omeara.bib

@book{edwards1984likelihood,
  title={Likelihood},
  author={Edwards, A.W.F.},
  isbn={9780521318716},
  lccn={lc84014282},
  series={Cambridge science classics},
  url={https://books.google.com/books?id=LL08AAAAIAAJ},
  year={1984},
  publisher={Cambridge University Press}
}

@article{RaboskyAndGoldberg2015,
author = {Rabosky, Daniel L. and Goldberg, Emma E.},
title = {Model Inadequacy and Mistaken Inferences of Trait-Dependent Speciation},
journal = {Systematic Biology},
volume = {64},
number = {2},
pages = {340-355},
year = {2015},
doi = {10.1093/sysbio/syu131},
URL = {http://dx.doi.org/10.1093/sysbio/syu131},
eprint = {/oup/backfile/content_public/journal/sysbio/64/2/10.1093_sysbio_syu131/4/syu131.pdf}
}

@article{BeaulieuAndOMeara2016,
author = {Beaulieu, Jeremy M. and OÕMeara, Brian C.},
title = {Detecting Hidden Diversification Shifts in Models of Trait-Dependent Speciation and Extinction},
journal = {Systematic Biology},
volume = {65},
number = {4},
pages = {583-601},
year = {2016},
doi = {10.1093/sysbio/syw022},
URL = {http://dx.doi.org/10.1093/sysbio/syw022},
eprint = {/oup/backfile/content_public/journal/sysbio/65/4/10.1093_sysbio_syw022/6/syw022.pdf}
}

@article{KosiolEtAl2007,
author = {Kosiol, Carolin and Holmes, Ian and Goldman, Nick},
title = {An Empirical Codon Model for Protein Sequence Evolution},
journal = {Molecular Biology and Evolution},
volume = {24},
number = {7},
pages = {1464-1479},
year = {2007},
doi = {10.1093/molbev/msm064},
URL = {http://dx.doi.org/10.1093/molbev/msm064},
eprint = {/oup/backfile/content_public/journal/mbe/24/7/10.1093_molbev_msm064/2/msm064.pdf}
}

@article {WhelanAndGoldman2004,
	author = {Whelan, Simon and Goldman, Nick},
	title = {Estimating the Frequency of Events That Cause Multiple-Nucleotide Changes},
	volume = {167},
	number = {4},
	pages = {2027--2043},
	year = {2004},
	doi = {10.1534/genetics.103.023226},
	publisher = {Genetics},
	abstract = {Existing mathematical models of DNA sequence evolution assume that all substitutions derive from point mutations. There is, however, increasing evidence that larger-scale events, involving two or more consecutive sites, may also be important. We describe a model, denoted SDT, that allows for single-nucleotide, doublet, and triplet mutations. Applied to protein-coding DNA, the SDT model allows doublet and triplet mutations to overlap codon boundaries but still permits data to be analyzed using the simplifying assumption of independence of sites. We have implemented the SDT model for maximum-likelihood phylogenetic inference and have applied it to an alignment of mammalian globin sequences and to 258 other protein-coding sequence alignments from the Pandit database. We find the SDT model{\textquoteright}s inclusion of doublet and triplet mutations to be overwhelmingly successful in giving statistically significant improvements in fit of model to data, indicating that larger-scale mutation events do occur. Distributions of inferred parameter values over all alignments analyzed suggest that these events are far more prevalent than previously thought. Detailed consideration of our results and the absence of any known mechanism causing three adjacent nucleotides to be substituted simultaneously, however, leads us to suggest that the actual evolutionary events occurring may include still-larger-scale events, such as gene conversion, inversion, or recombination, or a series of rapid compensatory changes.},
	issn = {0016-6731},
	URL = {http://www.genetics.org/content/167/4/2027},
	eprint = {http://www.genetics.org/content/167/4/2027.full.pdf},
	journal = {Genetics}
}

@Article{SchneiderEtAl2005,
author="Schneider, Adrian
and Cannarozzi, Gina M.
and Gonnet, Gaston H.",
title="Empirical codon substitution matrix",
journal="BMC Bioinformatics",
year="2005",
month="Jun",
day="01",
volume="6",
number="1",
pages="134",
abstract="Codon substitution probabilities are used in many types of molecular evolution studies such as determining Ka/Ks ratios, creating ancestral DNA sequences or aligning coding DNA. Until the recent dramatic increase in genomic data enabled construction of empirical matrices, researchers relied on parameterized models of codon evolution. Here we present the first empirical codon substitution matrix entirely built from alignments of coding sequences from vertebrate DNA and thus provide an alternative to parameterized models of codon evolution.",
issn="1471-2105",
doi="10.1186/1471-2105-6-134",
url="https://doi.org/10.1186/1471-2105-6-134"
}



@article{NguyenEtAl2015,
author = {Nguyen, Lam-Tung and Schmidt, Heiko A. and von Haeseler, Arndt and Minh, Bui Quang},
title = {IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies},
journal = {Molecular Biology and Evolution},
volume = {32},
number = {1},
pages = {268-274},
year = {2015},
doi = {10.1093/molbev/msu300},
URL = {http://dx.doi.org/10.1093/molbev/msu300},
eprint = {/oup/backfile/content_public/journal/mbe/32/1/10.1093_molbev_msu300/1/msu300.pdf}
},
author = {Nguyen, Lam-Tung and Schmidt, Heiko A. and von Haeseler, Arndt and Minh, Bui Quang},
title = {IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies},
journal = {Molecular Biology and Evolution},
volume = {32},
number = {1},
pages = {268-274},
year = {2015},
doi = {10.1093/molbev/msu300},
URL = {http://dx.doi.org/10.1093/molbev/msu300},
eprint = {/oup/backfile/content_public/journal/mbe/32/1/10.1093_molbev_msu300/1/msu300.pdf}
}

@article{YangEtAl1998,
author = {Yang, Z and Nielsen, R and Hasegawa, M},
title = {Models of amino acid substitution and applications to mitochondrial protein evolution.},
journal = {Molecular Biology and Evolution},
volume = {15},
number = {12},
pages = {1600-1611},
year = {1998},
doi = {10.1093/oxfordjournals.molbev.a025888},
URL = {http://dx.doi.org/10.1093/oxfordjournals.molbev.a025888},
eprint = {/oup/backfile/content_public/journal/mbe/15/12/10.1093_oxfordjournals.molbev.a025888/1/mbev_15_12_1600.pdf}
}

@Article{BlazejEtAl2017,
author="B{\l}a{\.{z}}ej, Pawe{\l}
and Mackiewicz, Dorota
and Grabi{\'{n}}ska, Ma{\l}gorzata
and Wn{\k{e}}trzak, Ma{\l}gorzata
and Mackiewicz, Pawe{\l}",
title="Optimization of amino acid replacement costs by mutational pressure in bacterial genomes",
journal="Scientific Reports",
year="2017",
month="Apr",
day="21",
volume="7",
number="1",
pages="1061",
abstract="Mutations are considered a spontaneous and random process, which is important component of evolution because it generates genetic variation. On the other hand, mutations are deleterious leading to non-functional genes and energetically costly repairs. Therefore, one can expect that the mutational pressure is optimized to simultaneously generate genetic diversity and preserve genetic information. To check if empirical mutational pressures are optimized in these ways, we compared matrices of nucleotide mutation rates derived from bacterial genomes with their best possible alternatives that minimized or maximized costs of amino acid replacements associated with differences in their physicochemical properties (e.g. hydropathy and polarity). It should be noted that the studied empirical nucleotide substitution matrices and the costs of amino acid replacements are independent because these matrices were derived from sites free of selection on amino acid properties and the amino acid costs assumed only amino acid physicochemical properties without any information about mutation at the nucleotide level. Obtained results indicate that the empirical mutational matrices show a tendency to minimize costs of amino acid replacements. It implies that bacterial mutational pressures can evolve to decrease consequences of amino acid substitutions. However, the optimization is not full, which enables generation of some genetic variability.",
issn="2045-2322",
doi="10.1038/s41598-017-01130-7",
url="https://doi.org/10.1038/s41598-017-01130-7"
}



@article{McClellanAndMcCracken2001,
author = {McClellan, David A. and McCracken, Kevin G.},
title = {Estimating the Influence of Selection on the Variable Amino Acid Sites of the Cytochrome b Protein Functional Domains},
journal = {Molecular Biology and Evolution},
volume = {18},
number = {6},
pages = {917-925},
year = {2001},
doi = {10.1093/oxfordjournals.molbev.a003892},
URL = {http://dx.doi.org/10.1093/oxfordjournals.molbev.a003892},
eprint = {/oup/backfile/content_public/journal/mbe/18/6/10.1093_oxfordjournals.molbev.a003892/3/i0737-4038-018-06-0917.pdf}
}

@article{WoolleyEtAl2003,
author = {Woolley, Steve and Johnson, Justin and Smith, Matthew J. and Crandall, Keith A. and McClellan, David A.},
title = {TreeSAAP: Selection on Amino Acid Properties using phylogenetic trees},
journal = {Bioinformatics},
volume = {19},
number = {5},
pages = {671-672},
year = {2003},
doi = {10.1093/bioinformatics/btg043},
URL = {http://dx.doi.org/10.1093/bioinformatics/btg043},
eprint = {/oup/backfile/content_public/journal/bioinformatics/19/5/10.1093/bioinformatics/btg043/2/btg043.pdf}
}

@article {ShahEtAl2015,
	author = {Shah, Premal and McCandlish, David M. and Plotkin, Joshua B.},
	title = {Contingency and entrenchment in protein evolution under purifying selection},
	volume = {112},
	number = {25},
	pages = {E3226--E3235},
	year = {2015},
	doi = {10.1073/pnas.1412933112},
	publisher = {National Academy of Sciences},
	abstract = {How large a role does history play in evolution? Do later events depend critically on specific earlier events, or do all events occur more or less independently? If a change occurs early in evolution, does it become easier or harder to revert the change as time proceeds? Here, we explore these ideas in the context of protein evolution, by simulating sequence evolution under purifying selection and then systematically permuting the order of amino acid substitutions. Our results suggest that the amino acid substitutions that occur in evolution are typically contingent on the presence of prior substitutions, and that substitutions that occur early in evolution become entrenched and difficult to modify as subsequent substitutions accrue.The phenotypic effect of an allele at one genetic site may depend on alleles at other sites, a phenomenon known as epistasis. Epistasis can profoundly influence the process of evolution in populations and shape the patterns of protein divergence across species. Whereas epistasis between adaptive substitutions has been studied extensively, relatively little is known about epistasis under purifying selection. Here we use computational models of thermodynamic stability in a ligand-binding protein to explore the structure of epistasis in simulations of protein sequence evolution. Even though the predicted effects on stability of random mutations are almost completely additive, the mutations that fix under purifying selection are enriched for epistasis. In particular, the mutations that fix are contingent on previous substitutions: Although nearly neutral at their time of fixation, these mutations would be deleterious in the absence of preceding substitutions. Conversely, substitutions under purifying selection are subsequently entrenched by epistasis with later substitutions: They become increasingly deleterious to revert over time. Our results imply that, even under purifying selection, protein sequence evolution is often contingent on history and so it cannot be predicted by the phenotypic effects of mutations assayed in the ancestral background.},
	issn = {0027-8424},
	URL = {http://www.pnas.org/content/112/25/E3226},
	eprint = {http://www.pnas.org/content/112/25/E3226.full.pdf},
	journal = {Proceedings of the National Academy of Sciences}
}


@article {PollockEtAl2012,
	author = {Pollock, David D. and Thiltgen, Grant and Goldstein, Richard A.},
	title = {Amino acid coevolution induces an evolutionary Stokes shift},
	volume = {109},
	number = {21},
	pages = {E1352--E1359},
	year = {2012},
	doi = {10.1073/pnas.1120084109},
	publisher = {National Academy of Sciences},
	abstract = {The process of amino acid replacement in proteins is context-dependent, with substitution rates influenced by local structure, functional role, and amino acids at other locations. Predicting how these differences affect replacement processes is difficult. To make such inference easier, it is often assumed that the acceptabilities of different amino acids at a position are constant. However, evolutionary interactions among residue positions will tend to invalidate this assumption. Here, we use simulations of purple acid phosphatase evolution to show that amino acid propensities at a position undergo predictable change after an amino acid replacement at that position. After a replacement, the new amino acid and similar amino acids tend to become gradually more acceptable over time at that position. In other words, proteins tend to equilibrate to the presence of an amino acid at a position through replacements at other positions. Such a shift is reminiscent of the spectroscopy effect known as the Stokes shift, where molecules receiving a quantum of energy and moving to a higher electronic state will adjust to the new state and emit a smaller quantum of energy whenever they shift back down to the original ground state. Predictions of changes in stability in real proteins show that mutation reversals become less favorable over time, and thus, broadly support our results. The observation of an evolutionary Stokes shift has profound implications for the study of protein evolution and the modeling of evolutionary processes.},
	issn = {0027-8424},
	URL = {http://www.pnas.org/content/109/21/E1352},
	eprint = {http://www.pnas.org/content/109/21/E1352.full.pdf},
	journal = {Proceedings of the National Academy of Sciences}
}


@article{ThieleEtAl2012,
    author = {Thiele, Ines AND Fleming, Ronan M. T. AND Que, Richard AND Bordbar, Aarash AND Diep, Dinh AND Palsson, Bernhard O.},
    journal = {PLOS ONE},
    publisher = {Public Library of Science},
    title = {Multiscale modeling of metabolism and macromolecular synthesis in E. coli and its application to the evolution of codon usage},
    year = {2012},
    month = {09},
    volume = {7},
    url = {https://doi.org/10.1371/journal.pone.0045635},
    pages = {1-18},
    abstract = {Biological systems are inherently hierarchal and multiscale in time and space. A major challenge of systems biology is to describe biological systems as a computational model, which can be used to derive novel hypothesis and drive experiments leading to new knowledge. The constraint-based reconstruction and analysis approach has been successfully applied to metabolism and to the macromolecular synthesis machinery assembly. Here, we present the first integrated stoichiometric multiscale model of metabolism and macromolecular synthesis for Escherichia coli K12 MG1655, which describes the sequence-specific synthesis and function of almost 2000 gene products at molecular detail. We added linear constraints, which couple enzyme synthesis and catalysis reactions. Comparison with experimental data showed improvement of growth phenotype prediction with the multiscale model over E. coli’s metabolic model alone. Many of the genes covered by this integrated model are well conserved across enterobacters and other, less related bacteria. We addressed the question of whether the bias in synonymous codon usage could affect the growth phenotype and environmental niches that an organism can occupy. We created two classes of in silico strains, one with more biased codon usage and one with more equilibrated codon usage than the wildtype. The reduced growth phenotype in biased strains was caused by tRNA supply shortage, indicating that expansion of tRNA gene content or tRNA codon recognition allow E. coli to respond to changes in codon usage bias. Our analysis suggests that in order to maximize growth and to adapt to new environmental niches, codon usage and tRNA content must co-evolve. These results provide further evidence for the mutation-selection-drift balance theory of codon usage bias. This integrated multiscale reconstruction successfully demonstrates that the constraint-based modeling approach is well suited to whole-cell modeling endeavors.},
    number = {9},
    doi = {10.1371/journal.pone.0045635}
}

@Article{LermanEtAl2012,
author="Lerman, Joshua A.
and Hyduke, Daniel R.
and Latif, Haythem
and Portnoy, Vasiliy A.
and Lewis, Nathan E.
and Orth, Jeffrey D.
and Schrimpe-Rutledge, Alexandra C.
and Smith, Richard D.
and Adkins, Joshua N.
and Zengler, Karsten
and Palsson, Bernhard O.",
title="In silico method for modelling metabolism and gene product expression at genome scale",
journal="Nature Communications",
year="2012",
month="Jul",
day="03",
publisher="The Author(s) SN  -",
volume="3",
pages="929 EP  -",
note="Article",
url="http://dx.doi.org/10.1038/ncomms1928"
}



@article{KingEtAl2015,
title = "Next-generation genome-scale models for metabolic engineering",
journal = "Current Opinion in Biotechnology",
volume = "35",
pages = "23 - 29",
year = "2015",
issn = "0958-1669",
doi = "https://doi.org/10.1016/j.copbio.2014.12.016",
url = "http://www.sciencedirect.com/science/article/pii/S0958166914002316",
author = "Zachary A King and Colton J Lloyd and Adam M Feist and Bernhard O Palsson"
}

@article{SullivanJoyce2005,
author = {Jack Sullivan and Paul Joyce},
title = {Model selection in phylogenetics},
journal = {Annual Review of Ecology, Evolution, and Systematics},
volume = {36},
number = {1},
pages = {445-466},
year = {2005},
doi = {10.1146/annurev.ecolsys.36.102003.152633},

URL = {
        https://doi.org/10.1146/annurev.ecolsys.36.102003.152633

},
eprint = {
        https://doi.org/10.1146/annurev.ecolsys.36.102003.152633

}
,
    abstract = { ‚ñ™ Abstract‚ÄÇInvestigation into model selection has a long history in the statistical literature. As model-based approaches begin dominating systematic biology, increased attention has focused on how models should be selected for distance-based, likelihood, and Bayesian phylogenetics. Here, we review issues that render model-based approaches necessary, briefly review nucleotide-based models that attempt to capture relevant features of evolutionary processes, and review methods that have been applied to model selection in phylogenetics: likelihood-ratio tests, AIC, BIC, and performance-based approaches. }
}


@article{posadaBuckley2004,
 ISSN = {10635157, 1076836X},
 URL = {http://www.jstor.org/stable/4135365},
 abstract = {Model selection is a topic of special relevance in molecular phylogenetics that affects many, if not all, stages of phylogenetic inference. Here we discuss some fundamental concepts and techniques of model selection in the context of phylogenetics. We start by reviewing different aspects of the selection of substitution models in phylogenetics from a theoretical, philosophical and practical point of view, and summarize this comparison in table format. We argue that the most commonly implemented model selection approach, the hierarchical likelihood ratio test, is not the optimal strategy for model selection in phylogenetics, and that approaches like the Akaike Information Criterion (AIC) and Bayesian methods offer important advantages. In particular, the latter two methods are able to simultaneously compare multiple nested or nonnested models, assess model selection uncertainty, and allow for the estimation of phylogenies and model parameters using all available models (model-averaged inference or multimodel inference). We also describe how the relative importance of the different parameters included in substitution models can be depicted. To illustrate some of these points, we have applied AIC-based model averaging to 37 mitochondrial DNA sequences from the subgenus Ohomopterus (genus Carabus) ground beetles described by Sota and Vogler (2001).},
 author = {David Posada and Thomas R. Buckley},
 journal = {Systematic Biology},
 number = {5},
 pages = {793--808},
 publisher = {[Oxford University Press, Society of Systematic Biologists]},
 title = {Model selection and model averaging in phylogenetics: advantages of Akaike Information Criterion and Bayesian approaches over likelihood ratio tests},
 volume = {53},
 year = {2004}
}



@article{revbayes,
author = {Hoehna, 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: Bayesian phylogenetic inference using graphical models and an interactive model-specification language},
journal = {Systematic Biology},
volume = {65},
number = {4},
pages = {726},
year = {2016},
doi = {10.1093/sysbio/syw021},
URL = { + http://dx.doi.org/10.1093/sysbio/syw021},
eprint = {/oup/backfile/Content_public/Journal/sysbio/65/4/10.1093_sysbio_syw021/3/syw021.pdf}
}

@article{goldman1993statistical,
  title={Statistical tests of models of DNA substitution},
  author={Goldman, Nick},
  journal={Journal of molecular evolution},
  volume={36},
  number={2},
  pages={182--198},
  year={1993},
  publisher={Springer}
}


@article{ButlerKing2004,
  title={Phylogenetic comparative analysis: a modeling approach for adaptive evolution},
  author={Butler, Marguerite A. and King, Aaron A.},
  journal={American Naturalist},
  volume={164},
  number={6},
  pages={683-695},
  year={2004},
  publisher={University of Chicago}
}


@article{OMearaetal2006,
  title={Testing for different rates of continuous trait evolution using likelihood},
  author={O'Meara, Brian C. and Ane, Cecile and Sanderson, Michael J and Wainwright P.C.},
  journal={Evolution},
  volume={60},
  number={5},
  pages={922-933},
  year={2006},
  publisher={Wiley}
}


@article{HurvichTsai1989,
  title={Regression and time series model selection in small samples},
  author={Hurvich, Clifford M. and Tsai, Chih-Ling},
  journal={Biometrika},
  volume={76},
  number={2},
  pages={297-307},
  year={1989},
  publisher={Oxford University Press}
}


@article{Jhwuengetal2014,
  title={Investigating the performance of AIC in selecting phylogenetic models},
  author={Jhwueng, Dwueng-Chwuan and Hurzurbazar Snehalata and O'Meara, Brian C. and Liu, Liang},
  journal={Statistical applications in genetics and moleculr biology},
  volume={13},
  number={4},
  pages={459-475},
  year={2014}
}


@article{IngramMahler2013,
  title={SURFACE: detecting convergent evolution from data by fitting Ornstein-Uhlenbeck models with stepwise Akaike Information Criterion},
  author={Ingram, Travis and Mahler, D. Luke},
  journal={Methods in ecology and evolution},
  volume={4},
  number={5},
  pages={416-425},
  year={2013}
}