% Encoding: windows-1252


@String { AN        = {The American Naturalist} }
@String { AREES     = {Annual Review of Ecology, Evolution, and Systematics} }
@String { ARG       = {Annual Review of Genetics} }
@String { BI        = {Bioinformatics} }
@String { BMCBIO    = {BMC Biology} }
@String { BMCEVOBIO = {BMC Evolutionary Biology} }
@String { CB        = {Current Biology} }
@String { EL        = {Ecology Letters} }
@String { EVOLUTION = {Evolution} }
@String { GENETICS  = {Genetics} }
@String { JASA      = {Journal of the American Statistical Association} }
@String { JME       = {Journal of Molecular Evolution} }
@String { JTB       = {Journal of Theoretical Biology} }
@String { MBE       = {Molecular Biology and Evolution} }
@String { ME        = {Molecular ecology} }
@String { MEE       = {Methods in Ecology and Evolution} }
@String { MPE       = {Molecular Phylogenetics and Evolution} }
@String { NAR       = {Nucl Acids Res}}
@String { NEE       = {Nature Ecology \& Evolution}}
@String { NP        = {New Phytologist} }
@String { PBIO      = {PLoS Biology} }
@String { PCB       = {PLoS Computational Biology} }
@String { PGENETICS = {PLoS Genetics} }
@String { PNAS      = {Proceedings of the National Academy of Sciences} }
@String { PONE      = {PLoS One} }
@String { ProcB     = {Proceedings of the Royal Society B: Biological Sciences} }
@String { SYSBIO    = {Systematic Biology} }
@String { TEE       = {Trends in Ecology \& Evolution} }
@String { TPB       = {Theoretical Population Biology} }

@article{Louca2020,
  author    = {Louca, Stilianos and Pennell, Matthew W.},
  journal   = {Nature},
  title     = {Extant timetrees are consistent with a myriad of diversification histories},
  year      = {2020},
  pages     = {1--4},
  publisher = {Nature Publishing Group},
}

@article{stadler2012,
  title     = {Estimating the basic reproductive number from viral sequence data},
  author    = {Stadler, Tanja and Kouyos, Roger and von Wyl, Viktor and Yerly, Sabine and B{\"o}ni, J{\"u}rg and B{\"u}rgisser, Philippe and Klimkait, Thomas and Joos, Beda and Rieder, Philip and Xie, Dong and others},
  journal   = {Molecular biology and evolution},
  volume    = {29},
  number    = {1},
  pages     = {347--357},
  year      = {2012},
  publisher = {Oxford University Press}
}

@article{MacPherson2020,
  title     = {A General Birth-Death-Sampling Model for Epidemiology and Macroevolution},
  author    = {MacPherson, Ailene and Louca, Stilianos and McLaughlin, Angela and Joy, Jeffrey B and Pennell, Matthew W},
  journal   = {bioRxiv},
  year      = {2020},
  publisher = {Cold Spring Harbor Laboratory}
}


@article{Green1995,
  title     = {{Reversible jump Markov chain Monte Carlo computation and Bayesian model determination}},
  author    = {Green, Peter J},
  journal   = {Biometrika},
  volume    = {82},
  number    = {4},
  pages     = {711--732},
  year      = {1995},
  publisher = {Oxford University Press}
}

@article{Culshaw2019,
  title     = {Exploring the power of {B}ayesian birth-death skyline models to detect mass extinction events from phylogenies with only extant taxa},
  author    = {Culshaw, Victoria and Stadler, Tanja and Sanmart{\'\i}n, Isabel},
  journal   = EVOLUTION,
  volume    = {73},
  number    = {6},
  pages     = {1133--1150},
  year      = {2019},
  publisher = {Wiley Online Library}
}

@article{May2016,
  title     = {A Bayesian approach for detecting the impact of mass-extinction events on molecular phylogenies when rates of lineage diversification may vary},
  author    = {May, Michael R and H{\"o}hna, Sebastian and Moore, Brian R},
  journal   = {Methods in Ecology and Evolution},
  volume    = {7},
  number    = {8},
  pages     = {947--959},
  year      = {2016},
  publisher = {Wiley Online Library}
}

@article{Brooks1998,
  title     = {General methods for monitoring convergence of iterative simulations},
  author    = {Brooks, Stephen P and Gelman, Andrew},
  journal   = {Journal of computational and graphical statistics},
  volume    = {7},
  number    = {4},
  pages     = {434--455},
  year      = {1998},
  publisher = {Taylor \& Francis Group}
}

@Article{Vehtari2020,
  author    = {Vehtari, Aki and Gelman, Andrew and Simpson, Daniel and Carpenter, Bob and B{\"u}rkner, Paul-Christian},
  journal   = {Bayesian Analysis},
  title     = {Rank-normalization, folding, and localization: An improved {$\widehat{R}$} for assessing convergence of {MCMC}},
  year      = {2020},
  volume    = {(advance access)},
  publisher = {International Society for Bayesian Analysis},
}

@article{Magallon2001,
  title     = {Absolute diversification rates in angiosperm clades},
  author    = {Magallon, Susana and Sanderson, Michael J},
  journal   = EVOLUTION,
  volume    = {55},
  number    = {9},
  pages     = {1762--1780},
  year      = {2001},
  publisher = {Wiley Online Library}
}

@article{Pybus2000,
  title     = {Testing macro--evolutionary models using incomplete molecular phylogenies},
  author    = {Pybus, Oliver G and Harvey, Paul H},
  journal   = ProcB,
  volume    = {267},
  number    = {1459},
  pages     = {2267--2272},
  year      = {2000},
  publisher = {The Royal Society}
}

@article{Colless1982,
  title  = {Review of {Phylogenetics: Theory and Practice of Phylogenetic Systematics}},
  author = {Colless, Donald H},
  journal= {Systematic Zoology},
  volume = {31},
  number = {1},
  pages  = {100--104},
  year   = {1982}
}

@article{Duchene2019,
  title     = {Phylodynamic model adequacy using posterior predictive simulations},
  author    = {Duchene, Sebastian and Bouckaert, Remco and Duchene, David A and Stadler, Tanja and Drummond, Alexei J},
  journal   = SYSBIO,
  volume    = {68},
  number    = {2},
  pages     = {358--364},
  year      = {2019},
  publisher = {Oxford University Press}
}

@article{Kuhnert2014,
  title     = {{Simultaneous reconstruction of evolutionary history and epidemiological dynamics from viral sequences with the birth--death SIR model}},
  author    = {K{\"u}hnert, Denise and Stadler, Tanja and Vaughan, Timothy G and Drummond, Alexei J},
  journal   = {{Journal of the Royal Society Interface}},
  volume    = {11},
  number    = {94},
  pages     = {20131106},
  year      = {2014},
  publisher = {The Royal Society}
}

@Article{Hoehna2015a,
  author    = {Sebastian H{\"o}hna},
  title     = {{The time-dependent reconstructed evolutionary process with a key-role for mass-extinction events}},
  journal   = {Journal of Theoretical Biology},
  year      = {2015},
  volume    = {380},
  pages     = {321--331},
  issn      = {0022-5193},
  doi       = {http://dx.doi.org/10.1016/j.jtbi.2015.06.005},
  keywords  = {Birth-death process},
  owner     = {hoehna},
  timestamp = {2015.08.13},
  url       = {http://www.sciencedirect.com/science/article/pii/S0022519315002842},
}

@Article{Hoehna2014a,
  author    = {H{\"o}hna, Sebastian},
  title     = {{Likelihood Inference of Non-Constant Diversification Rates with Incomplete Taxon Sampling}},
  journal   = PONE,
  year      = {2014},
  volume    = {9},
  number    = {1},
  pages     = {e84184},
  owner     = {hoehna},
  publisher = {Public Library of Science},
  timestamp = {2013.10.13},
}

@Article{Hoehna2013,
  author    = {H{\"o}hna, Sebastian},
  title     = {{Fast simulation of reconstructed phylogenies under global time-dependent birth-death processes}},
  journal   = BI,
  year      = {2013},
  volume    = {29},
  number    = {11},
  pages     = {1367--1374},
  owner     = {hoehna},
  publisher = {Oxford Univ Press},
  timestamp = {2013.01.11},
}

@Article{Hoehna2016b,
  author    = {H\"{o}hna, Sebastian and Landis, Michael J. and Heath, Tracy A. and Boussau, Bastien and Lartillot, Nicolas and Moore, Brian R. and Huelsenbeck, John P. and Ronquist, Fredrik},
  title     = {{RevBayes}: {B}ayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language},
  journal   = SYSBIO,
  year      = {2016},
  volume    = {65},
  number    = {4},
  pages     = {726--736},
  doi       = {10.1093/sysbio/syw021},
  owner     = {hoehna},
  timestamp = {2016.08.12},
}

@Article{Hoehna2016a,
  author    = {H{\"o}hna, Sebastian and May, Michael R. and Moore, Brian R.},
  title     = {{TESS: an R package for efficiently simulating phylogenetic trees and performing Bayesian inference of lineage diversification rates}},
  journal   = BI,
  year      = {2016},
  volume    = {32},
  number    = {5},
  pages     = {789-791},
  doi       = {10.1093/bioinformatics/btv651},
  eprint    = {http://bioinformatics.oxfordjournals.org/content/32/5/789.full.pdf+html},
  owner     = {hoehna},
  timestamp = {2016.02.28},
  url       = {http://bioinformatics.oxfordjournals.org/content/32/5/789.abstract},
}

@Article{Hoehna2011,
  author  = {H{\"o}hna, Sebastian and Stadler, Tanja and Ronquist, Fredrik and Britton, Tom},
  title   = {{Inferring speciation and extinction rates under different species sampling schemes}},
  journal = MBE,
  year    = {2011},
  volume  = {28},
  number  = {9},
  pages   = {2577--2589},
  eprint  = {http://mbe.oxfordjournals.org/content/early/2011/04/10/molbev.msr095.full.pdf+html},
}

@Article{Wilberg2019,
  author    = {Wilberg, Eric W. and Turner, Alan H. and Brochu, Christopher A.},
  title     = {{Evolutionary structure and timing of major habitat shifts in Crocodylomorpha}},
  journal   = {Scientific reports},
  year      = {2019},
  volume    = {9},
  number    = {1},
  pages     = {514},
  publisher = {Nature Publishing Group},
}

@Article{Stadler2011,
  author    = {Stadler, T.},
  title     = {{Mammalian phylogeny reveals recent diversification rate shifts}},
  journal   = PNAS,
  year      = {2011},
  volume    = {108},
  number    = {15},
  pages     = {6187--6192},
  owner     = {hoehna},
  publisher = {National Acad Sciences},
  timestamp = {2012.07.27},
}

@Article{Silvestro2019,
  author  = {Silvestro, Daniele and Tejedor, Marcelo F. and Serrano-Serrano, Martha L. and Loiseau, Oriane and Rossier, Victor and Rolland, Jonathan and Zizka, Alexander and H{\"o}hna, Sebastian and Antonelli, Alexandre and Salamin, Nicolas},
  title   = {{Early arrival and climatically-linked geographic expansion of New World monkeys from tiny African ancestors}},
  journal = SYSBIO,
  year    = {2019},
  volume  = {68},
  number  = {1},
  pages   = {78--92},
}

@Article{Gavryushkina2014,
  author    = {Gavryushkina, Alexandra and Welch, David and Stadler, Tanja and Drummond, Alexei J.},
  title     = {{Bayesian inference of sampled ancestor trees for epidemiology and fossil calibration}},
  journal   = PCB,
  year      = {2014},
  volume    = {10},
  number    = {12},
  pages     = {e1003919},
  publisher = {Public Library of Science},
}

@Article{Stadler2010,
  author    = {Stadler, T.},
  title     = {{Sampling-through-time in birth-death trees}},
  journal   = JTB,
  year      = {2010},
  volume    = {267},
  number    = {3},
  pages     = {396--404},
  owner     = {Hoehna},
  publisher = {Elsevier},
  timestamp = {2010.10.10},
}

@Article{Stadler2013,
  author    = {Stadler, Tanja and K{\"u}hnert, Denise and Bonhoeffer, Sebastian and Drummond, Alexei J},
  journal   = PNAS,
  title     = {{Birth-death skyline plot reveals temporal changes of epidemic spread in HIV and hepatitis C virus (HCV)}},
  year      = {2013},
  number    = {1},
  pages     = {228--233},
  volume    = {110},
  owner     = {hoehna},
  publisher = {National Acad Sciences},
  timestamp = {2014.03.09},
}

@Article{Zhang2016,
  author    = {Zhang, Chi and Stadler, Tanja and Klopfstein, Seraina and Heath, Tracy A. and Ronquist, Fredrik},
  title     = {Total-evidence dating under the fossilized birth--death process},
  journal   = SYSBIO,
  year      = {2016},
  volume    = {65},
  number    = {2},
  pages     = {228--249},
  publisher = {Oxford University Press},
}

@Article{Oaks2019,
  author    = {Oaks, Jamie R.},
  journal   = SYSBIO,
  title     = {{Full Bayesian comparative phylogeography from genomic data}},
  year      = {2019},
  number    = {3},
  pages     = {371--395},
  volume    = {68},
  publisher = {Oxford University Press},
}

@Article{Magee2020,
  author    = {Magee, Andrew F. and H{\"o}hna, Sebastian and Vasylyeva, Tetyana I. and Leach{\'e}, Adam D. and Minin, Vladimir N.},
  journal   = PCB,
  title     = {{Locally adaptive Bayesian birth-death model successfully detects slow and rapid rate shifts}},
  year      = {2020},
  number    = {10},
  pages     = {e1007999},
  volume    = {16},
  publisher = {Public Library of Science San Francisco, CA USA},
}

@Article{Markwick1998,
  author    = {Markwick, Paul J.},
  journal   = {Paleobiology},
  title     = {{Crocodilian diversity in space and time: the role of climate in paleoecology and its implication for understanding K/T extinctions}},
  year      = {1998},
  number    = {4},
  pages     = {470--497},
  volume    = {24},
  publisher = {JSTOR},
}

@Article{Brochu2003,
  author    = {Brochu, Christopher A.},
  journal   = {Annual Review of Earth and Planetary Sciences},
  title     = {{Phylogenetic approaches toward crocodylian history}},
  year      = {2003},
  number    = {1},
  pages     = {357--397},
  volume    = {31},
  publisher = {Annual Reviews 4139 El Camino Way, PO Box 10139, Palo Alto, CA 94303-0139, USA},
}

@Article{Bronzati2015,
  author    = {Bronzati, Mario and Montefeltro, Felipe C. and Langer, Max C.},
  journal   = {Royal Society open science},
  title     = {{Diversification events and the effects of mass extinctions on Crocodyliformes evolutionary history}},
  year      = {2015},
  number    = {5},
  pages     = {140385},
  volume    = {2},
  publisher = {The Royal Society Publishing},
}

@Article{Mannion2015,
  author    = {Mannion, Philip D. and Benson, Roger B. J. and Carrano, Matthew T. and Tennant, Jonathan P. and Judd, Jack and Butler, Richard J.},
  journal   = {Nature communications},
  title     = {Climate constrains the evolutionary history and biodiversity of crocodylians},
  year      = {2015},
  number    = {1},
  pages     = {1--9},
  volume    = {6},
  publisher = {Nature Publishing Group},
}

@Article{Tennant2016,
  author    = {Tennant, Jonathan P. and Mannion, Philip D. and Upchurch, Paul},
  journal   = ProcB,
  title     = {{Environmental drivers of crocodyliform extinction across the Jurassic/Cretaceous transition}},
  year      = {2016},
  number    = {1826},
  pages     = {20152840},
  volume    = {283},
  publisher = {The Royal Society},
}

@Article{Fanti2016,
  author    = {Fanti, Federico and Miyashita, Tetsuto and Cantelli, Luigi and Mnasri, Fawsi and Dridi, Jihed and Contessi, Michela and Cau, Andrea},
  journal   = {Cretaceous Research},
  title     = {{The largest thalattosuchian (Crocodylomorpha) supports teleosaurid survival across the Jurassic-Cretaceous boundary}},
  year      = {2016},
  pages     = {263--274},
  volume    = {61},
  publisher = {Elsevier},
}

@Article{Oaks2011,
  author    = {Oaks, Jamie R.},
  journal   = {Evolution: International Journal of Organic Evolution},
  title     = {{A time-calibrated species tree of Crocodylia reveals a recent radiation of the true crocodiles}},
  year      = {2011},
  number    = {11},
  pages     = {3285--3297},
  volume    = {65},
  publisher = {Wiley Online Library},
}

@Article{Crisp2009,
  Title                    = {Explosive radiation or cryptic mass extinction? Interpreting signatures in molecular phylogenies},
  Author                   = {Crisp, Michael D and Cook, Lyn G},
  Journal                  = {Evolution},
  Year                     = {2009},
  Number                   = {9},
  Pages                    = {2257--2265},
  Volume                   = {63},

  Owner                    = {hoehna},
  Publisher                = {Wiley Online Library},
  Timestamp                = {2015.09.28}
}

@Article{Heath2014,
  Title                    = {{The fossilized birth-death process for coherent calibration of divergence-time estimates}},
  Author                   = {Heath, Tracy A and Huelsenbeck, John P and Stadler, Tanja},
  Journal                  = PNAS,
  Year                     = {2014},
  Number                   = {29},
  Pages                    = {E2957--E2966},
  Volume                   = {111},

  Owner                    = {hoehna},
  Publisher                = {National Acad Sciences},
  Timestamp                = {2015.05.31}
}

@Article{Arcila2017,
  author  = {Arcila, Dahiana and Tyler, James C.},
  journal = ProcB,
  title   = {{Mass extinction in tetraodontiform fishes linked to the Palaeocene--Eocene thermal maximum}},
  year    = {2017},
  number  = {1866},
  pages   = {20171771},
  volume  = {284},
}

@Article{Brennan2017,
  author  = {Brennan, Ian G and Oliver, Paul M},
  journal = {Evolution},
  title   = {{Mass turnover and recovery dynamics of a diverse Australian continental radiation}},
  year    = {2017},
  number  = {5},
  pages   = {1352--1365},
  volume  = {71},
}

@Article{Rohlf1990,
  author  = {Rohlf, F. James and Chang, W. S. and Sokal, R. R. and Kim, Junhyong},
  journal = {Evolution},
  title   = {Accuracy of estimated phylogenies: effects of tree topology and evolutionary model},
  year    = {1990},
  number  = {6},
  pages   = {1671--1684},
  volume  = {44},
}

@Article{Fiala1985,
  author  = {Fiala, Kent L. and Sokal, Robert R.},
  journal = {Evolution},
  title   = {Factors determining the accuracy of cladogram estimation: evaluation using computer simulation},
  year    = {1985},
  number  = {3},
  pages   = {609--622},
  volume  = {39},
}

@Article{Morlon2011,
  Title                    = {{Reconciling molecular phylogenies with the fossil record}},
  Author                   = {Morlon, H. and Parsons, T.L. and Plotkin, J.B.},
  Journal                  = PNAS,
  Year                     = {2011},
  Number                   = {39},
  Pages                    = {16327--16332},
  Volume                   = {108},

  Owner                    = {hoehna},
  Publisher                = {National Acad Sciences},
  Timestamp                = {2012.03.15}
}

@Article{Quental2010,
  author    = {Quental, T. B. and Marshall, C. R.},
  journal   = TEE,
  title     = {{Diversity dynamics: molecular phylogenies need the fossil record}},
  year      = {2010},
  pages     = {434--441},
  volume    = {25},
  owner     = {Hoehna},
  publisher = {Elsevier},
  timestamp = {2010.08.05},
}

@Article{Freyman2018,
  author    = {Freyman, William A. and H{\"o}hna, Sebastian},
  title     = {{Cladogenetic and anagenetic models of chromosome number evolution: a Bayesian model averaging approach}},
  journal   = SYSBIO,
  year      = {2018},
  volume    = {67},
  number    = {2},
  pages     = {1995--215},
  publisher = {Oxford University Press},
}

@Article{Stadler2013a,
  Title                    = {How can we improve accuracy of macroevolutionary rate estimates?},
  Author                   = {Stadler, Tanja},
  Journal                  = SYSBIO,
  Year                     = {2013},
  Number                   = {2},
  Pages                    = {321--329},
  Volume                   = {62},

  Owner                    = {hoehna},
  Publisher                = {Oxford University Press},
  Timestamp                = {2013.09.10}
}

@Article{Nee1994,
  author              = {Nee, Sean and May, Robert M. and Harvey, Paul H.},
  journal             = {Philosophical Transactions: Biological Sciences},
  title               = {{The Reconstructed Evolutionary Process}},
  year                = {1994},
  number              = {1309},
  pages               = {305--311},
  volume              = {344},
  jstor_articletype   = {primary_article},
  jstor_formatteddate = {May 28, 1994},
  owner               = {hoehna},
  publisher           = {The Royal Society},
  timestamp           = {2009.08.05},
}

@Article{Gernhard2008,
  author    = {Gernhard, T.},
  title     = {{The conditioned reconstructed process}},
  journal   = JTB,
  year      = {2008},
  volume    = {253},
  number    = {4},
  pages     = {769--778},
  comment   = {Advances in the Birth-Death process. A new model for estimating prior and simulations.},
  owner     = {hoehna},
  publisher = {Elsevier},
  timestamp = {2009.07.27},
}

@Article{Stadler2009,
  Title                    = {{On incomplete sampling under birth-death models and connections to the sampling-based coalescent}},
  Author                   = {Stadler, Tanja},
  Journal                  = JTB,
  Year                     = {2009},
  Number                   = {1},
  Pages                    = {58--66},
  Volume                   = {261},

  Keywords                 = {Birth-death trees},
  Owner                    = {hoehna},
  Publisher                = {Elsevier},
  Timestamp                = {2009.08.03}
}

@Article{Talts2018,
  author  = {Talts, Sean and Betancourt, Michael and Simpson, Daniel and Vehtari, Aki and Gelman, Andrew},
  title   = {Validating Bayesian inference algorithms with simulation-based calibration},
  journal = {arXiv preprint arXiv:1804.06788},
  year    = {2018},
}

@Article{Cook2006,
  author    = {Cook, Samantha R. and Gelman, Andrew and Rubin, Donald B.},
  journal   = {Journal of Computational and Graphical Statistics},
  title     = {{Validation of software for Bayesian models using posterior quantiles}},
  year      = {2006},
  number    = {3},
  pages     = {675--692},
  volume    = {15},
  publisher = {Taylor \& Francis},
}

@Article{Huelsenbeck2004a,
  Title                    = {{Frequentist Properties of Bayesian Posterior Probabilities of Phylogenetic Trees Under Simple and Complex Substitution Models}},
  Author                   = {Huelsenbeck, John P. and Rannala, Bruce},
  Journal                  = SYSBIO,
  Year                     = {2004},
  Number                   = {6},
  Pages                    = {904-913},
  Volume                   = {53},

  Doi                      = {10.1080/10635150490522629},
  Eprint                   = {http://sysbio.oxfordjournals.org/content/53/6/904.full.pdf+html},
  Owner                    = {hoehna},
  Timestamp                = {2011.09.14}
}

@Article{Springer2012,
  author    = {Springer, Mark S. and Meredith, Robert W. and Gatesy, John and Emerling, Christopher A. and Park, Jong and Rabosky, Daniel L. and Stadler, Tanja and Steiner, Cynthia and Ryder, Oliver A. and Jane{\v{c}}ka, Jan E. and others},
  title     = {Macroevolutionary dynamics and historical biogeography of primate diversification inferred from a species supermatrix},
  journal   = PONE,
  year      = {2012},
  volume    = {7},
  number    = {11},
  pages     = {e49521},
  publisher = {Public Library of Science},
}

@Article{Paradis2019,
  author    = {Paradis, Emmanuel and Schliep, Klaus},
  journal   = BI,
  title     = {{ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R}},
  year      = {2019},
  number    = {3},
  pages     = {526--528},
  volume    = {35},
  publisher = {Oxford University Press},
}

@article{Andreoletti2023,
  author = {Andréoletti, Jérémy and Morlon, Hélène},
  title = {Exploring congruent diversification histories with flexibility and parsimony},
  journal = MEE,
  year = {2023},
  publisher = {Wiley Online Library},
}

@Comment{jabref-meta: databaseType:bibtex;}
