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@article{Blanquart:2008gl,
author = {Blanquart, S and Lartillot, N},
title = {{A Site- and Time-Heterogeneous Model of Amino Acid Replacement}},
journal = {Molecular Biology and Evolution},
year = {2008},
volume = {25},
number = {5},
pages = {842--858},
month = feb,
keywords = {PHYLOGENETIC METHODS},
doi = {10.1093/molbev/msn018},
language = {English},
read = {Yes},
rating = {0},
date-added = {2011-05-26T18:17:26GMT},
date-modified = {2017-09-28T14:14:01GMT},
url = {https://doi.org/10.1093/molbev/msn018},
local-url = {file://localhost/Users/cdunn/Dropbox/articles/Library.papers3/Articles/2008/Blanquart/Molecular%20Biology%20and%20Evolution%202008%20Blanquart.pdf},
file = {{Molecular Biology and Evolution 2008 Blanquart.pdf:/Users/cdunn/Dropbox/articles/Library.papers3/Articles/2008/Blanquart/Molecular Biology and Evolution 2008 Blanquart.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.1093/molbev/msn018}}
}
@article{Bollback:2002to,
author = {Bollback, Jonathan P},
title = {{Bayesian model adequacy and choice in phylogenetics}},
journal = {Molecular Biology and Evolution},
year = {2002},
volume = {19},
number = {7},
pages = {1171--1180},
month = jul,
affiliation = {Department of Biology, University of Rochester, NY 14627, USA. [email protected]},
keywords = {PHYLOGENETIC METHODS},
pmid = {12082136},
language = {English},
read = {Yes},
rating = {0},
date-added = {2011-04-21T20:42:38GMT},
date-modified = {2018-04-10T16:13:33GMT},
abstract = {Bayesian inference is becoming a common statistical approach to phylogenetic estimation because, among other reasons, it allows for rapid analysis of large data sets with complex evolutionary models. Conveniently, Bayesian phylogenetic methods use currently available stochastic models of sequence evolution. However, as with other model-based approaches, the results of Bayesian inference are conditional on the assumed model of evolution: inadequate models (models that poorly fit the data) may result in erroneous inferences. In this article, I present a Bayesian phylogenetic method that evaluates the adequacy of evolutionary models using posterior predictive distributions. By evaluating a model's posterior predictive performance, an adequate model can be selected for a Bayesian phylogenetic study. Although I present a single test statistic that assesses the overall (global) performance of a phylogenetic model, a variety of test statistics can be tailored to evaluate specific features (local performance) of evolutionary models to identify sources failure. The method presented here, unlike the likelihood-ratio test and parametric bootstrap, accounts for uncertainty in the phylogeny and model parameters.},
url = {https://doi.org/10.1093/oxfordjournals.molbev.a004175},
local-url = {file://localhost/Users/cdunn/Dropbox/articles/Library.papers3/Articles/2002/Bollback/Mol%20Biol%20Evol%202002%20Bollback.pdf},
file = {{Mol Biol Evol 2002 Bollback.pdf:/Users/cdunn/Dropbox/articles/Library.papers3/Articles/2002/Bollback/Mol Biol Evol 2002 Bollback.pdf:application/pdf}},
uri = {\url{papers3://publication/uuid/1034C006-7FD5-4B23-AB57-5C17EBF249BA}}
}
@article{Chang:2015hl,
author = {Chang, E S and Neuhof, M and Rubinstein, N D and Diamant, A and Philippe, H and Huchon, D and Cartwright, P},
title = {{Genomic insights into the evolutionary origin of Myxozoa within Cnidaria}},
journal = {Proceedings of the National Academy of Sciences},
year = {2015},
pages = {1--6},
month = nov,
doi = {10.1073/pnas.1511468112},
language = {English},
read = {Yes},
rating = {0},
date-added = {2015-11-23T17:57:31GMT},
date-modified = {2018-03-22T12:34:48GMT},
url = {https://doi.org/10.1073/pnas.1511468112},
local-url = {file://localhost/Users/cdunn/Dropbox/articles/Library.papers3/Files/36/36C84BEB-BBC5-4A2E-BB05-DC6DD43EF06C.pdf},
file = {{36C84BEB-BBC5-4A2E-BB05-DC6DD43EF06C.pdf:/Users/cdunn/Dropbox/articles/Library.papers3/Files/36/36C84BEB-BBC5-4A2E-BB05-DC6DD43EF06C.pdf:application/pdf;36C84BEB-BBC5-4A2E-BB05-DC6DD43EF06C.pdf:/Users/cdunn/Dropbox/articles/Library.papers3/Files/36/36C84BEB-BBC5-4A2E-BB05-DC6DD43EF06C.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.1073/pnas.1511468112}}
}
@article{Feuda:2017ew,
author = {Feuda, Roberto and Dohrmann, Martin and Pett, Walker and Philippe, Hervé and Rota-Stabelli, Omar and Lartillot, Nicolas and Wörheide, Gert and Pisani, Davide},
title = {{Improved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals}},
journal = {Current Biology},
year = {2017},
volume = {27},
number = {24},
pages = {1--12},
month = nov,
publisher = {Elsevier Ltd.},
doi = {10.1016/j.cub.2017.11.008},
language = {English},
read = {Yes},
rating = {0},
date-added = {2017-11-30T17:44:47GMT},
date-modified = {2018-06-20T14:37:02GMT},
abstract = {Current Biology, Corrected proof. doi:10.1016/j.cub.2017.11.008},
url = {https://doi.org/10.1016/j.cub.2017.11.008},
local-url = {file://localhost/Users/cdunn/Dropbox/articles/Library.papers3/Files/03/03E86186-0E72-4B49-8578-5B783B2D511B.pdf},
file = {{03E86186-0E72-4B49-8578-5B783B2D511B.pdf:/Users/cdunn/Dropbox/articles/Library.papers3/Files/03/03E86186-0E72-4B49-8578-5B783B2D511B.pdf:application/pdf;03E86186-0E72-4B49-8578-5B783B2D511B.pdf:/Users/cdunn/Dropbox/articles/Library.papers3/Files/03/03E86186-0E72-4B49-8578-5B783B2D511B.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.1016/j.cub.2017.11.008}}
}
@article{Foster:2004tw,
author = {Foster, Peter G},
title = {{Modeling compositional heterogeneity.}},
journal = {Systematic biology},
year = {2004},
volume = {53},
number = {3},
pages = {485--495},
month = jun,
affiliation = {Department of Zoology, The Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom. [email protected]},
pmid = {15503675},
language = {English},
read = {Yes},
rating = {0},
date-added = {2018-06-20T15:00:34GMT},
date-modified = {2018-06-20T15:00:43GMT},
abstract = {Compositional heterogeneity among lineages can compromise phylogenetic analyses, because models in common use assume compositionally homogeneous data. Models that can accommodate compositional heterogeneity with few extra parameters are described here, and used in two examples where the true tree is known with confidence. It is shown using likelihood ratio tests that adequate modeling of compositional heterogeneity can be achieved with few composition parameters, that the data may not need to be modelled with separate composition parameters for each branch in the tree. Tree searching and placement of composition vectors on the tree are done in a Bayesian framework using Markov chain Monte Carlo (MCMC) methods. Assessment of fit of the model to the data is made in both maximum likelihood (ML) and Bayesian frameworks. In an ML framework, overall model fit is assessed using the Goldman-Cox test, and the fit of the composition implied by a (possibly heterogeneous) model to the composition of the data is assessed using a novel tree-and model-based composition fit test. In a Bayesian framework, overall model fit and composition fit are assessed using posterior predictive simulation. It is shown that when composition is not accommodated, then the model does not fit, and incorrect trees are found; but when composition is accommodated, the model then fits, and the known correct phylogenies are obtained.},
url = {https://doi.org/10.1080/10635150490445779},
uri = {\url{papers3://publication/uuid/nr--24E2C9CF-92FE-4289-9366-F6B230B71489}}
}
@article{King:2017ie,
author = {King, Nicole and Rokas, Antonis},
title = {{Embracing Uncertainty in Reconstructing Early Animal Evolution.}},
journal = {Current biology : CB},
year = {2017},
volume = {27},
number = {19},
pages = {R1081--R1088},
month = oct,
affiliation = {Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA. Electronic address: [email protected].},
doi = {10.1016/j.cub.2017.08.054},
pmid = {29017048},
pmcid = {PMC5679448},
language = {English},
read = {Yes},
rating = {0},
date-added = {2018-06-20T14:33:50GMT},
date-modified = {2018-06-20T14:34:30GMT},
abstract = {The origin of animals, one of the major transitions in evolution, remains mysterious. Many key aspects of animal evolution can be reconstructed by comparing living species within a robust phylogenetic framework.~However, uncertainty remains regarding the evolutionary relationships between two ancient animal lineages - sponges and ctenophores - and the remaining animal phyla. Comparative morphology and some phylogenomic analyses support the view that sponges represent the sister lineage to the rest of the animals, while other phylogenomic analyses support ctenophores, a phylum of carnivorous, gelatinous marine organisms, as the sister lineage. Here, we explore why different studies yield different answers and discuss the implications of the two alternative hypotheses for understanding the origin of animals. Reconstruction of ancient evolutionary radiations is devilishly difficult and will likely require broader sampling of sponge and ctenophore genomes, improved analytical strategies and critical analyses of the phylogenetic distribution and molecular mechanisms underlying apparently conserved traits. Rather than staking out positions in favor of the ctenophores-sister or the sponges-sister hypothesis, we submit that research programs aimed at understanding the biology of the first animals should instead embrace the uncertainty surrounding early animal evolution in their experimental designs.},
url = {https://doi.org/10.1016/j.cub.2017.08.054},
local-url = {file://localhost/Users/cdunn/Dropbox/articles/Library.papers3/Files/88/88673B3A-D2DB-47CD-A2DF-FC57E9D8FB9C.pdf},
file = {{88673B3A-D2DB-47CD-A2DF-FC57E9D8FB9C.pdf:/Users/cdunn/Dropbox/articles/Library.papers3/Files/88/88673B3A-D2DB-47CD-A2DF-FC57E9D8FB9C.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.1016/j.cub.2017.08.054}}
}
@article{Lartillot:2013fg,
author = {Lartillot, Nicolas and Rodrigue, Nicolas and Stubbs, Daniel and Richer, Jacques},
title = {{PhyloBayes MPI: phylogenetic reconstruction with infinite mixtures of profiles in a parallel environment.}},
journal = {Systematic biology},
year = {2013},
volume = {62},
number = {4},
pages = {611--615},
month = jul,
publisher = {Oxford University Press},
affiliation = {Centre Robert Cedergren pour la Bioinformatique, D{\'e}partement de Biochimie, Universit{\'e} de Montr{\'e}al, C.P. 6128, Succursale Centre-ville. Montr{\'e}al, Qu{\'e}bec H3C 3J7, Canada. [email protected]},
doi = {10.1093/sysbio/syt022},
pmid = {23564032},
language = {English},
rating = {0},
date-added = {2014-11-21T00:11:50GMT},
date-modified = {2018-06-20T14:58:21GMT},
abstract = {Modeling across site variation of the substitution process is increasingly recognized as important for obtaining more accurate phylogenetic reconstructions. Both finite and infinite mixture models have been proposed and have been shown to significantly improve on classical single-matrix models. Compared with their finite counterparts, infinite mixtures have a greater expressivity. However, they are computationally more challenging. This has resulted in practical compromises in the design of infinite mixture models. In particular, a fast but simplified version of a Dirichlet process model over equilibrium frequency profiles implemented in PhyloBayes has often been used in recent phylogenomics studies, while more refined model structures, more realistic and empirically more fit, have been practically out of reach. We introduce a message passing interface version of PhyloBayes, implementing the Dirichlet process mixture models as well as more classical empirical matrices and finite mixtures. The parallelization is made efficient thanks to the combination of two algorithmic strategies: a partial Gibbs sampling update of the tree topology and the use of a truncated stick-breaking representation for the Dirichlet process prior. The implementation shows close to linear gains in computational speed for up to 64 cores, thus allowing faster phylogenetic reconstruction under complex mixture models. PhyloBayes MPI is freely available from our website www.phylobayes.org.},
url = {https://doi.org/10.1093/sysbio/syt022},
local-url = {file://localhost/Users/cdunn/Dropbox/articles/Library.papers3/Files/94/94A04B5E-75DB-4826-8566-C5EC3C233B20.pdf},
file = {{94A04B5E-75DB-4826-8566-C5EC3C233B20.pdf:/Users/cdunn/Dropbox/articles/Library.papers3/Files/94/94A04B5E-75DB-4826-8566-C5EC3C233B20.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.1093/sysbio/syt022}}
}
@article{Susko:2007ds,
author = {Susko, Edward and Roger, Andrew J.},
title = {{On reduced amino acid alphabets for phylogenetic inference}},
journal = {Molecular Biology and Evolution},
year = {2007},
volume = {24},
number = {9},
pages = {2139--2150},
month = sep,
affiliation = {Department of Mathematics and Statistics, Dalhousie University, Halifax, Nova Scotia, Canada. [email protected]},
doi = {10.1093/molbev/msm144},
pmid = {17652333},
language = {English},
read = {Yes},
rating = {0},
date-added = {2017-12-15T13:44:44GMT},
date-modified = {2018-06-19T17:04:19GMT},
abstract = {We investigate the use of Markov models of evolution for reduced amino acid alphabets or bins of amino acids. The use of reduced amino acid alphabets can ameliorate effects of model misspecification and saturation. We present algorithms for 2 different ways of automating the construction of bins: minimizing criteria based on properties of rate matrices and minimizing criteria based on properties of alignments. By simulation, we show that in the absence of model misspecification, the loss of information due to binning is found to be insubstantial, and the use of Markov models at the binned level is found to be almost as effective as the more appropriate missing data approach. By applying these approaches to real data sets where compositional heterogeneity and/or saturation appear to be causing biased tree estimation, we find that binning can improve topological estimation in practice.},
url = {https://doi.org/10.1093/molbev/msm144},
local-url = {file://localhost/Users/cdunn/Dropbox/articles/Library.papers3/Files/20/20FF4402-67DD-4554-9DA7-7E837C945AB1.pdf},
file = {{20FF4402-67DD-4554-9DA7-7E837C945AB1.pdf:/Users/cdunn/Dropbox/articles/Library.papers3/Files/20/20FF4402-67DD-4554-9DA7-7E837C945AB1.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.1093/molbev/msm144}}
}
@article{Whelan:2015jj,
author = {Whelan, Nathan V and Kocot, Kevin M and Moroz, Leonid L and Halanych, Kenneth M},
title = {{Error, signal, and the placement of Ctenophora sister to all other animals.}},
journal = {Proceedings of the National Academy of Sciences},
year = {2015},
volume = {112},
number = {18},
pages = {201503453--6},
month = apr,
publisher = {National Acad Sciences},
affiliation = {Molette Biology Laboratory for Environmental and Climate Change Studies, Department of Biological Sciences, Auburn University, Auburn, AL 36849; [email protected].},
doi = {10.1073/pnas.1503453112},
pmid = {25902535},
language = {English},
read = {Yes},
rating = {0},
date-added = {2015-04-27T14:45:13GMT},
date-modified = {2017-12-10T04:42:31GMT},
abstract = {Elucidating relationships among early animal lineages has been difficult, and recent phylogenomic analyses place Ctenophora sister to all other extant animals, contrary to the traditional view of Porifera as the earliest-branching animal lineage. To date, phylogenetic support for either ctenophores or sponges as sister to other animals has been limited and inconsistent among studies. Lack of agreement among phylogenomic analyses using different data and methods obscures how complex traits, such as epithelia, neurons, and muscles evolved. A consensus view of animal evolution will not be accepted until datasets and methods converge on a single hypothesis of early metazoan relationships and putative sources of systematic error (e.g., long-branch attraction, compositional bias, poor model choice) are assessed. Here, we investigate possible causes of systematic error by expanding taxon sampling with eight novel transcriptomes, strictly enforcing orthology inference criteria, and progressively examining potential causes of systematic error while using both maximum-likelihood with robust data partitioning and Bayesian inference with a site-heterogeneous model. We identified ribosomal protein genes as possessing a conflicting signal compared with other genes, which caused some past studies to infer ctenophores and cnidarians as sister. Importantly, biases resulting from elevated compositional heterogeneity or elevated substitution rates are ruled out. Placement of ctenophores as sister to all other animals, and sponge monophyly, are strongly supported under multiple analyses, herein.},
url = {https://doi.org/10.1073/pnas.1503453112},
local-url = {file://localhost/Users/cdunn/Dropbox/articles/Library.papers3/Files/90/9031AA65-696B-41C7-9C58-4505900885EF.pdf},
file = {{9031AA65-696B-41C7-9C58-4505900885EF.pdf:/Users/cdunn/Dropbox/articles/Library.papers3/Files/90/9031AA65-696B-41C7-9C58-4505900885EF.pdf:application/pdf;9031AA65-696B-41C7-9C58-4505900885EF.pdf:/Users/cdunn/Dropbox/articles/Library.papers3/Files/90/9031AA65-696B-41C7-9C58-4505900885EF.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.1073/pnas.1503453112}}
}