@article{Harmon:2010gh,
author = {Harmon, Luke J and Losos, Jonathan B and Jonathan Davies, T and Gillespie, Rosemary G and Gittleman, John L and Bryan Jennings, W and Kozak, Kenneth H and McPeek, Mark A and Moreno-Roark, Franck and Near, Thomas J and Purvis, Andy and Ricklefs, Robert E and Schluter, Dolph and Schulte Ii, James A and Seehausen, Ole and Sidlauskas, Brian L and Torres-Carvajal, Omar and Weir, Jason T and Mooers, Arne {\O}},
title = {{Early bursts of body size and shape evolution are rare in comparative data.}},
journal = {Evolution},
year = {2010},
volume = {64},
number = {8},
pages = {2385--2396},
month = aug
}

@article{Lynch:1991db,
author = {Lynch, Michael},
title = {{Methods for the Analysis of Comparative Data in Evolutionary Biology}},
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}

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author = {Butler, M A and King, A A},
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pages = {683--695},
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}

@article{Mitov:2018co,
author = {Mitov, Venelin and Stadler, Tanja},
title = {A Practical Guide to Estimating the Heritability of Pathogen Traits},
journal = {Molecular Biology and Evolution},
volume = {35},
number = {3},
pages = {756-772},
year = {2018},
doi = {10.1093/molbev/msx328},
URL = {http://dx.doi.org/10.1093/molbev/msx328},
eprint = {/oup/backfile/content_public/journal/mbe/35/3/10.1093_molbev_msx328/3/msx328.pdf}
}

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}

@article{Hansen:2012et,
author = {Hansen, Thomas F and Bartoszek, Krzysztof},
title = {{Interpreting the evolutionary regression: the interplay between observational and biological errors in phylogenetic comparative studies.}},
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}

@article {Mitov:2017eg,
	author = {Mitov, Venelin and Stadler, Tanja},
	title = {Parallel Likelihood Calculation for Phylogenetic Comparative Models: the SPLITT C++ Library},
	year = {2019},
	doi = {10.1111/2041-210X.13136},
	publisher = {John Wiley & Sons, Inc.},
	abstract = {1. Phylogenetic comparative models (PCMs) have been used to study macroevolutionary patterns, to characterize adaptive phenotypic landscapes, to quantify rates of evolution, to measure the heritability of traits, and to test various evolutionary hypotheses. A major obstacle to applying these models has been the complexity of evaluating their likelihood function. Recent works have shown that for many PCMs, the likelihood can be obtained in time proportional to the size of the tree based on post-order tree traversal, also known as pruning. Despite this progress, inferring complex multi-trait PCMs on large trees remains a time-intensive task. Here, we study parallelizing the pruning algorithm as a generic technique for speeding-up PCM-inference. 2. We implement several parallel traversal algorithms in the form of a generic C++ library for Serial and Parallel LIneage Traversal of Trees (SPLITT). Based on SPLITT, we provide examples of parallel likelihood evaluation for several popular PCMs, ranging from a single-trait Brownian motion model to complex multi-trait Ornstein-Uhlenbeck and mixed Gaussian phylogenetic models. 3. Using the phylogenetic Ornstein-Uhlenbeck mixed model (POUMM) as a showcase, we run benchmarks on up to 24 CPU cores, reporting up to an order of magnitude parallel speed-up on simulated balanced and unbalanced trees of up to 100,000 tips with up to 16 traits. Noticing that the parallel speed-up depends on multiple factors, the SPLITT library is capable to automatically select the fastest traversal strategy for a given hardware, tree-topology, and data. Combining SPLITT likelihood calculation with adaptive Metropolis sampling on real data, we show that the time for Bayesian POUMM inference on a tree of 10,000 tips can be reduced from several days to minutes. 4. We conclude that parallel pruning effectively accelerates the likelihood calculation and, thus, the statistical inference of Gaussian phylogenetic models. For time-intensive Bayesian inferences, we recommend combining this technique with adaptive Metropolis sampling. Beyond Gaussian models, the parallel tree traversal can be applied to numerous other models, including discrete trait and birth-death population dynamics models. Currently, SPLITT supports multi-core shared memory architectures, but can be extended to distributed memory architectures as well as graphical processing units.},
	URL = {https://doi.org/10.1111/2041-210X.13136},
	journal = {Methods in Ecology and Evolution}
}

@Manual{R-ape,
  title = {ape: Analyses of Phylogenetics and Evolution},
  author = {Emmanuel Paradis and Simon Blomberg and Ben Bolker and Julien Claude and Hoa Sien Cuong and Richard Desper and Gilles Didier and Benoit Durand and Julien Dutheil and Olivier Gascuel and Christoph Heibl and Anthony Ives and Bradley Jones and Daniel Lawson and Vincent Lefort and Pierre Legendre and Jim Lemon and Rosemary McCloskey and Johan Nylander and Rainer Opgen-Rhein and Andrei-Alin Popescu and Manuela Royer-Carenzi and Klaus Schliep and Korbinian Strimmer and Damien {de Vienne}},
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  note = {R package version 4.0},
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@Manual{R-coda,
  title = {coda: Output Analysis and Diagnostics for MCMC},
  author = {Martyn Plummer and Nicky Best and Kate Cowles and Karen Vines and Deepayan Sarkar and Douglas Bates and Russell Almond and Arni Magnusson},
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  note = {R package version 0.19-1},
  url = {https://CRAN.R-project.org/package=coda},
}
@Manual{R-data.table,
  title = {data.table: Extension of `data.frame`},
  author = {Matt Dowle and Arun Srinivasan},
  year = {2016},
  note = {R package version 1.10.0},
  url = {https://CRAN.R-project.org/package=data.table},
}
@Manual{R-foreach,
  title = {foreach: Provides Foreach Looping Construct for R},
  author = {{Revolution Analytics} and Steve Weston}},
  year = {2015},
  note = {R package version 1.4.3},
  url = {https://CRAN.R-project.org/package=foreach},
}
@Manual{R-parallel,
  title = {Support for Parallel computation in R},
  author = {R Core Team}},
  year = {2016},
  note = {R package version 3.3.2},
  url = {https://CRAN.R-project.org/package=parallel},
}
@Manual{R-GGally,
  title = {GGally: Extension to 'ggplot2'},
  author = {Barret Schloerke and Jason Crowley and Di Cook and Francois Briatte and Moritz Marbach and Edwin Thoen and Amos Elberg and Joseph Larmarange},
  year = {2016},
  note = {R package version 1.3.0},
  url = {https://CRAN.R-project.org/package=GGally},
}
@Manual{R-ggplot2,
  title = {ggplot2: Create Elegant Data Visualisations Using the Grammar of Graphics},
  author = {Hadley Wickham and Winston Chang},
  year = {2016},
  note = {R package version 2.2.1},
  url = {https://CRAN.R-project.org/package=ggplot2},
}
@Manual{R-gsl,
  title = {gsl: Wrapper for the Gnu Scientific Library},
  author = {Robin K. S. Hankin; qrng functions by Duncan Murdoch and multimin by Andrew Clausen},
  year = {2017},
  note = {R package version 1.9-10.3},
  url = {https://CRAN.R-project.org/package=gsl},
}
@Manual{R-knitr,
  title = {knitr: A General-Purpose Package for Dynamic Report Generation in R},
  author = {Yihui Xie},
  year = {2016},
  note = {R package version 1.15.1},
  url = {https://CRAN.R-project.org/package=knitr},
}
@Manual{R-lmtest,
  title = {lmtest: Testing Linear Regression Models},
  author = {Torsten Hothorn and Achim Zeileis and Richard W. Farebrother and Clint Cummins},
  year = {2015},
  note = {R package version 0.9-34},
  url = {https://CRAN.R-project.org/package=lmtest},
}
@Manual{R-Matrix,
  title = {Matrix: Sparse and Dense Matrix Classes and Methods},
  author = {Douglas Bates and Martin Maechler},
  year = {2017},
  note = {R package version 1.2-8},
  url = {https://CRAN.R-project.org/package=Matrix},
}
@Manual{R-mvtnorm,
  title = {mvtnorm: Multivariate Normal and t Distributions},
  author = {Alan Genz and Frank Bretz and Tetsuhisa Miwa and Xuefei Mi and Torsten Hothorn},
  year = {2016},
  note = {R package version 1.0-5},
  url = {https://CRAN.R-project.org/package=mvtnorm},
}
@Manual{R-Rcpp,
  title = {Rcpp: Seamless R and C++ Integration},
  author = {Dirk Eddelbuettel and Romain Francois and JJ Allaire and Kevin Ushey and Qiang Kou and Nathan Russell and Douglas Bates and John Chambers},
  year = {2017},
  note = {R package version 0.12.9},
  url = {https://CRAN.R-project.org/package=Rcpp},
}
@Manual{R-RcppArmadillo,
  title = {RcppArmadillo: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra
Library},
  author = {Dirk Eddelbuettel and Romain Francois and Doug Bates},
  year = {2016},
  note = {R package version 0.7.600.1.0},
  url = {https://CRAN.R-project.org/package=RcppArmadillo},
}
@Manual{R-rmarkdown,
  title = {rmarkdown: Dynamic Documents for R},
  author = {JJ Allaire and Joe Cheng and Yihui Xie and Jonathan McPherson and Winston Chang and Jeff Allen and Hadley Wickham and Aron Atkins and Rob Hyndman},
  year = {2016},
  note = {R package version 1.3},
  url = {https://CRAN.R-project.org/package=rmarkdown},
}
@Manual{R-Rmpfr,
  title = {Rmpfr: R MPFR - Multiple Precision Floating-Point Reliable},
  author = {Martin Maechler},
  year = {2016},
  note = {R package version 0.6-1},
  url = {https://CRAN.R-project.org/package=Rmpfr},
}
@Manual{R-testthat,
  title = {testthat: Unit Testing for R},
  author = {Hadley Wickham},
  year = {2016},
  note = {R package version 1.0.2},
  url = {https://CRAN.R-project.org/package=testthat},
}
@Manual{R-TreeSim,
  title = {TreeSim: Simulating Phylogenetic Trees},
  author = {Tanja Stadler},
  year = {2015},
  note = {R package version 2.2},
  url = {https://CRAN.R-project.org/package=TreeSim},
}
@Manual{R-adaptMCMC,
  title = {adaptMCMC: Implementation of a generic adaptive Monte Carlo Markov Chain sampler},
  author = {Andreas Scheidegger},
  year = {2012},
  note = {R package version 1.1},
  url = {https://CRAN.R-project.org/package=adaptMCMC},
}


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@article{Mitov:2016kd,
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year = {2016},
pages = {058503},
month = jun
}


@article{Mitov:2017ku,
author = {Mitov, Venelin and Stadler, Tanja},
title = {{Fast and Robust Inference of Phylogenetic Ornstein-Uhlenbeck Models Using Parallel Likelihood Calculation}},
journal = {bioRxiv},
year = {2017},
pages = {115089},
month = mai
}