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@article{Allman2011,
	abstract = {Gene trees are evolutionary trees representing the ancestry of genes sampled from multiple populations. Species trees represent populations of individuals-each with many genes-splitting into new populations or species. The coalescent process, which models ancestry of gene copies within populations, is often used to model the probability distribution of gene trees given a fixed species tree. This multispecies coalescent model provides a framework for phylogeneticists to infer species trees from gene trees using maximum likelihood or Bayesian approaches. Because the coalescent models a branching process over time, all trees are typically assumed to be rooted in this setting. Often, however, gene trees inferred by traditional phylogenetic methods are unrooted. We investigate probabilities of unrooted gene trees under the multispecies coalescent model. We show that when there are four species with one gene sampled per species, the distribution of unrooted gene tree topologies identifies the unrooted species tree topology and some, but not all, information in the species tree edges (branch lengths). The location of the root on the species tree is not identifiable in this situation. However, for 5 or more species with one gene sampled per species, we show that the distribution of unrooted gene tree topologies identifies the rooted species tree topology and all its internal branch lengths. The length of any pendant branch leading to a leaf of the species tree is also identifiable for any species from which more than one gene is sampled.},
	author = {Allman, E.S. and Degnan, J.H. and Rhodes, J.A.},
	date-added = {2020-12-30 15:05:57 -0900},
	date-modified = {2020-12-30 15:06:43 -0900},
	doi = {10.1007/s00285-010-0355-7},
	journal = {Journal of Mathematical Biology},
	number = {6},
	pages = {833--862},
	title = {Identifying the rooted species tree from the distribution of unrooted gene trees under the coalescent},
	volume = {62},
	year = {2011},
	Bdsk-Url-1 = {https://dx.doi.org/10.1007/s00285-010-0355-7}}

@article{AMR2020,
	abstract = {A simple graphical device, the simplex plot of quartet concordance factors, is introduced to aid in the exploration of a collection of gene trees on a common set of taxa. A single plot summarizes all gene tree discord, and allows for visual comparison to the expected discord from the multispecies coalescent model (MSC) of incomplete lineage sorting on a species tree. A formal statistical procedure is described that can quantify the deviation from expectation for each subset of four taxa, suggesting when the data is not in accord with the MSC, and thus either gene tree inference error is substantial or a more complex model such as that on a network may be required. If the collection of gene trees appears to be in accord with the MSC, the plots may reveal when substantial incomplete lineage sorting is present and coalescent based species tree inference is preferred over concatenation approaches. Applications to both simulated and empirical multilocus data sets illustrate the insights provided.},
	author = {Allman, E.S. and Mitchell, J.D. and Rhodes, J.A.},
	date-added = {2020-12-30 13:08:57 -0900},
	date-modified = {2020-12-30 13:09:46 -0900},
	doi = {10.1101/2020.02.13.948083},
	journal = {bioRxiv},
	title = {Gene tree discord, simplex plots, and statistical tests under the coalescent},
	year = {2020},
	Bdsk-Url-1 = {https://www.biorxiv.org/content/early/2020/02/13/2020.02.13.948083},
	Bdsk-Url-2 = {https://doi.org/10.1101/2020.02.13.948083}}

@article{RBMA2020,
	author = {Rhodes, J.A. and Ba{\~n}os, H. and Mitchell, J.D. and Allman, E.S.},
	doi = {10.1093/bioinformatics/btaa868},
	journal = {Bioinformatics},
	month = {10},
	title = {{MSCquartets 1.0: Quartet methods for species trees and networks under the multispecies coalescent model in R}},
	year = {2020},
	Bdsk-Url-1 = {https://doi.org/10.1093/bioinformatics/btaa868}}

@article{ABR19,
	author = {E.S. Allman and H. Ba{\~n}os and J.A. Rhodes},
	doi = {10.1186/s13015-019-0159-2},
	journal = {Algorithms Mol. Biol.},
	number = {24},
	pages = {1-25},
	title = {{NANUQ}: A method for inferring species networks from gene trees under the coalescent model},
	volume = {14},
	year = {2019},
	Bdsk-Url-1 = {https://doi.org/10.1186/s13015-019-0159-2}}

@article{SplitsTree,
	author = {D.H. Huson and D. Bryant},
	date-added = {2019-11-06 09:44:52 -0900},
	date-modified = {2019-11-06 13:57:53 -0900},
	journal = {Molecular Biology and Evolution},
	number = {2},
	pages = {254-267},
	title = {Application of Phylogenetic Networks in Evolutionary Studies},
	volume = {23},
	year = {2006}}

@article{HolmBonf79,
	author = {S. Holm},
	date-added = {2019-10-31 09:16:28 -0800},
	date-modified = {2019-10-31 09:18:40 -0800},
	journal = {Scand. J. Statist.},
	number = {2},
	pages = {65-70},
	title = {A simple sequentially rejective multiple test procedure},
	volume = {6},
	year = {1979}}

@article{simphy,
	author = {Mallo, D. and De Oliveira Martins, L. and Posada, D.},
	date-added = {2019-10-26 15:37:17 -0800},
	date-modified = {2019-10-27 17:19:04 -0800},
	doi = {10.1093/sysbio/syv082},
	journal = {Syst. Biol.},
	number = {2},
	pages = {334-344},
	title = {{SimPhy}: Phylogenomic Simulation of Gene, Locus, and Species Trees},
	url = {http://dx.doi.org/10.1093/sysbio/syv082},
	volume = {65},
	year = {2016},
	Bdsk-Url-1 = {http://dx.doi.org/10.1093/sysbio/syv082}}

@article{SayMir16,
	author = {E. Sayyari and S. Mirarab},
	date-added = {2019-10-26 09:04:24 -0800},
	date-modified = {2019-10-26 09:06:11 -0800},
	journal = {Mol. Biol. Evol.},
	number = {7},
	pages = {1654-1668},
	title = {Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies},
	volume = {33},
	year = {2016}}

@article{Martin2013,
	author = {Martin, S.H. and Dasmahapatra K.K. and Nadeau, N.J. and Salazar, C. and Walters, J.R. and Simpson, F. and Blaxter, M. and Manica, A. and Mallet, J. and Jiggins, C.D.},
	date-added = {2019-10-17 14:40:28 -0800},
	date-modified = {2019-10-17 14:40:28 -0800},
	journal = {Genome Res},
	pages = {1817-1828},
	title = {Genome-wide evidence for speciation with gene flow in {H}eliconius butterflies},
	volume = {23},
	year = {2013}}

@article{Rokas03,
	author = {Rokas, A. and Williams, B. and Carrol, S.},
	date-added = {2019-10-17 14:40:00 -0800},
	date-modified = {2019-10-17 14:40:39 -0800},
	journal = {Nature},
	month = {10},
	pages = {798--804},
	title = {Genome-scale approaches to resolving incongruence in molecular phylogenies},
	volume = {425},
	year = {2003}}

@article{CR84,
	author = {N. Cressie and T.R.C. Read},
	journal = {J. Royal Stat. Soc. B},
	number = {3},
	pages = {440-464},
	title = {Multinomial Goodness-Of-Fit Tests},
	volume = {46},
	year = {1984}}

@article{YR19,
	author = {S. Yourdkhani and J.A. Rhodes},
	doi = {10.1007/s11538-020-00773-4},
	journal = {Bul. Math. Biol.},
	number = {97},
	title = {Inferring metric trees from weighted quartets via an intertaxon distance},
	volume = {82},
	year = {2020},
	Bdsk-Url-1 = {https://doi.org/10.1007/s11538-020-00773-4}}

@article{MAR19,
	author = {J. Mitchell and E.S. Allman and J.A. Rhodes},
	doi = {10.1214/19-EJS1576},
	journal = {Electron. J. Statist.},
	number = {1},
	pages = {2150-2193},
	title = {Hypothesis testing near singularities and boundaries},
	volume = {13},
	year = {2019},
	Bdsk-Url-1 = {https://doi.org/10.1214/19-EJS1576}}

@article{Rho19,
	author = {J.A. Rhodes},
	date-added = {2019-05-15 13:07:37 -0800},
	date-modified = {2020-12-21 08:44:21 -0900},
	doi = {10.1109/TCBB.2019.2917204},
	journal = {IEEE/ACM Trans. Comput. Biol. Bioinform.},
	number = {6},
	pages = {2107-2118},
	title = {Topological metrizations of trees, and new quartet methods of tree inference},
	volume = {17},
	year = {2020},
	Bdsk-Url-1 = {https://doi.org/10.1109/TCBB.2019.2917204}}
