/2400422},
	Volume = {11},
	Year = {1985}
	}
@article{Nee2001,
	Abstract = {It is possible to estimate the rate of diversification of clades from phylogenies with a temporal dimension. First, I present several methods for constructing confidence intervals for the speciation rate under the simple assumption of a pure birth process. I discuss the relationships among these methods in the hope of clarifying some fundamental theory in this area. Their performances are compared in a simulation study and one is recommended for use as a result. A variety of other questions that may, in fact, be the questions of primary interest (e.g., Has the rate of cladogenesis been declining?) are then recast as biological variants of the purely statistical question-Is the birth process model appropriate for my data? Seen in this way, a preexisting arsenal of statistical techniques is opened up for use in this area: in particular, techniques developed for the analysis of Poisson processes and the analysis of survival data. These two approaches start from different representations of the data-the branch lengths in the tree-and I explicitly relate the two. Aiming for a synoptic account of useful theory in this area, I briefly discuss some important results from the analysis of two distinct birth-death processes: the one introduced into this area by Hey (1992) is refitted with some powerful statistical tools.},
	Author = {Nee, S},
	Doi = {10.1554/0014-3820(2001)055},
	Issn = {00143820},
	Journal = {Evolution: International Journal of Organic Evolution},
	Keywords = {animals,biological evolution,computer simulation,confidence intervals,genetic,genetic variation,likelihood functions,models,phylogeny,species specificity},
	Number = {4},
	Pages = {661--8},
	Publisher = {Wiley Online Library},
	Title = {Inferring speciation rates from phylogenies},
	Url = {http://www.ncbi.nlm.nih.gov/pubmed/11392383},
	Volume = {55},
	Year = {2001}
	}
@article{Rabosky2006,
	Abstract = {Maximum likelihood is a potentially powerful approach for investigating the tempo of diversification using molecular phylogenetic data. Likelihood methods distinguish between rate-constant and rate-variable models of diversification by fitting birth-death models to phylogenetic data. Because model selection in this context is a test of the null hypothesis that diversification rates have been constant over time, strategies for selecting best-fit models must minimize Type I error rates while retaining power to detect rate variation when it is present. Here I examine model selection, parameter estimation, and power to reject the null hypothesis using likelihood models based on the birth-death process. The Akaike information criterion (AIC) has often been used to select among diversification models; however, I find that selecting models based on the lowest AIC score leads to a dramatic inflation of the Type I error rate. When appropriately corrected to reduce Type I error rates, the birth-death likelihood approach performs as well or better than the widely used gamma statistic, at least when diversification rates have shifted abruptly over time. Analyses of datasets simulated under a range of rate-variable diversification scenarios indicate that the birth-death likelihood method has much greater power to detect variation in diversification rates when extinction is present. Furthermore, this method appears to be the only approach available that can distinguish between a temporal increase in diversification rates and a rate-constant model with nonzero extinction. I illustrate use of the method by analyzing a published phylogeny for Australian agamid lizards.},
	Author = {Rabosky, Daniel L},
	Institution = {Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York 14853-2701, USA. DLR32@cornell.edu},
	Journal = {Evolution: International Journal of Organic Evolution},
	Keywords = {animals,biodiversity,computer simulation,likelihood functions,lizards,lizards physiology,phylogeny,population dynamics,time factors},
	Number = {6},
	Pages = {1152--1164},
	Publisher = {Wiley Online Library},
	Title = {Likelihood methods for detecting temporal shifts in diversification rates},
	Url = {http://www.ncbi.nlm.nih.gov/pubmed/16892966},
	Volume = {60},
	Year = {2006}
	}
@article{McConway2004,
	Abstract = {Observed variations in rates of taxonomic diversification have been attributed to a range of factors including biological innovations, ecosystem restructuring, and environmental changes. Before inferring causality of any particular factor, however, it is critical to demonstrate that the observed variation in diversity is significantly greater than that expected from natural stochastic processes. Relative tests that assess whether observed asymmetry in species richness between sister taxa in monophyletic pairs is greater than would be expected under a symmetric model have been used widely in studies of rate heterogeneity and are particularly useful for groups in which paleontological data are problematic. Although one such test introduced by Slowinski and Guyer a decade ago has been applied to a wide range of clades and evolutionary questions, the statistical behavior of the test has not been examined extensively, particularly when used with Fisher's procedure for combining probabilities to analyze data from multiple independent taxon pairs. Here, certain pragmatic difficulties with the Slowinski-Guyer test are described, further details of the development of a recently introduced likelihood-based relative rates test are presented, and standard simulation procedures are used to assess the behavior of the two tests in a range of situations to determine: (I) the accuracy of the tests' nominal Type I error rate; (2) the statistical power of the tests; (3) the sensitivity of the tests to inclusion of taxon pairs with few species; (4) the behavior of the tests with datasets comprised of few taxon pairs; and (5) the sensitivity of the tests to certain violations of the null model assumptions. Our results indicate that in most biologically plausible scenarios, the likelihood-based test has superior statistical properties in terms of both Type I error rate and power, and we found no scenario in which the Slowinski-Guyer test was distinctly superior, although the degree of the discrepancy varies among the different scenarios. The Slowinski-Guyer test tends to be much more conservative (i.e., very disinclined to reject the null hypothesis) in datasets with many small pairs. In most situations, the performance of both the likelihood-based test and particularly the Slowinski-Guyer test improve when pairs with few species are excluded from the computation, although this is balanced against a decline in the tests' power and accuracy as fewer pairs are included in the dataset. The performance of both tests is quite poor when they are applied to datasets in which the taxon sizes do not conform to the distribution implied by the usual null model. Thus, results of analyses of taxonomic rate heterogeneity using the Slowinski-Guyer test can be misleading because the test's ability to reject the null hypothesis (equal rates) when true is often inaccurate and its ability to reject the null hypothesis when the alternative (unequal rates) is true is poor, particularly when small taxon pairs are included. Although not always perfect, the likelihood-based test provides a more accurate and powerful alternative as a relative rate, test.},
	Author = {McConway, K J and Sims, H J},
	Journal = {Evolution},
	Keywords = {adaptive zones,confidence intervals,diversity,estimating divergence times,evolutionary rates,extinction,floral nectar spurs,fossil preservation,innovation,key,likelihood,molecular clock,species diversity,stratigraphic ranges,taxon pairs,taxonomic diversity},
	Number = {1},
	Pages = {12--23},
	Title = {A likelihood-based method for testing for nonstochastic variation of diversification rates in phylogenies},
	Volume = {58},
	Year = {2004}}
@article{Paradis1997,
	Abstract = {A new method to estimate the diversification rate of a lineage from a phylogeny of recent species is presented. This uses survival models to analyse the ages of the species as derived from the phylogeny. Survival models can analyse missing data where the exact date of death is unknown (censoring). This approach allows us to include missing data (species not included in a detailed phylogenetic study) in the analysis, provided a minimum age is known for these species. Three models are presented, with emphasis on temporal variation in diversification rates. The maximum likelihood method and Akaike information criteria are used to derive estimators and tests of hypotheses. A simulation study demonstrates that the method is able to detect a temporal variation in diversification rate only when it is present, avoiding type I and type II errors. A lineage with ten species may be sufficient to detect a temporal variation in diversification rate even with 50 per cent of missing data. An application is presented with data from a phylogeny of birds of the genus Ramphocelus.},
	Author = {Paradis, E},
	Journal = {Proceedings of the Royal Society B Biological Sciences},
	Keywords = {akaike information criterion diversification evolu},
	Number = {1385},
	Pages = {1141--1147},
	Publisher = {The Royal Society},
	Title = {Assessing temporal variations in diversification rates from phylogenies: estimation and hypothesis testing},
	Url = {http://rspb.royalsocietypublishing.org/cgi/doi/10.1098/rspb.1997.0158},
	Volume = {264},
	Year = {1997}
	}
@article{NeeMH1992,
	Abstract = {The analysis of the tempo and mode of evolution has a strong tradition in paleontology. Recent advances in molecular phylogenetic reconstruction make it possible to complement this work by using data from extant species.},
	Author = {Nee, S and Mooers, A O and Harvey, P H},
	Issn = {00278424},
	Journal = {Proceedings of the National Academy of Sciences of the United States of America},
	Number = {17},
	Pages = {8322--8326},
	Title = {Tempo and mode of evolution revealed from molecular phylogenies},
	Url = {http://www.pnas.org/content/89/17/8322.abstract},
	Volume = {89},
	Year = {1992}
	}
@article{Nee2006,
	Abstract = {Birth-death models, and their subsetsthe pure birth and pure death modelshave a long history of use for informing thinking about macroevolutionary patterns. Here we illustrate with examples the wide range of questions they have been used to address, including estimating and comparing rates of diversification of clades, investi- gating the shapes of clades, and some rather surprising uses such as estimating speciation rates from data that are not resolved below the level of the genus. The raw data for inference can be the fossil record or the molecular phylogeny of a clade, and we explore the similarites and differences in the behavior of the birth-death models when applied to these different forms of data.},
	Author = {Nee, Sean},
	Doi = {10.1146/annurev.ecolsys.37.091305.110035},
	Isbn = {9780824314378},
	Issn = {1543592X},
	Journal = {Annual Review of Ecology Evolution and Systematics},
	Keywords = {fossil record,paleobiology,phylogenetics},
	Number = {1},
	Pages = {1--17},
	Publisher = {Annual Reviews},
	Series = {Annual Review of Ecology Evolution and Systematics},
	Title = {Birth-Death Models in Macroevolution},
	Url = {http://www.annualreviews.org/doi/abs/10.1146/annurev.ecolsys.37.091305.110035},
	Volume = {37},
	Year = {2006}
	}
@article{LiebermanK2010,
	Abstract = {Trilobites are a highly diverse group of extinct arthropods that persisted for nearly 300 million years. During that time, there was a profusion of morphological form, and they occupied a plethora of marine habitats. Their diversity, relative abundance, and complex morphology make them excellent candidates for phylogenetic analysis, and partly as a consequence they have been the subject of many cladistic studies. Although phylogenetic knowledge is certainly incomplete, our understanding of evolutionary patterns within the group has dramatically increased over the last 30 years. Moreover, trilobites have formed an important component of various studies of macroevolutionary processes. Here, we summarize the phylogenetic breadth of knowledge on the Trilobita, and present various hypotheses about phylogenetic patterns within the group, from the highest to the lowest taxonomic levels. Key topics we consider include the question of trilobite monophyly, the phylogenetic position of trilobites vis \`{a} vis extant arthropod groups, and inter- and intra-ordinal relationships.},
	Author = {Bruce S. Lieberman and Karim, Talia S},
	Institution = {Department of Geology, University of Kansas, 1475 Jayhawk Boulevard, Lawrence, KS 66045, USA.},
	Journal = {Arthropod structure development},
	Number = {2-3},
	Pages = {111--123},
	Publisher = {Elsevier Ltd},
	Title = {Tracing the trilobite tree from the root to the tips: a model marriage of fossils and phylogeny},
	Url = {http://www.ncbi.nlm.nih.gov/pubmed/19854298},
	Volume = {39},
	Year = {2010}
	}
@article{Lieberman2002,
	Abstract = {This paper presents a phylogenetic analysis of the "Fallotaspidoidea," a determination of the biogeographic origins of the eutrilobites, and art evaluation of the timing of the Cambrian radiation based on biogeographic evidence. Phylogenetic analysis incorporated 29 exoskeletal characters and 16 ingroup taxa. In the single most parsimonious tree the genus Fallotaspidella Repina, 1961, is the sister taxon of the sutured members of the Redlichiina Richter, 1932. Phylogenetic analysis is also used to determine the evolutionary relationships of two new species of "fallotaspidoids" distributed in the White-Inyo Range of California that have been previously illustrated but not described. These species had been referred to Fallotaspis Hupe, 1953, and used to define the occurrence of the eponymous Fallotaspis Zone in Southwestern Laurentia. However, these two new species need to be reassigned to Archaeaspis Repina in Khomentovskii and Repina, 1965. They are described as Archaeaspis nelsoni and A. macropleuron. Their phylogenetic status Suggests that the Fallotaspis Zone in southwestern Laurentia is not exactly analogous to the Fallotaspis Zone in Morocco, where that division was originally defined. Thus, changes to the biostratigraphy of the Early Cambrian of Southwestern Laurentia may be in order. Furthermore, specimens of a new species referable to Nevadia Walcott, 1910, are recognized in strata traditionally treated as within the Fallotaspis Zone, which is held to underlie the Nevadella Zone, suggesting further biostratigraphic complexity within the basal Lower Cambrian of southwestern Laurentia. Phylogenetic analyses of the Olenellina and Olenelloidea, along with the phylogenetic analysis presented here, are used to consider the biogeographic origins of the eutrilobites. The group appears to have originated in Siberia. Biogeographic patterns in trilobites, especially those relating to the split between the Olenellid and Redlichiid faunal provinces are important for determining the timing of the Cambrian radiation. Some authors have argued that there was a hidden radiation that significantly predated the Cambrian, whereas others have suggested that the radiation occurred right at the start of the Cambrian. The results from trilobite biogeography presented here support an early radiation. They are most compatible with the notion that there was a vicariance event relating to the origin of the redlichimid trilobites, and thus the eponymous Redlichiid faunal province, from the "fallotaspidoids." whose representatives were part of the Olenellid faunal province. This vicariance event, based on biogeographic patterns. is likely related to the breakup of Pannotia which occurred sometime between 600-550 Ma. suggesting that the initial episodes of trilobite cladogenesis occurred within that interval. As trilobites are relatively derived arthropods, this suggests that numerous important episodes of metazoan cladogeriesis precede both the earliest trilobitic part of the Early Cambrian, and indeed. even the Early Cambrian.},
	Author = {Bruce S. Lieberman},
	Doi = {10.1666/0022-3360(2002)076<0692:PAOSBE>2.0.CO;2},
	Issn = {00223360},
	Journal = {Journal of Paleontology},
	Number = {4},
	Pages = {692--708},
	Publisher = {Paleontological Society},
	Title = {Phylogenetic Analysis of Some Basal Early {Cambrian} Trilobites, the Biogeographic Origins of the {Eutrilobita}, and the Timing of the {Cambrian} Radiation},
	Url = {http://jpaleontol.geoscienceworld.org/cgi/content/abstract/76/4/692},
	Volume = {76},
	Year = {2002}
	}
@article{RonquistKVSMR2012,
	Author = {F. Ronquist and S. Klopfstein and L. Vilhelmsen and S. Schulmeister and D. L. Murray and A. P. Rasnitsyn},
	Journal = {Systematic Biology},
	Title = {A total-evidence approach to dating with fossils, applied to the early radiation of the {H}ymenoptera},
	Volume = {doi: 10.1093/sysbio/sys058},
	Year = {2012}}
@article{Heath2012,
	Author = {Tracy A. Heath},
	Journal = {Systematic Biology},
	Title = {A hierarchical {B}ayesian model for calibrating estimates of species divergence times},
	Volume = {doi: 10.1093/sysbio/sys032},
	Year = {2012}}
@article{SilvestroSZ2011,
	Author = {Daniele Silvestro and Jan Schnitzler and Georg Zizka},
	Doi = {10.1186/1471-2148-11-311},
	Journal = {BMC Evolutionary Biology},
	Month = {Jan},
	Pages = {311},
	Pii = {1471-2148-11-311},
	Title = {A {B}ayesian framework to estimate diversification rates and their variation through time and space},
	Volume = {11},
	Year = {2011}
	}
@article{WilkinsonSSMYT2011,
	Author = {Wilkinson, Richard D. and Steiper, Michael E. and Soligo, Christophe and Martin, Robert D. and Yang, Ziheng and {Tavar\'e}, Simon},
	Doi = {10.1093/sysbio/syq054},
	Journal = {Systematic Biology},
	Number = {1},
	Pages = {16-31},
	Title = {Dating Primate Divergences through an Integrated Analysis of Palaeontological and Molecular Data},
	Url = {http://sysbio.oxfordjournals.org/content/60/1/16.abstract},
	Volume = {60},
	Year = {2011}
	}
@article{QuentalM2010,
	Author = {Quental, Tiago B and Marshall, Charles R},
	Journal = {Trends in Ecology \& Evolution},
	Number = {8},
	Pages = {434--441},
	Title = {{Diversity dynamics: molecular phylogenies need the fossil record.}},
	Url = {http://linkinghub.elsevier.com/retrieve/pii/S0169534710001011},
	Volume = {25},
	Year = {2010}
	}
@article{HohnaEtAl2011,
	Author = {H\"ohna, Sebastian and Stadler, Tanja and Ronquist, Fredrik and Britton, Tom},
	Doi = {10.1093/molbev/msr095},
	Eprint = {http://mbe.oxfordjournals.org/content/28/9/2577.full.pdf+html},
	Journal = {Molecular Biology and Evolution},
	Number = {9},
	Pages = {2577-2589},
	Title = {Inferring Speciation and Extinction Rates under Different Sampling Schemes},
	Url = {http://mbe.oxfordjournals.org/content/28/9/2577.abstract},
	Volume = {28},
	Year = {2011}
	}
@article{Stadler2011,
	Author = {Tanja Stadler},
	Journal = {Systematic Biology},
	Pages = {668--675},
	Title = {Simulating trees on a fixed number of extant species},
	Volume = 60,
	Year = 2011}
@article{VendittiEtAl2006,
	Author = {Venditti, Chris and Meade, Andrew and Pagel, Mark},
	Journal = {Systematic Biology},
	Number = {4},
	Pages = {637--643},
	Title = {Detecting the node-density artifact in phylogeny reconstruction},
	Url = {http://centaur.reading.ac.uk/10244/},
	Volume = {55},
	Year = {2006}
	}
@article{AtkinsonEtAl2008,
	Author = {Atkinson, Quentin D and Meade, Andrew and Venditti, Chris and Greenhill, Simon J and Pagel, Mark},
	Journal = {Science},
	Number = {5863},
	Pages = {588},
	Title = {Languages evolve in punctuational bursts.},
	Url = {http://www.ncbi.nlm.nih.gov/pubmed/18239118},
	Volume = {319},
	Year = {2008}
	}
@article{WebsterEtAl2003,
	Author = {Webster, M and Gaines, R R and Hughes, N C},
	Journal = {Palaeogeography, Palaeoclimatology, Palaeoecology},
	Number = {1-2},
	Pages = {100--122},
	Title = {Microstratigraphy, trilobite biostratinomy, and depositional environment of the ``{L}ower {C}ambrian'' {R}uin {W}ash {L}agerst\"atte, {P}ioche {F}ormation, {N}evada},
	Url = {http://www.scopus.com/scopus/inward/record.url?eid=2-s2.0-45049087726&partnerID=40},
	Volume = {264},
	Year = {2008}
	}
@article{MorlonEtAl2011,
	Author = {Morlon, H and Parsons, T L and Plotkin, J B},
	Journal = {Proceedings of the National Academy of Sciences},
	Number = {11},
	Pages = {16327--32},
	Publisher = {National Acad Sciences},
	Title = {Reconciling molecular phylogenies with the fossil record},
	Url = {http://www.pnas.org/cgi/doi/10.1073/pnas.1102543108},
	Volume = {19104},
	Year = {2011}
	}
@article{BrockEtAl2011,
	Author = {Brock, Chad D and Harmon, Luke J and Alfaro, Michael E},
	Journal = {Systematic Biology},
	Number = {4},
	Pages = {410--9},
	Title = {Testing for Temporal Variation in Diversification Rates When Sampling is Incomplete and Nonrandom},
	Url = {http://www.ncbi.nlm.nih.gov/pubmed/21378083},
	Volume = {60},
	Year = {2011}
	}
@article{CusimanoRenner2010,
	Author = {Cusimano, Natalie and Renner, Susanne S},
	Journal = {Systematic Biology},
	Number = {4},
	Pages = {458--464},
	Publisher = {Oxford University Press},
	Title = {Slowdowns in diversification rates from real phylogenies may not be real.},
	Url = {http://www.ncbi.nlm.nih.gov/pubmed/20547781},
	Volume = {59},
	Year = {2010}
	}
@article{StadlerPNAS2011,
	title={Mammalian phylogeny reveals recent diversification rate shifts.},
	author={Stadler, Tanja},
	volume={108},
	url={http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3076834&tool=pmcentrez&rendertype=abstract},
	number={15},
	journal={Proceedings of the National Academy of Sciences of the United States of America},
	publisher={National Acad Sciences},
	year={2011},
	pages={6187--6192}}
@article{Lepage2006,
	author    = {T. Lepage and S. Lawi and P. Tupper and D. Bryant},
	title     = {Continuous and tractable models for the variation of evolutionary rates},
	journal   = {Mathematical Biosciences},
	year      = 2006,
	volume    = 199,
	pages     = {216--233}}
@article{Rannala2007,
	author    = {B. Rannala and Z. Yang},
	title     = {Inferring speciation times under an episodic molecular clock},
	journal   = {Systematic Biology},
	year      = 2007,
	volume    = 56,
	pages     = {453--466}}
@article{KishinoT2001,
	author    = {H. Kishino and J. L. Thorne and W. Bruno},
	title     = {Performance of a divergence time estimation method under a probabilistic model of rate evolution},
	journal   = {Molecular Biology and Evolution},
	year      = 2001,
	volume    = 18,
	pages     = {352--361}}
@article{HuelsenbeckLS2000,
	author    = {J. P. Huelsenbeck and B. Larget and D. L. Swofford},
	title     = {A compound {P}oisson process for relaxing the molecular clock},
	journal   = {Genetics},
	year      = 2000,
	volume    = 154,
	pages     = {1879--1892}}
@article{Drummond2006,
	author    = {A. J. Drummond and S. Y. Ho and M. J. Phillips and A. Rambaut},
	title     = {Relaxed phylogenetics and dating with confidence},
	journal   = {PLoS Biology},
	year      = 2006,
	volume    = 4,
	pages     = {e88}}
@article{Drummond2010,
	author    = {A. J. Drummond and M. A. Suchard},
	title     = {Bayesian random local clocks, or one rate to rule them all},
	journal   = {BMC Biology},
	year      = 2010,
	volume    = 8,
	pages     = {114}}