text:
@article{Barrow201478,
	Abstract = {Abstract The field of phylogenetics is changing rapidly with the application of high-throughput sequencing to non-model organisms. Cost-effective use of this technology for phylogenetic studies, which often include a relatively small portion of the genome but several taxa, requires strategies for genome partitioning and sequencing multiple individuals in parallel. In this study we estimated a multilocus phylogeny for the North American chorus frog genus Pseudacris using anonymous nuclear loci that were recently developed using a reduced representation library approach. We sequenced 27 nuclear loci and three mitochondrial loci for 44 individuals on 1/3 of an Illumina MiSeq run, obtaining 96.5% of the targeted amplicons at less than 20% of the cost of traditional Sanger sequencing. We found heterogeneity among gene trees, although four major clades (Trilling Frog, Fat Frog, crucifer, and West Coast) were consistently supported, and we resolved the relationships among these clades for the first time with strong support. We also found discordance between the mitochondrial and nuclear datasets that we attribute to mitochondrial introgression and a possible selective sweep. Bayesian concordance analysis in \{BUCKy\} and species tree analysis in *BEAST produced largely similar topologies, although we identify taxa that require additional investigation in order to clarify taxonomic and geographic range boundaries. Overall, we demonstrate the utility of a reduced representation library approach for marker development and parallel tagged sequencing on an Illumina MiSeq for phylogenetic studies of non-model organisms. },
	Author = {Lisa N. Barrow and Hannah F. Ralicki and Sandra A. Emme and Emily Moriarty Lemmon},
	Doi = {http://dx.doi.org/10.1016/j.ympev.2014.02.007},
	Issn = {1055-7903},
	Journal = {Molecular Phylogenetics and Evolution},
	Keywords = {Pseudacris},
	Pages = {78--90},
	Title = {Species tree estimation of {North American} chorus frogs ({Hylidae}: \textit{Pseudacris}) with parallel tagged amplicon sequencing},
	Url = {http://www.sciencedirect.com/science/article/pii/S105579031400058X},
	Volume = {75},
	Year = {2014},
	Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/pii/S105579031400058X},
	Bdsk-Url-2 = {http://dx.doi.org/10.1016/j.ympev.2014.02.007}}

@article{Ogilvie01052016,
	Abstract = {Under the multispecies coalescent model of molecular evolution, gene trees have independent evolutionary histories within a shared species tree. In comparison, supermatrix concatenation methods assume that gene trees share a single common genealogical history, thereby equating gene coalescence with species divergence. The multispecies coalescent is supported by previous studies which found that its predicted distributions fit empirical data, and that concatenation is not a consistent estimator of the species tree. *BEAST, a fully Bayesian implementation of the multispecies coalescent, is popular but computationally intensive, so the increasing size of phylogenetic data sets is both a computational challenge and an opportunity for better systematics. Using simulation studies, we characterize the scaling behavior of *BEAST, and enable quantitative prediction of the impact increasing the number of loci has on both computational performance and statistical accuracy. Follow-up simulations over a wide range of parameters show that the statistical performance of *BEAST relative to concatenation improves both as branch length is reduced and as the number of loci is increased. Finally, using simulations based on estimated parameters from two phylogenomic data sets, we compare the performance of a range of species tree and concatenation methods to show that using *BEAST with tens of loci can be preferable to using concatenation with thousands of loci. Our results provide insight into the practicalities of Bayesian species tree estimation, the number of loci required to obtain a given level of accuracy and the situations in which supermatrix or summary methods will be outperformed by the fully Bayesian multispecies coalescent.},
	Author = {Ogilvie, Huw A. and Heled, Joseph and Xie, Dong and Drummond, Alexei J.},
	Doi = {10.1093/sysbio/syv118},
	Eprint = {http://sysbio.oxfordjournals.org/content/65/3/381.full.pdf+html},
	Journal = {Systematic Biology},
	Number = {3},
	Pages = {381--396},
	Title = {Computational Performance and Statistical Accuracy of {*BEAST} and Comparisons with Other Methods},
	Url = {http://sysbio.oxfordjournals.org/content/65/3/381.abstract},
	Volume = {65},
	Year = {2016},
	Bdsk-Url-1 = {http://sysbio.oxfordjournals.org/content/65/3/381.abstract},
	Bdsk-Url-2 = {http://dx.doi.org/10.1093/sysbio/syv118}}

@article{Mendes01072016,
	Abstract = {Substitution rates are known to be variable among genes, chromosomes, species, and lineages due to multifarious biological processes. Here, we consider another source of substitution rate variation due to a technical bias associated with gene tree discordance. Discordance has been found to be rampant in genome-wide data sets, often due to incomplete lineage sorting (ILS). This apparent substitution rate variation is caused when substitutions that occur on discordant gene trees are analyzed in the context of a single, fixed species tree. Such substitutions have to be resolved by proposing multiple substitutions on the species tree, and we therefore refer to this phenomenon as Substitutions Produced by ILS (SPILS). We use simulations to demonstrate that SPILS has a larger effect with increasing levels of ILS, and on trees with larger numbers of taxa. Specific branches of the species trees are consistently, but erroneously, inferred to be longer or shorter, and we show that these branches can be predicted based on discordant tree topologies. Moreover, we observe that fixing a species tree topology when performing tests of positive selection increases the false positive rate, particularly for genes whose discordant topologies are most affected by SPILS. Finally, we use data from multiple Drosophila species to show that SPILS can be detected in nature. Although the effects of SPILS are modest per gene, it has the potential to affect substitution rate variation whenever high levels of ILS are present, particularly in rapid radiations. The problems outlined here have implications for character mapping of any type of trait, and for any biological process that causes discordance. We discuss possible solutions to these problems, and areas in which they are likely to have caused faulty inferences of convergence and accelerated evolution.},
	Author = {Mendes, F\'abio K. and Hahn, Matthew W.},
	Doi = {10.1093/sysbio/syw018},
	Eprint = {http://sysbio.oxfordjournals.org/content/65/4/711.full.pdf+html},
	Journal = {Systematic Biology},
	Number = {4},
	Pages = {711--721},
	Title = {Gene Tree Discordance Causes Apparent Substitution Rate Variation},
	Url = {http://sysbio.oxfordjournals.org/content/65/4/711.abstract},
	Volume = {65},
	Year = {2016},
	Bdsk-Url-1 = {http://sysbio.oxfordjournals.org/content/65/4/711.abstract},
	Bdsk-Url-2 = {http://dx.doi.org/10.1093/sysbio/syw018}}

@article{10.1371/journal.pcbi.1003537,
	Abstract = {
We present a new open source, extensible and flexible software platform for Bayesian evolutionary analysis called BEAST 2. This software platform is a re-design of the popular BEAST 1 platform to correct structural deficiencies that became evident as the BEAST 1 software evolved. Key among those deficiencies was the lack of post-deployment extensibility. BEAST 2 now has a fully developed package management system that allows third party developers to write additional functionality that can be directly installed to the BEAST 2 analysis platform via a package manager without requiring a new software release of the platform. This package architecture is showcased with a number of recently published new models encompassing birth-death-sampling tree priors, phylodynamics and model averaging for substitution models and site partitioning. A second major improvement is the ability to read/write the entire state of the MCMC chain to/from disk allowing it to be easily shared between multiple instances of the BEAST software. This facilitates checkpointing and better support for multi-processor and high-end computing extensions. Finally, the functionality in new packages can be easily added to the user interface (BEAUti 2) by a simple XML template-based mechanism because BEAST 2 has been re-designed to provide greater integration between the analysis engine and the user interface so that, for example BEAST and BEAUti use exactly the same XML file format.
},
	Author = {Bouckaert, Remco AND Heled, Joseph AND K\"uhnert, Denise AND Vaughan, Tim AND Wu, Chieh-Hsi AND Xie, Dong AND Suchard, Marc A. AND Rambaut, Andrew AND Drummond, Alexei J.},
	Doi = {10.1371/journal.pcbi.1003537},
	Journal = {PLoS Computational Biology},
	Month = {04},
	Number = {4},
	Pages = {e1003537},
	Publisher = {Public Library of Science},
	Title = {{BEAST} 2: A Software Platform for {Bayesian} Evolutionary Analysis},
	Url = {http://dx.doi.org/10.1371%2Fjournal.pcbi.1003537},
	Volume = {10},
	Year = {2014},
	Bdsk-Url-1 = {http://dx.doi.org/10.1371%2Fjournal.pcbi.1003537},
	Bdsk-Url-2 = {http://dx.doi.org/10.1371/journal.pcbi.1003537}}

@article{Yang01122014,
	Abstract = {A method was developed for simultaneous Bayesian inference of species delimitation and species phylogeny using the multispecies coalescent model. The method eliminates the need for a user-specified guide tree in species delimitation and incorporates phylogenetic uncertainty in a Bayesian framework. The nearest-neighbor interchange algorithm was adapted to propose changes to the species tree, with the gene trees for multiple loci altered in the proposal to avoid conflicts with the newly proposed species tree. We also modify our previous scheme for specifying priors for species delimitation models to construct joint priors for models of species delimitation and species phylogeny. As in our earlier method, the modified algorithm integrates over gene trees, taking account of the uncertainty of gene tree topology and branch lengths given the sequence data. We conducted a simulation study to examine the statistical properties of the method using six populations (two sequences each) and a true number of three species, with values of divergence times and ancestral population sizes that are realistic for recently diverged species. The results suggest that the method tends to be conservative with high posterior probabilities being a confident indicator of species status. Simulation results also indicate that the power of the method to delimit species increases with an increase of the divergence times in the species tree, and with an increased number of gene loci. Reanalyses of two data sets of cavefish and coast horned lizards suggest considerable phylogenetic uncertainty even though the data are informative about species delimitation. We discuss the impact of the prior on models of species delimitation and species phylogeny and of the prior on population size parameters (θ) on Bayesian species delimitation.},
	Author = {Yang, Ziheng and Rannala, Bruce},
	Doi = {10.1093/molbev/msu279},
	Eprint = {http://mbe.oxfordjournals.org/content/31/12/3125.full.pdf+html},
	Journal = {Molecular Biology and Evolution},
	Number = {12},
	Pages = {3125--3135},
	Title = {Unguided Species Delimitation Using {DNA} Sequence Data from Multiple Loci},
	Url = {http://mbe.oxfordjournals.org/content/31/12/3125.abstract},
	Volume = {31},
	Year = {2014},
	Bdsk-Url-1 = {http://mbe.oxfordjournals.org/content/31/12/3125.abstract},
	Bdsk-Url-2 = {http://dx.doi.org/10.1093/molbev/msu279}}

@article{rannala2017efficient,
	title={Efficient {Bayesian} species tree inference under the multispecies coalescent},
	author={Rannala, Bruce and Yang, Ziheng},
	journal={Systematic Biology},
	note={Advance Access},
	year={2017},
	publisher={Oxford University Press}
}

@Article{Jones2017,
author="Jones, Graham",
title="Algorithmic improvements to species delimitation and phylogeny estimation under the multispecies coalescent",
journal="Journal of Mathematical Biology",
year="2017",
volume="74",
number="1",
pages="447--467",
abstract="The focus of this article is a Bayesian method for inferring both species delimitations and species trees under the multispecies coalescent model using molecular sequences from multiple loci. The species delimitation requires no a priori assignment of individuals to species, and no guide tree. The method is implemented in a package called STACEY for BEAST2, and is a extension of the author's DISSECT package. Here we demonstrate considerable efficiency improvements by using three new operators for sampling from the posterior using the Markov chain Monte Carlo algorithm, and by using a model for the population size parameters along the branches of the species tree which allows these parameters to be integrated out. The correctness of the moves is demonstrated by tests of the implementation. The practice of using a pipeline approach to species delimitation under the multispecies coalescent, has been shown to have major problems on simulated data (Olave et al. in Syst Biol 63:263--271. doi:                  10.1093/sysbio/syt106                                  , 2014). The same simulated data set is used to demonstrate the accuracy and improved convergence of the present method. We also compare performance with *BEAST for a fixed delimitation analysis on a large data set, and again show improved convergence.",
issn="1432-1416",
doi="10.1007/s00285-016-1034-0",
url="http://dx.doi.org/10.1007/s00285-016-1034-0"
}

@article{Andrieu2008,
	Abstract = {We review adaptive Markov chain Monte Carlo algorithms (MCMC) as a mean to optimise their performance. Using simple toy examples we review their theoretical underpinnings, and in particular show why adaptive MCMC algorithms might fail when some fundamental properties are not satisfied. This leads to guidelines concerning the design of correct algorithms. We then review criteria and the useful framework of stochastic approximation, which allows one to systematically optimise generally used criteria, but also analyse the properties of adaptive MCMC algorithms. We then propose a series of novel adaptive algorithms which prove to be robust and reliable in practice. These algorithms are applied to artificial and high dimensional scenarios, but also to the classic mine disaster dataset inference problem.},
	Author = {Andrieu, Christophe and Thoms, Johannes},
	Doi = {10.1007/s11222-008-9110-y},
	Issn = {1573-1375},
	Journal = {Statistics and Computing},
	Number = {4},
	Pages = {343--373},
	Title = {A tutorial on adaptive {MCMC}},
	Url = {http://dx.doi.org/10.1007/s11222-008-9110-y},
	Volume = {18},
	Year = {2008},
	Bdsk-Url-1 = {http://dx.doi.org/10.1007/s11222-008-9110-y}}

@article{EVO:EVO414,
	Abstract = {Several techniques, such as concatenation and consensus methods, are available for combining data from multiple loci to produce a single statement of phylogenetic relationships. However, when multiple alleles are sampled from individual species, it becomes more challenging to estimate relationships at the level of species, either because concatenation becomes inappropriate due to conflicts among individual gene trees, or because the species from which multiple alleles have been sampled may not form monophyletic groups in the estimated tree. We propose a Bayesian hierarchical model to reconstruct species trees from multiple-allele, multilocus sequence data, building on a recently proposed method for estimating species trees from single allele multilocus data. A two-step Markov Chain Monte Carlo (MCMC) algorithm is adopted to estimate the posterior distribution of the species tree. The model is applied to estimate the posterior distribution of species trees for two multiple-allele datasets---yeast (Saccharomyces) and birds (Manacus---manakins). The estimates of the species trees using our method are consistent with those inferred from other methods and genetic markers, but in contrast to other species tree methods, it provides credible regions for the species tree. The Bayesian approach described here provides a powerful framework for statistical testing and integration of population genetics and phylogenetics.},
	Author = {Liu, Liang and Pearl, Dennis K. and Brumfield, Robb T. and Edwards, Scott V.},
	Doi = {10.1111/j.1558-5646.2008.00414.x},
	Issn = {1558-5646},
	Journal = {Evolution},
	Keywords = {Bayesian hierarchical model, coalescent theory, gene tree, species tree},
	Number = {8},
	Pages = {2080--2091},
	Publisher = {Blackwell Publishing Inc},
	Title = {ESTIMATING SPECIES TREES USING MULTIPLE-ALLELE {DNA} SEQUENCE DATA},
	Url = {http://dx.doi.org/10.1111/j.1558-5646.2008.00414.x},
	Volume = {62},
	Year = {2008},
	Bdsk-Url-1 = {http://dx.doi.org/10.1111/j.1558-5646.2008.00414.x}}

@article{Yang1994,
	Abstract = {Two approximate methods are proposed for maximum likelihood phylogenetic estimation, which allow variable rates of substitution across nucleotide sites. Three data sets with quite different characteristics were analyzed to examine empirically the performance of these methods. The first, called the ``discrete gamma model,'' uses several categories of rates to approximate the gamma distribution, with equal probability for each category. The mean of each category is used to represent all the rates falling in the category. The performance of this method is found to be quite good, and four such categories appear to be sufficient to produce both an optimum, or near-optimum fit by the model to the data, and also an acceptable approximation to the continuous distribution. The second method, called ``fixed-rates model,'' classifies sites into several classes according to their rates predicted assuming the star tree. Sites in different classes are then assumed to be evolving at these fixed rates when other tree topologies are evaluated. Analyses of the data sets suggest that this method can produce reasonable results, but it seems to share some properties of a least-squares pairwise comparison; for example, interior branch lengths in nonbest trees are often found to be zero. The computational requirements of the two methods are comparable to that of Felsenstein's (1981, J Mol Evol 17:368--376) model, which assumes a single rate for all the sites.},
	Author = {Yang, Ziheng},
	Doi = {10.1007/BF00160154},
	Issn = {1432-1432},
	Journal = {Journal of Molecular Evolution},
	Number = {3},
	Pages = {306--314},
	Title = {Maximum likelihood phylogenetic estimation from {DNA} sequences with variable rates over sites: Approximate methods},
	Url = {http://dx.doi.org/10.1007/BF00160154},
	Volume = {39},
	Year = {1994},
	Bdsk-Url-1 = {http://dx.doi.org/10.1007/BF00160154}}

@article{Berv2014120,
	Abstract = {Abstract The Neotropical cotingas (Cotingidae: Aves) are a group of passerine birds that are characterized by extreme diversity in morphology, ecology, breeding system, and behavior. Here, we present a comprehensive phylogeny of the Neotropical cotingas based on six nuclear and mitochondrial loci (∼7500 bp) for a sample of 61 cotinga species in all 25 genera, and 22 species of suboscine outgroups. Our taxon sample more than doubles the number of cotinga species studied in previous analyses, and allows us to test the monophyly of the cotingas as well as their intrageneric relationships with high resolution. We analyze our genetic data using a Bayesian species tree method, and concatenated Bayesian and maximum likelihood methods, and present a highly supported phylogenetic hypothesis. We confirm the monophyly of the cotingas, and present the first phylogenetic evidence for the relationships of Phibalura flavirostris as the sister group to Ampelion and Doliornis, and the paraphyly of Lipaugus with respect to Tijuca. In addition, we resolve the diverse radiations within the Cotinga, Lipaugus, Pipreola, and Procnias genera. We find no support for Darwin's (1871) hypothesis that the increase in sexual selection associated with polygynous breeding systems drives the evolution of color dimorphism in the cotingas, at least when analyzed at a broad categorical scale. Finally, we present a new comprehensive phylogenetic classification of all cotinga species. },
	Author = {Jacob S. Berv and Richard O. Prum},
	Doi = {http://dx.doi.org/10.1016/j.ympev.2014.09.001},
	Issn = {1055-7903},
	Journal = {Molecular Phylogenetics and Evolution},
	Keywords = {Monogamy},
	Pages = {120--136},
	Title = {A comprehensive multilocus phylogeny of the {Neotropical} cotingas ({Cotingidae, Aves}) with a comparative evolutionary analysis of breeding system and plumage dimorphism and a revised phylogenetic classification},
	Url = {http://www.sciencedirect.com/science/article/pii/S1055790314003133},
	Volume = {81},
	Year = {2014},
	Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/pii/S1055790314003133},
	Bdsk-Url-2 = {http://dx.doi.org/10.1016/j.ympev.2014.09.001}}

@article{Lambert2015146,
	Abstract = {Abstract Simulation studies suggest that coalescent-based species-tree methods are generally more accurate than concatenated analyses. However, these species-tree methods remain impractical for many large datasets. Thus, a critical but unresolved issue is when and why concatenated and coalescent species-tree estimates will differ. We predict such differences for branches in concatenated trees that are short, weakly supported, and have conflicting gene trees. We test these predictions in Scincidae, the largest lizard family, with data from 10 nuclear genes for 17 ingroup taxa and 44 genes for 12 taxa. We support our initial predictions, and suggest that simply considering uncertainty in concatenated trees may sometimes encompass the differences between these methods. We also found that relaxed-clock concatenated trees can be surprisingly similar to the species-tree estimate. Remarkably, the coalescent species-tree estimates had slightly lower support values when based on many more genes (44 vs. 10) and a small (∼30%) reduction in taxon sampling. Thus, taxon sampling may be more important than gene sampling when applying species-tree methods to deep phylogenetic questions. Finally, our coalescent species-tree estimates tentatively support division of Scincidae into three monophyletic subfamilies, a result otherwise found only in concatenated analyses with extensive species sampling. },
	Author = {Shea M. Lambert and Tod W. Reeder and John J. Wiens},
	Doi = {http://dx.doi.org/10.1016/j.ympev.2014.10.004},
	Issn = {1055-7903},
	Journal = {Molecular Phylogenetics and Evolution},
	Keywords = {Taxon sampling},
	Pages = {146--155},
	Title = {When do species-tree and concatenated estimates disagree? {An} empirical analysis with higher-level scincid lizard phylogeny},
	Url = {http://www.sciencedirect.com/science/article/pii/S1055790314003558},
	Volume = {82, Part A},
	Year = {2015},
	Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/pii/S1055790314003558},
	Bdsk-Url-2 = {http://dx.doi.org/10.1016/j.ympev.2014.10.004}}

@article{doi:10.1146/annurev.es.18.110187.001413,
	Author = {C Moritz and T E Dowling and W M Brown},
	Doi = {10.1146/annurev.es.18.110187.001413},
	Eprint = {http://dx.doi.org/10.1146/annurev.es.18.110187.001413},
	Journal = {Annual Review of Ecology and Systematics},
	Pages = {269--292},
	Title = {Evolution of Animal Mitochondrial {DNA}: Relevance for Population Biology and Systematics},
	Url = {http://dx.doi.org/10.1146/annurev.es.18.110187.001413},
	Volume = {18},
	Year = {1987},
	Bdsk-Url-1 = {http://dx.doi.org/10.1146/annurev.es.18.110187.001413}}

@article{10.1371/journal.pbio.0040088,
	Abstract = {This new method can simultaneously infer phylogeny and estimate the molecular clock. The authors run their method on several large alignments to show its phylogenetic accuracy and ability to infer a timescale to evolution.},
	Author = {Drummond, Alexei J AND Ho, Simon Y. W AND Phillips, Matthew J AND Rambaut, Andrew},
	Doi = {10.1371/journal.pbio.0040088},
	Journal = {PLoS Biology},
	Month = {03},
	Number = {5},
	Pages = {e88},
	Publisher = {Public Library of Science},
	Title = {Relaxed Phylogenetics and Dating with Confidence},
	Url = {http://dx.doi.org/10.1371%2Fjournal.pbio.0040088},
	Volume = {4},
	Year = {2006},
	Bdsk-Url-1 = {http://dx.doi.org/10.1371%2Fjournal.pbio.0040088},
	Bdsk-Url-2 = {http://dx.doi.org/10.1371/journal.pbio.0040088}}

@article{dryad_23rc0,
	Author = {Lisa N. Barrow and Hannah F. Ralicki and Sandra A. Emme and Emily Moriarty Lemmon},
	Doi = {doi:10.5061/dryad.23rc0},
	Journal = {Dryad Digital Repository},
	Publisher = {Dryad Digital Repository},
	Title = {Data from: Species tree estimation of {North American} chorus frogs ({Hylidae: Pseudacris}) with parallel tagged amplicon sequencing},
	Url = {http://dx.doi.org/10.5061/dryad.23rc0},
	Year = {2014},
	Bdsk-Url-1 = {http://dx.doi.org/10.5061/dryad.23rc0}}

@article{Hasegawa1985,
	Abstract = {A new statistical method for estimating divergence dates of species from DNA sequence data by a molecular clock approach is developed. This method takes into account effectively the information contained in a set of DNA sequence data. The molecular clock of mitochondrial DNA (mtDNA) was calibrated by setting the date of divergence between primates and ungulates at the Cretaceous-Tertiary boundary (65 million years ago), when the extinction of dinosaurs occurred. A generalized leastsquares method was applied in fitting a model to mtDNA sequence data, and the clock gave dates of 92.3{\textpm}11.7, 13.3{\textpm}1.5, 10.9{\textpm}1.2, 3.7{\textpm}0.6, and 2.7{\textpm}0.6 million years ago (where the second of each pair of numbers is the standard deviation) for the separation of mouse, gibbon, orangutan, gorilla, and chimpanzee, respectively, from the line leading to humans. Although there is some uncertainty in the clock, this dating may pose a problem for the widely believed hypothesis that the bipedal creatureAustralopithecus afarensis, which lived some 3.7 million years ago at Laetoli in Tanzania and at Hadar in Ethiopia, was ancestral to man and evolved after the human-ape splitting. Another likelier possibility is that mtDNA was transferred through hybridization between a proto-human and a protochimpanzee after the former had developed bipedalism.},
	Author = {Hasegawa, Masami and Kishino, Hirohisa and Yano, Takaaki},
	Doi = {10.1007/BF02101694},
	Issn = {1432-1432},
	Journal = {Journal of Molecular Evolution},
	Number = {2},
	Pages = {160--174},
	Title = {Dating of the human-ape splitting by a molecular clock of mitochondrial {DNA}},
	Url = {http://dx.doi.org/10.1007/BF02101694},
	Volume = {22},
	Year = {1985},
	Bdsk-Url-1 = {http://dx.doi.org/10.1007/BF02101694}}

@article{Goldman1993,
	Abstract = {Penny et al. have written that ``The most fundamental criterion for a scientific method is that the data must, in principle, be able to reject the model. Hardly any [phylogenetic] tree-reconstruction methods meet this simple requirement.'' The ability to reject models is of such great importance because the results of all phylogenetic analyses depend on their underlying models---to have confidence in the inferences, it is necessary to have confidence in the models. In this paper, a test statistics suggested by Cox is employed to test the adequacy of some statistical models of DNA sequence evolution used in the phylogenetic inference method introduced by Felsentein. Monte Carlo simulations are used to assess significance levels. The resulting statistical tests provide an objective and very general assessment of all the components of a DNA substitution model; more specific versions of the test are devised to test individual components of a model. In all cases, the new analyses have the additional advantage that values of phylogenetic parameters do not have to be assumed in order to perform the tests.},
	Author = {Goldman, Nick},
	Doi = {10.1007/BF00166252},
	Issn = {1432-1432},
	Journal = {Journal of Molecular Evolution},
	Number = {2},
	Pages = {182--198},
	Title = {Statistical tests of models of {DNA} substitution},
	Url = {http://dx.doi.org/10.1007/BF00166252},
	Volume = {36},
	Year = {1993},
	Bdsk-Url-1 = {http://dx.doi.org/10.1007/BF00166252}}

@misc{biopy,
	Author = {Heled, Joseph},
	Howpublished = {\url{https://figshare.com/articles/biopy_a_Library_for_Phylogenetic_Exploration/761224}},
	Note = {Last accessed July 17, 2016},
	Title = {biopy --- a Library for Phylogenetic Exploration},
	Year = {unpublished data}}

@article{Gernhard2008769,
	Abstract = {We investigate a neutral model for speciation and extinction, the constant rate birth--death process. The process is conditioned to have n extant species today, we look at the tree distribution of the reconstructed trees--i.e. the trees without the extinct species. Whereas the tree shape distribution is well-known and actually the same as under the pure birth process, no analytic results for the speciation times were known. We provide the distribution for the speciation times and calculate the expectations analytically. This characterizes the reconstructed trees completely. We will show how the results can be used to date phylogenies.},
	Author = {Tanja Gernhard},
	Doi = {http://dx.doi.org/10.1016/j.jtbi.2008.04.005},
	Issn = {0022-5193},
	Journal = {Journal of Theoretical Biology},
	Keywords = {Reconstructed process},
	Number = {4},
	Pages = {769--778},
	Title = {The conditioned reconstructed process},
	Url = {http://www.sciencedirect.com/science/article/pii/S0022519308001811},
	Volume = {253},
	Year = {2008},
	Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/pii/S0022519308001811},
	Bdsk-Url-2 = {http://dx.doi.org/10.1016/j.jtbi.2008.04.005}}

@article{10.2307/1446044,
	Abstract = {The demography and life history of two populations of two species of chorus frogs (Pseudacris ornata and P. nigrita) were studied for 4 yr on the Savannah River Plant near Aiken, South Carolina. Sexual maturity in both species is reached within the first year of life, and the population turnover is nearly annual. The sex ratio of adults that entered the breeding ponds each year at each locality was 1:1. The operational sex ratio was skewed toward males during the first breeding peak in P. ornata, but was 1:1 in P. nigrita. All females that entered the ponds for the first time were gravid, but the percentage of females depositing eggs within a season and within localities was variable. In general, when the number of adults breeding in one year was low, survival of these adults to the next breeding season was high, suggesting that there may be a cost to reproduction in terms of survival. Juvenile recruitment was highest in the wettest year of the study. Recruitment of P. nigrita was never as high as that of P. ornata. One of the study sites had an artificially lowered water level, and juvenile recruitment of P. ornata was low during all years at this site compared to the other pond. These species best fit a bet-hedging model of life history tactics. The breeding habitat is unpredictable in time and space. Juvenile mortality is predictably high, but where and when it occurs is random. Selection apparently has favored juvenile dispersal as an alternative to longevity and iteroparity of individual females.},
	Author = {Janalee P. Caldwell},
	Issn = {00458511, 19385110},
	Journal = {Copeia},
	Number = {1},
	Pages = {114--127},
	Publisher = {[American Society of Ichthyologists and Herpetologists (ASIH), Allen Press]},
	Title = {Demography and Life History of Two Species of Chorus Frogs ({Anura: Hylidae}) in {South Carolina}},
	Url = {http://www.jstor.org/stable/1446044},
	Volume = {1987},
	Year = {1987},
	Bdsk-Url-1 = {http://www.jstor.org/stable/1446044}}

@article{Rambaut01061997,
	Abstract = {Motivation: Seq-Gen is a program that will simulate the evolution of nucleotide sequences along a phylogeny, using common models of the substitution process. A range of models of molecular evolution are implemented, including the general reversible model. Nucleotide frequencies and other parameters of the model may be given and site-specific rate heterogeneity can also be incorporated in a number of ways. Any number of trees may be read in and the program will produce any number of data sets for each tree. Thus, large sets of replicate simulations can be easily created. This can be used to test phylogenetic hypotheses using the parametric bootstrap.Availability: Seq-Gen can be obtained by WWW from http://evolve.zoo.ox.ac.uk/Seq-Gen/seq-gen.html or by FTP from ftp://evolve.zoo.ox.ac.uk/packages/Seq-Gen/. The package includes the source code, manual and example files. An Apple Macintosh version is available from the same sites.},
	Author = {Rambaut, Andrew and Grassly, Nicholas C.},
	Doi = {10.1093/bioinformatics/13.3.235},
	Eprint = {http://bioinformatics.oxfordjournals.org/content/13/3/235.full.pdf+html},
	Journal = {Computer applications in the biosciences},
	Number = {3},
	Pages = {235--238},
	Title = {{Seq-Gen}: an application for the {Monte Carlo} simulation of {DNA} sequence evolution along phylogenetic trees},
	Url = {http://bioinformatics.oxfordjournals.org/content/13/3/235.abstract},
	Volume = {13},
	Year = {1997},
	Bdsk-Url-1 = {http://bioinformatics.oxfordjournals.org/content/13/3/235.abstract},
	Bdsk-Url-2 = {http://dx.doi.org/10.1093/bioinformatics/13.3.235}}

@article{ROBINSON1981131,
	Abstract = {A metric on general phylogenetic trees is presented. This extends the work of most previous authors, who constructed metrics for binary trees. The metric presented in this paper makes possible the comparison of the many nonbinary phylogenetic trees appearing in the literature. This provides an objective procedure for comparing the different methods for constructing phylogenetic trees. The metric is based on elementary operations which transform one tree into another. Various results obtained in applying these operations are given. They enable the distance between any pair of trees to be calculated efficiently. This generalizes previous work by Bourque to the case where interior vertices can be labeled, and labels may contain more than one element or may be empty.},
	Author = {D.F. Robinson and L.R. Foulds},
	Doi = {http://dx.doi.org/10.1016/0025-5564(81)90043-2},
	Issn = {0025-5564},
	Journal = {Mathematical Biosciences},
	Pages = {131--147},
	Title = {Comparison of phylogenetic trees},
	Url = {http://www.sciencedirect.com/science/article/pii/0025556481900432},
	Volume = {53},
	Year = {1981},
	Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/pii/0025556481900432},
	Bdsk-Url-2 = {http://dx.doi.org/10.1016/0025-5564(81)90043-2}}

@article{Heled2013,
	Abstract = {Bayesian phylogenetic analysis generates a set of trees which are often condensed into a single tree representing the whole set. Many methods exist for selecting a representative topology for a set of unrooted trees, few exist for assigning branch lengths to a fixed topology, and even fewer for simultaneously setting the topology and branch lengths. However, there is very little research into locating a good representative for a set of rooted time trees like the ones obtained from a BEAST analysis.},
	Author = {Heled, Joseph and Bouckaert, Remco R.},
	Doi = {10.1186/1471-2148-13-221},
	Issn = {1471-2148},
	Journal = {BMC Evolutionary Biology},
	Pages = {221},
	Title = {Looking for trees in the forest: summary tree from posterior samples},
	Url = {http://dx.doi.org/10.1186/1471-2148-13-221},
	Volume = {13},
	Year = {2013},
	Bdsk-Url-1 = {http://dx.doi.org/10.1186/1471-2148-13-221}}

@article{Moen2014190,
	Abstract = {Studies of phylogenetic diversification often show evidence for slowdowns in diversification rates over the history of clades. Recent studies seeking biological explanations for this pattern have emphasized the role of niche differentiation, as in hypotheses of adaptive radiation and ecological limits to diversity. Yet many other biological explanations might underlie diversification slowdowns. In this paper, we focus on the geographic context of diversification, environment-driven bursts of speciation, failure of clades to keep pace with a changing environment, and protracted speciation. We argue that, despite being currently underemphasized, these alternatives represent biologically plausible explanations that should be considered along with niche differentiation. Testing the importance of these alternative hypotheses might yield fundamentally different explanations for what influences species richness within clades through time. },
	Author = {Daniel Moen and H{\'e}l{\`e}ne Morlon},
	Doi = {http://dx.doi.org/10.1016/j.tree.2014.01.010},
	Issn = {0169-5347},
	Journal = {Trends in Ecology \& Evolution},
	Keywords = {wax--wane dynamics},
	Number = {4},
	Pages = {190--197},
	Title = {Why does diversification slow down?},
	Url = {http://www.sciencedirect.com/science/article/pii/S016953471400024X},
	Volume = {29},
	Year = {2014},
	Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/pii/S016953471400024X},
	Bdsk-Url-2 = {http://dx.doi.org/10.1016/j.tree.2014.01.010}}

@article{annurev-ecolsys-110512-135822,
	Author = {Lemmon, Emily Moriarty and Lemmon, Alan R.},
	Doi = {10.1146/annurev-ecolsys-110512-135822},
	Journal = {Annual Review of Ecology, Evolution, and Systematics},
	Number = {1},
	Pages = {99--121},
	Title = {High-Throughput Genomic Data in Systematics and Phylogenetics},
	Url = {http://dx.doi.org/10.1146/annurev-ecolsys-110512-135822},
	Volume = {44},
	Year = {2013},
	Bdsk-Url-1 = {http://dx.doi.org/10.1146/annurev-ecolsys-110512-135822}}

@article{NYAS:NYAS12747,
	Abstract = {The heterogeneity of signals in the genomes of diverse organisms poses challenges for traditional phylogenetic analysis. Phylogenetic methods known as ``species tree'' methods have been proposed to directly address one important source of gene tree heterogeneity, namely the incomplete lineage sorting that occurs when evolving lineages radiate rapidly, resulting in a diversity of gene trees from a single underlying species tree. Here we review theory and empirical examples that help clarify conflicts between species tree and concatenation methods, and misconceptions in the literature about the performance of species tree methods. Considering concatenation as a special case of the multispecies coalescent model helps explain differences in the behavior of the two methods on phylogenomic data sets. Recent work suggests that species tree methods are more robust than concatenation approaches to some of the classic challenges of phylogenetic analysis, including rapidly evolving sites in DNA sequences and long-branch attraction. We show that approaches, such as binning, designed to augment the signal in species tree analyses can distort the distribution of gene trees and are inconsistent. Computationally efficient species tree methods incorporating biological realism are a key to phylogenetic analysis of whole-genome data.},
	Author = {Liu, Liang and Xi, Zhenxiang and Wu, Shaoyuan and Davis, Charles C. and Edwards, Scott V.},
	Doi = {10.1111/nyas.12747},
	Issn = {1749-6632},
	Journal = {Annals of the New York Academy of Sciences},
	Keywords = {bias--variance dilemma, transcriptome, isochore, anomaly zone, recombination},
	Number = {1},
	Pages = {36--53},
	Title = {Estimating phylogenetic trees from genome-scale data},
	Url = {http://dx.doi.org/10.1111/nyas.12747},
	Volume = {1360},
	Year = {2015},
	Bdsk-Url-1 = {http://dx.doi.org/10.1111/nyas.12747}}

@article{Stamatakis01052014,
	Author = {Stamatakis, Alexandros},
	Doi = {10.1093/bioinformatics/btu033},
	Eprint = {http://bioinformatics.oxfordjournals.org/content/30/9/1312.full.pdf+html},
	Journal = {Bioinformatics},
	Number = {9},
	Pages = {1312--1313},
	Title = {{RAxML} version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies},
	Url = {http://bioinformatics.oxfordjournals.org/content/30/9/1312.abstract},
	Volume = {30},
	Year = {2014},
	Bdsk-Url-1 = {http://bioinformatics.oxfordjournals.org/content/30/9/1312.abstract},
	Bdsk-Url-2 = {http://dx.doi.org/10.1093/bioinformatics/btu033}}

@article{Kozlov01082015,
	Author = {Kozlov, Alexey M. and Aberer, Andre J. and Stamatakis, Alexandros},
	Doi = {10.1093/bioinformatics/btv184},
	Eprint = {http://bioinformatics.oxfordjournals.org/content/31/15/2577.full.pdf+html},
	Journal = {Bioinformatics},
	Number = {15},
	Pages = {2577--2579},
	Title = {{ExaML} version 3: a tool for phylogenomic analyses on supercomputers},
	Url = {http://bioinformatics.oxfordjournals.org/content/31/15/2577.abstract},
	Volume = {31},
	Year = {2015},
	Bdsk-Url-1 = {http://bioinformatics.oxfordjournals.org/content/31/15/2577.abstract},
	Bdsk-Url-2 = {http://dx.doi.org/10.1093/bioinformatics/btv184}}

@article{Aberer01102014,
	Author = {Aberer, Andre J. and Kobert, Kassian and Stamatakis, Alexandros},
	Doi = {10.1093/molbev/msu236},
	Eprint = {http://mbe.oxfordjournals.org/content/31/10/2553.full.pdf+html},
	Journal = {Molecular Biology and Evolution},
	Number = {10},
	Pages = {2553--2556},
	Title = {{ExaBayes}: Massively Parallel {Bayesian} Tree Inference for the Whole-Genome Era},
	Url = {http://mbe.oxfordjournals.org/content/31/10/2553.abstract},
	Volume = {31},
	Year = {2014},
	Bdsk-Url-1 = {http://mbe.oxfordjournals.org/content/31/10/2553.abstract},
	Bdsk-Url-2 = {http://dx.doi.org/10.1093/molbev/msu236}}

@article{Drummond2007,
	Author = {Drummond, Alexei J. and Rambaut, Andrew},
	Doi = {10.1186/1471-2148-7-214},
	Issn = {1471-2148},
	Journal = {BMC Evolutionary Biology},
	Pages = {214},
	Title = {{BEAST}: Bayesian evolutionary analysis by sampling trees},
	Url = {http://dx.doi.org/10.1186/1471-2148-7-214},
	Volume = {7},
	Year = {2007},
	Bdsk-Url-1 = {http://dx.doi.org/10.1186/1471-2148-7-214}}

@article{journal.pgen.0020068,
	Author = {Degnan, James H AND Rosenberg, Noah A},
	Doi = {10.1371/journal.pgen.0020068},
	Journal = {PLoS Genetics},
	Month = {05},
	Number = {5},
	Pages = {e68},
	Publisher = {Public Library of Science},
	Title = {Discordance of Species Trees with Their Most Likely Gene Trees},
	Url = {http://dx.plos.org/10.1371%2Fjournal.pgen.0020068},
	Volume = {2},
	Year = {2006},
	Bdsk-Url-1 = {http://dx.plos.org/10.1371%2Fjournal.pgen.0020068},
	Bdsk-Url-2 = {http://dx.doi.org/10.1371/journal.pgen.0020068}}

@article{Kubatko01022007,
	Author = {Kubatko, Laura Salter and Degnan, James H.},
	Doi = {10.1080/10635150601146041},
	Eprint = {http://sysbio.oxfordjournals.org/content/56/1/17.full.pdf+html},
	Journal = {Systematic Biology},
	Number = {1},
	Pages = {17--24},
	Title = {Inconsistency of Phylogenetic Estimates from Concatenated Data under Coalescence},
	Url = {http://sysbio.oxfordjournals.org/content/56/1/17.abstract},
	Volume = {56},
	Year = {2007},
	Bdsk-Url-1 = {http://sysbio.oxfordjournals.org/content/56/1/17.abstract},
	Bdsk-Url-2 = {http://dx.doi.org/10.1080/10635150601146041}}

@article{Liu2010,
	Author = {Liu, Liang and Yu, Lili and Edwards, Scott V.},
	Doi = {10.1186/1471-2148-10-302},
	Issn = {1471-2148},
	Journal = {BMC Evolutionary Biology},
	Pages = {302},
	Title = {A maximum pseudo-likelihood approach for estimating species trees under the coalescent model},
	Url = {http://dx.doi.org/10.1186/1471-2148-10-302},
	Volume = {10},
	Year = {2010},
	Bdsk-Url-1 = {http://dx.doi.org/10.1186/1471-2148-10-302}}

@article{Mirarab01092014,
	Author = {Mirarab, S. and Reaz, R. and Bayzid, Md. S. and Zimmermann, T. and Swenson, M. S. and Warnow, T.},
	Doi = {10.1093/bioinformatics/btu462},
	Eprint = {http://bioinformatics.oxfordjournals.org/content/30/17/i541.full.pdf+html},
	Journal = {Bioinformatics},
	Number = {17},
	Pages = {i541--i548},
	Title = {{ASTRAL}: genome-scale coalescent-based species tree estimation},
	Url = {http://bioinformatics.oxfordjournals.org/content/30/17/i541.abstract},
	Volume = {30},
	Year = {2014},
	Bdsk-Url-1 = {http://bioinformatics.oxfordjournals.org/content/30/17/i541.abstract},
	Bdsk-Url-2 = {http://dx.doi.org/10.1093/bioinformatics/btu462}}

@article{Mirarab15062015,
	Author = {Mirarab, Siavash and Warnow, Tandy},
	Doi = {10.1093/bioinformatics/btv234},
	Eprint = {http://bioinformatics.oxfordjournals.org/content/31/12/i44.full.pdf+html},
	Journal = {Bioinformatics},
	Number = {12},
	Pages = {i44--i52},
	Title = {{ASTRAL-II}: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes},
	Url = {http://bioinformatics.oxfordjournals.org/content/31/12/i44.abstract},
	Volume = {31},
	Year = {2015},
	Bdsk-Url-1 = {http://bioinformatics.oxfordjournals.org/content/31/12/i44.abstract},
	Bdsk-Url-2 = {http://dx.doi.org/10.1093/bioinformatics/btv234}}

@article{Xi201563,
	Author = {Zhenxiang Xi and Liang Liu and Charles C. Davis},
	Doi = {http://dx.doi.org/10.1016/j.ympev.2015.06.009},
	Issn = {1055-7903},
	Journal = {Molecular Phylogenetics and Evolution},
	Keywords = {PhyML},
	Pages = {63--71},
	Title = {Genes with minimal phylogenetic information are problematic for coalescent analyses when gene tree estimation is biased},
	Url = {http://www.sciencedirect.com/science/article/pii/S1055790315001797},
	Volume = {92},
	Year = {2015},
	Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/pii/S1055790315001797},
	Bdsk-Url-2 = {http://dx.doi.org/10.1016/j.ympev.2015.06.009}}

@article{Degnan2009332,
	Abstract = {The field of phylogenetics is entering a new era in which trees of historical relationships between species are increasingly inferred from multilocus and genomic data. A major challenge for incorporating such large amounts of data into inference of species trees is that conflicting genealogical histories often exist in different genes throughout the genome. Recent advances in genealogical modeling suggest that resolving close species relationships is not quite as simple as applying more data to the problem. Here we discuss the complexities of genealogical discordance and review the issues that new methods for multilocus species tree inference will need to address to account successfully for naturally occurring genomic variability in evolutionary histories. },
	Author = {James H. Degnan and Noah A. Rosenberg},
	Doi = {http://dx.doi.org/10.1016/j.tree.2009.01.009},
	Issn = {0169-5347},
	Journal = {Trends in Ecology \& Evolution},
	Number = {6},
	Pages = {332--340},
	Title = {Gene tree discordance, phylogenetic inference and the multispecies coalescent},
	Url = {http://www.sciencedirect.com/science/article/pii/S0169534709000846},
	Volume = {24},
	Year = {2009},
	Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/pii/S0169534709000846},
	Bdsk-Url-2 = {http://dx.doi.org/10.1016/j.tree.2009.01.009}}

@article{Drummond2010,
	Abstract = {Relaxed molecular clock models allow divergence time dating and ``relaxed phylogenetic'' inference, in which a time tree is estimated in the face of unequal rates across lineages. We present a new method for relaxing the assumption of a strict molecular clock using Markov chain Monte Carlo to implement Bayesian modeling averaging over random local molecular clocks. The new method approaches the problem of rate variation among lineages by proposing a series of local molecular clocks, each extending over a subregion of the full phylogeny. Each branch in a phylogeny (subtending a clade) is a possible location for a change of rate from one local clock to a new one. Thus, including both the global molecular clock and the unconstrained model results, there are a total of 22n-2 possible rate models available for averaging with 1, 2, ..., 2n-2 different rate categories.},
	Author = {Drummond, Alexei J. and Suchard, Marc A.},
	Doi = {10.1186/1741-7007-8-114},
	Issn = {1741-7007},
	Journal = {BMC Biology},
	Pages = {114},
	Title = {Bayesian random local clocks, or one rate to rule them all},
	Url = {http://dx.doi.org/10.1186/1741-7007-8-114},
	Volume = {8},
	Year = {2010},
	Bdsk-Url-1 = {http://dx.doi.org/10.1186/1741-7007-8-114}}

@article{Rasmussen01122007,
	Abstract = {Comparative genomics provides a general methodology for discovering functional DNA elements and understanding their evolution. The availability of many related genomes enables more powerful analyses, but requires rigorous phylogenetic methods to resolve orthologous genes and regions. Here, we use 12 recently sequenced Drosophila genomes and nine fungal genomes to address the problem of accurate gene-tree reconstruction across many complete genomes. We show that existing phylogenetic methods that treat each gene tree in isolation show large-scale inaccuracies, largely due to insufficient phylogenetic information in individual genes. However, we find that gene trees exhibit common properties that can be exploited for evolutionary studies and accurate phylogenetic reconstruction. Evolutionary rates can be decoupled into gene-specific and species-specific components, which can be learned across complete genomes. We develop a phylogenetic reconstruction methodology that exploits these properties and achieves significantly higher accuracy, addressing the species-level heterotachy and enabling studies of gene evolution in the context of species evolution.},
	Author = {Rasmussen, Matthew D. and Kellis, Manolis},
	Doi = {10.1101/gr.7105007},
	Eprint = {http://genome.cshlp.org/content/17/12/1932.full.pdf+html},
	Journal = {Genome Research},
	Number = {12},
	Pages = {1932--1942},
	Title = {Accurate gene-tree reconstruction by learning gene- and species-specific substitution rates across multiple complete genomes},
	Url = {http://genome.cshlp.org/content/17/12/1932.abstract},
	Volume = {17},
	Year = {2007},
	Bdsk-Url-1 = {http://genome.cshlp.org/content/17/12/1932.abstract},
	Bdsk-Url-2 = {http://dx.doi.org/10.1101/gr.7105007}}

@article{Gossmann01032014,
	Abstract = {Sex-biased genes are genes with a preferential or specific expression in one sex and tend to show an accelerated rate of evolution in animals. Various hypotheses---which are not mutually exclusive---have been put forth to explain observed patterns of rapid evolution. One possible explanation is positive selection, but this has been shown only in few animal species and mostly for male-specific genes. Here, we present a large-scale study that investigates evolutionary patterns of sex-biased genes in the predominantly self-fertilizing plant Arabidopsis thaliana. Unlike most animal species, A. thaliana does not possess sex chromosomes, its flowers develop both male and female sexual organs, and it is characterized by low outcrossing rates. Using cell-specific gene expression data, we identified genes whose expression is enriched in comparison with all other tissues in the male and female gametes (sperm, egg, and central cell), as well as in synergids, pollen, and pollen tubes, which also play an important role in reproduction. Genes specifically expressed in gametes and synergids show higher rates of protein evolution compared with the genome-wide average and no evidence for positive selection. In contrast, pollen- and pollen tube-specific genes not only have lower rates of protein evolution but also exhibit a higher proportion of adaptive amino acid substitutions. We show that this is the result of increased levels of purifying and positive selection among genes with pollen- and pollen tube-specific expression. The increased proportion of adaptive substitutions cannot be explained by the fact that pollen- and pollen tube-expressed genes are enriched in segmental duplications, are on average older, or have a larger effective population size. Our observations are consistent with prezygotic sexual selection as a result of interactions during pollination and pollen tube growth such as pollen tube competition.},
	Author = {Gossmann, Toni I. and Schmid, Marc W. and Grossniklaus, Ueli and Schmid, Karl J.},
	Doi = {10.1093/molbev/mst226},
	Eprint = {http://mbe.oxfordjournals.org/content/31/3/574.full.pdf+html},
	Journal = {Molecular Biology and Evolution},
	Number = {3},
	Pages = {574--583},
	Title = {Selection-Driven Evolution of Sex-Biased Genes Is Consistent with Sexual Selection in \textit{Arabidopsis thaliana}},
	Url = {http://mbe.oxfordjournals.org/content/31/3/574.abstract},
	Volume = {31},
	Year = {2014},
	Bdsk-Url-1 = {http://mbe.oxfordjournals.org/content/31/3/574.abstract},
	Bdsk-Url-2 = {http://dx.doi.org/10.1093/molbev/mst226}}

@article{Bromham2503,
	Abstract = {DNA sequences evolve at different rates in different species. This rate variation has been most closely examined in mammals, revealing a large number of characteristics that can shape the rate of molecular evolution. Many of these traits are part of the mammalian life-history continuum: species with small body size, rapid generation turnover, high fecundity and short lifespans tend to have faster rates of molecular evolution. In addition, rate of molecular evolution in mammals might be influenced by behaviour (such as mating system), ecological factors (such as range restriction) and evolutionary history (such as diversification rate). I discuss the evidence for these patterns of rate variation, and the possible explanations of these correlations. I also consider the impact of these systematic patterns of rate variation on the reliability of the molecular date estimates that have been used to suggest a Cretaceous radiation of modern mammals, before the final extinction of the dinosaurs.},
	Author = {Bromham, Lindell},
	Doi = {10.1098/rstb.2011.0014},
	Eprint = {http://rstb.royalsocietypublishing.org/content/366/1577/2503.full.pdf},
	Issn = {0962-8436},
	Journal = {Philosophical Transactions of the Royal Society of London B: Biological Sciences},
	Number = {1577},
	Pages = {2503--2513},
	Publisher = {The Royal Society},
	Title = {The genome as a life-history character: why rate of molecular evolution varies between mammal species},
	Url = {http://rstb.royalsocietypublishing.org/content/366/1577/2503},
	Volume = {366},
	Year = {2011},
	Bdsk-Url-1 = {http://rstb.royalsocietypublishing.org/content/366/1577/2503},
	Bdsk-Url-2 = {http://dx.doi.org/10.1098/rstb.2011.0014}}

@article{Thorne01092002,
	Abstract = {Bayesian methods for estimating evolutionary divergence times are extended to multigene data sets, and a technique is described for detecting correlated changes in evolutionary rates among genes. Simulations are employed to explore the effect of multigene data on divergence time estimation, and the methodology is illustrated with a previously published data set representing diverse plant taxa. The fact that evolutionary rates and times are confounded when sequence data are compared is emphasized and the importance of fossil information for disentangling rates and times is stressed.},
	Author = {Thorne, Jeffrey L. and Kishino, Hirohisa},
	Doi = {10.1080/10635150290102456},
	Eprint = {http://sysbio.oxfordjournals.org/content/51/5/689.full.pdf+html},
	Journal = {Systematic Biology},
	Number = {5},
	Pages = {689--702},
	Title = {Divergence Time and Evolutionary Rate Estimation with Multilocus Data},
	Url = {http://sysbio.oxfordjournals.org/content/51/5/689.abstract},
	Volume = {51},
	Year = {2002},
	Bdsk-Url-1 = {http://sysbio.oxfordjournals.org/content/51/5/689.abstract},
	Bdsk-Url-2 = {http://dx.doi.org/10.1080/10635150290102456}}

@article{Hastings1970,
	Abstract = {A generalization of the sampling method introduced by Metropolis et al. (1953) is presented along with an exposition of the relevant theory, techniques of application and methods and difficulties of assessing the error in Monte Carlo estimates. Examples of the methods, including the generation of random orthogonal matrices and potential applications of the methods to numerical problems arising in statistics, are discussed.},
	Author = {W. K. Hastings},
	Issn = {00063444},
	Journal = {Biometrika},
	Number = {1},
	Pages = {97--109},
	Publisher = {[Oxford University Press, Biometrika Trust]},
	Title = {{Monte Carlo} Sampling Methods Using {Markov} Chains and Their Applications},
	Url = {http://www.jstor.org/stable/2334940},
	Volume = {57},
	Year = {1970},
	Bdsk-Url-1 = {http://www.jstor.org/stable/2334940}}

@article{Metropolis1953,
	Author = {Metropolis, Nicholas and Rosenbluth, Arianna W. and Rosenbluth, Marshall N. and Teller, Augusta H. and Teller, Edward},
	Doi = {http://dx.doi.org/10.1063/1.1699114},
	Journal = {The Journal of Chemical Physics},
	Number = {6},
	Pages = {1087--1092},
	Title = {Equation of State Calculations by Fast Computing Machines},
	Url = {http://scitation.aip.org/content/aip/journal/jcp/21/6/10.1063/1.1699114},
	Volume = {21},
	Year = {1953},
	Bdsk-Url-1 = {http://scitation.aip.org/content/aip/journal/jcp/21/6/10.1063/1.1699114},
	Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.1699114}}

@article{Heled01032010,
	Abstract = {Until recently, it has been common practice for a phylogenetic analysis to use a single gene sequence from a single individual organism as a proxy for an entire species. With technological advances, it is now becoming more common to collect data sets containing multiple gene loci and multiple individuals per species. These data sets often reveal the need to directly model intraspecies polymorphism and incomplete lineage sorting in phylogenetic estimation procedures.For a single species, coalescent theory is widely used in contemporary population genetics to model intraspecific gene trees. Here, we present a Bayesian Markov chain Monte Carlo method for the multispecies coalescent. Our method coestimates multiple gene trees embedded in a shared species tree along with the effective population size of both extant and ancestral species. The inference is made possible by multilocus data from multiple individuals per species.Using a multiindividual data set and a series of simulations of rapid species radiations, we demonstrate the efficacy of our new method. These simulations give some insight into the behavior of the method as a function of sampled individuals, sampled loci, and sequence length. Finally, we compare our new method to both an existing method (BEST 2.2) with similar goals and the supermatrix (concatenation) method. We demonstrate that both BEST and our method have much better estimation accuracy for species tree topology than concatenation, and our method outperforms BEST in divergence time and population size estimation.},
	Author = {Heled, Joseph and Drummond, Alexei J.},
	Doi = {10.1093/molbev/msp274},
	Eprint = {http://mbe.oxfordjournals.org/content/27/3/570.full.pdf+html},
	Journal = {Molecular Biology and Evolution},
	Number = {3},
	Pages = {570--580},
	Title = {Bayesian Inference of Species Trees from Multilocus Data},
	Url = {http://mbe.oxfordjournals.org/content/27/3/570.abstract},
	Volume = {27},
	Year = {2010},
	Bdsk-Url-1 = {http://mbe.oxfordjournals.org/content/27/3/570.abstract},
	Bdsk-Url-2 = {http://dx.doi.org/10.1093/molbev/msp274}}

@article{Blom20160181,
	Abstract = {Recent radiations are important to evolutionary biologists, because they provide an opportunity to study the mechanisms that link micro- and macroevolution. The role of ecological speciation during adaptive radiation has been intensively studied, but radiations can arise from a diversity of evolutionary processes; in particular, on large continental landmasses where allopatric speciation might frequently precede ecological differentiation. It is therefore important to establish a phylogenetic and ecological framework for recent continental-scale radiations that are species-rich and ecologically diverse. Here, we use a genomic (approx. 1 200 loci, exon capture) approach to fit branch lengths on a summary-coalescent species tree and generate a time-calibrated phylogeny for a recent and ecologically diverse radiation of Australian scincid lizards; the genus Cryptoblepharus. We then combine the phylogeny with a comprehensive phenotypic dataset for over 800 individuals across the 26 species, and use comparative methods to test whether habitat specialization can explain current patterns of phenotypic variation in ecologically relevant traits. We find significant differences in morphology between species that occur in distinct environments and convergence in ecomorphology with repeated habitat shifts across the continent. These results suggest that isolated analogous habitats have provided parallel ecological opportunity and have repeatedly promoted adaptive diversification. By contrast, speciation processes within the same habitat have resulted in distinct lineages with relatively limited morphological variation. Overall, our study illustrates how alternative diversification processes might have jointly stimulated species proliferation across the continent and generated a remarkably diverse group of Australian lizards.},
	Author = {Blom, Mozes P. K. and Horner, Paul and Moritz, Craig},
	Doi = {10.1098/rspb.2016.0181},
	Eprint = {http://rspb.royalsocietypublishing.org/content/283/1832/20160181.full.pdf},
	Issn = {0962-8452},
	Journal = {Proceedings of the Royal Society of London B: Biological Sciences},
	Number = {1832},
	Publisher = {The Royal Society},
	Title = {Convergence across a continent: adaptive diversification in a recent radiation of {Australian} lizards},
	Url = {http://rspb.royalsocietypublishing.org/content/283/1832/20160181},
	Volume = {283},
	Year = {2016},
	Bdsk-Url-1 = {http://rspb.royalsocietypublishing.org/content/283/1832/20160181},
	Bdsk-Url-2 = {http://dx.doi.org/10.1098/rspb.2016.0181}}

@article{Angelis874,
	Abstract = {Although the effects of the coalescent process on sequence divergence and genealogies are well understood, the virtual majority of studies that use molecular sequences to estimate times of divergence among species have failed to account for the coalescent process. Here we study the impact of ancestral population size and incomplete lineage sorting on Bayesian estimates of species divergence times under the molecular clock when the inference model ignores the coalescent process. Using a combination of mathematical analysis, computer simulations and analysis of real data, we find that the errors on estimates of times and the molecular rate can be substantial when ancestral populations are large and when there is substantial incomplete lineage sorting. For example, in a simple three-species case, we find that if the most precise fossil calibration is placed on the root of the phylogeny, the age of the internal node is overestimated, while if the most precise calibration is placed on the internal node, then the age of the root is underestimated. In both cases, the molecular rate is overestimated. Using simulations on a phylogeny of nine species, we show that substantial errors in time and rate estimates can be obtained even when dating ancient divergence events. We analyse the hominoid phylogeny and show that estimates of the neutral mutation rate obtained while ignoring the coalescent are too high. Using a coalescent-based technique to obtain geological times of divergence, we obtain estimates of the mutation rate that are within experimental estimates and we also obtain substantially older divergence times within the phylogeny.},
	Author = {Angelis, Konstantinos and Dos Reis, Mario},
	Doi = {10.1093/czoolo/61.5.874},
	Eprint = {http://cz.oxfordjournals.org/content/61/5/874.full.pdf},
	Issn = {1674-5507},
	Journal = {Current Zoology},
	Number = {5},
	Pages = {874--885},
	Publisher = {The Oxford University Press},
	Title = {The impact of ancestral population size and incomplete lineage sorting on {Bayesian} estimation of species divergence times},
	Url = {http://cz.oxfordjournals.org/content/61/5/874},
	Volume = {61},
	Year = {2015},
	Bdsk-Url-1 = {http://cz.oxfordjournals.org/content/61/5/874},
	Bdsk-Url-2 = {http://dx.doi.org/10.1093/czoolo/61.5.874}}

@article{Yang01082007,
	Abstract = {PAML, currently in version 4, is a package of programs for phylogenetic analyses of DNA and protein sequences using maximum likelihood (ML). The programs may be used to compare and test phylogenetic trees, but their main strengths lie in the rich repertoire of evolutionary models implemented, which can be used to estimate parameters in models of sequence evolution and to test interesting biological hypotheses. Uses of the programs include estimation of synonymous and nonsynonymous rates (dN and dS) between two protein-coding DNA sequences, inference of positive Darwinian selection through phylogenetic comparison of protein-coding genes, reconstruction of ancestral genes and proteins for molecular restoration studies of extinct life forms, combined analysis of heterogeneous data sets from multiple gene loci, and estimation of species divergence times incorporating uncertainties in fossil calibrations. This note discusses some of the major applications of the package, which includes example data sets to demonstrate their use. The package is written in ANSI C, and runs under Windows, Mac OSX, and UNIX systems. It is available at http://abacus.gene.ucl.ac.uk/software/paml.html.},
	Author = {Yang, Ziheng},
	Doi = {10.1093/molbev/msm088},
	Eprint = {http://mbe.oxfordjournals.org/content/24/8/1586.full.pdf+html},
	Journal = {Molecular Biology and Evolution},
	Number = {8},
	Pages = {1586--1591},
	Title = {{PAML} 4: Phylogenetic Analysis by Maximum Likelihood},
	Url = {http://mbe.oxfordjournals.org/content/24/8/1586.abstract},
	Volume = {24},
	Year = {2007},
	Bdsk-Url-1 = {http://mbe.oxfordjournals.org/content/24/8/1586.abstract},
	Bdsk-Url-2 = {http://dx.doi.org/10.1093/molbev/msm088}}

@article{Guindon01052010,
	Abstract = {PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm performing nearest neighbor interchanges to improve a reasonable starting tree topology. Since the original publication (Guindon S., Gascuel O. 2003. A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696--704), PhyML has been widely used (>2500 citations in ISI Web of Science) because of its simplicity and a fair compromise between accuracy and speed. In the meantime, research around PhyML has continued, and this article describes the new algorithms and methods implemented in the program. First, we introduce a new algorithm to search the tree space with user-defined intensity using subtree pruning and regrafting topological moves. The parsimony criterion is used here to filter out the least promising topology modifications with respect to the likelihood function. The analysis of a large collection of real nucleotide and amino acid data sets of various sizes demonstrates the good performance of this method. Second, we describe a new test to assess the support of the data for internal branches of a phylogeny. This approach extends the recently proposed approximate likelihood-ratio test and relies on a nonparametric, Shimodaira--Hasegawa--like procedure. A detailed analysis of real alignments sheds light on the links between this new approach and the more classical nonparametric bootstrap method. Overall, our tests show that the last version (3.0) of PhyML is fast, accurate, stable, and ready to use. A Web server and binary files are available from http://www.atgc-montpellier.fr/phyml/.},
	Author = {Guindon, St{\'e}phane and Dufayard, Jean-Fran{\c c}ois and Lefort, Vincent and Anisimova, Maria and Hordijk, Wim and Gascuel, Olivier},
	Doi = {10.1093/sysbio/syq010},
	Eprint = {http://sysbio.oxfordjournals.org/content/59/3/307.full.pdf+html},
	Journal = {Systematic Biology},
	Number = {3},
	Pages = {307--321},
	Title = {New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of {PhyML} 3.0},
	Url = {http://sysbio.oxfordjournals.org/content/59/3/307.abstract},
	Volume = {59},
	Year = {2010},
	Bdsk-Url-1 = {http://sysbio.oxfordjournals.org/content/59/3/307.abstract},
	Bdsk-Url-2 = {http://dx.doi.org/10.1093/sysbio/syq010}}

@article{Yule21,
	Author = {Yule, G. Udny},
	Doi = {10.1098/rstb.1925.0002},
	Eprint = {http://rstb.royalsocietypublishing.org/content/213/402-410/21.full.pdf},
	Issn = {0264-3960},
	Journal = {Philosophical Transactions of the Royal Society B: Biological Sciences},
	Number = {403},
	Pages = {21--87},
	Publisher = {The Royal Society},
	Title = {A Mathematical Theory of Evolution, Based on the Conclusions of {Dr. J. C. Willis, F.R.S.}},
	Url = {http://rstb.royalsocietypublishing.org/content/213/402-410/21},
	Volume = {213},
	Year = {1925},
	Bdsk-Url-1 = {http://rstb.royalsocietypublishing.org/content/213/402-410/21},
	Bdsk-Url-2 = {http://dx.doi.org/10.1098/rstb.1925.0002}}

@incollection{JUKES196921,
	Author = {THOMAS H. Jukes and CHARLES R. Cantor},
	Booktitle = {Mammalian Protein Metabolism},
	Doi = {http://dx.doi.org/10.1016/B978-1-4832-3211-9.50009-7},
	Isbn = {978-1-4832-3211-9},
	Pages = {21--132},
	Publisher = {Academic Press},
	Title = {Evolution of Protein Molecules},
	Url = {http://www.sciencedirect.com/science/article/pii/B9781483232119500097},
	Year = {1969},
	Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/pii/B9781483232119500097},
	Bdsk-Url-2 = {http://dx.doi.org/10.1016/B978-1-4832-3211-9.50009-7}}

@article{Felsenstein1981,
	Abstract = {The application of maximum likelihood techniques to the estimation of evolutionary trees from nucleic acid sequence data is discussed. A computationally feasible method for finding such maximum likelihood estimates is developed, and a computer program is available. This method has advantages over the traditional parsimony algorithms, which can give misleading results if rates of evolution differ in different lineages. It also allows the testing of hypotheses about the constancy of evolutionary rates by likelihood ratio tests, and gives rough indication of the error of the estimate of the tree.},
	Author = {Felsenstein, Joseph},
	Doi = {10.1007/BF01734359},
	Issn = {1432-1432},
	Journal = {Journal of Molecular Evolution},
	Number = {6},
	Pages = {368--376},
	Title = {Evolutionary trees from {DNA} sequences: A maximum likelihood approach},
	Url = {http://dx.doi.org/10.1007/BF01734359},
	Volume = {17},
	Year = {1981},
	Bdsk-Url-1 = {http://dx.doi.org/10.1007/BF01734359}}

@article{Baer2007,
	Author = {Baer, Charles F. and Miyamoto, Michael M. and Denver, Dee R.},
	Doi = {10.1038/nrg2158},
	Issn = {1471-0056},
	Journal = {Nature Reviews Genetics},
	Month = {Aug},
	Number = {8},
	Pages = {619--631},
	Title = {Mutation rate variation in multicellular eukaryotes: causes and consequences},
	Url = {http://dx.doi.org/10.1038/nrg2158},
	Volume = {8},
	Year = {2007},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nrg2158}}

@article{doi:10.1146/annurev.ecolsys.33.010802.150500,
	Abstract = { ▪ Abstract Molecular clocks have profoundly influenced modern views on the timing of important events in evolutionary history. We review recent advances in estimating divergence times from molecular data, emphasizing the continuum between processes at the phylogenetic and population genetic scales. On the phylogenetic scale, we address the complexities of DNA sequence evolution as they relate to estimating divergences, focusing on models of nucleotide substitution and problems associated with among-site and among-lineage rate variation. On the population genetic scale, we review advances in the incorporation of ancestral population processes into the estimation of divergence times between recently separated species. Throughout the review we emphasize new statistical methods and the importance of model testing during the process of divergence time estimation. },
	Author = {Brian S. Arbogast and Scott V. Edwards and John Wakeley and Peter Beerli and Joseph B. Slowinski},
	Doi = {10.1146/annurev.ecolsys.33.010802.150500},
	Eprint = {http://dx.doi.org/10.1146/annurev.ecolsys.33.010802.150500},
	Journal = {Annual Review of Ecology and Systematics},
	Pages = {707--740},
	Title = {Estimating Divergence Times from Molecular Data on Phylogenetic and Population Genetic Timescales},
	Url = {http://dx.doi.org/10.1146/annurev.ecolsys.33.010802.150500},
	Volume = {33},
	Year = {2002},
	Bdsk-Url-1 = {http://dx.doi.org/10.1146/annurev.ecolsys.33.010802.150500}}

@article{Yang854,
	Abstract = {This paper provides an overview and a tutorial of the BPP program, which is a Bayesian MCMC program for analyzing multi-locus genomic sequence data under the multispecies coalescent model. An example dataset of five nuclear loci from the East Asian brown frogs is used to illustrate four different analyses, including estimation of species divergence times and population size parameters under the multispecies coalescent model on a fixed species phylogeny (A00), species tree estimation when the assignment and species delimitation are fixed (A01), species delimitation using a fixed guide tree (A10), and joint species delimitation and species-tree estimation or unguided species delimitation (A11). For the joint analysis (A11), two new priors are introduced, which assign uniform probabilities for the different numbers of delimited species, which may be useful when assignment, species delimitation, and species phylogeny are all inferred in one joint analysis. The paper ends with a discussion of the assumptions, the strengths and weaknesses of the BPP analysis.},
	Author = {Yang, Ziheng},
	Doi = {10.1093/czoolo/61.5.854},
	Eprint = {http://cz.oxfordjournals.org/content/61/5/854.full.pdf},
	Issn = {1674-5507},
	Journal = {Current Zoology},
	Number = {5},
	Pages = {854--865},
	Publisher = {The Oxford University Press},
	Title = {The {BPP} program for species tree estimation and species delimitation},
	Url = {http://cz.oxfordjournals.org/content/61/5/854},
	Volume = {61},
	Year = {2015},
	Bdsk-Url-1 = {http://cz.oxfordjournals.org/content/61/5/854},
	Bdsk-Url-2 = {http://dx.doi.org/10.1093/czoolo/61.5.854}}

@article{Liu01112008,
	Abstract = {Summary: BEST implements a Bayesian hierarchical model to jointly estimate gene trees and the species tree from multilocus sequences. It provides a new option for estimating species phylogenies within the popular Bayesian phylogenetic program MrBayes. The technique of simulated annealing is adopted along with Metropolis coupling as performed in MrBayes to improve the convergence rate of the Markov Chain Monte Carlo algorithm.Availability: http://www.stat.osu.edu/~dkp/BEST.Contact: lliu@oeb.harvard.edu},
	Author = {Liu, Liang},
	Doi = {10.1093/bioinformatics/btn484},
	Eprint = {http://bioinformatics.oxfordjournals.org/content/24/21/2542.full.pdf+html},
	Journal = {Bioinformatics},
	Number = {21},
	Pages = {2542--2543},
	Title = {{BEST}: {Bayesian} estimation of species trees under the coalescent model},
	Url = {http://bioinformatics.oxfordjournals.org/content/24/21/2542.abstract},
	Volume = {24},
	Year = {2008},
	Bdsk-Url-1 = {http://bioinformatics.oxfordjournals.org/content/24/21/2542.abstract},
	Bdsk-Url-2 = {http://dx.doi.org/10.1093/bioinformatics/btn484}}

@article{Giarla01092015,
	Abstract = {Phylogenetic relationships in recent, rapid radiations can be difficult to resolve due to incomplete lineage sorting and reliance on genetic markers that evolve slowly relative to the rate of speciation. By incorporating hundreds to thousands of unlinked loci, phylogenomic analyses have the potential to mitigate these difficulties. Here, we attempt to resolve phylogenetic relationships among eight shrew species (genus Crocidura) from the Philippines, a phylogenetic problem that has proven intractable with small (< 10 loci) data sets. We sequenced hundreds of ultraconserved elements and whole mitochondrial genomes in these species and estimated phylogenies using concatenation, summary coalescent, and hierarchical coalescent methods. The concatenated approach recovered a maximally supported and fully resolved tree. In contrast, the coalescent-based approaches produced similar topologies, but each had several poorly supported nodes. Using simulations, we demonstrate that the concatenated tree could be positively misleading. Our simulations also show that the tree shape we tend to infer, which involves a series of short internal branches, is difficult to resolve, even if substitution models are known and multiple individuals per species are sampled. As such, the low support we obtained for backbone relationships in our coalescent-based inferences reflects a real and appropriate lack of certainty. Our results illuminate the challenges of estimating a bifurcating tree in a rapid and recent radiation, providing a rare empirical example of a nearly simultaneous series of speciation events in a terrestrial animal lineage as it spreads across an oceanic archipelago.},
	Author = {Giarla, Thomas C. and Esselstyn, Jacob A.},
	Doi = {10.1093/sysbio/syv029},
	Eprint = {http://sysbio.oxfordjournals.org/content/64/5/727.full.pdf+html},
	Journal = {Systematic Biology},
	Number = {5},
	Pages = {727--740},
	Title = {The Challenges of Resolving a Rapid, Recent Radiation: Empirical and Simulated Phylogenomics of {Philippine} Shrews},
	Url = {http://sysbio.oxfordjournals.org/content/64/5/727.abstract},
	Volume = {64},
	Year = {2015},
	Bdsk-Url-1 = {http://sysbio.oxfordjournals.org/content/64/5/727.abstract},
	Bdsk-Url-2 = {http://dx.doi.org/10.1093/sysbio/syv029}}

@incollection{Tavare1986,
	Address = {Providence, Rhode Island},
	Author = {Tavar{\'e}, Simon},
	Booktitle = {Some Mathematical Questions in Biology: {DNA} Sequence Analysis},
	Editor = {Miura, R.M.},
	Isbn = {9780821897119},
	Pages = {57--86},
	Publisher = {American Mathematical Society},
	Series = {Lectures on mathematics in the life sciences},
	Title = {Some probabilistic and statistical problems in the analysis of {DNA} sequences},
	Volume = {17},
	Year = {1986}}

@article{Zimmermann2014,
	Abstract = {Species tree estimation can be challenging in the presence of gene tree conflict due to incomplete lineage sorting (ILS), which can occur when the time between speciation events is short relative to the population size. Of the many methods that have been developed to estimate species trees in the presence of ILS, *BEAST, a Bayesian method that co-estimates the species tree and gene trees given sequence alignments on multiple loci, has generally been shown to have the best accuracy. However, *BEAST is extremely computationally intensive so that it cannot be used with large numbers of loci; hence, *BEAST is not suitable for genome-scale analyses.},
	Author = {Zimmermann, Th{\'e}o and Mirarab, Siavash and Warnow, Tandy},
	Doi = {10.1186/1471-2164-15-S6-S11},
	Issn = {1471-2164},
	Journal = {BMC Genomics},
	Number = {Suppl 6},
	Pages = {S11},
	Title = {{BBCA}: Improving the scalability of {*BEAST} using random binning},
	Url = {http://dx.doi.org/10.1186/1471-2164-15-S6-S11},
	Volume = {15},
	Year = {2014},
	Bdsk-Url-1 = {http://dx.doi.org/10.1186/1471-2164-15-S6-S11}}

@article{Faircloth01102012,
	Abstract = {Although massively parallel sequencing has facilitated large-scale DNA sequencing, comparisons among distantly related species rely upon small portions of the genome that are easily aligned. Methods are needed to efficiently obtain comparable DNA fragments prior to massively parallel sequencing, particularly for biologists working with non-model organisms. We introduce a new class of molecular marker, anchored by ultraconserved genomic elements (UCEs), that universally enable target enrichment and sequencing of thousands of orthologous loci across species separated by hundreds of millions of years of evolution. Our analyses here focus on use of UCE markers in Amniota because UCEs and phylogenetic relationships are well-known in some amniotes. We perform an in silico experiment to demonstrate that sequence flanking 2030 UCEs contains information sufficient to enable unambiguous recovery of the established primate phylogeny. We extend this experiment by performing an in vitro enrichment of 2386 UCE-anchored loci from nine, non-model avian species. We then use alignments of 854 of these loci to unambiguously recover the established evolutionary relationships within and among three ancient bird lineages. Because many organismal lineages have UCEs, this type of genetic marker and the analytical framework we outline can be applied across the tree of life, potentially reshaping our understanding of phylogeny at many taxonomic levels.},
	Author = {Faircloth, Brant C. and McCormack, John E. and Crawford, Nicholas G. and Harvey, Michael G. and Brumfield, Robb T. and Glenn, Travis C.},
	Doi = {10.1093/sysbio/sys004},
	Eprint = {http://sysbio.oxfordjournals.org/content/61/5/717.full.pdf+html},
	Journal = {Systematic Biology},
	Number = {5},
	Pages = {717--726},
	Title = {Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales},
	Url = {http://sysbio.oxfordjournals.org/content/61/5/717.abstract},
	Volume = {61},
	Year = {2012},
	Bdsk-Url-1 = {http://sysbio.oxfordjournals.org/content/61/5/717.abstract},
	Bdsk-Url-2 = {http://dx.doi.org/10.1093/sysbio/sys004}}

@article{Springer20161,
	Abstract = {Abstract Higher-level relationships among placental mammals are mostly resolved, but several polytomies remain contentious. Song et al. (2012) claimed to have resolved three of these using shortcut coalescence methods (MP-EST, STAR) and further concluded that these methods, which assume no within-locus recombination, are required to unravel deep-level phylogenetic problems that have stymied concatenation. Here, we reanalyze Song et al.'s (2012) data and leverage these re-analyses to explore key issues in systematics including the recombination ratchet, gene tree stoichiometry, the proportion of gene tree incongruence that results from deep coalescence versus other factors, and simulations that compare the performance of coalescence and concatenation methods in species tree estimation. Song et al. (2012) reported an average locus length of 3.1 kb for the 447 protein-coding genes in their phylogenomic dataset, but the true mean length of these loci (start codon to stop codon) is 139.6 kb. Empirical estimates of recombination breakpoints in primates, coupled with consideration of the recombination ratchet, suggest that individual coalescence genes (c-genes) approach ∼12 bp or less for Song et al.'s (2012) dataset, three to four orders of magnitude shorter than the c-genes reported by these authors. This result has general implications for the application of coalescence methods in species tree estimation. We contend that it is illogical to apply coalescence methods to complete protein-coding sequences. Such analyses amalgamate c-genes with different evolutionary histories (i.e., exons separated by >100,000 bp), distort true gene tree stoichiometry that is required for accurate species tree inference, and contradict the central rationale for applying coalescence methods to difficult phylogenetic problems. In addition, Song et al.'s (2012) dataset of 447 genes includes 21 loci with switched taxonomic names, eight duplicated loci, 26 loci with non-homologous sequences that are grossly misaligned, and numerous loci with >50% missing data for taxa that are misplaced in their gene trees. These problems were compounded by inadequate tree searches with nearest neighbor interchange branch swapping and inadvertent application of substitution models that did not account for among-site rate heterogeneity. Sixty-six gene trees imply unrealistic deep coalescences that exceed 100 million years (MY). Gene trees that were obtained with better justified models and search parameters show large increases in both likelihood scores and congruence. Coalescence analyses based on a curated set of 413 improved gene trees and a superior coalescence method (ASTRAL) support a Scandentia (treeshrews) + Glires (rabbits, rodents) clade, contradicting one of the three primary systematic conclusions of Song et al. (2012). Robust support for a Perissodactyla + Carnivora clade within Laurasiatheria is also lost, contradicting a second major conclusion of this study. Song et al.'s (2012) MP-EST species tree provided the basis for circular simulations that led these authors to conclude that the multispecies coalescent accounts for 77% of the gene tree conflicts in their dataset, but many internal branches of their MP-EST tree are stunted by an order of magnitude or more due to wholesale gene tree reconstruction errors. An independent assessment of branch lengths suggests the multispecies coalescent accounts for ⩽15% of the conflicts among Song et al.'s (2012) 447 gene trees. Unfortunately, Song et al.'s (2012) flawed phylogenomic dataset has been used as a model for additional simulation work that suggests the superiority of shortcut coalescence methods relative to concatenation. Investigator error was passed on to the subsequent simulation studies, which also incorporated further logical errors that should be avoided in future simulation studies. Illegitimate branch length switches in the simulation routines unfairly protected coalescence methods from their Achilles' heel, high gene tree reconstruction error at short internodes. These simulations therefore provide no evidence that shortcut coalescence methods out-compete concatenation at deep timescales. In summary, the long c-genes that are required for accurate reconstruction of species trees using shortcut coalescence methods do not exist and are a delusion. Coalescence approaches based on \{SNPs\} that are widely spaced in the genome avoid problems with the recombination ratchet and merit further pursuit in both empirical systematic research and simulations. },
	Author = {Mark S. Springer and John Gatesy},
	Doi = {http://dx.doi.org/10.1016/j.ympev.2015.07.018},
	Issn = {1055-7903},
	Journal = {Molecular Phylogenetics and Evolution},
	Keywords = {Species tree},
	Pages = {1--33},
	Title = {The gene tree delusion},
	Url = {http://www.sciencedirect.com/science/article/pii/S1055790315002225},
	Volume = {94, Part A},
	Year = {2016},
	Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/pii/S1055790315002225},
	Bdsk-Url-2 = {http://dx.doi.org/10.1016/j.ympev.2015.07.018}}

@article{Szollosi01012015,
	Abstract = {This article reviews the various models that have been used to describe the relationships between gene trees and species trees. Molecular phylogeny has focused mainly on improving models for the reconstruction of gene trees based on sequence alignments. Yet, most phylogeneticists seek to reveal the history of species. Although the histories of genes and species are tightly linked, they are seldom identical, because genes duplicate, are lost or horizontally transferred, and because alleles can coexist in populations for periods that may span several speciation events. Building models describing the relationship between gene and species trees can thus improve the reconstruction of gene trees when a species tree is known, and vice versa. Several approaches have been proposed to solve the problem in one direction or the other, but in general neither gene trees nor species trees are known. Only a few studies have attempted to jointly infer gene trees and species trees. These models account for gene duplication and loss, transfer or incomplete lineage sorting. Some of them consider several types of events together, but none exists currently that considers the full repertoire of processes that generate gene trees along the species tree. Simulations as well as empirical studies on genomic data show that combining gene tree--species tree models with models of sequence evolution improves gene tree reconstruction. In turn, these better gene trees provide a more reliable basis for studying genome evolution or reconstructing ancestral chromosomes and ancestral gene sequences. We predict that gene tree--species tree methods that can deal with genomic data sets will be instrumental to advancing our understanding of genomic evolution.},
	Author = {Sz\"{o}ll\H{o}si, Gergely J. and Tannier, Eric and Daubin, Vincent and Boussau, Bastien},
	Doi = {10.1093/sysbio/syu048},
	Eprint = {http://sysbio.oxfordjournals.org/content/64/1/e42.full.pdf+html},
	Journal = {Systematic Biology},
	Number = {1},
	Pages = {e42--e62},
	Title = {The Inference of Gene Trees with Species Trees},
	Url = {http://sysbio.oxfordjournals.org/content/64/1/e42.abstract},
	Volume = {64},
	Year = {2015},
	Bdsk-Url-1 = {http://sysbio.oxfordjournals.org/content/64/1/e42.abstract},
	Bdsk-Url-2 = {http://dx.doi.org/10.1093/sysbio/syu048}}

@article{Phillips06102009,
	Abstract = {The semiaquatic platypus and terrestrial echidnas (spiny anteaters) are the only living egg-laying mammals (monotremes). The fossil record has provided few clues as to their origins and the evolution of their ecological specializations; however, recent reassignment of the Early Cretaceous Teinolophos and Steropodon to the platypus lineage implies that platypuses and echidnas diverged >112.5 million years ago, reinforcing the notion of monotremes as living fossils. This placement is based primarily on characters related to a single feature, the enlarged mandibular canal, which supplies blood vessels and dense electrosensory receptors to the platypus bill. Our reevaluation of the morphological data instead groups platypus and echidnas to the exclusion of Teinolophos and Steropodon and suggests that an enlarged mandibular canal is ancestral for monotremes (partly reversed in echidnas, in association with general mandibular reduction). A multigene evaluation of the echidna--platypus divergence using both a relaxed molecular clock and direct fossil calibrations reveals a recent split of 19--48 million years ago. Platypus-like monotremes (Monotrematum) predate this divergence, indicating that echidnas had aquatically foraging ancestors that reinvaded terrestrial ecosystems. This ecological shift and the associated radiation of echidnas represent a recent expansion of niche space despite potential competition from marsupials. Monotremes might have survived the invasion of marsupials into Australasia by exploiting ecological niches in which marsupials are restricted by their reproductive mode. Morphology, ecology, and molecular biology together indicate that Teinolophos and Steropodon are basal monotremes rather than platypus relatives, and that living monotremes are a relatively recent radiation.},
	Author = {Phillips, Matthew J. and Bennett, Thomas H. and Lee, Michael S. Y.},
	Doi = {10.1073/pnas.0904649106},
	Eprint = {http://www.pnas.org/content/106/40/17089.full.pdf},
	Journal = {Proceedings of the National Academy of Sciences},
	Number = {40},
	Pages = {17089--17094},
	Title = {Molecules, morphology, and ecology indicate a recent, amphibious ancestry for echidnas},
	Url = {http://www.pnas.org/content/106/40/17089.abstract},
	Volume = {106},
	Year = {2009},
	Bdsk-Url-1 = {http://www.pnas.org/content/106/40/17089.abstract},
	Bdsk-Url-2 = {http://dx.doi.org/10.1073/pnas.0904649106}}

@article{Gatesy26032013,
	Author = {Gatesy, John and Springer, Mark S.},
	Doi = {10.1073/pnas.1221121110},
	Eprint = {http://www.pnas.org/content/110/13/E1179.full.pdf},
	Journal = {Proceedings of the National Academy of Sciences},
	Number = {13},
	Pages = {E1179},
	Title = {Concatenation versus coalescence versus ``concatalescence''},
	Url = {http://www.pnas.org/content/110/13/E1179.short},
	Volume = {110},
	Year = {2013},
	Bdsk-Url-1 = {http://www.pnas.org/content/110/13/E1179.short},
	Bdsk-Url-2 = {http://dx.doi.org/10.1073/pnas.1221121110}}

@article{Xu1353,
	Abstract = {The multispecies coalescent (MSC) model has emerged as a powerful framework for inferring species phylogenies while accounting for ancestral polymorphism and gene tree-species tree conflict. A number of methods have been developed in the past few years to estimate the species tree under the MSC. The full likelihood methods (including maximum likelihood and Bayesian inference) average over the unknown gene trees and accommodate their uncertainties properly but involve intensive computation. The approximate or summary coalescent methods are computationally fast and are applicable to genomic datasets with thousands of loci, but do not make an efficient use of information in the multilocus data. Most of them take the two-step approach of reconstructing the gene trees for multiple loci by phylogenetic methods and then treating the estimated gene trees as observed data, without accounting for their uncertainties appropriately. In this article we review the statistical nature of the species tree estimation problem under the MSC, and explore the conceptual issues and challenges of species tree estimation by focusing mainly on simple cases of three or four closely related species. We use mathematical analysis and computer simulation to demonstrate that large differences in statistical performance may exist between the two classes of methods. We illustrate that several counterintuitive behaviors may occur with the summary methods but they are due to inefficient use of information in the data by summary methods and vanish when the data are analyzed using full-likelihood methods. These include (i) unidentifiability of parameters in the model, (ii) inconsistency in the so-called anomaly zone, (iii) singularity on the likelihood surface, and (iv) deterioration of performance upon addition of more data. We discuss the challenges and strategies of species tree inference for distantly related species when the molecular clock is violated, and highlight the need for improving the computational efficiency and model realism of the likelihood methods as well as the statistical efficiency of the summary methods.},
	Author = {Xu, Bo and Yang, Ziheng},
	Doi = {10.1534/genetics.116.190173},
	Eprint = {http://www.genetics.org/content/204/4/1353.full.pdf},
	Issn = {0016-6731},
	Journal = {Genetics},
	Number = {4},
	Pages = {1353--1368},
	Publisher = {Genetics},
	Title = {Challenges in Species Tree Estimation Under the Multispecies Coalescent Model},
	Url = {http://www.genetics.org/content/204/4/1353},
	Volume = {204},
	Year = {2016},
	Bdsk-Url-1 = {http://www.genetics.org/content/204/4/1353},
	Bdsk-Url-2 = {http://dx.doi.org/10.1534/genetics.116.190173}}

@article{doi:10.1093/bioinformatics/btu530,
author = {Chifman, Julia and Kubatko, Laura},
title = {Quartet Inference from SNP Data Under the Coalescent Model},
journal = {Bioinformatics},
volume = {30},
number = {23},
pages = {3317},
year = {2014},
doi = {10.1093/bioinformatics/btu530},
URL = { + http://dx.doi.org/10.1093/bioinformatics/btu530},
eprint = {/oup/backfile/Content_public/Journal/bioinformatics/30/23/10.1093/bioinformatics/btu530/2/btu530.pdf}
}

@article {Liu171,
	author = {Liu, Liang and Edwards, Scott V.},
	title = {Comment on ``{Statistical binning enables an accurate coalescent-based estimation of the avian tree}''},
	volume = {350},
	number = {6257},
	pages = {171},
	year = {2015},
	doi = {10.1126/science.aaa7343},
	publisher = {American Association for the Advancement of Science},
	abstract = {Mirarab et al. (Research Article, 12 December 2014, p. 1250463) introduced statistical binning to improve the signal in phylogenetic methods using the multispecies coalescent model. We show that all forms of binning{\textemdash}na{\"\i}ve, statistical, and weighted statistical{\textemdash}display poor performance and are statistically inconsistent in large regions of parameter space, unlike unbinned sequence data used with species tree methods.},
	issn = {0036-8075},
	URL = {http://science.sciencemag.org/content/350/6257/171.1},
	eprint = {http://science.sciencemag.org/content/350/6257/171.1.full.pdf},
	journal = {Science}
}

@article {Mirarab1250463,
	author = {Mirarab, Siavash and Bayzid, Md. Shamsuzzoha and Boussau, Bastien and Warnow, Tandy},
	title = {Statistical binning enables an accurate coalescent-based estimation of the avian tree},
	volume = {346},
	number = {6215},
	year = {2014},
	pages = {1337},
	doi = {10.1126/science.1250463},
	publisher = {American Association for the Advancement of Science},
	abstract = {IntroductionReconstructing species trees for rapid radiations, as in the early diversification of birds, is complicated by biological processes such as incomplete lineage sorting (ILS) that can cause different parts of the genome to have different evolutionary histories. Statistical methods, based on the multispecies coalescent model and that combine gene trees, can be highly accurate even in the presence of massive ILS; however, these methods can produce species trees that are topologically far from the species tree when estimated gene trees have error. We have developed a statistical binning technique to address gene tree estimation error and have explored its use in genome-scale species tree estimation with MP-EST, a popular coalescent-based species tree estimation method.The statistical binning pipeline for estimating species trees from gene trees. Loci are grouped into bins based on a statistical test for combinabilty, before estimating gene trees.RationaleIn statistical binning, phylogenetic trees on different genes are estimated and then placed into bins, so that the differences between trees in the same bin can be explained by estimation error (see the figure). A new tree is then estimated for each bin by applying maximum likelihood to a concatenated alignment of the multiple sequence alignments of its genes, and a species tree is estimated using a coalescent-based species tree method from these supergene trees.ResultsUnder realistic conditions in our simulation study, statistical binning reduced the topological error of species trees estimated using MP-EST and enabled a coalescent-based analysis that was more accurate than concatenation even when gene tree estimation error was relatively high. Statistical binning also reduced the error in gene tree topology and species tree branch length estimation, especially when the phylogenetic signal in gene sequence alignments was low. Species trees estimated using MP-EST with statistical binning on four biological data sets showed increased concordance with the biological literature. When MP-EST was used to analyze 14,446 gene trees in the avian phylogenomics project, it produced a species tree that was discordant with the concatenation analysis and conflicted with prior literature. However, the statistical binning analysis produced a tree that was highly congruent with the concatenation analysis and was consistent with the prior scientific literature.ConclusionsStatistical binning reduces the error in species tree topology and branch length estimation because it reduces gene tree estimation error. These improvements are greatest when gene trees have reduced bootstrap support, which was the case for the avian phylogenomics project. Because using unbinned gene trees can result in overestimation of ILS, statistical binning may be helpful in providing more accurate estimations of ILS levels in biological data sets. Thus, statistical binning enables highly accurate species tree estimations, even on genome-scale data sets.Gene tree incongruence arising from incomplete lineage sorting (ILS) can reduce the accuracy of concatenation-based estimations of species trees. Although coalescent-based species tree estimation methods can have good accuracy in the presence of ILS, they are sensitive to gene tree estimation error. We propose a pipeline that uses bootstrapping to evaluate whether two genes are likely to have the same tree, then it groups genes into sets using a graph-theoretic optimization and estimates a tree on each subset using concatenation, and finally produces an estimated species tree from these trees using the preferred coalescent-based method. Statistical binning improves the accuracy of MP-EST, a popular coalescent-based method, and we use it to produce the first genome-scale coalescent-based avian tree of life.},
	issn = {0036-8075},
	URL = {http://science.sciencemag.org/content/346/6215/1250463},
	eprint = {http://science.sciencemag.org/content/346/6215/1250463.full.pdf},
	journal = {Science}
}

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