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@article{HansonSmith:2010fz,
author = {Hanson-Smith, Victor and Kolaczkowski, Bryan and Thornton, Joseph W},
title = {{Robustness of ancestral sequence reconstruction to phylogenetic uncertainty}},
journal = {Molecular Biology and Evolution},
year = {2010},
volume = {27},
number = {9},
pages = {1988--1999},
month = sep
}

@article{Ren:2005bi,
author = {Ren, Fengrong and Tanaka, Hiroshi and Yang, Ziheng},
title = {{An empirical examination of the utility of codon-substitution models in phylogeny reconstruction}},
journal = {Systematic Biology},
year = {2005},
volume = {54},
number = {5},
pages = {808--818},
month = oct
}

@article{Holder:2003jw,
author = {Holder, Mark and Lewis, Paul O},
title = {{Phylogeny estimation: traditional and Bayesian approaches}},
journal = {Nature Reviews Genetics},
year = {2003},
volume = {4},
number = {4},
pages = {275--284},
month = apr
}

@article{deQueiroz:2007di,
author = {de Queiroz, Kevin},
title = {{Species concepts and species delimitation}},
journal = {Systematic Biology},
year = {2007},
volume = {56},
number = {6},
pages = {879--886},
month = dec
}

@article{Suchard:2001we,
author = {Suchard, M A and Weiss, R E and Sinsheimer, J S},
title = {{Bayesian selection of continuous-time Markov chain evolutionary models}},
journal = {Molecular Biology and Evolution},
year = {2001},
volume = {18},
number = {6},
pages = {1001--1013},
month = jun
}

@article{Sisson:2005kb,
author = {Sisson, S A},
title = {{Transdimensional Markov chains: A decade of progress and future perspectives}},
journal = {Journal of the American Statistical Association},
year = {2005},
volume = {100},
number = {471},
pages = {1077--1089},
month = sep
}

@article{Slatkin:1991wx,
author = {Slatkin, M and Hudson, R R},
title = {{Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations}},
journal = {Genetics},
year = {1991},
volume = {129},
number = {2},
pages = {555--562},
month = oct
}

@article{Watterson:1975ur,
author = {Watterson, G A},
title = {{On the number of segregating sites in genetical models without recombination}},
journal = {Theoretical Population Biology},
year = {1975},
volume = {7},
number = {2},
pages = {256--276},
month = apr
}

@article{Kimura:1980vd,
author = {Kimura, M},
title = {{A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences}},
journal = {Journal of Molecular Evolution},
year = {1980},
volume = {16},
number = {2},
pages = {111--120},
month = dec
}

@article{Kumar:2012gv,
author = {Kumar, Sudhir and Filipski, Alan J and Battistuzzi, Fabia U and Kosakovsky Pond, Sergei L and Tamura, Koichiro},
title = {{Statistics and truth in phylogenomics}},
journal = {Molecular Biology and Evolution},
year = {2012},
volume = {29},
number = {2},
pages = {457--472},
month = feb
}

@article{Yu:2011ck,
author = {Yu, Yun and Than, Cuong and Degnan, James H and Nakhleh, Luay},
title = {{Coalescent histories on phylogenetic networks and detection of hybridization despite incomplete lineage sorting}},
journal = {Systematic Biology},
year = {2011},
volume = {60},
number = {2},
pages = {138--149},
month = mar
}

@article{Huelsenbeck:2007kz,
author = {Huelsenbeck, John P and Suchard, Marc A},
title = {{A nonparametric method for accommodating and testing across-site rate variation}},
journal = {Systematic Biology},
year = {2007},
volume = {56},
number = {6},
pages = {975--987},
month = dec
}

@article{Zhang:2013fu,
author = {Zhang, Jiajie and Kapli, Paschalia and Pavlidis, Pavlos and Stamatakis, Alexandros},
title = {{A general species delimitation method with applications to phylogenetic placements}},
journal = {Bioinformatics},
year = {2013},
volume = {29},
number = {22},
pages = {2869--2876}
}

@article{Kaplan:1991uk,
author = {Kaplan, N and Hudson, R R and Iizuka, M},
title = {{The coalescent process in models with selection, recombination and geographic subdivision}},
journal = {Genetical research},
year = {1991},
volume = {57},
number = {1},
pages = {83--91},
month = feb
}

@article{Paabo:2004kw,
author = {P{\"a}{\"a}bo, Svante and Poinar, Hendrik and Serre, David and Jaenicke-Despres, Viviane and Hebler, Juliane and Rohland, Nadin and Kuch, Melanie and Krause, Johannes and Vigilant, Linda and Hofreiter, Michael},
title = {{Genetic analyses from ancient DNA}},
journal = {Annual Review of Genetics},
year = {2004},
volume = {38},
number = {1},
pages = {645--679}
}

@article{Whelan:2001id,
author = {Whelan, S and Lio, P and Goldman, N},
title = {{Molecular phylogenetics: state-of-the-art methods for looking into the past}},
journal = {Trends in Genetics},
year = {2001},
volume = {17},
number = {5},
pages = {262--272},
month = may
}

@article{Sforza:1964ta,
author = {Sforza, Cavalli LL and Edwards, Anthony William Fairbank},
title = {{Reconstruction of evolutionary trees}},
journal = {in: Phenetic and Phylogenetic Classification},
year = {1964},
pages = {67--76}
}

@article{Heath:2012dr,
author = {Heath, Tracy A and Holder, Mark T and Huelsenbeck, John P},
title = {{A Dirichlet process prior for estimating lineage-specific substitution rates}},
journal = {Molecular Biology and Evolution},
year = {2012},
volume = {29},
number = {3},
pages = {939--955},
month = mar
}

@article{Leng:2011gf,
author = {Leng, Liang and Zhang, De-Xing},
title = {{Measuring population differentiation using GST or D? A simulation study with microsatellite DNA markers under a finite island model and nonequilibrium conditions}},
journal = {Molecular Ecology},
year = {2011},
volume = {20},
number = {12},
pages = {2494--2509},
month = jun
}

@article{Berger:1999eu,
author = {Berger, James O and Liseo, Brunero and Wolpert, Robert L},
title = {{Integrated likelihood methods for eliminating nuisance parameters}},
journal = {Statistical Science},
year = {1999},
volume = {14},
number = {1},
pages = {1--22},
month = feb
}

@article{Gernhard:2008jy,
author = {Gernhard, Tanja},
title = {{The conditioned reconstructed process}},
journal = {Journal of theoretical biology},
year = {2008},
volume = {253},
number = {4},
pages = {769--778},
month = aug
}

@article{Lewis:2015jf,
author = {Lewis, Paul O and Holder, Mark T and Swofford, David L},
title = {{Phycas: software for Bayesian phylogenetic analysis}},
journal = {Systematic Biology},
year = {2015},
volume = {64},
number = {3},
pages = {525--531},
month = may
}

@article{Gamble:2008fe,
author = {Gamble, Tony and Berendzen, Peter B and Shaffer, H Bradley and Starkey, David E and Simons, Andrew M},
title = {{Species limits and phylogeography of North American cricket frogs (Acris: Hylidae)}},
journal = {Molecular Phylogenetics and Evolution},
year = {2008},
volume = {48},
number = {1},
pages = {112--125},
month = jul
}

@article{McVean:2004ca,
author = {McVean, Gilean A T and Myers, Simon R and Hunt, Sarah and Deloukas, Panos and Bentley, David R and Donnelly, Peter},
title = {{The fine-scale structure of recombination rate variation in the human genome}},
journal = {Science},
year = {2004},
volume = {304},
number = {5670},
pages = {581--584},
month = apr
}

@article{Yang:2007gq,
author = {Yang, Ziheng},
title = {{Fair-balance paradox, star-tree paradox, and Bayesian phylogenetics}},
journal = {Molecular Biology and Evolution},
year = {2007},
volume = {24},
number = {8},
pages = {1639--1655},
month = aug
}

@article{Susko:2015ig,
author = {Susko, Edward},
title = {{Bayesian long branch attraction bias and corrections}},
journal = {Systematic Biology},
year = {2015},
volume = {64},
number = {2},
pages = {243--255},
month = mar
}

@article{Peskun:1973gi,
author = {Peskun, P H},
title = {{Optimum Monte-Carlo sampling using Markov chains}},
journal = {Biometrika},
year = {1973},
volume = {60},
number = {3},
pages = {607--612},
month = dec
}

@article{Yang:2002wz,
author = {Yang, Ziheng},
title = {{Likelihood and Bayes estimation of ancestral population sizes in hominoids using data from multiple loci}},
journal = {Genetics},
year = {2002},
volume = {162},
number = {4},
pages = {1811--1823},
month = dec
}

@article{Excoffier:2006kt,
author = {Excoffier, Laurent and Heckel, Gerald},
title = {{Computer programs for population genetics data analysis: a survival guide}},
journal = {Nature Reviews Genetics},
year = {2006},
volume = {7},
number = {10},
pages = {745--758},
month = oct
}

@article{Susko:2008ci,
author = {Susko, Edward},
title = {{On the distributions of bootstrap support and posterior distributions for a star tree}},
journal = {Systematic Biology},
year = {2008},
volume = {57},
number = {4},
pages = {602--612},
month = aug
}

@article{Rannala:2007kh,
author = {Rannala, Bruce and Yang, Ziheng},
title = {{Inferring speciation times under an episodic molecular clock}},
journal = {Systematic Biology},
year = {2007},
volume = {56},
number = {3},
pages = {453--466},
month = jun
}

@article{Leache:2014jg,
author = {Leach{\'e}, Adam D and Fujita, Matthew K and Minin, Vladimir N and Bouckaert, Remco R},
title = {{Species delimitation using genome-wide SNP data}},
journal = {Systematic Biology},
year = {2014},
volume = {63},
number = {4},
pages = {534--542},
month = jul
}

@article{Grimm:2015dq,
author = {Grimm, Guido W and Kapli, Paschalia and Bomfleur, Benjamin and McLoughlin, Stephen and Renner, Susanne S},
title = {{Using more than the oldest fossils: Dating osmundaceae with three Bayesian clock approaches}},
journal = {Systematic Biology},
year = {2015},
volume = {64},
number = {3},
pages = {396--405},
month = may
}

@article{Stadler:2013bp,
author = {Stadler, Tanja},
title = {{Recovering speciation and extinction dynamics based on phylogenies}},
journal = {Journal of evolutionary biology},
year = {2013},
volume = {26},
number = {6},
pages = {1203--1219},
month = jun
}

@article{Yang:1997tp,
author = {Yang, Z and Rannala, B},
title = {{Bayesian phylogenetic inference using DNA sequences: a Markov Chain Monte Carlo Method}},
journal = {Molecular Biology and Evolution},
year = {1997},
volume = {14},
number = {7},
pages = {717--724},
month = jul
}

@article{Hill:1974va,
author = {Hill, W G},
title = {{Estimation of linkage disequilibrium in randomly mating populations}},
journal = {Heredity},
year = {1974},
volume = {33},
number = {2},
pages = {229--239},
month = oct
}

@article{Mueller:2004ui,
author = {Mueller, Jakob C},
title = {{Linkage disequilibrium for different scales and applications}},
journal = {Briefings in bioinformatics},
year = {2004},
volume = {5},
number = {4},
pages = {355--364},
month = dec
}

@article{Stephens:2003je,
author = {Stephens, Matthew and Donnelly, Peter},
title = {{A comparison of bayesian methods for haplotype reconstruction from population genotype data}},
journal = {American Journal of Human Genetics},
year = {2003},
volume = {73},
number = {5},
pages = {1162--1169},
month = nov
}

@article{Semple:2006gs,
author = {Semple, C and Steel, M},
title = {{Unicyclic networks: compatibility and enumeration}},
journal = {Ieee-Acm Transactions on Computational Biology and Bioinformatics},
year = {2006},
volume = {3},
number = {1},
pages = {84--91}
}

@article{OReilly:2015ey,
author = {O'Reilly, Joseph E and Dos Reis, Mario and Donoghue, Philip C J},
title = {{Dating tips for divergence-time estimation}},
journal = {Trends in Genetics},
year = {2015},
volume = {31},
number = {11},
pages = {637--650},
month = nov
}

@article{Wright:1931ub,
author = {Wright, S},
title = {{Evolution in Mendelian populations}},
journal = {Genetics},
year = {1931},
volume = {16},
number = {2},
pages = {97--159},
month = mar
}

@article{Beaumont:2002ue,
author = {Beaumont, Mark A and Zhang, Wenyang and Balding, David J},
title = {{Approximate Bayesian computation in population genetics}},
journal = {Genetics},
year = {2002},
volume = {162},
number = {4},
pages = {2025--2035},
month = dec
}

@article{Griffiths:1994iz,
author = {Griffiths, R C and Tavar{\'e}, S},
title = {{Sampling theory for neutral alleles in a varying environment}},
journal = {Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences},
year = {1994},
volume = {344},
number = {1310},
pages = {403--410},
month = jun
}

@article{Collins:2014jl,
author = {Collins, Rupert A and Cruickshank, Robert H},
title = {{Known knowns, known unknowns, unknown unknowns and unknown knowns in DNA barcoding: a comment on Dowton et al.}},
journal = {Systematic Biology},
year = {2014},
volume = {63},
number = {6},
pages = {1005--1009},
month = nov
}

@article{Hohna:2011hd,
author = {H{\"o}hna, Sebastian and Stadler, Tanja and Ronquist, Fredrik and Britton, Tom},
title = {{Inferring speciation and extinction rates under different sampling schemes}},
journal = {Molecular Biology and Evolution},
year = {2011},
volume = {28},
number = {9},
pages = {2577--2589},
month = sep
}

@article{Yang:1994vo,
author = {Yang, Z},
title = {{Estimating the pattern of nucleotide substitution}},
journal = {Journal of Molecular Evolution},
year = {1994},
volume = {39},
number = {1},
pages = {105--111},
month = jul
}

@article{Nee:1994ty,
author = {Nee, Sean and May, Robert M and Harvey, Paul H},
title = {{The reconstructed evolutionary process}},
journal = {Philosophical Transactions of the Royal Society B: Biological Sciences},
year = {1994},
volume = {344},
number = {1309},
pages = {305--311}
}

@article{Yang:2000jv,
author = {Yang, Z},
title = {{Complexity of the simplest phylogenetic estimation problem}},
journal = {Proceedings of the Royal Society B: Biological Sciences},
year = {2000},
volume = {267},
number = {1439},
pages = {109--116},
month = jan
}

@article{Watson:1953jg,
author = {Watson, J D and Crick, F H C},
title = {{Molecular structure of Nucleic Acids: a structure for Deoxyribose Nucleic Acid}},
journal = {Nature},
year = {1953},
volume = {171},
number = {4356},
pages = {737--738}
}

@article{BouchardCote:2013ga,
author = {Bouchard-C{\^o}t{\'e}, Alexandre and Jordan, Michael I},
title = {{Evolutionary inference via the Poisson Indel Process}},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
year = {2013},
volume = {110},
number = {4},
pages = {1160--1166},
month = jan
}

@article{Heath:2012dk,
author = {Heath, Tracy A},
title = {{A hierarchical Bayesian model for calibrating estimates of species divergence times}},
journal = {Systematic Biology},
year = {2012},
volume = {61},
number = {5},
pages = {793--809},
month = oct
}

@article{Excoffier:2010cc,
author = {Excoffier, Laurent and Lischer, Heidi E L},
title = {{Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows}},
journal = {Molecular ecology resources},
year = {2010},
volume = {10},
number = {3},
pages = {564--567},
month = may
}

@article{Huelsenbeck:2001id,
author = {Huelsenbeck, J P and Ronquist, F and Nielsen, R and Bollback, J P},
title = {{Bayesian inference of phylogeny and its impact on evolutionary biology}},
journal = {Science},
year = {2001},
volume = {294},
number = {5550},
pages = {2310--2314},
month = dec
}

@article{Nielsen:2006en,
author = {Nielsen, Rasmus and Matz, Mikhail},
title = {{Statistical approaches for DNA barcoding}},
journal = {Systematic Biology},
year = {2006},
volume = {55},
number = {1},
pages = {162--169},
month = feb
}

@article{Redelings:2005et,
author = {Redelings, Benjamin D and Suchard, Marc A},
title = {{Joint Bayesian estimation of alignment and phylogeny}},
journal = {Systematic Biology},
year = {2005},
volume = {54},
number = {3},
pages = {401--418},
month = jun
}

@article{Kumar:2016hy,
author = {Kumar, Sudhir and Hedges, S Blair},
title = {{Advances in time estimation methods for molecular data}},
journal = {Molecular Biology and Evolution},
year = {2016},
volume = {33},
number = {4},
pages = {863--869},
month = apr
}

@article{Yu:2012hh,
author = {Yu, Yun and Degnan, James H and Nakhleh, Luay},
title = {{The probability of a gene tree topology within a phylogenetic network with applications to hybridization detection}},
journal = {PLoS genetics},
year = {2012},
volume = {8},
number = {4},
pages = {e1002660}
}

@article{Stadler:2012hn,
author = {Stadler, Tanja and Kouyos, Roger and von Wyl, Viktor and Yerly, Sabine and B{\"o}ni, J{\"u}rg and B{\"u}rgisser, Philippe and Klimkait, Thomas and Joos, Beda and Rieder, Philip and Xie, Dong and G{\"u}nthard, Huldrych F and Drummond, Alexei J and Bonhoeffer, Sebastian and {Swiss HIV Cohort Study}},
title = {{Estimating the basic reproductive number from viral sequence data}},
journal = {Molecular Biology and Evolution},
year = {2012},
volume = {29},
number = {1},
pages = {347--357},
month = jan
}

@article{Charlesworth:2009jz,
author = {Charlesworth, Brian},
title = {{Effective population size and patterns of molecular evolution and variation}},
journal = {Nature Reviews Genetics},
year = {2009},
volume = {10},
number = {3},
pages = {195--205},
month = mar
}

@article{Hartmann:2010db,
author = {Hartmann, Klaas and Wong, Dennis and Stadler, Tanja},
title = {{Sampling trees from evolutionary models}},
journal = {Systematic Biology},
year = {2010},
volume = {59},
number = {4},
pages = {465--476},
month = jul
}

@article{Xie:2011it,
author = {Xie, Wangang and Lewis, Paul O and Fan, Yu and Kuo, Lynn and Chen, Ming-Hui},
title = {{Improving marginal likelihood estimation for Bayesian phylogenetic model selection}},
journal = {Systematic Biology},
year = {2011},
volume = {60},
number = {2},
pages = {150--160},
month = mar
}

@article{Brown:2014ex,
author = {Brown, Jeremy M},
title = {{Predictive approaches to assessing the fit of evolutionary models}},
journal = {Systematic Biology},
year = {2014},
volume = {63},
number = {3},
pages = {289--292},
month = may
}

@article{Takezaki:2008hd,
author = {Takezaki, Naoko and Nei, Masatoshi},
title = {{Empirical tests of the reliability of phylogenetic trees constructed with microsatellite DNA}},
journal = {Genetics},
year = {2008},
volume = {178},
number = {1},
pages = {385--392},
month = jan
}

@article{Minin:2003vn,
author = {Minin, Vladimir and Abdo, Zaid and Joyce, Paul and Sullivan, Jack},
title = {{Performance-based selection of likelihood models for phylogeny estimation}},
journal = {Systematic Biology},
year = {2003},
volume = {52},
number = {5},
pages = {674--683},
month = oct
}

@article{Hedrick:1987vk,
author = {Hedrick, P W},
title = {{Gametic disequilibrium measures: proceed with caution}},
journal = {Genetics},
year = {1987},
volume = {117},
number = {2},
pages = {331--341},
month = oct
}

@article{Huelsenbeck:2000ic,
author = {Huelsenbeck, J P and Larget, B and Swofford, David L},
title = {{A compound poisson process for relaxing the molecular clock}},
journal = {Genetics},
year = {2000},
volume = {154},
number = {4},
pages = {1879--1892},
month = apr
}

@article{Zhu:2012hu,
author = {Zhu, Tianqi and Yang, Ziheng},
title = {{Maximum likelihood implementation of an isolation-with-migration model with three species for testing speciation with gene flow}},
journal = {Molecular Biology and Evolution},
year = {2012},
volume = {29},
number = {10},
pages = {3131--3142},
month = oct
}

@article{Guindon:2010gf,
author = {Guindon, St{\'e}phane and Dufayard, Jean-Fran{\c c}ois and Lefort, Vincent and Anisimova, Maria and Hordijk, Wim and Gascuel, Olivier},
title = {{New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0}},
journal = {Systematic Biology},
year = {2010},
volume = {59},
number = {3},
pages = {307--321},
month = may
}

@article{Pritchard:2000uv,
author = {Pritchard, J K and Stephens, M and Donnelly, P},
title = {{Inference of population structure using multilocus genotype data}},
journal = {Genetics},
year = {2000},
volume = {155},
number = {2},
pages = {945--959},
month = jun
}

@article{Heath:2014hn,
author = {Heath, Tracy A and Huelsenbeck, John P and Stadler, Tanja},
title = {{The fossilized birth-death process for coherent calibration of divergence-time estimates}},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
year = {2014},
volume = {111},
number = {29},
pages = {E2957--66},
month = jul
}

@article{Rannala:2008im,
author = {Rannala, Bruce and Yang, Ziheng},
title = {{Phylogenetic inference using whole Genomes}},
journal = {Annual Review of Genomics and Human Genetics},
year = {2008},
volume = {9},
number = {1},
pages = {217--231}
}

@article{Griffiths:1996vt,
author = {Griffiths, R C and Tavar{\'e}, S},
title = {{Monte Carlo inference methods in population genetics}},
journal = {Mathematical and Computer Modelling},
year = {1996},
volume = {23},
number = {8-9},
pages = {141--158}
}

@article{Huelsenbeck:2008gz,
author = {Huelsenbeck, John P and Ane, Cecile and Larget, Bret and Ronquist, Fredrik},
title = {{A Bayesian perspective on a non-parsimonious parsimony model}},
journal = {Systematic Biology},
year = {2008},
volume = {57},
number = {3},
pages = {406--419}
}

@article{Brown:2010hj,
author = {Brown, Jeremy M and Hedtke, Shannon M and Lemmon, Alan R and Lemmon, Emily Moriarty},
title = {{When trees grow too long: investigating the causes of highly inaccurate bayesian branch-length estimates}},
journal = {Systematic Biology},
year = {2010},
volume = {59},
number = {2},
pages = {145--161},
month = mar
}

@article{Szollosi:2013hs,
author = {Sz{\"o}ll{\H o}si, Gergely J and Tannier, Eric and Lartillot, Nicolas and Daubin, Vincent},
title = {{Lateral gene transfer from the dead}},
journal = {Systematic Biology},
year = {2013},
volume = {62},
number = {3},
pages = {386--397},
month = may
}

@article{Valdes:1993ww,
author = {Valdes, A M and Slatkin, M and Freimer, N B},
title = {{Allele frequencies at microsatellite loci: the stepwise mutation model revisited}},
journal = {Genetics},
year = {1993},
volume = {133},
number = {3},
pages = {737--749},
month = mar
}

@article{BouchardCote:2012ie,
author = {Bouchard-C{\^o}t{\'e}, Alexandre and Sankararaman, Sriram and Jordan, Michael I},
title = {{Phylogenetic inference via sequential Monte Carlo}},
journal = {Systematic Biology},
year = {2012},
volume = {61},
number = {4},
pages = {579--593},
month = jul
}

@article{Liu:2007du,
author = {Liu, Liang and Pearl, Dennis K},
title = {{Species trees from gene trees: reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions}},
journal = {Systematic Biology},
year = {2007},
volume = {56},
number = {3},
pages = {504--514},
month = jun
}

@article{Hellenthal:2006dy,
author = {Hellenthal, Garrett and Stephens, Matthew},
title = {{Insights into recombination from population genetic variation}},
journal = {Current opinion in genetics {\&} development},
year = {2006},
volume = {16},
number = {6},
pages = {565--572},
month = dec
}

@article{Hohna:2008ec,
author = {H{\"o}hna, Sebastian and Defoin-Platel, Michael and Drummond, Alexei J},
title = {{Clock-constrained tree proposal operators in Bayesian phylogenetic inference}},
journal = {8th IEEE International Conference on Bioinformatics and BioEngineering (BIBE)},
year = {2008},
pages = {1--7}
}

@article{Leache:2010ks,
author = {Leach{\'e}, Adam D and Fujita, Matthew K},
title = {{Bayesian species delimitation in West African forest geckos (Hemidactylus fasciatus)}},
journal = {Proceedings of the Royal Society B: Biological Sciences},
year = {2010},
volume = {277},
number = {1697},
pages = {3071--3077},
month = oct
}

@article{Neher:2014eu,
author = {Neher, Richard A and Russell, Colin A and Shraiman, Boris I},
title = {{Predicting evolution from the shape of genealogical trees}},
journal = {eLife},
year = {2014},
volume = {3},
pages = {e03568}
}

@article{Varki:2008kt,
author = {Varki, Ajit and Geschwind, Daniel H and Eichler, Evan E},
title = {{Explaining human uniqueness: genome interactions with environment, behaviour and culture}},
journal = {Nature Reviews Genetics},
year = {2008},
volume = {9},
number = {10},
pages = {749--763},
month = oct
}

@article{Frazer:2009hg,
author = {Frazer, Kelly A and Murray, Sarah S and Schork, Nicholas J and Topol, Eric J},
title = {{Human genetic variation and its contribution to complex traits}},
journal = {Nature Reviews Genetics},
year = {2009},
volume = {10},
number = {4},
pages = {241--251},
month = apr
}

@article{Rosenberg:2002ff,
author = {Rosenberg, Noah A and Nordborg, Magnus},
title = {{Genealogical trees, coalescent theory and the analysis of genetic polymorphisms}},
journal = {Nature Reviews Genetics},
year = {2002},
volume = {3},
number = {5},
pages = {380--390},
month = may
}

@article{Green:1995ut,
author = {Green, P J},
title = {{Reversible jump Markov chain Monte Carlo computation and Bayesian model determination}},
journal = {Biometrika},
year = {1995},
volume = {82},
number = {4},
pages = {711--732},
month = dec
}

@article{McVean:2002ws,
author = {McVean, Gil and Awadalla, Philip and Fearnhead, Paul},
title = {{A coalescent-based method for detecting and estimating recombination from gene sequences.}},
journal = {Genetics},
year = {2002},
volume = {160},
number = {3},
pages = {1231--1241},
month = mar
}

@article{Fujita:2011gy,
author = {Fujita, Matthew K and Leach{\'e}, Adam D},
title = {{A coalescent perspective on delimiting and naming species: a reply to Bauer et al.}},
journal = {Proceedings of the Royal Society B: Biological Sciences},
year = {2011},
volume = {278},
number = {1705},
pages = {493--495},
month = feb
}

@article{Rannala:2013gk,
author = {Rannala, Bruce and Yang, Ziheng},
title = {{Improved reversible jump algorithms for Bayesian species delimitation}},
journal = {Genetics},
year = {2013},
volume = {194},
number = {1},
pages = {245--253},
month = may
}

@article{Gaunt:2007dv,
author = {Gaunt, Tom R and Rodriguez, Santiago and Day, Ian N M},
title = {{Cubic exact solutions for the estimation of pairwise haplotype frequencies: implications for linkage disequilibrium analyses and a web tool 'CubeX'}},
journal = {Bmc Bioinformatics},
year = {2007},
volume = {8},
number = {1}
}

@article{Takahata:1995kl,
author = {Takahata, N and Satta, Y and Klein, J},
title = {{Divergence time and population size in the lineage leading to modern humans}},
journal = {Theoretical Population Biology},
year = {1995},
volume = {48},
number = {2},
pages = {198--221},
month = oct
}

@article{Leache:2011bt,
author = {Leach{\'e}, Adam D and Rannala, Bruce},
title = {{The accuracy of species tree estimation under simulation: a comparison of methods}},
journal = {Systematic Biology},
year = {2011},
volume = {60},
number = {2},
pages = {126--137},
month = mar
}

@article{Lewis:2001wu,
author = {Lewis, P O},
title = {{A likelihood approach to estimating phylogeny from discrete morphological character data}},
journal = {Systematic Biology},
year = {2001},
volume = {50},
number = {6},
pages = {913--925},
month = nov
}

@article{Brooks:1998tg,
author = {Brooks, S P},
title = {{Markov chain Monte Carlo method and its application}},
journal = {Journal of the Royal Statistical Society Series D-the Statistician},
year = {1998},
volume = {47},
number = {1},
pages = {69--100}
}

@article{Gavryushkina:2014fw,
author = {Gavryushkina, Alexandra and Welch, David and Stadler, Tanja and Drummond, Alexei J},
title = {{Bayesian inference of sampled ancestor trees for epidemiology and fossil calibration}},
journal = {PLoS Computational Biology},
year = {2014},
volume = {10},
number = {12},
pages = {e1003919},
month = dec
}

@article{Lambert:2013cs,
author = {Lambert, Amaury and Stadler, Tanja},
title = {{Birth-death models and coalescent point processes: The shape and probability of reconstructed phylogenies}},
journal = {Theoretical Population Biology},
year = {2013},
volume = {90},
pages = {113--128},
month = dec
}

@article{Sanger:1977vp,
author = {Sanger, Frederick and Nicklen, Steven and Coulson, Alan R},
title = {{DNA sequencing with chain-terminating inhibitors}},
journal = {Proceedings of the National Academy of Sciences},
year = {1977},
volume = {74},
number = {12},
pages = {5463--5467}
}

@article{Choi:2011fj,
author = {Choi, Sang Chul and Hey, Jody},
title = {{Joint inference of population assignment and demographic history}},
journal = {Genetics},
year = {2011},
volume = {189},
number = {2},
pages = {561--577},
month = oct
}

@article{Metropolis:1953vj,
author = {Metropolis, N and Rosenbluth, A W and Rosenbluth, M N and Teller, A H and Teller, E},
title = {{Equation of state calculations by fast computing machines}},
journal = {Journal of Chemical Physics},
year = {1953},
volume = {21},
pages = {1087--1092}
}

@book{Felsenstein:2004ws,
author = {Felsenstein, Joseph},
title = {{Inferring phylogenies}},
publisher = {Sinauer associates Sunderland},
year = {2004}
}

@article{Edwards:1970dz,
author = {Edwards, A W F},
title = {{Estimation of the branch points of a branching diffusion process}},
journal = {Journal of the Royal Statistical Society. Series B (Methodological)},
year = {1970},
volume = {32},
number = {2},
pages = {155--174},
month = jan
}

@article{Leache:2007ke,
author = {Leach{\'e}, Adam D and Mulcahy, Daniel G},
title = {{Phylogeny, divergence times and species limits of spiny lizards (Sceloporus magister species group) in western North American deserts and Baja California}},
journal = {Molecular Ecology},
year = {2007},
volume = {16},
number = {24},
pages = {5216--5233},
month = dec
}

@article{Gavryushkina:2013ia,
author = {Gavryushkina, Alexandra and Welch, David and Drummond, Alexei J},
title = {{Recursive algorithms for phylogenetic tree counting}},
journal = {Algorithms for Molecular Biology},
year = {2013},
volume = {8},
number = {1}
}

@article{Hastings:1970ew,
author = {Hastings, W K},
title = {{Monte Carlo sampling methods using Markov chains and their applications}},
journal = {Biometrika},
year = {1970},
volume = {57},
number = {1},
pages = {97--109},
month = apr
}

@article{Yang:2012jc,
author = {Yang, Ziheng and Rannala, Bruce},
title = {{Molecular phylogenetics: principles and practice}},
journal = {Nature Reviews Genetics},
year = {2012},
volume = {13},
number = {5},
pages = {303--314},
month = may
}

@article{Liu:2009jh,
author = {Liu, Kevin and Raghavan, Sindhu and Nelesen, Serita and Linder, C Randal and Warnow, Tandy},
title = {{Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees}},
journal = {Science},
year = {2009},
volume = {324},
number = {5934},
pages = {1561--1564}
}

@article{Rannala:2003vt,
author = {Rannala, Bruce and Yang, Ziheng},
title = {{Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci}},
journal = {Genetics},
year = {2003},
volume = {164},
number = {4},
pages = {1645--1656},
month = aug
}

@article{Degnan:2009hr,
author = {Degnan, James H and Rosenberg, Noah A},
title = {{Gene tree discordance, phylogenetic inference and the multispecies coalescent}},
journal = {Trends in Ecology {\&} Evolution},
year = {2009},
volume = {24},
number = {6},
pages = {332--340},
month = jun
}

@article{Heled:2008et,
author = {Heled, Joseph and Drummond, Alexei J},
title = {{Bayesian inference of population size history from multiple loci}},
journal = {BMC Evolutionary Biology},
year = {2008},
volume = {8},
number = {1},
pages = {289}
}

@article{Yang:1995th,
author = {Yang, Z and Kumar, S and Nei, M},
title = {{A new method of inference of ancestral nucleotide and amino acid sequences}},
journal = {Genetics},
year = {1995},
volume = {141},
number = {4},
pages = {1641--1650},
month = dec
}

@article{Fu:1993ts,
author = {Fu, Y X and Li, W H},
title = {{Statistical tests of neutrality of mutations}},
journal = {Genetics},
year = {1993},
volume = {133},
number = {3},
pages = {693--709},
month = mar
}

@article{Stephens:2000dw,
author = {Stephens, Matthew and Donnelly, Peter},
title = {{Inference in molecular population genetics}},
journal = {Journal of the Royal Statistical Society Series B-Statistical Methodology},
year = {2000},
volume = {62},
number = {4},
pages = {605--655},
month = jan
}

@article{Li:2000cy,
author = {Li, Shuying and Pearl, Dennis K and Doss, Hani},
title = {{Phylogenetic tree construction using Markov chain Monte Carlo}},
journal = {Journal of the American Statistical Association},
year = {2000},
volume = {95},
number = {450},
pages = {508},
month = jun
}

@article{Jukes:1969wx,
author = {Jukes, T H and Cantor, C R},
title = {{Evolution of protein molecules}},
journal = {Mammalian Protein Metabolism},
year = {1969},
number = {ed. H. N. Munro},
pages = {21--132}
}

@article{Harrison:2015cy,
author = {Harrison, Luke B and Larsson, Hans C E},
title = {{Among-character rate variation distributions in phylogenetic analysis of discrete morphological characters}},
journal = {Systematic Biology},
year = {2015},
volume = {64},
number = {2},
pages = {307--324},
month = mar
}

@article{SabetiPC:2006ha,
author = {{Sabeti, P. C.} and Schaffner, S F and Fry, B and Lohmueller, J and Varilly, P and Shamovsky, O and Palma, A and Mikkelsen, T S and Altshuler, D and Lander, E S},
title = {{Positive natural selection in the human lineage}},
journal = {Science},
year = {2006},
volume = {312},
number = {5780},
pages = {1614--1620},
month = jun
}

@article{Rannala:2012ke,
author = {Rannala, Bruce and Zhu, Tianqi and Yang, Ziheng},
title = {{Tail paradox, partial identifiability, and influential priors in Bayesian branch length inference}},
journal = {Molecular Biology and Evolution},
year = {2012},
volume = {29},
number = {1},
pages = {325--335},
month = jan
}

@article{Yang:2005iu,
author = {Yang, Ziheng and Rannala, Bruce},
title = {{Branch-length prior influences Bayesian posterior probability of phylogeny}},
journal = {Systematic Biology},
year = {2005},
volume = {54},
number = {3},
pages = {455--470},
month = jun
}

@article{CHIB:2001gq,
author = {CHIB, S and Jeliazkov, I},
title = {{Marginal likelihood from the Metropolis-Hastings output}},
journal = {Journal of the American Statistical Association},
year = {2001},
volume = {96},
number = {453},
pages = {270--281},
month = mar
}

@article{Lindley:1957vo,
author = {Lindley, D V},
title = {{A statistical paradox}},
journal = {Biometrika},
year = {1957},
volume = {44},
number = {1-2},
pages = {187--192}
}

@article{Stadler:2013dc,
author = {Stadler, Tanja and Bokma, Folmer},
title = {{Estimating speciation and extinction rates for phylogenies of higher taxa}},
journal = {Systematic Biology},
year = {2013},
volume = {62},
number = {2},
pages = {220--230},
month = mar
}

@article{Beerenwinkel:2015eb,
author = {Beerenwinkel, Niko and Schwarz, Roland F and Gerstung, Moritz and Markowetz, Florian},
title = {{Cancer evolution: mathematical models and computational inference}},
journal = {Systematic Biology},
year = {2015},
volume = {64},
number = {1},
pages = {E1--E25},
month = jan
}

@article{Zhai:2009dv,
author = {Zhai, Weiwei and Nielsen, Rasmus and Slatkin, Montgomery},
title = {{An investigation of the statistical power of neutrality tests based on comparative and population genetic data}},
journal = {Molecular Biology and Evolution},
year = {2009},
volume = {26},
number = {2},
pages = {273--283},
month = feb
}

@article{Brown:2007ee,
author = {Brown, Jeremy M and Lemmon, Alan R},
title = {{The importance of data partitioning and the utility of Bayes factors in Bayesian phylogenetics}},
journal = {Systematic Biology},
year = {2007},
volume = {56},
number = {4},
pages = {643--655},
month = aug
}

@article{Rannala:q4RoHlBN,
author = {Rannala, Bruce and Yang, Ziheng},
title = {{Efficient Bayesian species tree inference under the multi-species coalescent}},
year = {2015}
}

@article{Pritchard:2001dj,
author = {Pritchard, J K and Przeworski, M},
title = {{Linkage disequilibrium in humans: models and data}},
journal = {American Journal of Human Genetics},
year = {2001},
volume = {69},
number = {1},
pages = {1--14},
month = jul
}

@article{Yang:2005hn,
author = {Yang, Z and Wong, WSW and Nielsen, R},
title = {{Bayes empirical Bayes inference of amino acid sites under positive selection}},
journal = {Molecular Biology and Evolution},
year = {2005},
volume = {22},
number = {4},
pages = {1107--1118},
month = apr
}

@article{McVean:2005ho,
author = {McVean, Gilean A T and Cardin, Niall J},
title = {{Approximating the coalescent with recombination}},
journal = {Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences},
year = {2005},
volume = {360},
number = {1459},
pages = {1387--1393},
month = jul
}

@article{Hedges:2004cl,
author = {Hedges, S Blair and Kumar, Sudhir},
title = {{Precision of molecular time estimates}},
journal = {Trends in Genetics},
year = {2004},
volume = {20},
number = {5},
pages = {242--247},
month = may
}

@article{Hudson:1990vo,
author = {Hudson, R R},
title = {{Gene genealogies and the coalescent process}},
journal = {Oxford Surveys in Evolutionary Biology},
year = {1990},
volume = {7},
pages = {1--44}
}

@article{Baele:2012gx,
author = {Baele, Guy and Lemey, Philippe and Bedford, Trevor and Rambaut, Andrew and Suchard, Marc A and Alekseyenko, Alexander V},
title = {{Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty}},
journal = {Molecular Biology and Evolution},
year = {2012},
volume = {29},
number = {9},
pages = {2157--2167},
month = sep
}

@article{Mau:1997wh,
author = {Mau, Bob and Newton, Michael A},
title = {{Phylogenetic inference for binary data on dendrograms using Markov chain Monte Carlo}},
journal = {Journal of Computational and Graphical Statistics},
year = {1997},
volume = {6},
number = {1},
pages = {122--131}
}

@article{Kingman:2000uy,
author = {Kingman, J F},
title = {{Origins of the coalescent. 1974-1982}},
journal = {Genetics},
year = {2000},
volume = {156},
number = {4},
pages = {1461--1463},
month = dec
}

@article{Liu:2010bw,
author = {Liu, Liang and Yu, Lili and Edwards, Scott V},
title = {{A maximum pseudo-likelihood approach for estimating species trees under the coalescent model}},
journal = {BMC Evolutionary Biology},
year = {2010},
volume = {10},
number = {1},
pages = {302}
}

@article{Silvestro:2014co,
author = {Silvestro, Daniele and Schnitzler, Jan and Liow, Lee Hsiang and Antonelli, Alexandre and Salamin, Nicolas},
title = {{Bayesian estimation of speciation and extinction from incomplete fossil occurrence data}},
journal = {Systematic Biology},
year = {2014},
volume = {63},
number = {3},
pages = {349--367},
month = may
}

@article{Suchard:2009dj,
author = {Suchard, Marc A and Rambaut, Andrew},
title = {{Many-core algorithms for statistical phylogenetics}},
journal = {Bioinformatics},
year = {2009},
volume = {25},
number = {11},
pages = {1370--1376}
}

@article{Brooks:2003jk,
author = {Brooks, S P and Giudici, P and Roberts, G O},
title = {{Efficient construction of reversible jump Markov chain Monte Carlo proposal distributions}},
journal = {Journal of the Royal Statistical Society Series B-Statistical Methodology},
year = {2003},
volume = {65},
number = {1},
pages = {3--55},
month = jan
}

@article{Yang:1997ts,
author = {Yang, Z},
title = {{PAML: a program package for phylogenetic analysis by maximum likelihood}},
journal = {Computer applications in the biosciences : CABIOS},
year = {1997},
volume = {13},
number = {5},
pages = {555--556},
month = oct
}

@article{Rogers:2014ka,
author = {Rogers, Jeffrey and Gibbs, Richard A},
title = {{Comparative primate genomics: emerging patterns of genome content and dynamics}},
journal = {Nature Reviews Genetics},
year = {2014},
volume = {15},
number = {5},
pages = {347--359},
month = may
}

@article{Excoffier:1995ux,
author = {Excoffier, L and Slatkin, M},
title = {{Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population}},
journal = {Molecular Biology and Evolution},
year = {1995},
volume = {12},
number = {5},
pages = {921--927},
month = sep
}

@article{Zhang:2014dy,
author = {Zhang, Chi and Rannala, Bruce and Yang, Ziheng},
title = {{Bayesian species delimitation can be robust to guide-tree inference errors}},
journal = {Systematic Biology},
year = {2014},
volume = {63},
number = {6},
pages = {993--1004},
month = nov
}

@article{Huelsenbeck:2001vw,
author = {Huelsenbeck, J P and Bollback, J P},
title = {{Empirical and hierarchical Bayesian estimation of ancestral states}},
journal = {Systematic Biology},
year = {2001},
volume = {50},
number = {3},
pages = {351--366},
month = jun
}

@article{Lewontin:1988vx,
author = {Lewontin, R C},
title = {{On measures of gametic disequilibrium}},
journal = {Genetics},
year = {1988},
volume = {120},
number = {3},
pages = {849--852},
month = nov
}

@article{Twyford:2012bw,
author = {Twyford, A D and Ennos, R A},
title = {{Next-generation hybridization and introgression}},
journal = {Heredity},
year = {2012},
volume = {108},
number = {3},
pages = {179--189},
month = mar
}

@article{Marjoram:2003fn,
author = {Marjoram, Paul and Molitor, John and Plagnol, Vincent and Tavar{\'e}, Simon},
title = {{Markov chain Monte Carlo without likelihoods}},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
year = {2003},
volume = {100},
number = {26},
pages = {15324--15328},
month = dec
}

@article{Yang:2015uc,
author = {Yang, Ziheng},
title = {{The BPP program for species tree estimation and species delimitation}},
journal = {Current Zoology},
year = {2015},
volume = {61},
number = {5},
pages = {854--865},
month = oct
}

@article{Ho:2009gn,
author = {Ho, Simon Y W and Phillips, Matthew J},
title = {{Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times}},
journal = {Systematic Biology},
year = {2009},
volume = {58},
number = {3},
pages = {367--380},
month = jun
}

@article{Hohna:2012fg,
author = {H{\"o}hna, Sebastian and Drummond, Alexei J},
title = {{Guided tree topology proposals for Bayesian phylogenetic inference}},
journal = {Systematic Biology},
year = {2012},
volume = {61},
number = {1},
pages = {1--11},
month = jan
}

@article{Nichols:2001jl,
author = {Nichols, Richard},
title = {{Gene trees and species trees are not the same}},
journal = {Trends in Ecology {\&} Evolution},
year = {2001},
volume = {16},
number = {7},
pages = {358--364},
month = jul
}

@article{Nielsen:2001ww,
author = {Nielsen, R and Wakeley, J},
title = {{Distinguishing migration from isolation: a Markov chain Monte Carlo approach}},
journal = {Genetics},
year = {2001},
volume = {158},
number = {2},
pages = {885--896},
month = jun
}

@article{Abecasis:2000vq,
author = {Abecasis, G R and Cookson, W O},
title = {{GOLD--graphical overview of linkage disequilibrium}},
journal = {Bioinformatics},
year = {2000},
volume = {16},
number = {2},
pages = {182--183},
month = feb
}

@article{Rannala:2002bp,
author = {Rannala, Bruce},
title = {{Identifiability of Parameters in MCMC Bayesian Inference of Phylogeny}},
journal = {Systematic Biology},
year = {2002},
volume = {51},
number = {5},
pages = {754--760},
month = sep
}

@article{Yu:2014dt,
author = {Yu, Yun and Dong, Jianrong and Liu, Kevin J and Nakhleh, Luay},
title = {{Maximum likelihood inference of reticulate evolutionary histories}},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
year = {2014},
volume = {111},
number = {46},
pages = {16448--16453}
}

@article{Cardona:2008dj,
author = {Cardona, Gabriel and Rossell{\'o}, Francesc and Valiente, Gabriel},
title = {{Extended Newick: it is time for a standard representation of phylogenetic networks}},
journal = {Bmc Bioinformatics},
year = {2008},
volume = {9},
number = {1},
pages = {532}
}

@article{Lartillot:2015bj,
author = {Lartillot, Nicolas},
title = {{Probabilistic models of eukaryotic evolution: time for integration}},
journal = {Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences},
year = {2015},
volume = {370},
number = {1678}
}

@article{Williams:2006eo,
author = {Williams, Paul D and Pollock, David D and Blackburne, Benjamin P and Goldstein, Richard A},
title = {{Assessing the accuracy of ancestral protein reconstruction methods}},
journal = {PLoS Computational Biology},
year = {2006},
volume = {2},
number = {6},
pages = {e69},
month = jun
}

@article{Hasegawa:1985ww,
author = {Hasegawa, M and Kishino, H and Yano, T},
title = {{Dating of the human-ape splitting by a molecular clock of mitochondrial DNA}},
journal = {Journal of Molecular Evolution},
year = {1985},
volume = {22},
number = {2},
pages = {160--174}
}

@article{Kingman:1982kq,
author = {Kingman, J F C},
title = {{On the genealogy of large populations}},
journal = {Journal of Applied Probability},
year = {1982},
volume = {19},
pages = {27--43}
}

@article{Szollosi:2012el,
author = {Sz{\"o}ll{\H o}si, Gergely J and Boussau, Bastien and Abby, Sophie S and Tannier, Eric and Daubin, Vincent},
title = {{Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations}},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
year = {2012},
volume = {109},
number = {43},
pages = {17513--17518},
month = oct
}

@article{Rannala:1996tb,
author = {Rannala, B and Yang, Z},
title = {{Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference}},
journal = {Journal of Molecular Evolution},
year = {1996},
volume = {43},
number = {3},
pages = {304--311},
month = sep
}

@article{Ho:2007ea,
author = {Ho, Simon Y W and Heupink, Tim H and Rambaut, Andrew and Shapiro, Beth},
title = {{Bayesian estimation of sequence damage in ancient DNA}},
journal = {Molecular Biology and Evolution},
year = {2007},
volume = {24},
number = {6},
pages = {1416--1422},
month = jun
}

@article{Stadler:2015kx,
author = {Stadler, Tanja and Vaughan, Timothy G and Gavryushkin, Alex and Guindon, St{\'e}phane and K{\"u}hnert, Denise and Leventhal, Gabriel E and Drummond, Alexei J},
title = {{How well can the exponential-growth coalescent approximate constant-rate birth-death population dynamics?}},
journal = {Proceedings of the Royal Society B: Biological Sciences},
year = {2015},
volume = {282},
number = {1806},
pages = {20150420--20150420},
month = may
}

@article{Goldman:2008dj,
author = {Goldman, Nick and Yang, Ziheng},
title = {{Introduction. Statistical and computational challenges in molecular phylogenetics and evolution}},
journal = {Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences},
year = {2008},
volume = {363},
number = {1512},
pages = {3889--3892},
month = dec
}

@article{Pardi:2015ei,
author = {Pardi, Fabio and Scornavacca, Celine},
title = {{Reconstructible phylogenetic networks: do not distinguish the indistinguishable}},
journal = {PLoS Computational Biology},
year = {2015},
volume = {11},
number = {4},
pages = {e1004135},
month = apr
}

@article{Geman:1984wt,
author = {Geman, S and Geman, D},
title = {{Stochastic relaxation, gibbs distributions, and the bayesian restoration of images}},
journal = {IEEE transactions on pattern analysis and machine intelligence},
year = {1984},
volume = {6},
number = {6},
pages = {721--741},
month = jun
}

@article{Sisson:2007il,
author = {Sisson, S A and Fan, Y and Tanaka, Mark M},
title = {{Sequential Monte Carlo without likelihoods}},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
year = {2007},
volume = {104},
number = {6},
pages = {1760--1765},
month = feb
}

@article{Carstens:2013bn,
author = {Carstens, Bryan C and Pelletier, Tara A and Reid, Noah M and Satler, Jordan D},
title = {{How to fail at species delimitation}},
journal = {Molecular Ecology},
year = {2013},
volume = {22},
number = {17},
pages = {4369--4383},
month = sep
}

@article{Stadler:2013hf,
author = {Stadler, Tanja and K{\"u}hnert, Denise and Bonhoeffer, Sebastian and Drummond, Alexei J},
title = {{Birth-death skyline plot reveals temporal changes of epidemic spread in HIV and hepatitis C virus (HCV)}},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
year = {2013},
volume = {110},
number = {1},
pages = {228--233},
month = jan
}

@article{Hajibabaei:2007bb,
author = {Hajibabaei, Mehrdad and Singer, Gregory A C and Hebert, Paul D N and Hickey, Donal A},
title = {{DNA barcoding: how it complements taxonomy, molecular phylogenetics and population genetics}},
journal = {Trends in Genetics},
year = {2007},
volume = {23},
number = {4},
pages = {167--172},
month = apr
}

@article{Altekar:2004jz,
author = {Altekar, Gautam and Dwarkadas, Sandhya and Huelsenbeck, John P and Ronquist, Fredrik},
title = {{Parallel Metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference}},
journal = {Bioinformatics},
year = {2004},
volume = {20},
number = {3},
pages = {407--415},
month = feb
}

@article{DosReis:2016eg,
author = {Dos Reis, Mario and Donoghue, Philip C J and Yang, Ziheng},
title = {{Bayesian molecular clock dating of species divergences in the genomics era}},
journal = {Nature Reviews Genetics},
year = {2016},
volume = {17},
number = {2},
pages = {71--80},
month = feb
}

@article{Felsenstein:1978vh,
author = {Felsenstein, Joseph},
title = {{The number of evolutionary trees}},
journal = {Systematic Biology},
year = {1978},
volume = {27},
number = {1},
pages = {27--33}
}

@article{Wang:2009gr,
author = {Wang, Ying and Rannala, Bruce},
title = {{Population genomic inference of recombination rates and hotspots}},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
year = {2009},
volume = {106},
number = {15},
pages = {6215--6219},
month = apr
}

@book{Yang:2014tn,
author = {Yang, Ziheng},
title = {{Molecular Evolution: A Statistical Approach}},
publisher = {Oxford University Press},
year = {2014},
month = may
}

@article{Beaumont:2004cl,
author = {Beaumont, Mark A and Rannala, Bruce},
title = {{The Bayesian revolution in genetics}},
journal = {Nature Reviews Genetics},
year = {2004},
volume = {5},
number = {4},
pages = {251--261},
month = apr
}

@article{DosReis:2013bk,
author = {Dos Reis, Mario and Yang, Ziheng},
title = {{The unbearable uncertainty of Bayesian divergence time estimation}},
journal = {Journal of Systematics and Evolution},
year = {2013},
volume = {51},
number = {1},
pages = {30--43},
month = jan
}

@article{Rambaut:2009io,
author = {Rambaut, Andrew and Ho, Simon Y W and Drummond, Alexei J and Shapiro, Beth},
title = {{Accommodating the effect of ancient DNA damage on inferences of demographic histories}},
journal = {Molecular Biology and Evolution},
year = {2009},
volume = {26},
number = {2},
pages = {245--248},
month = feb
}

@article{Fearnhead:2001vb,
author = {Fearnhead, P and Donnelly, P},
title = {{Estimating recombination rates from population genetic data}},
journal = {Genetics},
year = {2001},
volume = {159},
number = {3},
pages = {1299--1318},
month = nov
}

@article{Marshall:2010hd,
author = {Marshall, David C},
title = {{Cryptic failure of partitioned Bayesian phylogenetic analyses: lost in the land of long trees}},
journal = {Systematic Biology},
year = {2010},
volume = {59},
number = {1},
pages = {108--117},
month = jan
}

@article{Ronquist:2012ir,
author = {Ronquist, Fredrik and Teslenko, Maxim and van der Mark, Paul and Ayres, Daniel L and Darling, Aaron and H{\"o}hna, Sebastian and Larget, Bret and Liu, Liang and Suchard, Marc A and Huelsenbeck, John P},
title = {{MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space}},
journal = {Systematic Biology},
year = {2012},
volume = {61},
number = {3},
pages = {539--542},
month = may
}

@article{Kubatko:2009jf,
author = {Kubatko, Laura S and Carstens, Bryan C and Knowles, L Lacey},
title = {{STEM: species tree estimation using maximum likelihood for gene trees under coalescence}},
journal = {Bioinformatics},
year = {2009},
volume = {25},
number = {7},
pages = {971--973},
month = apr
}

@article{WilkinsonHerbots:1998tn,
author = {Wilkinson-Herbots, H M},
title = {{Genealogy and subpopulation differentiation under various models of population structure}},
journal = {Journal of Mathematical Biology},
year = {1998},
volume = {37},
number = {6},
pages = {535--585},
month = dec
}

@article{Alhaddad:2016cl,
author = {Alhaddad, Hasan and Zhang, Chi and Rannala, Bruce and Lyons, Leslie A},
title = {{A glance at recombination hotspots in the domestic cat}},
journal = {PloS one},
year = {2016},
volume = {11},
number = {2},
pages = {e0148710}
}

@article{Wu:2004ib,
author = {Wu, Chung-I and Ting, Chau-Ti},
title = {{Genes and speciation}},
journal = {Nature Reviews Genetics},
year = {2004},
volume = {5},
number = {2},
pages = {114--122},
month = feb
}

@article{Yang:1994wd,
author = {Yang, Z},
title = {{Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods}},
journal = {Journal of Molecular Evolution},
year = {1994},
volume = {39},
number = {3},
pages = {306--314},
month = sep
}

@article{Hohna:2014fw,
author = {H{\"o}hna, Sebastian and Heath, Tracy A and Boussau, Bastien and Landis, Michael J and Ronquist, Fredrik and Huelsenbeck, John P},
title = {{Probabilistic graphical model representation in phylogenetics}},
journal = {Systematic Biology},
year = {2014},
volume = {63},
number = {5},
pages = {753--771},
month = sep
}

@article{Stephens:2001kh,
author = {Stephens, M and Smith, N J and Donnelly, P},
title = {{A new statistical method for haplotype reconstruction from population data}},
journal = {American Journal of Human Genetics},
year = {2001},
volume = {68},
number = {4},
pages = {978--989},
month = apr
}

@article{Rasmussen:2012kk,
author = {Rasmussen, Matthew D and Kellis, Manolis},
title = {{Unified modeling of gene duplication, loss, and coalescence using a locus tree}},
journal = {Genome Research},
year = {2012},
volume = {22},
number = {4},
pages = {755--765},
month = apr
}

@article{Yang:2006eu,
author = {Yang, Ziheng and Rannala, Bruce},
title = {{Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds}},
journal = {Molecular Biology and Evolution},
year = {2006},
volume = {23},
number = {1},
pages = {212--226},
month = jan
}

@article{Moret:2004gu,
author = {Moret, BME and Nakhleh, L and Warnow, T and Linder, C R and Tholse, A and Padolina, A and Sun, J and Timme, R},
title = {{Phylogenetic networks: modeling, reconstructibility, and accuracy}},
journal = {Ieee-Acm Transactions on Computational Biology and Bioinformatics},
year = {2004},
volume = {1},
number = {1},
pages = {13--23}
}

@article{Symula:2008jj,
author = {Symula, R and Keogh, J S and Cannatella, D C},
title = {{Ancient phylogeographic divergence in southeastern Australia among populations of the widespread common froglet, Crinia signifera}},
journal = {Molecular Phylogenetics and Evolution},
year = {2008},
volume = {47},
number = {2},
pages = {569--580},
month = may
}

@article{Lipinski:2008gg,
author = {Lipinski, Monika J and Froenicke, Lutz and Baysac, Kathleen C and Billings, Nicholas C and Leutenegger, Christian M and Levy, Alon M and Longeri, Maria and Niini, Tirri and Ozpinar, Haydar and Slater, Margaret R and Pedersen, Niels C and Lyons, Leslie A},
title = {{The ascent of cat breeds: Genetic evaluations of breeds and worldwide random-bred populations}},
journal = {Genomics},
year = {2008},
volume = {91},
number = {1},
pages = {12--21},
month = jan
}

@article{Hey:2004hr,
author = {Hey, Jody and Nielsen, Rasmus},
title = {{Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis}},
journal = {Genetics},
year = {2004},
volume = {167},
number = {2},
pages = {747--760},
month = jun
}

@article{Stadler:2011bn,
author = {Stadler, Tanja},
title = {{Mammalian phylogeny reveals recent diversification rate shifts}},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
year = {2011},
volume = {108},
number = {15},
pages = {6187--6192}
}

@article{Hofreiter:2001if,
author = {Hofreiter, M and Serre, D and Poinar, H N and Kuch, M and Paabo, S},
title = {{Ancient DNA}},
journal = {Nature Reviews Genetics},
year = {2001},
volume = {2},
number = {5},
pages = {353--359},
month = may
}

@article{Niemiller:2012cd,
author = {Niemiller, Matthew L and Near, Thomas J and Fitzpatrick, Benjamin M},
title = {{Delimiting species using multilocus data: diagnosing cryptic diversity in the southern cavefish, Typhlichthys subterraneus (Teleostei: Amblyopsidae)}},
journal = {Evolution; international journal of organic evolution},
year = {2012},
volume = {66},
number = {3},
pages = {846--866},
month = mar
}

@article{Jeffreys:2001ku,
author = {Jeffreys, A J and Kauppi, L and Neumann, R},
title = {{Intensely punctate meiotic recombination in the class II region of the major histocompatibility complex}},
journal = {Nature genetics},
year = {2001},
volume = {29},
number = {2},
pages = {217--222},
month = oct
}

@article{Guang:2016fl,
author = {Guang, August and Zapata, Felipe and Howison, Mark and Lawrence, Charles E and Dunn, Casey W},
title = {{An integrated perspective on phylogenetic workflows}},
journal = {Trends in Ecology {\&} Evolution},
year = {2016},
volume = {31},
number = {2},
pages = {116--126},
month = feb
}

@article{Cowles:1996bv,
author = {Cowles, M K and Carlin, B P},
title = {{Markov chain Monte Carlo convergence diagnostics: a comparative review}},
journal = {Journal of the American Statistical Association},
year = {1996},
volume = {91},
number = {434},
pages = {883--904},
month = jun
}

@article{Arcila:2015hm,
author = {Arcila, Dahiana and Alexander Pyron, R and Tyler, James C and Ort{\'\i}, Guillermo and Betancur-R, Ricardo},
title = {{An evaluation of fossil tip-dating versus node-age calibrations in tetraodontiform fishes (Teleostei: Percomorphaceae)}},
journal = {Molecular Phylogenetics and Evolution},
year = {2015},
volume = {82 Pt A},
pages = {131--145},
month = jan
}

@article{Redelings:2007eb,
author = {Redelings, Benjamin D and Suchard, Marc A},
title = {{Incorporating indel information into phylogeny estimation for rapidly emerging pathogens}},
journal = {BMC Evolutionary Biology},
year = {2007},
volume = {7},
number = {1},
pages = {40}
}

@article{Wheeler:2008cc,
author = {Wheeler, Ward C and Pickett, Kurt M},
title = {{Topology-Bayes versus Clade-Bayes in phylogenetic analysis}},
journal = {Molecular Biology and Evolution},
year = {2008},
volume = {25},
number = {2},
pages = {447--453},
month = feb
}

@article{Stadler:2013dd,
author = {Stadler, Tanja and Yang, Ziheng},
title = {{Dating phylogenies with sequentially sampled tips}},
journal = {Systematic Biology},
year = {2013},
volume = {62},
number = {5},
pages = {674--688},
month = sep
}

@article{Zuckerkandl:1965vq,
author = {Zuckerkandl, Emile and Pauling, Linus},
title = {{Evolutionary divergence and convergence in proteins}},
journal = {Evolving genes and proteins},
year = {1965},
volume = {97},
pages = {97--166}
}

@article{Sukumaran:2010id,
author = {Sukumaran, Jeet and Holder, Mark T},
title = {{DendroPy: a Python library for phylogenetic computing}},
journal = {Bioinformatics},
year = {2010},
volume = {26},
number = {12},
pages = {1569--1571},
month = jun
}

@article{Lakner:2008dn,
author = {Lakner, Clemens and van der Mark, Paul and Huelsenbeck, John P and Larget, Bret and Ronquist, Fredrik},
title = {{Efficiency of Markov chain Monte Carlo tree proposals in Bayesian phylogenetics}},
journal = {Systematic Biology},
year = {2008},
volume = {57},
number = {1},
pages = {86--103},
month = feb
}

@article{Hickerson:2006dr,
author = {Hickerson, Michael J and Meyer, Christopher P and Moritz, Craig},
title = {{DNA barcoding will often fail to discover new animal species over broad parameter space}},
journal = {Systematic Biology},
year = {2006},
volume = {55},
number = {5},
pages = {729--739},
month = oct
}

@article{Kuhner:2007ev,
author = {Kuhner, Mary K and Smith, Lucian P},
title = {{Comparing likelihood and Bayesian coalescent estimation of population parameters}},
journal = {Genetics},
year = {2007},
volume = {175},
number = {1},
pages = {155--165},
month = jan
}

@article{Zhang:2003wm,
author = {Zhang, De-Xing and Hewitt, Godfrey M},
title = {{Nuclear DNA analyses in genetic studies of populations: practice, problems and prospects}},
journal = {Molecular Ecology},
year = {2003},
volume = {12},
number = {3},
pages = {563--584},
month = mar
}

@article{Pagel:2004es,
author = {Pagel, Mark and Meade, Andrew and Barker, Daniel},
title = {{Bayesian estimation of ancestral character states on phylogenies}},
journal = {Systematic Biology},
year = {2004},
volume = {53},
number = {5},
pages = {673--684},
month = oct
}

@article{Zhang:2016kf,
author = {Zhang, Chi and Stadler, Tanja and Klopfstein, Seraina and Heath, Tracy A and Ronquist, Fredrik},
title = {{Total-evidence dating under the fossilized birth-death process}},
journal = {Systematic Biology},
year = {2016},
volume = {65},
number = {2},
pages = {228--249},
month = mar
}

@article{Reid:2014gu,
author = {Reid, Noah M and Hird, Sarah M and Brown, Jeremy M and Pelletier, Tara A and McVay, John D and Satler, Jordan D and Carstens, Bryan C},
title = {{Poor fit to the multispecies coalescent is widely detectable in empirical data}},
journal = {Systematic Biology},
year = {2014},
volume = {63},
number = {3},
pages = {322--333},
month = may
}

@article{Mateiu:2008by,
author = {Mateiu, Ligia M and Rannala, Bruce},
title = {{Bayesian inference of errors in ancient DNA caused by postmortem degradation}},
journal = {Molecular Biology and Evolution},
year = {2008},
volume = {25},
number = {7},
pages = {1503--1511},
month = jul
}

@article{Hey:2010fa,
author = {Hey, Jody},
title = {{Isolation with migration models for more than two populations}},
journal = {Molecular Biology and Evolution},
year = {2010},
volume = {27},
number = {4},
pages = {905--920},
month = apr
}

@article{Bloomquist:2010jf,
author = {Bloomquist, Erik W and Suchard, Marc A},
title = {{Unifying vertical and nonvertical evolution: a stochastic ARG-based framework}},
journal = {Systematic Biology},
year = {2010},
volume = {59},
number = {1},
pages = {27--41},
month = jan
}

@article{Yang:1995uh,
author = {Yang, Z},
title = {{A space-time process model for the evolution of DNA sequences}},
journal = {Genetics},
year = {1995},
volume = {139},
number = {2},
pages = {993--1005},
month = feb
}

@article{Strasburg:2011di,
author = {Strasburg, Jared L and Rieseberg, Loren H},
title = {{Interpreting the estimated timing of migration events between hybridizing species}},
journal = {Molecular Ecology},
year = {2011},
volume = {20},
number = {11},
pages = {2353--2366},
month = jun
}

@article{Huelsenbeck:1995cj,
author = {Huelsenbeck, John P},
title = {{Performance of phylogenetic methods in simulation}},
journal = {Systematic Biology},
year = {1995},
volume = {44},
number = {1},
pages = {17--48},
month = mar
}

@article{Myers:2005dy,
author = {Myers, Simon and Bottolo, Leonardo and Freeman, Colin and McVean, Gil and Donnelly, Peter},
title = {{A fine-scale map of recombination rates and hotspots across the human genome}},
journal = {Science},
year = {2005},
volume = {310},
number = {5746},
pages = {321--324},
month = oct
}

@article{Kulle:2008is,
author = {Kulle, B and Frigessi, A and Edvardsen, H and Kristensen, V and Wojnowski, L},
title = {{Accounting for haplotype phase uncertainty in linkage disequilibrium estimation}},
journal = {Genetic epidemiology},
year = {2008},
volume = {32},
number = {2},
pages = {168--178},
month = feb
}

@article{Zhang:2011jf,
author = {Zhang, Chi and Zhang, De-Xing and Zhu, Tianqi and Yang, Ziheng},
title = {{Evaluation of a Bayesian coalescent method of species delimitation}},
journal = {Systematic Biology},
year = {2011},
volume = {60},
number = {6},
pages = {747--761},
month = dec
}

@article{Degnan:2005ux,
author = {Degnan, J H and Salter, L A},
title = {{Gene tree distributions under the coalescent process}},
journal = {Evolution; international journal of organic evolution},
year = {2005},
volume = {59},
number = {1},
pages = {24--37},
month = jan
}

@article{Efron:2013dn,
author = {Efron, Bradley},
title = {{Bayes' Theorem in the 21st Century}},
journal = {Science},
year = {2013},
volume = {340},
number = {6137},
pages = {1177--1178}
}

@article{Boussau:2013ba,
author = {Boussau, Bastien and Sz{\"o}ll{\H o}si, Gergely J and Duret, Laurent and Gouy, Manolo and Tannier, Eric and Daubin, Vincent},
title = {{Genome-scale coestimation of species and gene trees}},
journal = {Genome Research},
year = {2013},
volume = {23},
number = {2},
pages = {323--330},
month = feb
}

@article{Yang:2010hm,
author = {Yang, Ziheng and Rannala, Bruce},
title = {{Bayesian species delimitation using multilocus sequence data}},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
year = {2010},
volume = {107},
number = {20},
pages = {9264--9269},
month = may
}

@article{Stumpf:2003fm,
author = {Stumpf, Michael P H and McVean, Gilean A T},
title = {{Estimating recombination rates from population-genetic data}},
journal = {Nature Reviews Genetics},
year = {2003},
volume = {4},
number = {12},
pages = {959--968},
month = dec
}

@article{Kuhner:2009ex,
author = {Kuhner, Mary K},
title = {{Coalescent genealogy samplers: windows into population history}},
journal = {Trends in Ecology {\&} Evolution},
year = {2009},
volume = {24},
number = {2},
pages = {86--93},
month = feb
}

@article{Misof:2014jv,
author = {Misof, Bernhard and Liu, Shanlin and Meusemann, Karen and Peters, Ralph S and Donath, Alexander and Mayer, Christoph and Frandsen, Paul B and Ware, Jessica and Flouri, Tom{\'a}{\v s} and Beutel, Rolf G and Niehuis, Oliver and Petersen, Malte and Izquierdo-Carrasco, Fernando and Wappler, Torsten and Rust, Jes and Aberer, Andre J and Asp{\"o}ck, Ulrike and Asp{\"o}ck, Horst and Bartel, Daniela and Blanke, Alexander and Berger, Simon and B{\"o}hm, Alexander and Buckley, Thomas R and Calcott, Brett and Chen, Junqing and Friedrich, Frank and Fukui, Makiko and Fujita, Mari and Greve, Carola and Grobe, Peter and Gu, Shengchang and Huang, Ying and Jermiin, Lars S and Kawahara, Akito Y and Krogmann, Lars and Kubiak, Martin and Lanfear, Robert and Letsch, Harald and Li, Yiyuan and Li, Zhenyu and Li, Jiguang and Lu, Haorong and Machida, Ryuichiro and Mashimo, Yuta and Kapli, Pashalia and McKenna, Duane D and Meng, Guanliang and Nakagaki, Yasutaka and Navarrete-Heredia, Jos{\'e} Luis and Ott, Michael and Ou, Yanxiang and Pass, G{\"u}nther and Podsiadlowski, Lars and Pohl, Hans and von Reumont, Bj{\"o}rn M and Sch{\"u}tte, Kai and Sekiya, Kaoru and Shimizu, Shota and Slipinski, Adam and Stamatakis, Alexandros and Song, Wenhui and Su, Xu and Szucsich, Nikolaus U and Tan, Meihua and Tan, Xuemei and Tang, Min and Tang, Jingbo and Timelthaler, Gerald and Tomizuka, Shigekazu and Trautwein, Michelle and Tong, Xiaoli and Uchifune, Toshiki and Walzl, Manfred G and Wiegmann, Brian M and Wilbrandt, Jeanne and Wipfler, Benjamin and Wong, Thomas K F and Wu, Qiong and Wu, Gengxiong and Xie, Yinlong and Yang, Shenzhou and Yang, Qing and Yeates, David K and Yoshizawa, Kazunori and Zhang, Qing and Zhang, Rui and Zhang, Wenwei and Zhang, Yunhui and Zhao, Jing and Zhou, Chengran and Zhou, Lili and Ziesmann, Tanja and Zou, Shijie and Li, Yingrui and Xu, Xun and Zhang, Yong and Yang, Huanming and Wang, Jian and Wang, Jun and Kjer, Karl M and Zhou, Xin},
title = {{Phylogenomics resolves the timing and pattern of insect evolution}},
journal = {Science},
year = {2014},
volume = {346},
number = {6210},
pages = {763--767},
month = nov
}

@article{Leigh:2015bm,
author = {Leigh, Jessica W and Bryant, David},
title = {{Monte Carlo strategies for selecting parameter values in simulation experiments}},
journal = {Systematic Biology},
year = {2015},
volume = {64},
number = {5},
pages = {741--751},
month = sep
}

@article{Sjostrand:2012kp,
author = {Sjostrand, Joel and Sennblad, Bengt and Arvestad, Lars and Lagergren, Jens},
title = {{DLRS: gene tree evolution in light of a species tree}},
journal = {Bioinformatics},
year = {2012},
volume = {28},
number = {22},
pages = {2994--2995}
}

@article{Bouckaert:2014iz,
author = {Bouckaert, Remco and Heled, Joseph and K{\"u}hnert, Denise and Vaughan, Tim and Wu, Chieh-Hsi and Xie, Dong and Suchard, Marc A and Rambaut, Andrew and Drummond, Alexei J},
title = {{BEAST 2: a software platform for Bayesian evolutionary analysis}},
journal = {PLoS Computational Biology},
year = {2014},
volume = {10},
number = {4},
pages = {e1003537},
month = apr
}

@book{Swofford:2003ic,
author = {Swofford, David L},
title = {{PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4}},
publisher = {Sinauer Associates},
year = {2003},
address = {Sunderland, Massachusetts}
}

@article{Meng:2009iw,
author = {Meng, Chen and Kubatko, Laura Salter},
title = {{Detecting hybrid speciation in the presence of incomplete lineage sorting using gene tree incongruence: a model}},
journal = {Theoretical Population Biology},
year = {2009},
volume = {75},
number = {1},
pages = {35--45},
month = feb
}

@article{Seo:2009bb,
author = {Seo, Tae-Kun and Kishino, Hirohisa},
title = {{Statistical comparison of nucleotide, amino acid, and codon substitution models for evolutionary analysis of protein-coding sequences}},
journal = {Systematic Biology},
year = {2009},
volume = {58},
number = {2},
pages = {199--210},
month = apr
}

@article{Heled:2012ef,
author = {Heled, Joseph and Drummond, Alexei J},
title = {{Calibrated tree priors for relaxed phylogenetics and divergence time estimation}},
journal = {Systematic Biology},
year = {2012},
volume = {61},
number = {1},
pages = {138--149},
month = jan
}

@article{Racimo:2015fz,
author = {Racimo, Fernando and Sankararaman, Sriram and Nielsen, Rasmus and Huerta-Sanchez, Emilia},
title = {{Evidence for archaic adaptive introgression in humans}},
journal = {Nature Reviews Genetics},
year = {2015},
volume = {16},
number = {6},
pages = {359--371},
month = jun
}

@article{Librado:2009ee,
author = {Librado, P and Rozas, J},
title = {{DnaSP v5: a software for comprehensive analysis of DNA polymorphism data}},
journal = {Bioinformatics},
year = {2009},
volume = {25},
number = {11},
pages = {1451--1452},
month = jun
}

@article{Falush:2003ts,
author = {Falush, Daniel and Stephens, Matthew and Pritchard, Jonathan K},
title = {{Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies}},
journal = {Genetics},
year = {2003},
volume = {164},
number = {4},
pages = {1567--1587},
month = aug
}

@article{Huelsenbeck:2004dv,
author = {Huelsenbeck, John P and Larget, Bret and Alfaro, Michael E},
title = {{Bayesian phylogenetic model selection using reversible jump Markov chain Monte Carlo}},
journal = {Molecular Biology and Evolution},
year = {2004},
volume = {21},
number = {6},
pages = {1123--1133},
month = jun
}

@article{Yu:2013kd,
author = {Yu, Yun and Ristic, Nikola and Nakhleh, Luay},
title = {{Fast algorithms and heuristics for phylogenomics under ILS and hybridization}},
journal = {Bmc Bioinformatics},
year = {2013},
volume = {14},
number = {Suppl 15}
}

@article{Stadler:2009ei,
author = {Stadler, Tanja},
title = {{On incomplete sampling under birth-death models and connections to the sampling-based coalescent}},
journal = {Journal of theoretical biology},
year = {2009},
volume = {261},
number = {1},
pages = {58--66}
}

@article{Posada:2004ix,
author = {Posada, David and Buckley, Thomas R},
title = {{Model selection and model averaging in phylogenetics: advantages of akaike information criterion and bayesian approaches over likelihood ratio tests}},
journal = {Systematic Biology},
year = {2004},
volume = {53},
number = {5},
pages = {793--808},
month = oct
}

@article{Pyron:2011dt,
author = {Pyron, R Alexander},
title = {{Divergence time estimation using fossils as terminal taxa and the origins of Lissamphibia}},
journal = {Systematic Biology},
year = {2011},
volume = {60},
number = {4},
pages = {466--481},
month = jul
}

@article{Larget:2013gs,
author = {Larget, Bret},
title = {{The estimation of tree posterior probabilities using conditional clade probability distributions}},
journal = {Systematic Biology},
year = {2013},
volume = {62},
number = {4},
pages = {501--511},
month = jul
}

@article{Balding:2006gk,
author = {Balding, David J},
title = {{A tutorial on statistical methods for population association studies}},
journal = {Nature Reviews Genetics},
year = {2006},
volume = {7},
number = {10},
pages = {781--791},
month = oct
}

@article{Nielsen:2004ga,
author = {Nielsen, Rasmus and Hubisz, Melissa J and Clark, Andrew G},
title = {{Reconstituting the frequency spectrum of ascertained single-nucleotide polymorphism data}},
journal = {Genetics},
year = {2004},
volume = {168},
number = {4},
pages = {2373--2382},
month = dec
}

@article{Szollosi:2013es,
author = {Sz{\"o}ll{\H o}si, Gergely J and Rosikiewicz, Wojciech and Boussau, Bastien and Tannier, Eric and Daubin, Vincent},
title = {{Efficient exploration of the space of reconciled gene trees}},
journal = {Systematic Biology},
year = {2013},
volume = {62},
number = {6},
pages = {901--912},
month = nov
}

@article{Vaughan:2014ha,
author = {Vaughan, Timothy G and Kuehnert, Denise and Popinga, Alex and Welch, David and Drummond, Alexei J},
title = {{Efficient Bayesian inference under the structured coalescent}},
journal = {Bioinformatics},
year = {2014},
volume = {30},
number = {16},
pages = {2272--2279}
}

@article{Weir:1979gh,
author = {Weir, B S and Cockerham, C C},
title = {{Estimation of linkage disequilibrium in randomly mating populations}},
journal = {Heredity},
year = {1979},
volume = {42},
number = {FEB},
pages = {105--111}
}

@article{Knowles:2007db,
author = {Knowles, L Lacey and Carstens, Bryan C},
title = {{Delimiting species without monophyletic gene trees}},
journal = {Systematic Biology},
year = {2007},
volume = {56},
number = {6},
pages = {887--895},
month = dec
}

@article{Liu:2008hl,
author = {Liu, Liang},
title = {{BEST: Bayesian estimation of species trees under the coalescent model}},
journal = {Bioinformatics},
year = {2008},
volume = {24},
number = {21},
pages = {2542--2543},
month = nov
}

@article{McDiarmid:2015kt,
author = {McDiarmid, Colin and Semple, Charles and Welsh, Dominic},
title = {{Counting Phylogenetic Networks}},
journal = {Annals of Combinatorics},
year = {2015},
volume = {19},
number = {1},
pages = {205--224},
month = mar
}

@article{Tofigh:2011fq,
author = {Tofigh, Ali and Hallett, Michael and Lagergren, Jens},
title = {{Simultaneous Identification of Duplications and Lateral Gene Transfers}},
journal = {Ieee-Acm Transactions on Computational Biology and Bioinformatics},
year = {2011},
volume = {8},
number = {2},
pages = {517--535}
}

@article{Chen:2015iu,
author = {Chen, Hua and Hey, Jody and Chen, Kun},
title = {{Inferring very recent population growth rate from population-scale sequencing data: using a large-sample coalescent estimator}},
journal = {Molecular Biology and Evolution},
year = {2015},
volume = {32},
number = {11},
pages = {2996--3011},
month = nov
}

@article{Sousa:2013hz,
author = {Sousa, Vitor and Hey, Jody},
title = {{Understanding the origin of species with genome-scale data: modelling gene flow}},
journal = {Nature Reviews Genetics},
year = {2013},
volume = {14},
number = {6},
pages = {404--414},
month = jun
}

@article{Stadler:2014vb,
author = {Stadler, Tanja and K{\"u}hnert, Denise and Rasmussen, David A and du Plessis, Louis},
title = {{Insights into the early epidemic spread of Ebola in Sierra Leone provided by viral sequence data}},
journal = {PLoS currents},
year = {2014},
volume = {6}
}

@article{Beerli:2001ga,
author = {Beerli, P and Felsenstein, J},
title = {{Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach}},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
year = {2001},
volume = {98},
number = {8},
pages = {4563--4568},
month = apr
}

@article{Huber:2015bn,
author = {Huber, Katharina T and Linz, Simone and Moulton, Vincent and Wu, Taoyang},
title = {{Spaces of phylogenetic networks from generalized nearest-neighbor interchange operations}},
journal = {Journal of Mathematical Biology},
year = {2015},
pages = {1--27},
month = jun
}

@article{Lockwood:2014ij,
author = {Lockwood, Sarah H and Guan, Anna and Yu, Abigail S and Zhang, Chi and Zykovich, Artem and Korf, Ian and Rannala, Bruce and Segal, David J},
title = {{The functional significance of common polymorphisms in zinc finger transcription factors}},
journal = {G3 (Bethesda)},
year = {2014},
volume = {4},
number = {9},
pages = {1647--1655},
month = sep
}

@article{Wang:2008fg,
author = {Wang, Ying and Rannala, Bruce},
title = {{Bayesian inference of fine-scale recombination rates using population genomic data}},
journal = {Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences},
year = {2008},
volume = {363},
number = {1512},
pages = {3921--3930},
month = dec
}

@article{Pybus:2000uu,
author = {Pybus, O G and Rambaut, A and Harvey, P H},
title = {{An integrated framework for the inference of viral population history from reconstructed genealogies}},
journal = {Genetics},
year = {2000},
volume = {155},
number = {3},
pages = {1429--1437},
month = jul
}

@article{Ronquist:2003gt,
author = {Ronquist, Fredrik and Huelsenbeck, John P},
title = {{MrBayes 3: Bayesian phylogenetic inference under mixed models}},
journal = {Bioinformatics},
year = {2003},
volume = {19},
number = {12},
pages = {1572--1574},
month = aug
}

@article{DeGiorgio:2014gx,
author = {DeGiorgio, Michael and Degnan, James H},
title = {{Robustness to divergence time underestimation when inferring species trees from estimated gene trees}},
journal = {Systematic Biology},
year = {2014},
volume = {63},
number = {1},
pages = {66--82},
month = jan
}

@article{Ronquist:2012ea,
author = {Ronquist, Fredrik and Klopfstein, Seraina and Vilhelmsen, Lars and Schulmeister, Susanne and Murray, Debra L and Rasnitsyn, Alexandr P},
title = {{A total-evidence approach to dating with fossils, applied to the early radiation of the Hymenoptera}},
journal = {Systematic Biology},
year = {2012},
volume = {61},
number = {6},
pages = {973--999},
month = dec
}

@article{Duchene:2015gl,
author = {Duch{\^e}ne, David A and Duch{\^e}ne, Sebastian and Holmes, Edward C and Ho, Simon Y W},
title = {{Evaluating the adequacy of molecular clock models using posterior predictive simulations}},
journal = {Molecular Biology and Evolution},
year = {2015},
volume = {32},
number = {11},
pages = {2986--2995},
month = nov
}

@article{Padhukasahasram:2011bt,
author = {Padhukasahasram, Badri and Rannala, Bruce},
title = {{Bayesian population genomic inference of crossing over and gene conversion}},
journal = {Genetics},
year = {2011},
volume = {189},
number = {2},
pages = {607--619},
month = oct
}

@article{Strimmer:2001wy,
author = {Strimmer, K and Pybus, O G},
title = {{Exploring the demographic history of DNA sequences using the generalized skyline plot}},
journal = {Molecular Biology and Evolution},
year = {2001},
volume = {18},
number = {12},
pages = {2298--2305},
month = dec
}

@article{Heled:2015df,
author = {Heled, Joseph and Drummond, Alexei J},
title = {{Calibrated birth-death phylogenetic time-tree priors for Bayesian inference}},
journal = {Systematic Biology},
year = {2015},
volume = {64},
number = {3},
pages = {369--383},
month = may
}

@article{Jones:2014cq,
author = {Jones, Graham and Aydin, Zeynep and Oxelman, Bengt},
title = {{DISSECT: an assignment-free Bayesian discovery method for species delimitation under the multispecies coalescent}},
journal = {Bioinformatics},
year = {2014},
pages = {btu770},
month = nov
}

@article{Drummond:2007gs,
author = {Drummond, Alexei J and Rambaut, Andrew},
title = {{BEAST: Bayesian evolutionary analysis by sampling trees}},
journal = {BMC Evolutionary Biology},
year = {2007},
volume = {7},
number = {1},
pages = {214}
}

@article{Olave:2014ce,
author = {Olave, Melisa and Sol{\`a}, Eduard and Knowles, L Lacey},
title = {{Upstream analyses create problems with DNA-based species delimitation.}},
journal = {Systematic Biology},
year = {2014},
volume = {63},
number = {2},
pages = {263--271},
month = mar
}

@article{Jones010199,
author = {Jones, Graham R},
title = {{Species delimitation and phylogeny estimation under the multispecies coalescent}},
journal = {bioRxiv},
year = {2015},
pages = {010199}
}

@article{Lepage:2007bq,
author = {Lepage, Thomas and Bryant, David and Philippe, Herv{\'e} and Lartillot, Nicolas},
title = {{A general comparison of relaxed molecular clock models}},
journal = {Molecular Biology and Evolution},
year = {2007},
volume = {24},
number = {12},
pages = {2669--2680},
month = dec
}

@article{WilkinsonHerbots:2008hd,
author = {Wilkinson-Herbots, Hilde M},
title = {{The distribution of the coalescence time and the number of pairwise nucleotide differences in the "isolation with migration" model}},
journal = {Theoretical Population Biology},
year = {2008},
volume = {73},
number = {2},
pages = {277--288},
month = mar
}

@article{Yang:2007ki,
author = {Yang, Ziheng},
title = {{PAML 4: phylogenetic analysis by maximum likelihood}},
journal = {Molecular Biology and Evolution},
year = {2007},
volume = {24},
number = {8},
pages = {1586--1591},
month = aug
}

@article{Lewis:2005kl,
author = {Lewis, P O and Holder, M T and Holsinger, K E},
title = {{Polytomies and Bayesian phylogenetic inference}},
journal = {Systematic Biology},
year = {2005},
volume = {54},
number = {2},
pages = {241--253},
month = apr
}

@article{deVladar:2011kz,
author = {de Vladar, Harold P and Barton, Nicholas H},
title = {{The contribution of statistical physics to evolutionary biology}},
journal = {Trends in Ecology {\&} Evolution},
year = {2011},
volume = {26},
number = {8},
pages = {424--432},
month = aug
}

@article{OMeara:2010jx,
author = {O'Meara, Brian C},
title = {{New heuristic methods for joint species delimitation and species tree inference}},
journal = {Systematic Biology},
year = {2010},
volume = {59},
number = {1},
pages = {59--73},
month = jan
}

@article{Donnelly:1995bf,
author = {Donnelly, P and Tavar{\'e}, S},
title = {{Coalescents and genealogical structure under neutrality}},
journal = {Annual Review of Genetics},
year = {1995},
volume = {29},
number = {1},
pages = {401--421}
}

@article{Stadler:2010fn,
author = {Stadler, Tanja},
title = {{Sampling-through-time in birth-death trees}},
journal = {Journal of theoretical biology},
year = {2010},
volume = {267},
number = {3},
pages = {396--404},
month = dec
}

@article{DosReis:2014jd,
author = {Dos Reis, Mario and Zhu, Tianqi and Yang, Ziheng},
title = {{The impact of the rate prior on Bayesian estimation of divergence times with multiple loci}},
journal = {Systematic Biology},
year = {2014},
volume = {63},
number = {4},
pages = {555--565},
month = jul
}

@article{Zhang:2012ke,
author = {Zhang, Chi and Rannala, Bruce and Yang, Ziheng},
title = {{Robustness of compound Dirichlet priors for Bayesian inference of branch lengths}},
journal = {Systematic Biology},
year = {2012},
volume = {61},
number = {5},
pages = {779--784},
month = oct
}

@article{Kass:1995vb,
author = {Kass, R E and Raftery, A E},
title = {{Bayes factors}},
journal = {Journal of the American Statistical Association},
year = {1995},
volume = {90},
number = {430},
pages = {773--795}
}

@article{Francis:2015kj,
author = {Francis, Andrew R and Steel, Mike},
title = {{Which phylogenetic networks are merely trees with additional arcs?}},
journal = {Systematic Biology},
year = {2015},
volume = {64},
number = {5},
pages = {768--777},
month = sep
}

@article{Nielsen:2005kx,
author = {Nielsen, Rasmus},
title = {{Molecular signatures of natural selection}},
journal = {Annual Review of Genetics},
year = {2005},
volume = {39},
number = {1},
pages = {197--218}
}

@article{Wall:2009fo,
author = {Wall, Jeffrey D and Lohmueller, Kirk E and Plagnol, Vincent},
title = {{Detecting ancient admixture and estimating demographic parameters in multiple human populations}},
journal = {Molecular Biology and Evolution},
year = {2009},
volume = {26},
number = {8},
pages = {1823--1827},
month = aug
}

@article{Kimura:1969tn,
author = {Kimura, M},
title = {{The number of heterozygous nucleotide sites maintained in a finite population due to steady flux of mutations}},
journal = {Genetics},
year = {1969},
volume = {61},
number = {4},
pages = {893--903},
month = apr
}

@article{Yu:2015jx,
author = {Yu, Yun and Nakhleh, Luay},
title = {{A maximum pseudo-likelihood approach for phylogenetic networks}},
journal = {BMC genomics},
year = {2015},
volume = {16 Suppl 10},
number = {Suppl 10},
pages = {S10},
month = oct
}

@article{Falush:2007kq,
author = {Falush, Daniel and Stephens, Matthew and Pritchard, Jonathan K},
title = {{Inference of population structure using multilocus genotype data: dominant markers and null alleles}},
journal = {Molecular ecology notes},
year = {2007},
volume = {7},
number = {4},
pages = {574--578},
month = jul
}

@article{Yang:2014it,
author = {Yang, Ziheng and Rannala, Bruce},
title = {{Unguided species delimitation using DNA sequence data from multiple loci}},
journal = {Molecular Biology and Evolution},
year = {2014},
volume = {31},
number = {12},
pages = {3125--3135},
month = dec
}

@article{Payseur:2016cm,
author = {Payseur, Bret A and Rieseberg, Loren H},
title = {{A Genomic Perspective on Hybridization and Speciation}},
journal = {Molecular Ecology},
year = {2016},
pages = {n/a--n/a},
month = feb
}

@article{Beaumont:2010fk,
author = {Beaumont, Mark A and Nielsen, Rasmus and Robert, Christian and Hey, Jody and Gaggiotti, Oscar and Knowles, Lacey and Estoup, Arnaud and Panchal, Mahesh and Corander, Jukka and Hickerson, Mike and Sisson, Scott A and Fagundes, Nelson and Chikhi, Lounes and Beerli, Peter and Vitalis, Renaud and Cornuet, Jean-Marie and Huelsenbeck, John and Foll, Matthieu and Yang, Ziheng and Rousset, Francois and Balding, David and Excoffier, Laurent},
title = {{In defence of model-based inference in phylogeography REPLY}},
journal = {Molecular Ecology},
year = {2010},
volume = {19},
number = {3},
pages = {436--446},
month = feb
}

@article{Kimura:1964wh,
author = {Kimura, M and Crow, J F},
title = {{The number of alleles that can be maintained in finite population}},
journal = {Genetics},
year = {1964},
volume = {49},
number = {4},
pages = {725--738}
}

@article{Bielawski:2001uu,
author = {Bielawski, J P and Yang, Z},
title = {{Positive and negative selection in the DAZ gene family}},
journal = {Molecular Biology and Evolution},
year = {2001},
volume = {18},
number = {4},
pages = {523--529},
month = apr
}

@article{Leventhal:2014el,
author = {Leventhal, Gabriel E and Guenthard, Huldrych F and Bonhoeffer, Sebastian and Stadler, Tanja},
title = {{Using an Epidemiological Model for Phylogenetic Inference Reveals Density Dependence in HIV Transmission}},
journal = {Molecular Biology and Evolution},
year = {2014},
volume = {31},
number = {1},
pages = {6--17},
month = jan
}

@article{Thomas:1999ww,
author = {Thomas, M J and Seto, E},
title = {{Unlocking the mechanisms of transcription factor YY1: are chromatin modifying enzymes the key?}},
journal = {Gene},
year = {1999},
volume = {236},
number = {2},
pages = {197--208},
month = aug
}

@article{Zaheri:2014cr,
author = {Zaheri, Maryam and Dib, Linda and Salamin, Nicolas},
title = {{A generalized mechanistic codon model}},
journal = {Molecular Biology and Evolution},
year = {2014},
volume = {31},
number = {9},
pages = {2528--2541},
month = sep
}

@article{Hinchliff:2015gi,
author = {Hinchliff, Cody E and Smith, Stephen A and Allman, James F and Burleigh, J Gordon and Chaudhary, Ruchi and Coghill, Lyndon M and Crandall, Keith A and Deng, Jiabin and Drew, Bryan T and Gazis, Romina and Gude, Karl and Hibbett, David S and Katz, Laura A and Laughinghouse, H Dail and McTavish, Emily Jane and Midford, Peter E and Owen, Christopher L and Ree, Richard H and Rees, Jonathan A and Soltis, Douglas E and Williams, Tiffani and Cranston, Karen A},
title = {{Synthesis of phylogeny and taxonomy into a comprehensive tree of life}},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
year = {2015},
volume = {112},
number = {41},
pages = {12764--12769},
month = oct
}

@article{Paigen:2010jv,
author = {Paigen, Kenneth and Petkov, Petko},
title = {{Mammalian recombination hot spots: properties, control and evolution}},
journal = {Nature Reviews Genetics},
year = {2010},
volume = {11},
number = {3},
pages = {221--233},
month = mar
}

@article{Kingman:1982jb,
author = {Kingman, J F C},
title = {{The coalescent}},
journal = {Stochastic Processes and their Applications},
year = {1982},
volume = {13},
number = {3},
pages = {235--248}
}

@article{Mateiu:2006gh,
author = {Mateiu, Ligia and Rannala, Bruce},
title = {{Inferring complex DNA substitution processes on phylogenies using uniformization and data augmentation}},
journal = {Systematic Biology},
year = {2006},
volume = {55},
number = {2},
pages = {259--269},
month = apr
}

@article{Slatkin:2008ks,
author = {Slatkin, Montgomery},
title = {{Linkage disequilibrium--understanding the evolutionary past and mapping the medical future}},
journal = {Nature Reviews Genetics},
year = {2008},
volume = {9},
number = {6},
pages = {477--485},
month = jun
}

@article{Ayres:2012gf,
author = {Ayres, Daniel L and Darling, Aaron and Zwickl, Derrick J and Beerli, Peter and Holder, Mark T and Lewis, Paul O and Huelsenbeck, John P and Ronquist, Fredrik and Swofford, David L and Cummings, Michael P and Rambaut, Andrew and Suchard, Marc A},
title = {{BEAGLE: an application programming interface and high-performance computing library for statistical phylogenetics}},
journal = {Systematic Biology},
year = {2012},
volume = {61},
number = {1},
pages = {170--173},
month = jan
}

@article{Liu:2009hf,
author = {Liu, Liang and Yu, Lili and Kubatko, Laura and Pearl, Dennis K and Edwards, Scott V},
title = {{Coalescent methods for estimating phylogenetic trees}},
journal = {Molecular Phylogenetics and Evolution},
year = {2009},
volume = {53},
number = {1},
pages = {320--328},
month = oct
}

@article{Drummond:2005dw,
author = {Drummond, A J and Rambaut, A and Shapiro, B and Pybus, O G},
title = {{Bayesian coalescent inference of past population dynamics from molecular sequences}},
journal = {Molecular Biology and Evolution},
year = {2005},
volume = {22},
number = {5},
pages = {1185--1192},
month = may
}

@article{Aberer:2014by,
author = {Aberer, Andre J and Kobert, Kassian and Stamatakis, Alexandros},
title = {{ExaBayes: massively parallel bayesian tree inference for the whole-genome era}},
journal = {Molecular Biology and Evolution},
year = {2014},
volume = {31},
number = {10},
pages = {2553--2556},
month = oct
}

@article{Yang:1996vi,
author = {Yang, Z},
title = {{Among-site rate variation and its impact on phylogenetic analyses}},
journal = {Trends in Ecology {\&} Evolution},
year = {1996},
volume = {11},
number = {9},
pages = {367--372},
month = sep
}

@article{Axelsson:2008bb,
author = {Axelsson, Erik and Willerslev, Eske and Gilbert, M Thomas P and Nielsen, Rasmus},
title = {{The effect of ancient DNA damage on inferences of demographic histories}},
journal = {Molecular Biology and Evolution},
year = {2008},
volume = {25},
number = {10},
pages = {2181--2187},
month = oct
}

@article{Ho:2014bc,
author = {Ho, Simon Y W},
title = {{The changing face of the molecular evolutionary clock}},
journal = {Trends in Ecology {\&} Evolution},
year = {2014},
volume = {29},
number = {9},
pages = {496--503},
month = sep
}

@article{Drummond:2006kt,
author = {Drummond, Alexei J and Ho, Simon Y W and Phillips, Matthew J and Rambaut, Andrew},
title = {{Relaxed phylogenetics and dating with confidence}},
journal = {PLoS biology},
year = {2006},
volume = {4},
number = {5},
pages = {e88},
month = may
}

@article{Whidden:2015bs,
author = {Whidden, Chris and Matsen, Frederick A},
title = {{Quantifying MCMC exploration of phylogenetic tree space}},
journal = {Systematic Biology},
year = {2015},
volume = {64},
number = {3},
pages = {472--491},
month = may
}

@article{Ramakrishnan:2009gk,
author = {Ramakrishnan, Uma and Hadly, Elizabeth A},
title = {{Using phylochronology to reveal cryptic population histories: review and synthesis of 29 ancient DNA studies}},
journal = {Molecular Ecology},
year = {2009},
volume = {18},
number = {7},
pages = {1310--1330},
month = apr
}

@article{Drummond:2002ub,
author = {Drummond, A J and Nicholls, G K and Rodrigo, A G and Solomon, W},
title = {{Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data}},
journal = {Genetics},
year = {2002},
volume = {161},
number = {3},
pages = {1307--1320},
month = jul
}

@article{Teare:2002if,
author = {Teare, M D and Dunning, A M and Durocher, F and Rennart, G and Easton, D F},
title = {{Sampling distribution of summary linkage disequilibrium measures}},
journal = {Annals of Human Genetics},
year = {2002},
volume = {66},
number = {Pt 3},
pages = {223--233},
month = may
}

@article{Saitou:1987wo,
author = {Saitou, Naruya and Nei, Masatoshi},
title = {{The neighbor-joining method: a new method for reconstructing phylogenetic trees}},
journal = {Molecular Biology and Evolution},
year = {1987},
volume = {4},
number = {4},
pages = {406--425}
}

@article{Robinson:1981bg,
author = {Robinson, D F and Foulds, L R},
title = {{Comparison of phylogenetic trees}},
journal = {Mathematical Biosciences},
year = {1981},
volume = {53},
number = {1-2},
pages = {131--147}
}

@article{Zhu:2015jg,
author = {Zhu, Tianqi and Dos Reis, Mario and Yang, Ziheng},
title = {{Characterization of the uncertainty of divergence time estimation under relaxed molecular clock models using multiple loci}},
journal = {Systematic Biology},
year = {2015},
volume = {64},
number = {2},
pages = {267--280},
month = mar
}

@article{Liu:2008dt,
author = {Liu, Liang and Pearl, Dennis K and Brumfield, Robb T and Edwards, Scott V},
title = {{Estimating species trees using multiple-allele DNA sequence data}},
journal = {Evolution; international journal of organic evolution},
year = {2008},
volume = {62},
number = {8},
pages = {2080--2091},
month = aug
}

@article{Zhang:1997tk,
author = {Zhang, J and Nei, M},
title = {{Accuracies of ancestral amino acid sequences inferred by the parsimony, likelihood, and distance methods}},
journal = {Journal of Molecular Evolution},
year = {1997},
volume = {44 Suppl 1},
pages = {S139--46}
}

@article{Li:2012be,
author = {Li, Wai Lok Sibon and Drummond, Alexei J},
title = {{Model averaging and Bayes factor calculation of relaxed molecular clocks in Bayesian phylogenetics}},
journal = {Molecular Biology and Evolution},
year = {2012},
volume = {29},
number = {2},
pages = {751--761},
month = feb
}

@article{Hellenthal:2007hb,
author = {Hellenthal, Garrett and Stephens, Matthew},
title = {{msHOT: modifying Hudson's ms simulator to incorporate crossover and gene conversion hotspots}},
journal = {Bioinformatics},
year = {2007},
volume = {23},
number = {4},
pages = {520--521},
month = feb
}

@article{Felsenstein:1981vk,
author = {Felsenstein, J},
title = {{Evolutionary trees from DNA sequences: a maximum likelihood approach}},
journal = {Journal of Molecular Evolution},
year = {1981},
volume = {17},
number = {6},
pages = {368--376}
}

@article{Lemmon:2004co,
author = {Lemmon, Alan R and Moriarty, Emily C},
title = {{The importance of proper model assumption in bayesian phylogenetics}},
journal = {Systematic Biology},
year = {2004},
volume = {53},
number = {2},
pages = {265--277},
month = apr
}

@article{Baele:2013cg,
author = {Baele, Guy and Li, Wai Lok Sibon and Drummond, Alexei J and Suchard, Marc A and Lemey, Philippe},
title = {{Accurate model selection of relaxed molecular clocks in Bayesian phylogenetics}},
journal = {Molecular Biology and Evolution},
year = {2013},
volume = {30},
number = {2},
pages = {239--243},
month = feb
}

@article{Szollosi:2015dp,
author = {Sz{\"o}ll{\H o}si, Gergely J and Tannier, Eric and Daubin, Vincent and Boussau, Bastien},
title = {{The Inference of Gene Trees with Species Trees}},
journal = {Systematic Biology},
year = {2015},
volume = {64},
number = {1},
pages = {E42--E62},
month = jan
}

@article{Hey:2007cb,
author = {Hey, Jody and Nielsen, Rasmus},
title = {{Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics}},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
year = {2007},
volume = {104},
number = {8},
pages = {2785--2790},
month = feb
}

@article{Inoue:2010ge,
author = {Inoue, Jun and Donoghue, Philip C J and Yang, Ziheng},
title = {{The impact of the representation of fossil calibrations on Bayesian estimation of species divergence times}},
journal = {Systematic Biology},
year = {2010},
volume = {59},
number = {1},
pages = {74--89},
month = jan
}

@article{Wood:2013ic,
author = {Wood, Hannah Marie and Matzke, Nicholas J and Gillespie, Rosemary G and Griswold, Charles E},
title = {{Treating fossils as terminal taxa in divergence time estimation reveals ancient vicariance patterns in the palpimanoid spiders}},
journal = {Systematic Biology},
year = {2013},
volume = {62},
number = {2},
pages = {264--284},
month = mar
}

@article{Yang:1998vj,
author = {Yang, Z},
title = {{Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution}},
journal = {Molecular Biology and Evolution},
year = {1998},
volume = {15},
number = {5},
pages = {568--573},
month = may
}

@article{Abbott:2013jl,
author = {Abbott, R and Albach, D and Ansell, S and Arntzen, J W and Baird, S J E and Bierne, N and Boughman, J and Brelsford, A and Buerkle, C A and Buggs, R and Butlin, R K and Dieckmann, U and Eroukhmanoff, F and Grill, A and Cahan, S H and Hermansen, J S and Hewitt, G and Hudson, A G and Jiggins, C and Jones, J and Keller, B and Marczewski, T and Mallet, J and Martinez-Rodriguez, P and M{\"o}st, M and Mullen, S and Nichols, R and Nolte, A W and Parisod, C and Pfennig, K and Rice, A M and Ritchie, M G and Seifert, B and Smadja, C M and Stelkens, R and Szymura, J M and V{\"a}in{\"o}l{\"a}, R and Wolf, J B W and Zinner, D},
title = {{Hybridization and speciation}},
journal = {Journal of evolutionary biology},
year = {2013},
volume = {26},
number = {2},
pages = {229--246},
month = feb
}

@article{Yang:2013hb,
author = {Yang, Ziheng and Rodriguez, Carlos E},
title = {{Searching for efficient Markov chain Monte Carlo proposal kernels}},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
year = {2013},
volume = {110},
number = {48},
pages = {19307--19312}
}

@article{Mallet:2007gy,
author = {Mallet, James},
title = {{Hybrid speciation}},
journal = {Nature},
year = {2007},
volume = {446},
number = {7133},
pages = {279--283},
month = mar
}

@article{Money:2012iu,
author = {Money, Daniel and Whelan, Simon},
title = {{Characterizing the phylogenetic tree-search problem}},
journal = {Systematic Biology},
year = {2012},
volume = {61},
number = {2},
pages = {228--239},
month = mar
}

@article{Pyron:2015cl,
author = {Pyron, R Alexander},
title = {{Post-molecular systematics and the future of phylogenetics}},
journal = {Trends in Ecology {\&} Evolution},
year = {2015},
volume = {30},
number = {7},
pages = {384--389},
month = jul
}

@article{Ross:2008hk,
author = {Ross, Howard A and Murugan, Sumathi and Li, Wai Lok Sibon},
title = {{Testing the reliability of genetic methods of species identification via simulation}},
journal = {Systematic Biology},
year = {2008},
volume = {57},
number = {2},
pages = {216--230},
month = apr
}

@article{Marjoram:2006ic,
author = {Marjoram, Paul and Tavar{\'e}, Simon},
title = {{Modern computational approaches for analysing molecular genetic variation data}},
journal = {Nature Reviews Genetics},
year = {2006},
volume = {7},
number = {10},
pages = {759--770},
month = oct
}

@article{Huelsenbeck:2001jt,
author = {Huelsenbeck, J P and Ronquist, F},
title = {{MRBAYES: Bayesian inference of phylogenetic trees}},
journal = {Bioinformatics},
year = {2001},
volume = {17},
number = {8},
pages = {754--755},
month = aug
}

@article{Nielsen:2009ey,
author = {Nielsen, Rasmus and Beaumont, Mark A},
title = {{Statistical inferences in phylogeography}},
journal = {Molecular Ecology},
year = {2009},
volume = {18},
number = {6},
pages = {1034--1047},
month = mar
}

@article{Heled:2010ia,
author = {Heled, Joseph and Drummond, Alexei J},
title = {{Bayesian inference of species trees from multilocus data}},
journal = {Molecular Biology and Evolution},
year = {2010},
volume = {27},
number = {3},
pages = {570--580},
month = mar
}

@article{Beerli:2006jb,
author = {Beerli, Peter},
title = {{Comparison of Bayesian and maximum-likelihood inference of population genetic parameters}},
journal = {Bioinformatics},
year = {2006},
volume = {22},
number = {3},
pages = {341--345},
month = feb
}

@article{Thorne:2002il,
author = {Thorne, Jeffrey L and Kishino, Hirohisa},
title = {{Divergence time and evolutionary rate estimation with multilocus data}},
journal = {Systematic Biology},
year = {2002},
volume = {51},
number = {5},
pages = {689--702},
month = oct
}

@article{Leache:2014ji,
author = {Leach{\'e}, Adam D and Harris, Rebecca B and Rannala, Bruce and Yang, Ziheng},
title = {{The influence of gene flow on species tree estimation: a simulation study}},
journal = {Systematic Biology},
year = {2014},
volume = {63},
number = {1},
pages = {17--30},
month = jan
}

@article{Stadler:2013hq,
author = {Stadler, Tanja},
title = {{How can we improve accuracy of macroevolutionary rate estimates?}},
journal = {Systematic Biology},
year = {2013},
volume = {62},
number = {2},
pages = {321--329},
month = mar
}

@article{Burgess:2008kf,
author = {Burgess, Ralph and Yang, Ziheng},
title = {{Estimation of hominoid ancestral population sizes under Bayesian coalescent models incorporating mutation rate variation and sequencing errors}},
journal = {Molecular Biology and Evolution},
year = {2008},
volume = {25},
number = {9},
pages = {1979--1994},
month = sep
}

@article{Lartillot:2006ds,
author = {Lartillot, N and Philippe, H},
title = {{Computing Bayes factors using thermodynamic integration}},
journal = {Systematic Biology},
year = {2006},
volume = {55},
number = {2},
pages = {195--207},
month = apr
}

