Akaike, H (1974). ‘A new look at the statistical model identification’. In: IEEE Transactions on Automatic Control 19.6, pp. 716–723 (page 18).
Aldous, D (2001). ‘Stochastic models and descriptive statistics for phylogenetic trees, from Yule to today’. In: Statistical Science 16, pp. 23–34 (pages 31, 39).
Alekseyenko, AV, CJ, Lee and MA, Suchard (2008). ‘Wagner and Dollo: a stochastic duet by composing two parsimonious solos’. In: Systematic Biology 57.5, pp. 772–784 (page 115).
Allen, LJ (2003). An introduction to stochastic processes with applications to biology. Upper Saddle River, NJ: Pearson Education (page 12).
Amenta, N and J, Klingner (2002). ‘Case study: visualizing sets of evolutionary trees’. In: INFOVIS 2002. IEEE Symposium on Information Visualization, pp. 71–74 (page 159).
Anderson, RM and RM, May (1991). Infectious diseases of humans: dynamics and control. Oxford: Oxford University Press (page 34).
Arunapuram, P, I Edvardsson, M Golden, et al. (2013). ‘StatAlign 2.0: combining statistical alignment with RNA secondary structure prediction’. In: Bioinformatics 29.5, pp. 654–655 (page 9).
Atarhouch, T, L Rüber, EG Gonzalez, et al. (2006). ‘Signature of an early genetic bottleneck in a population of Moroccan sardines (Sardina pilchardus)’. In: Molecular Phylogenetics and Evolution 39.2, pp. 373–383 (page 133).
Avise, J (2000). Phylogeography: the history and formation of species. Cambridge, MA: Harvard University Press (page 68).
Ayres, D, A Darling, D Zwickl, et al. (2012). ‘BEAGLE: a common application programming interface and high-performance computing library for statistical phylogenetics’. In: Systematic Biology 61, pp. 170–173 (page 114).
Baele, G, P Lemey, T Bedford, et al. (2012). ‘Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty’. In: Molecular Biology and Evolution 29.9, pp. 2157–2167 (pages 18, 19, 136, 137).
Baele, G, WLS Li, AJ Drummond, MA, Suchard and P, Lemey (2013a). ‘Accurate model selection of relaxed molecular clocks in Bayesian phylogenetics’. In: Molecular Biology and Evolution 30.2, pp. 239–243 (pages 18, 137).
Baele, G, P, Lemey and S, Vansteelandt (2013b). ‘Make the most of your samples: Bayes factor estimators for high-dimensional models of sequence evolution’. In: BMC Bioinformatics 14.1, p. 85 (page 19).
Bahl, J, MC Lau, GJ Smith, et al. (2011). ‘Ancient origins determine global biogeography of hot and cold desert cyanobacteria’. In: Nature Communications 2, art. 163 (page 96).
Bahlo, M and RC, Griffiths (2000). ‘Inference from gene trees in a subdivided population’. In: Theoretical Population Biology 57.2, pp. 79–95 (page 31).
Barnes, I, P Matheus, B Shapiro, D, Jensen and A, Cooper (2002). ‘Dynamics of Pleistocene population extinctions in Beringian brown bears’. In: Science 295, p. 2267 (page 31).
Barrett, M, MJ, Donoghue and E, Sober (1991). ‘Against consensus’. In: Systematic Zoology 40.4, pp. 486–493 (page 159).
Barton, NH, F, Depaulis and AM, Etheridge (2002). ‘Neutral evolution in spatially continuous populations’. In: Theoretical Population Biology 61.1, pp. 31–48 (page 74).
Barton, NH, J, Kelleher and AM, Etheridge (2010a). ‘A new model for extinction and recolonization in two dimensions: quantifying phylogeography’. In: Evolution 64.9, pp. 2701–2715 (page 74).
Barton, NH, AM, Etheridge and A, Veber (2010b). ‘A new model for evolution in a spatial continuum’. In: Electronic Journal of Probability 15, pp. 162–216 (page 74).
Beaumont, MA, R, Nielsen, C, Robert, et al. (2010). ‘In defence of model-based inference in phylogeography’. In: Molecular Ecology 19.3, pp. 436–446 (page 69).
Bedford, T, S Cobey, P Beerli and M, Pascual (2010). ‘Global migration dynamics underlie evolution and persistence of human influenza A (H3N2)’. In: PLoS Pathogens 6.5, e1000918 (page 71).
Beerli, P (2004). ‘Effect of unsampled populations on the estimation of population sizes and migration rates between sampled populations’. In: Molecular Ecology 13.4, pp. 827–836 (page 72).
Beerli, P (2006). ‘Comparison of Bayesian and maximum-likelihood inference of population genetic parameters.’ In: Bioinformatics 22.3, pp. 341–345 (page 14).
Beerli, P and J, Felsenstein (1999). ‘Maximum-likelihood estimation of migration rates and effective population numbers in two populations using a coalescent approach’. In: Genetics 152.2, pp. 763–773 (pages 6, 31).
Beerli, P and J, Felsenstein (2001). ‘Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach.’ In: Proceedings of the National Academy of Sciences USA 98.8, pp. 4563–4568 (pages 6, 31, 69, 71, 72).
Belfiore, N, L, Liu and C, Moritz (2008). ‘Multilocus phylogenetics of a rapid radiation in the genus Thomomys (Rodentia: Geomyidae)’. In: Systematic Biology 57.2, pp. 294–310 (page 120).
Benner, P, M, Bačák and PY, Bourguignon (2014). ‘Point estimates in phylogenetic reconstructions’. In: Bioinformatics 30.17, pp. i534–i540 (page 154).
Berger, JO (2006). ‘The case for objective Bayesian analysis’. In: Bayesian Analysis 1.3, pp. 385–402 (page 20).
Berger, JO and JM, Bernardo (1992). ‘On the development of reference priors’. In: Bayesian statistics. Ed. by JM, Bernardo, JO Berger, AP Dawid and AFM, Smith. Vol. 4. Oxford: Oxford University Press, pp. 35–60 (pages 14, 127).
Biek, R, AJ, Drummond and M, Poss (2006). ‘A virus reveals population structure and recent demographic history of its carnivore host’. In: Science 311, pp. 538–541 (pages 73, 133).
Biek, R, JC Henderson, LA Waller, CE, Rupprecht and LA, Real (2007). ‘A high-resolution genetic signature of demographic and spatial expansion in epizootic rabies virus’. In: Proceedings of the National Academy of Sciences USA 104.19, pp. 7993–7998 (page 73).
Bielejec, F, A Rambaut, MA Suchard and P, Lemey (2011). ‘SPREAD: spatial phylogenetic reconstruction of evolutionary dynamics’. In: Bioinformatics 27.20, pp. 2910–2912 (page 135).
Bielejec, F, P Lemey, G Baele, A, Rambaut and MA, Suchard (2014). ‘Inferring heterogeneous evolutionary processes through time: from sequence substitution to phylogeography’. In: Systematic Biology 63.4, pp. 493–504 (page 113).
Billera, L, S Holmes and K, Vogtmann (2001). ‘Geometry of the space of phylogenetic trees’. In: Advances in Applied Mathematics 27, pp. 733–767 (page 154).
Bloomquist, EW and MA, Suchard (2010). ‘Unifying vertical and nonvertical evolution: a stochastic ARG-based framework’. In: Systematic Biology 59.1, pp. 27–41 (pages 6, 10).
Bofkin, L and N, Goldman (2007). ‘Variation in evolutionary processes at different codon positions’. In: Molecular Biology and Evolution 24.2, pp. 513–521 (pages 100, 104, 146).
Bolstad, WM (2011). Understanding computational Bayesian statistics. Vol. 644. Hoboken, NJ: Wiley (page 10).
Boni, MF, D, Posada and MW, Feldman (2007). ‘An exact nonparametric method for inferring mosaic structure in sequence triplets’. In: Genetics 176.2, pp. 1035–1047 (page 97).
Bouckaert, RR (2010). ‘DensiTree: making sense of sets of phylogenetic trees’. In: Bioinformatics 26.10, pp. 1372–1373 (pages 156, 163).
Bouckaert, RR and D, Bryant (2012). ‘A rough guide to SNAPP’. In: BEAST 2 wiki (pages x, 124).
Bouckaert, RR, P, Lemey, M, Dunn, et al. (2012). ‘Mapping the origins and expansion of the Indo-European language family’. In: Science 337, pp. 957–960 (pages 57, 135).
Bouckaert, RR, M, Alvarado-Mora and J Rebello, Pinho (2013). ‘Evolutionary rates and HBV: issues of rate estimation with Bayesian molecular methods’. In: Antiviral Therapy 18, pp. 497–503 (pages 57, 100, 145).
Bouckaert, RR, J Heled, D Kühnert, et al. (2014). ‘BEAST 2: a software platform for Bayesian evolutionary analysis’. In: PLoS Computational Biology 10.4, e1003537 (page 16).
Bradley, RK, A Roberts, M Smoot, et al. (2009). ‘Fast statistical alignment’. In: PLoS Computational Biology 5.5, e1000392 (page 9).
Brooks, S and A, Gelman (1998). ‘Assessing convergence of Markov chain Monte Carlo algorithms’. In: Journal of Computational and Graphical Statistics 7, pp. 434–455 (page 140).
Brooks, S, A Gelman, GL Jones and XL, Meng (2010). Handbook of Markov chain Monte Carlo. Boca Raton, FL: Chapman & Hall/CRC. (page 10).
Brown, JM (2014). ‘Predictive approaches to assessing the fit of evolutionary models’. In: Systematic Biology 63.3, pp. 289–292 (page 18).
Brown, RP and Z, Yang (2011). ‘Rate variation and estimation of divergence times using strict and relaxed clocks’. In: BMC Evolutionary Biology 11, art. 271 (pages 105, 106, 144, 146).
Bryant, D (2003). ‘A classification of consensus methods for phylogenetics’. In: BioConsensus (Piscataway, NJ, 2000/2001). Providence, RI: AMS, pp. 163–184 (page 159).
Bryant, D, RR, Bouckaert, J, Felsenstein, N, Rosenberg, and A, RoyChoudhury (2012). ‘Inferring species trees directly from biallelic genetic markers: bypassing gene trees in a full coalescent analysis’. In: Molecular Biology and Evolution 29.8, pp. 1917–1932 (pages 7, 115, 119, 123).
Bunce, M, TH, Worthy, T, Ford, et al. (2003). ‘Extreme reversed sexual size dimorphism in the extinct New Zealand moa Dinornis.’In: Nature 425, pp. 172–175 (page 129).
Burnham, K and D, Anderson (2002). Model selection and multimodel inference: a practical information-theoretic approach. New York: Springer Verlag (page 32).
Camargo, A, LJ, Avila M Morando and J, WSites (2012). ‘Accuracy and precision of species trees: effects of locus, individual, and base pair sampling on inference of species trees in lizards of the Liolaemus darwinii group (Squamata, Liolaemidae)’. In: Systematic Biology 61.2, pp. 272–288 (page 120).
Campos, PF, E Willerslev, A Sher, et al. (2010). ‘Ancient DNA analyses exclude humans as the driving force behind late Pleistocene musk ox (Ovibos moschatus) population dynamics’. In: Proceedings of the National Academy of Sciences USA 107.12, pp. 5675–5680 (page 134).
Cavalli-Sforza, L and A, Edwards (1967). ‘Phylogenetic analysis: models and estimation procedures’. In: American Journal of Human Genetics 19, pp. 233–257 (pages 24, 25).
Chaves, JA and TB, Smith (2011). ‘Evolutionary patterns of diversification in the Andean hummingbird genus Adelomyia’. In: Molecular Phylogenetics and Evolution 60.2, pp. 207–218 (page 165).
Chung, Y and C, Ané (2011). ‘Comparing two Bayesian methods for gene tree/species tree reconstruction: simulations with incomplete lineage sorting and horizontal gene transfer’.In: Systematic Biology 60.3, pp. 261–275 (page 120).
Coop, G and RC, Griffiths (2004). ‘Ancestral inference on gene trees under selection’. In: Theoretical Population Biology 66.3, pp. 219–232 (pages 69, 76).
Cox, J, J, Ingersoll and S, Ross (1985). ‘A theory of the term structure of interest rates’. In: Econometrica 53, pp. 385–407 (page 125).
Currie, TE, SJ Greenhill, R Mace, et al. (2010). ‘Is horizontal transmission really a problem for phylogenetic comparative methods? A simulation study using continuous cultural traits’. In: Philosophical Transactions of the Royal Society B: Biological Sciences 365, pp. 3903–3912 (page 97).
Debruyne, R, G Chu, CE King, et al. (2008). ‘Out of America: ancient DNA evidence for a new world origin of late quaternary woolly mammoths’. In: Current Biology 18.17, pp. 1320–1326 (page 133).
Degnan, JH and NA, Rosenberg (2006). ‘Discordance of species trees with their most likely gene trees’. In: PLoS Genetics 2.5, e68 (page 116).
Didelot, X, J, Gardy and C, Colijn (2014). ‘Bayesian inference of infectious disease transmission from whole genome sequence data’. In: Molecular Biology and Evolution, msu121 (page 41).
Dinča, V, VA, Lukhtanov, G, Talavera and R, Vila (2011). ‘Unexpected layers of cryptic diversity in wood white Leptidea butterflies’. In: Nature Communications 2, art. 324 (pages 121, 165).
Drummond, AJ (2002). ‘Computational statistical inference for molecular evolution and population genetics’. PhD thesis. University of Auckland (page 106).
Drummond, AJ and A, Rambaut (2007). ‘BEAST: Bayesian evolutionary analysis by sampling trees’. In: BMC Evolutionary Biology 7, art. 214 (pages 14, 74, 79).
Drummond, AJ and AG, Rodrigo (2000). ‘Reconstructing genealogies of serial samples under the assumption of a molecular clock using serial-sample UPGMA’. In: Molecular Biology and Evolution 17.12, pp. 1807–1815 (page 31).
Drummond, AJ and MA, Suchard (2008). ‘Fully Bayesian tests of neutrality using genealogical summary statistics’. In: BMC Genetics 9, art. 68 (page 18).
Drummond, AJ and MA, Suchard (2010). ‘Bayesian random local clocks, or one rate to rule them all’. In: BMC Biology 8.1, art. 114 (pages 63–65, 83, 146).
Drummond, AJ, R, Forsberg and AG, Rodrigo (2001). ‘The inference of stepwise changes in substitution rates using serial sequence samples.’In: Molecular Biology and Evolution 18.7, pp. 1365–1371 (page 31).
Drummond, AJ, GK Nicholls, AG Rodrigo andW, Solomon (2002). ‘Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data’. In: Genetics 161.3, pp. 1307–1320 (pages 6, 14, 31, 33, 34, 66, 74, 109).
Drummond, AJ, OG Pybus, A Rambaut, R, Forsberg and AG, Rodrigo (2003a). ‘Measurably evolving populations’. In: Trends in Ecology & Evolution 18, pp. 481–488 (pages 8, 66, 128, 152).
Drummond, AJ, OG, Pybus and A, Rambaut (2003b). ‘Inference of viral evolutionary rates from molecular sequences’. In: Advances in Parasitology 54, pp. 331–358 (page 149).
Drummond, AJ, A, Rambaut, B, Shapiro and OG, Pybus (2005). ‘Bayesian coalescent inference of past population dynamics from molecular sequences’. In: Molecular Biology and Evolution 22.5, pp. 1185–1192 (pages 32, 108, 130, 133).
Drummond, AJ, SYW Ho, MJ Phillips and A, Rambaut (2006). ‘Relaxed phylogenetics and dating with confidence’. In: PLoS Biology 4.5, e88 (pages 62, 63, 73, 144).
Drummond, AJ, MA Suchard, D Xie and A, Rambaut (2012). ‘Bayesian phylogenetics with BEAUti and the BEAST 1.7’. In: Molecular Biology and Evolution 29.8, pp. 1969–1973 (pages 16, 74).
Duffy, S, LA, Shackelton and EC, Holmes (2008). ‘Rates of evolutionary change in viruses: patterns and determinants’. In: Nature Reviews Genetics 9.4, pp. 267–276 (pages 20, 152).
Durbin, R, SR Eddy, A Krogh and G, Mitchison (1998). Biological sequence analysis: probabilistic models of proteins and nucleic acids. Cambridge: Cambridge University Press (page 8).
Edgar, RC (2004a). ‘MUSCLE: a multiple sequence alignment method with reduced time and space complexity’. In: BMC Bioinformatics 5, p. 113 (page 9).
Edgar, RC (2004b). ‘MUSCLE: multiple sequence alignment with high accuracy and high throughput’. In: Nucleic Acids Research 32.5, pp. 1792–1797 (page 9).
Edwards, A (1970). ‘Estimation of the branch points of a branching diffusion process (with discussion)’. In: Journal of the Royal Statistical Society, Series B 32, pp. 155–174 (page 38).
Edwards, A and L, Cavalli-Sforza (1965). ‘A method for cluster analysis’. In: Biometrics, pp. 362–375 (page 6).
Edwards, CTT, EC Holmes, DJ Wilson, et al. (2006). ‘Population genetic estimation of the loss of genetic diversity during horizontal transmission of HIV-1’. In: BMC Evolutionary Biology 6, art. 28 (page 32).
Etienne, R, B Haegeman, T Stadler, et al. (2012). ‘Diversity-dependence brings molecular phylogenies closer to agreement with the fossil record’. In: Proceedings of the Royal Society B:Biological Sciences, doi:10.1098/rspb.2011.1439 (page 39).
Ewing, G and AG, Rodrigo (2006a). ‘Coalescent-based estimation of population parameters when the number of demes changes over time’. In: Molecular Biology and Evolution 23.5, pp. 988–996 (pages 6, 71).
Ewing, G and AG, Rodrigo (2006b). ‘Estimating population parameters using the structured serial coalescent with Bayesian MCMC inference when some demes are hidden’. In: Evolutionary Bioinformatics 2, pp. 227–235 (page 72).
Ewing, G, G, Nicholls and AG, Rodrigo (2004). ‘Using temporally spaced sequences to simultaneously estimate migration rates, mutation rate and population sizes in measurably evolving populations’. In: Genetics 168.4, pp. 2407–2420 (pages 6, 14, 69, 71, 72).
Faria, NR, MA Suchard, A Abecasis, et al. (2012). ‘Phylodynamics of the HIV-1 CRF02_AG clade in Cameroon’. In: Infection, Genetics and Evolution 12.2, pp. 453–460 (page 135).
Fearnhead, P and P, Donnelly (2001). ‘Estimating recombination rates from population genetic data’. In: Genetics 159.3, pp. 1299–1318 (page31).
Fearnhead, P and C, Sherlock (2006). ‘An exact Gibbs sampler for the Markov-modulated Poisson process’. In: Journal of the Royal Statistical Society, Series B 68.5, pp. 767–784 (page 72).
Felsenstein, J (1981). ‘Evolutionary trees from DNA sequences: a maximum likelihood approach’. In: Journal of Molecular Evolution 17, pp. 368–376 (pages 6, 49, 53, 55, 69, 70).
Felsenstein, J (1985). ‘Phylogenies and the comparative method’. In: The American Naturalist 125.1, pp. 1–15 (page 73).
Felsenstein, J (1988). ‘Phylogenies from molecular sequences: inference and reliability’. In: Annual Review of Genetics 22, pp. 521–565 (page 31).
Felsenstein, J (1992). ‘Estimating effective population size from samples of sequences: inefficiency of pairwise and segregating sites as compared to phylogenetic estimates’. In: Genetical Research 59, pp. 139–147 (pages 29, 31).
Felsenstein, J (2001). ‘The troubled growth of statistical phylogenetics’. In: Systematic Biology 50.4, pp. 465–467 (pages 6, 19, 68).
Felsenstein, J (2004). Inferring phylogenies. Sunderland, MA: Sinauer Associates (pages 14, 98).
Felsenstein, J (2006). ‘Accuracy of coalescent likelihood estimates: do we need more sites, more sequences, or more loci?’In: Molecular Biology and Evolution 23.3, pp. 691–700 (pages 6, 131, 151).
Finlay, EK, C Gaillard, S Vahidi, et al. (2007). ‘Bayesian inference of population expansions in domestic bovines’. In: Biology Letters 3.4, pp. 449–452 (page 133).
Firth, C, A Kitchen, B Shapiro, et al. (2010). ‘Using time-structured data to estimate evolutionary rates of double-stranded DNA viruses’. In: Molecular Biology and Evolution 27, pp. 2038–2051 (page 152).
Fisher, R (1930). Genetical theory of natural selection. Oxford: Clarendon Press (page 28).
FitzJohn, R (2010). ‘Quantitative traits and diversification’. In: Systematic Biology 59.6, pp. 619–633 (page 39).
FitzJohn, RG, WP, Maddison and SP, Otto (2009). ‘Estimating trait-dependent speciation and extinction rates from incompletely resolved phylogenies’. In: Systematic Biology 58.6, pp. 595–611 (page 39).
Ford, CB, PL Lin, MR Chase, et al. (2011). ‘Use of whole genome sequencing to estimate the mutation rate of Mycobacterium tuberculosis during latent infection’. In: Nature Genetics 43.5, pp. 482–486 (page 66).
Fraser, C, CA Donnelly, S Cauchemenz, et al. (2009). ‘Pandemic potential of a strain of influenza A (H1N1): early findings’. In: Science 324, pp. 1557–1561 (page 133).
Fu, YX (1994). ‘A phylogenetic estimator of effective population size or mutation rate’. In: Genetics 136.2, pp. 685–692 (page 29).
Gavryushkina, A, D, Welch and AJ, Drummond (2013). ‘Recursive algorithms for phylogenetic tree counting’. In: Algorithms in Molecular Biology 8, p. 26 (pages 25, 42).
Gavryushkina, A, D Welch, T Stadler and AJ, Drummond (2014). ‘Bayesian inference of sampled ancestor trees for epidemiology and fossil calibration’. In: arXiv preprint arXiv:1406.4573 (pages 42, 67, 111, 112).
Gelman, A and DB, Rubin (1992). ‘A single series from the Gibbs sampler provides a false sense of security’. In: Bayesian statistics. Ed. by J Bernardo, JO Berger, JO, Dawid and AFM, Smith. Vol. 4. Oxford: Oxford University Press, pp. 625–631 (page 140).
Gelman, A, GO, Roberts and WR, Gilks (1996). ‘Efficient Metropolis jumping rules’. In: Bayesian statistics. Ed. by JM, Bernardo, JO, Berger, AP, Dawid and AFM, Smith. Vol. 5. Oxford: Oxford University Press, pp. 599–608 (page 89).
Gelman, A, J Carlin, H Stern and D, Rubin (2004). Bayesian data analysis. 2nd edn. New York: Chapman & Hall/CRC (pages 10, 140).
Geman, S and D, Geman (1984). ‘Stochastic relaxation, Gibbs distribution, and the Bayesian restoration of images’. In: IEEE Transactions on Pattern Analysis and Machine Intelligence 6, pp. 721–741 (pages 16, 139).
Gernhard, T (2008). ‘The conditioned reconstructed process’.In: Journal of Theoretical Biology 253.4, pp. 769–778 (page 38).
Geweke, J (1992). ‘Evaluating the accuracy of sampling-based approaches to the calculation of posterior moments’. In: Bayesian statistics. Ed. by JM Bernardo, JO Berger, JO, Dawid and AFM, Smith. Vol. 4. Oxford: Oxford University Press, pp. 169–193 (page 140).
Gill, MS, P Lemey, NR Faria, et al. (2013). ‘Improving Bayesian population dynamics inference: a coalescent-based model for multiple loci’. In: Molecular Biology and Evolution 30.3, pp. 713–724 (page 33).
Gillespie, JH (2001). ‘Is the population size of a species relevant to its evolution?’In: Evolution 55.11, pp. 2161–2169 (page 29).
Goldman, N and Z, Yang (1994). ‘A codon-based model of nucleotide substitution for proteincoding DNA sequences’. In: Molecular Biology and Evolution 11, pp. 725–736 (page 51).
Goldstein, M (2006). ‘Subjective Bayesian analysis: principles and practice’. In: Bayesian Analysis 1.3, pp. 403–420 (page 20).
Graham, M and J, Kennedy (2010). ‘A survey of multiple tree visualisation’. In: Information Visualization 9.4, pp. 235–252 (page 156).
Gray, RD and QD, Atkinson (2003). ‘Language-tree divergence times support the Anatolian theory of Indo-European origin’. In: Nature 426, pp. 435–439 (page 57).
Gray, RD, AJ, Drummond and SJ, Greenhill (2009). ‘Language phylogenies reveal expansion pulses and pauses in Pacific settlement’. In: Science 323, pp. 479–483 (page 57).
Gray, RR, AJ Tatem, JA Johnson, et al. (2011). ‘Testing spatiotemporal hypothesis of bacterial evolution using methicillin-resistant Staphylococcus aureus ST239 genome-wide data within a Bayesian framework’. In: Molecular Biology and Evolution 28.5, pp. 1593–1603 (page 75).
Green, P (1995). ‘Reversible jump Markov chain Monte Carlo computation and Bayesian model determination’.In: Biometrika 82, pp. 711–732 (pages 16, 17).
Green, P, N, Hjort and S, Richardson (2003). Highly structured stochastic systems. Oxford: Oxford University Press (page 16).
Greenhill, SJ, AJ, Drummond and RD, Gray (2010). ‘How accurate and robust are the phylogenetic estimates of Austronesian language relationships?’In: PloS One 5.3, e9573 (page 97).
Grenfell, BT, OG Pybus, JR Gog, et al. (2004). ‘Unifying the epidemiological and evolutionary dynamics of pathogens’. In: Science 303, pp. 327–332 (page 74).
Griffiths, RC (1989). ‘Genealogical-tree probabilities in the infinitely-many-site model’. In: Journal of Mathematical Biology 27.6, pp. 667–680 (page 31).
Griffiths, RC and P, Marjoram (1996). ‘Ancestral inference from samples of DNA sequences with recombination’. In: Journal of Computational Biology 3.4, pp. 479–502 (pages 10, 31).
Griffiths, RC and S, Tavaré (1994). ‘Sampling theory for neutral alleles in a varying environment’. In: Philosophical Transactions of the Royal Society B: Biological Sciences 344, pp. 403–410 (pages 29, 31).
Grummer, JA, RW, Bryson and TW, Reeder (2014). ‘Species delimitation using Bayes factors: simulations and application to the Sceloporus scalaris species group (Squamata: Phrynosomatidae)’. In: Systematic Biology 63.2, pp. 119–133 (page 122).
Gu, X,, YX Fu and WH, Li (1995). ‘Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites’. In: Molecular Biology and Evolution 12.4, pp. 546–557 (page 54).
Hailer, F, VE Kutschera, BM Hallström, et al. (2012).‘Nuclear genomic sequences reveal that polar bears are an old and distinct bear lineage’. In: Science 336, pp. 344–347. eprint: www.sciencemag.org/content/336/6079/344.full.pdf (page 121).
Harding, E (1971). ‘The probabilities of rooted tree-shapes generated by random bifurcation’. In: Advances in Applied Probability 3, pp. 44–77 (page 36).
Harvey, PH and MD, Pagel (1991). The comparative method in evolutionary biology. Oxford: Oxford University Press (page 73).
Hasegawa, M, H, Kishino and T, Yano (1985). ‘Dating the human–ape splitting by a molecular clock of mitochondrial DNA’. In: Journal of Molecular Evolution 22, pp. 160–174 (pages 50,104).
Hastings, W (1970). ‘Monte Carlo sampling methods using Markov chains and their applications’. In: Biometrika 57, pp. 97–109 (pages 14, 16, 20, 31).
He, M, F Miyajima, P, Roberts, et al. (2013). ‘Emergence and global spread of epidemic healthcare-associated Clostridium difficile’. In: Nature Genetics 45.1, pp. 109–113 (page 134).
Heath, TA, JP, Huelsenbeck and T, Stadler (2014). ‘The fossilized birth–death process for coherent calibration of divergence-time estimates’. In: Proceedings of the National Academy of Sciences USA 111.29, pp. 2957–2966 (pages 67, 112).
Heidelberger, P and PD, Welch (1983). ‘Simulation run length control in the presence of an initial transient’. In: Operations Research 31.6, pp. 1109–1144 (page 140).
Hein, J, M, Schierup and C, Wiuf (2004). Gene genealogies, variation and evolution: a primer in coalescent theory. Oxford: Oxford University Press (page 27).
Heled, J and RR, Bouckaert (2013). ‘Looking for trees in the forest: summary tree from posterior samples’. In: BMC Evolutionary Biology 13.1, art. 221 (pages 159, 160, 163).
Heled, J and AJ, Drummond (2008). ‘Bayesian inference of population size history from multiple loci’. In: BMC Evolutionary Biology 8.1, art. 289 (pages 6, 17, 32, 110, 130, 131, 151).
Heled, J and AJ, Drummond (2010). ‘Bayesian inference of species trees from multilocus data’. In: Molecular Biology and Evolution 27.3, pp. 570–580 (pages 7, 8, 100, 113, 116, 119, 122).
Heled, J and AJ, Drummond (2012). ‘Calibrated tree priors for relaxed phylogenetics and divergence time estimation’. In: Systematic Biology 61.1, pp. 138–149 (pages 66, 84, 110, 111, 127).
Heled, JandAJ, Drummond(2013). ‘Calibrated birth–death phylogenetic time-tree priors for Bayesian inference’. In: arXiv preprint arXiv:1311.4921 (pages 66, 110, 111, 127).
Hey, J (2010). ‘Isolation with migration models for more than two populations’. In: Molecular Biology and Evolution 27.4, pp. 905–920 (page 8).
Hillis, D, T Heath and K St, John (2005). ‘Analysis and visualization of tree space’. In: Systematic Biology 54.3, pp. 471–482 (page 159).
Ho, SY and B, Shapiro (2011). ‘Skyline-plot methods for estimating demographic history from nucleotide sequences’. In: Molecular Ecology Resources 11.3, pp. 423–434 (page 97).
Ho, SYW, MJ, Phillips, AJ, Drummond and A, Cooper (2005). ‘Accuracy of rate estimation using relaxed-clock models with a critical focus on the early Metazoan radiation’. In: Molecular Biology and Evolution 22, pp. 1355–1363 (page 144).
Hoffman, J, S Grant, J, Forcada and C, Phillips (2011). ‘Bayesian inference of a historical bottleneck in a heavily exploited marine mammal’.In: Molecular Ecology 20.19, pp. 3989– 4008 (page 133).
Hoffman, MD and A, Gelman (2014). ‘The no-U-turn sampler: adaptively setting path lengths in Hamiltonian Monte Carlo’.In: Journal of Machine Learning Research 15, pp. 1593–1623 (page 156).
Höhna, S and AJ, Drummond (2012). ‘Guided tree topology proposals for Bayesian phylogenetic inference’. In: Systematic Biology 61.1, pp. 1–11 (pages 113, 150, 156, 159, 161).
Höhna, S, T Stadler, F, Ronquist and T, Britton (2011). ‘Inferring speciation and extinction rates under different sampling schemes’. In: Molecular Biology and Evolution 28.9, pp. 2577–2589 (page 98).
Holder, MT, PO, Lewis, DL, Swofford and B, Larget (2005). ‘Hastings ratio of the LOCAL proposal used in Bayesian phylogenetics’. In: Systematic Biology 54, pp. 961–965 (page 16).
Holder, MT, J, Sukumaran and PO, Lewis (2008). ‘A justification for reporting the majorityrule consensus tree in Bayesian phylogenetics’. In: Systematic Biology 57.5, pp. 814–821 (page 160).
Holmes, EC and BT, Grenfell (2009). ‘Discovering the phylodynamics of RNA viruses’. In: PLoS Computational Biology 5.10, e1000505 (page 74).
Holmes, EC, LQ, Zhang, P, Simmonds, AS, Rogers and AJ Leigh, Brown (1993). ‘Molecular investigation of human immunodeficiency virus (HIV) infection in a patient of an HIV-infected surgeon’. In: Journal of Infectious Diseases 167.6, pp. 1411–1414 (page 31).
Hudson, RR (1987). ‘Estimating the recombination parameter of a finite population model without selection’. In: Genetics Research 50.3, pp. 245–250 (page 29).
Hudson, RR (1990). ‘Gene genealogies and the coalescent process’. In: Oxford surveys in evolutionary biology. Ed. by D, Futuyma and J, Antonovics. Vol. 7. Oxford: Oxford University Press, pp. 1–44 (pages 29, 71, 72).
Hudson, RR and NL, Kaplan (1985). ‘Statistical properties of the number of recombination events in the history of a sample of DNA sequences’. In: Genetics 111.1, pp. 147–164 (page 29).
Huelsenbeck, JP and F, Ronquist (2001). ‘MrBayes: Bayesian inference of phylogenetic trees’. In: Bioinformatics 17, pp. 754–755 (page 14).
Huelsenbeck, JP, B, Larget and DL, Swofford (2000). ‘A compound Poisson process for relaxing the molecular clock’. In: Genetics 154, pp. 1879–1892 (page 62).
Huelsenbeck, JP, F Ronquist, R Nielsen and JP, Bollback (2001). ‘Bayesian inference of phylogeny and its impact on evolutionary biology’. In: Science 294, pp. 2310–2314 (pages 6, 111).
Huelsenbeck, JP, B, Larget and ME, Alfaro (2004). ‘Bayesian phylogenetic model selection using reversible jump Markov chain Monte Carlo’. In: Molecular Biology and Evolution 21.6, pp. 1123–1133 (page 57).
Hurvich, CM and CL, Tsai (1989). ‘Regression and time series model selection in small samples’. In: Biometrika 76.2, pp. 297–307 (page 32).
Huson, DH and D, Bryant (2006). ‘Application of phylogenetic networks in evolutionary studies’. In: Molecular Biology and Evolution 23.2, pp. 254–267 (page 97).
Jackman, T, A Larson, KD Queiroz and J, Losos (1999). ‘Phylogenetic relationships and tempo of early diversification in Anolis lizards’. In: Systematic Biology 48.2, pp. 254–285 (page 157).
Jaynes, ET (2003). Probability theory: the logic of science. Cambridge: Cambridge University Press (pages 10, 19).
Jeffreys, H (1946). ‘An invariant form for the prior probability in estimation problems’. In: Proceedings of the Royal Society A: Mathematical and Physical Sciences 186.1007, pp. 453–461 (page 14).
Jeffreys, H (1961). Theory of probability. 1st edn. London: Oxford University Press (page 14).
Jenkins, GM, A Rambaut, OG Pybus and EC, Holmes (2002). ‘Rates of molecular evolution in RNA viruses: a quantitative phylogenetic analysis’. In: Journal of Molecular Evolution 54.2, pp. 156–165 (pages 66, 152).
Jones, G (2011). ‘Calculations for multi-type age-dependent binary branching processes’. In: Journal of Mathematical Biology 63.1, pp. 33–56 (page 39).
Jukes, T and C, Cantor (1969). ‘Evolution of protein molecules’. In: Mammaliam protein metabolism. Ed. by H, Munro. New York: Academic Press, pp. 21–132 (pages 44, 46, 103).
Kass, R and A, Raftery (1995). ‘Bayes factors’. In: Journal of the American Statistical Association 90, pp. 773–795 (page 18).
Kass, RE, BP, Carlin, A, Gelman and RM, Neal (1998). ‘Markov chain Monte Carlo in practice: a roundtable discussion’. In: The American Statistician 52.2, pp. 93–100 (pages 140, 141).
Katoh, K and DM, Standley (2013). ‘MAFFT multiple sequence alignment software version 7: improvements in performance and usability’. In: Molecular Biology and Evolution 30.4, pp. 772–780 (page 9).
Katoh, K and DM, Standley (2014). ‘MAFFT: iterative refinement and additional methods’. In: Methods in Molecular Biology 1079, pp. 131–146 (page 9).
Katoh, K, K Misawa, K Kuma and T, Miyata (2002). ‘MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform’. In: Nucleic Acids Research 30.14, pp. 3059–3066 (page 9).
Keeling, MJ and P, Rohani (2008). Modeling infectious diseases in humans and animals. Princeton, NJ: Princeton, University Press (page 34).
Kendall, DG (1948). ‘On the generalized “birth-and-death” process’. In: Annals of Mathematical Statistics 19.1, pp. 1–15 (page 36).
Kendall, DG (1949). ‘Stochastic processes and population growth’.In: Journal of the Royal Statistical Society, Series B 11.2, pp. 230–282 (page 73).
Kimura, M (1980). ‘A simple model for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences’. In: Journal of Molecular Evolution 16, pp. 111–120 (page 48).
Kingman, J (1982). ‘The coalescent’. In: Stochastic Processes and Their Applications 13.3, pp. 235–248 (pages 6, 28).
Kishino, H, JL, Thorne and WJ, Bruno (2001). ‘Performance of a divergence time estimation method under a probabilistic model of rate evolution’. In: Molecular Biology and Evolution 18.3, pp. 352–361 (page 62).
Knuth, D (1997). The art of computer programming. Vol. 2. Seminumerical algorithms. Reading, MA: Addison-Wesley (page 114).
Kouyos, RD, CL, Althaus and S, Bonhoeffer (2006). ‘Stochastic or deterministic: what is the effective population size of HIV-1?’In: Trends in Microbiology 14.12, pp. 507–511 (page 29).
Kubatko, LS and JH, Degnan (2007). ‘Inconsistency of phylogenetic estimates from concatenated data under coalescence’. In: Systematic Biology 56.1, pp. 17–24 (page 116).
Kuhner, MK (2006). ‘LAMARC 2.0: maximum likelihood and Bayesian estimation of population parameters’. In: Bioinformatics 22.6, pp. 768–770 (pages 10, 14).
Kuhner, MK, J, Yamato and J, Felsenstein (1995). ‘Estimating effective population size and mutation rate from sequence data using Metropolis–Hastings sampling’. In: Genetics 140, pp. 1421–1430 (pages 6, 31).
Kuhner, MK, J, Yamato and J, Felsenstein (1998). ‘Maximum likelihood estimation of population growth rates based on the coalescent’. In: Genetics 149, pp. 429–434 (pages 6, 31, 109).
Kuhner, MK, J, Yamato and J, Felsenstein (2000). ‘Maximum likelihood estimation of recombination rates from population data’. In: Genetics 156.3, pp. 1393–1401 (pages 6, 10, 31).
Kühnert, D, CH, Wu and AJ, Drummond (2011). ‘Phylogenetic and epidemic modeling of rapidly evolving infectious diseases’. In: Infection, Genetics and Evolution 11.8, pp. 1825–1841 (pages 8, 66, 75).
Kühnert, D, T, Stadler, TG, Vaughan and AJ, Drummond (2014). ‘Simultaneous reconstruction of evolutionary history and epidemiological dynamics from viral sequences with the birth–death SIR model’. In: Journal of the Royal Society Interface 11.94 (pages 40, 75, 130).
Kuo, L and B, Mallick (1998). ‘Variable selection for regression models’. In: Sankhya B 60, pp. 65–81 (page 17).
Lakner, C, P van der, Mark, JP, Huelsenbeck, B, Larget and F, Ronquist (2008). ‘Efficiency of Markov chain Monte Carlo tree proposals in Bayesian phylogenetics’. In: Systematic Biology 57.1, pp. 86–103 (page 156).
Lambert, DM, PA Ritchie, CD Millar, et al. (2002). ‘Rates of evolution in ancient DNA from Adelie penguins’.In: Science 295, pp. 2270–2273 (pages 31, 66, 129).
Laplace, P (1812). Théorie analytique des probabilités. Paris: Courcier (page 13).
Larget, B (2013). ‘The estimation of tree posterior probabilities using conditional clade probability distributions’. In: Systematic Biology 62.4, pp. 501–511 (pages 159, 161).
Larget, B and D, Simon (1999). ‘Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees’. In: Molecular Biology and Evolution 16, pp. 750–759 (page 14).
Larkin, M, G, Blackshields, NP, Brown, et al. (2007). ‘Clustal W and Clustal X version 2.0’. In: Bioinformatics 23, pp. 2947–2948 (page 9).
Lartillot, N and H, Philippe (2006). ‘Computing Bayes factors using thermodynamic integration’.In: Systematic Biology 55, pp. 195–207 (page 136).
Lartillot, N, T, Lepage and S, Blanquart (2009). ‘PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating’. In: Bioinformatics 25.17, pp. 2286–2288 (page 14).
Leaché, AD and MK, Fujita (2010). ‘Bayesian species delimitation in West African forest geckos (Hemidactylus fasciatus)’. In: Proceedings of the Royal Society B: Biological Sciences 277, pp. 3071–3077 (page 121).
Leaché, AD and B, Rannala (2011). ‘The accuracy of species tree estimation under simulation: a comparison of methods’. In: Systematic Biology 60.2, pp. 126–137 (page 119).
Leaché, AD, MK, Fujita, VN, Minin and RR, Bouckaert (2014). ‘Species delimitation using genome-wide SNP data’. In: Systematic Biology, syu018 (page 126).
Leitner, T and W, Fitch (1999). ‘The phylogenetics of known transmission histories’. In: The evolution of HIV. Ed. by KA, Crandall. Baltimore, MD: Johns Hopkins University Press, pp. 315–345 (page 41).
Lemey, P, OG Pybus, B Wang, et al. (2003). ‘Tracing the origin and history of the HIV-2 epidemic’. In: Proceedings of the National Academy of Sciences USA 100.11, pp. 6588–6592 (page 32).
Lemey, P, OG, Pybus, Rambaut, A, et al. (2004). ‘The molecular population genetics of HIV-1 group O’. In: Genetics 167.3, pp. 1059–1068 (pages 32, 152).
Lemey, P, A, Rambaut, AJ, Drummond andMA, Suchard (2009a). ‘Bayesian phylogeography finds its roots’. In: PLoS Computational Biology 5.9, e1000520 (pages 17, 69, 71, 72, 76, 134).
Lemey, P, MA, Suchard and A, Rambaut (2009b). ‘Reconstructing the initial global spread of a human influenza pandemic: a Bayesian spatial–temporal model for the global spread of H1N1pdm’. In: PLoS Currents RRN1031 (pages 71, 129, 134).
Lemey, P, A Rambaut, JJ Welch and MA, Suchard (2010). ‘Phylogeography takes a relaxed random walk in continuous space and time’. In: Molecular Biology and Evolution 27.8, pp. 1877–1885 (pages 73, 134).
Lemey, P, A, Rambaut, T, Bedford, et al. (2014). ‘Unifying viral genetics and human transportation data to predict the global transmission dynamics of human influenza H3N2’.In: PLoS Pathogens 10.2, e1003932 (page 135).
Leonard, J, R, Wayne, J, Wheeler, et al. (2002). ‘Ancient DNA evidence for Old World origin of New World dogs’. In: Science 298, p. 1613 (page 31).
Lepage, T, D, Bryant, H, Philippe and N, Lartillot (2007). ‘A general comparison of relaxed molecular clock models’. In: Molecular Biology and Evolution 24.12, pp. 2669–2680 (page 63).
Leventhal, GE, H, Guenthard, S, Bonhoeffer and T, Stadler (2014). ‘Using an epidemiological model for phylogenetic inference reveals density-dependence in HIV transmission’. In: Molecular Biology and Evolution 31.1, pp. 6–17 (pages 34, 40, 75).
Levinson, G and GA, Gutman (1987). ‘High frequencies of short frameshifts in poly-CA/TG tandem repeats borne by bacteriophage M13 in Escherichia coli K-12’. In: Nucleic Acids Research 15.13, pp. 5323–5338 (page 52).
Lewis, PO (2001). ‘A likelihood approach to estimating phylogeny from discrete morphological character data’. In: Systematic Biology 50.6, pp. 913–925 (page 57).
Lewis, PO, MT, Holder and KE, Holsinger (2005). ‘Polytomies and Bayesian phylogenetic inference.’In: Systematic Biology 54.2, pp. 241–253 (page 14).
Li, S, D, Pearl and H, Doss (2000). ‘Phylogenetic tree construction using Markov chain Monte Carlo’. In: Journal of the American Statistical Association 95, pp. 493–508 (page 14).
Li, WLS and AJ, Drummond (2012). ‘Model averaging and Bayes factor calculation of relaxed molecular clocks in Bayesian phylogenetics’. In: Molecular Biology and Evolution 29.2, pp. 751–761 (pages 63, 145).
Liu, L (2008). ‘BEST: Bayesian estimation of species trees under the coalescent model’. In: Bioinformatics 24.21, pp. 2542–2543 (page 119).
Liu, L, DK Pearl, RT Brumfield and SV, Edwards (2008). ‘Estimating species trees using multipleallele DNA sequence data’. In: Evolution 62.8, pp. 2080–2091 (page 7).
Liu, L, L Yu, L Kubatko, DK, Pearl and SV, Edwards (2009a). ‘Coalescent methods for estimating phylogenetic trees’. In: Molecular Phylogenetics and Evolution 53.1, pp. 320–328 (page 7).
Liu, L, L, Yu, DK, Pearl and SV, Edwards (2009b). ‘Estimating species phylogenies using coalescence times among sequences’. In: Systematic Biology 58.5, pp. 468–477 (page 7).
Loreille, O, L Orlando, M Patou-Mathis, et al. (2001). ‘Ancient DNA analysis reveals divergence of the cave bear, Ursus spelaeus, and brown bear, Ursus arctos, lineages’. In: Current Biology 11.3, pp. 200–203 (page 31).
Lunn, DJ, A Thomas, N Best and D, Spiegelhalter (2000). ‘WinBUGS – a Bayesian modelling framework: concepts, structure, and extensibility’. In: Statistics and Computing 10.4, pp. 325–337 (page 156).
Lunn, D, D, Spiegelhalter, A, Thomas and N, Best (2009). ‘The BUGS project: evolution, critique and future directions’. In: Statistics in Medicine 28.25, pp. 3049–3067 (page 156).
Lunter, G, I Miklos, AJ Drummond, JL, Jensen and J, Hein (2005). ‘Bayesian coestimation of phylogeny and sequence alignment’. In: BMC Bioinformatics 6, art. 83 (pages 4, 9, 99).
MacKay, DJ (2003). Information theory, inference and learning algorithms. Cambridge: Cambridge University Press (page 10).
Maddison, DR and WP, Maddison (2005). MacClade 4.08. Sunderland, MA: Sinauer Associates (page 68).
Maddison, WP (2007). ‘Estimating a binary character's effect on speciation and extinction’. In: Systematic Biology 56.5, pp. 701–710 (pages 39, 69).
Matschiner, M and RR, Bouckaert (2013). ‘A rough guide to CladeAge’. In: BEAST 2 wiki (pages 66, 111).
Matsumoto, M and T, Nishimura (1998). ‘Mersenne twister: a 623-dimensionally equidistributed uniform pseudo-random number generator’. In: ACMTransactions on Modeling and Computer Simulation 8.1, pp. 3–30 (page 114).
Mau, B and M, Newton (1997). ‘Phylogenetic inference for binary data on dendrograms using Markov chainMonte Carlo’. In: Journal of Computational and Graphical Statistics 6, pp. 122–131 (page 14).
Mau, B, MA, Newton and B, Larget (1999). ‘Bayesian phylogenetic inference via Markov chain Monte Carlo methods’. In: Biometrics 55.1, pp. 1–12 (pages 14, 157).
McCormack, JE, J Heled, KS Delaney, AT, Peterson and LL, Knowles (2011). <‘Calibrating divergence times on species trees versus gene trees: implications for speciation history of Aphelocoma jays’. In: Evolution 65.1, pp.184–202 (page 165).
Meredith, R, J, Janecka, J, Gatesy, et al. (2011). ‘Impacts of the Cretaceous terrestrial revolution and KPg extinction on mammal diversification’. In: Science 334, pp. 521–524 (page 39).
Metropolis, N, A, Rosenbluth, M, Rosenbluth, A, Teller and E, Teller (1953). ‘Equations of state calculations by fast computing machines’. In: Journal of Chemistry and Physics 21, pp. 1087–1092 (pages 14, 20, 31).
Minin, VN, EW, Bloomquist and MA, Suchard (2008). ‘Smooth skyride through a rough skyline: Bayesian coalescent-based inference of population dynamics’. In: Molecular Biology and Evolution 25.7, pp. 1459–1471 (pages 33, 108).
Molina, J, M, Sikora, N, Garud, et al. (2011). ‘Molecular evidence for a single evolutionary origin of domesticated rice’. In: Proceedings of the National Academy of Sciences USA 108.20, pp. 8351–8356 (page 121).
Mollentze, N, LH, Nel, S, Townsend, et al. (2014). ‘A Bayesian approach for inferring the dynamics of partially observed endemic infectious diseases from space-time-genetic data’. In: Proceedings of the Royal Society B: Biological Sciences 281.1782, p. 20133251 (page 75).
Monjane, AL, GW Harkins, DP Martin, et al. (2011). ‘Reconstructing the history of Maize streak virus strain A dispersal to reveal diversification hot spots and its origin in southern Africa’. In: Journal of Virology 85.18, pp. 9623–9636 (page 135).
Mooers, A and S, Heard (1997). ‘Inferring evolutionary process from phylogenetic tree shape’. In: Quarterly Review of Biology 72, pp. 31–54 (page 107).
Moran, PAP (1962). The statistical processes of evolutionary theory. Oxford: Clarendon Press (page 28).
Moran, PAP (1958). ‘Random processes in genetics’. In: Mathematical Proceedings of the Cambridge Philosophical Society 54, pp. 60–71 (page 28).
Morlon, H, T, Parsons and J, Plotkin (2011). ‘Reconciling molecular phylogenies with the fossil record’. In: Proceedings of the National Academy of Sciences USA 108.39, pp. 16 327–16 332 (page 39).
Mourier, T, SY Ho, MTP Gilbert, E, Willerslev and L, Orlando (2012). ‘Statistical guidelines for detecting past population shifts using ancient DNA’. In: Molecular Biology and Evolution 29.9, pp. 2241–2251 (page 97).
Muse, S and B, Gaut (1994). ‘A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with applications to the chloroplast genome’. In: Molecular Biology and Evolution 11, pp. 715–725 (page 51).
Mutreja, A, DW, Kim, NR, Thomson, et al. (2011). ‘Evidence for several waves of global transmission in the seventh cholera pandemic’.In: Nature 477.7365, pp. 462–465 (page 129).
Nagalingum, N, C Marshall, T Quental, et al. (2011). ‘Recent synchronous radiation of a living fossil’. In: Science 334, pp. 796–799 (page 96).
Nee, SC (2001). ‘Inferring speciation rates from phylogenies’. In: Evolution 55.4, pp. 661–668 (page 107).
Nee, SC, EC, Holmes, RM, May and PH, Harvey (1994a). ‘Extinction rates can be estimated from molecular phylogenies’. In: Philosophical Transactions of the Royal Society B: Biological Sciences 344.1307, pp. 77–82 (page 107).
Nee, SC, RM, May and PH, Harvey (1994b). ‘The reconstructed evolutionary process’. In: Philosophical Transactions of the Royal Society B: Biological Sciences 344, pp. 305–311 (page 39).
Nee, SC, EC, Holmes, A, Rambaut and PH, Harvey (1995). ‘Inferring population history from molecular phylogenies’. In: Philosophical Transactions of the Royal Society B: Biological Sciences 349.1327, pp. 25–31 (page 29).
Newton, Mand A, Raftery (1994). ‘Approximate Bayesian inference with the weighted likelihood bootstrap’. In: Journal of the Royal Statistical Society, Series B 56, pp. 3–48 (page 18).
Nicholls, GK and RD, Gray (2006). ‘Quantifying uncertainty in a stochastic model of vocabulary evolution’. In: Phylogenetic methods and the prehistory of languages. Ed. by P, Forster and C, Renfrew. Cambridge:McDonald Institute for Archaeological Research, pp. 161–171 (page 57).
Nicholls, GK and RD, Gray (2008). ‘Dated ancestral trees from binary trait data and their application to the diversification of languages’. In: Journal of the Royal Statistical Society, Series B 70.3, pp. 545–566 (page 115).
Nielsen, R and Z, Yang (1998). ‘Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene’. In: Genetics 148, pp. 929–936 (page 111).
Notredame, C, DG, Higgins and J, Heringa (2000). ‘T-coffee: a novel method for fast and accurate multiple sequence alignment’. In: Journal of Molecular Biology 302.1, pp. 205 –217 (page 9).
Novák, A, I Miklós, R Lyngsø and J, Hein (2008). ‘StatAlign: an extendable software package for joint Bayesian estimation of alignments and evolutionary trees’. In: Bioinformatics 24.20, pp. 2403–2404 (pages 9, 99).
Nylander, JAA, JC, Wilgenbusch, DL, Warren and DL, Swofford (2008). ‘AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics’. In: Bioinformatics 24.4, pp. 581–583 (pages 141, 156).
Ohta, T and M, Kimura (1973). ‘A model of mutation appropriate to estimate the number of electrophoretically detectable alleles in a finite population’. In: Genetics 22.2, pp. 201–204 (page 52).
Opgen-Rhein, R, L, Fahrmeir and K, Strimmer (2005). ‘Inference of demographic history from genealogical trees using reversible jump Markov chain Monte Carlo’. In: BMC Evolutionary Biology 5.1, art. 6 (page 32).
Owen, Mand JS, Provan (2011). ‘A fast algorithm for computing geodesic distances in tree space’. In: IEEE/ACM Transactions on Computational Biology and Bioinformatics 8.1, pp. 2–13 (page 154).
Pagel, MD and A, Meade (2004). ‘A phylogenetic mixture model for detecting patternheterogeneity in gene sequence or character-state data’. In: Systematic Biology 53.4, pp. 571–581 (page 14).
Palacios, JA and VN, Minin (2012). ‘Integrated nested Laplace approximation for Bayesian nonparametric phylodynamics.’In: Proceedings of the 28th Conference on Uncertainty in Artificial Intelligence. Ed. by N de, Freitas and K Murphy., Sterling, VA: AUAI Press, pp. 726–735 (page 33).
Palacios, JA and VN, Minin (2013). ‘Gaussian process-based Bayesian nonparametric inference of population trajectories from gene genealogies’. In: Biometrics 69.1, pp. 8–18 (page 33).
Palmer, D, J, Frater, R, Phillips, AR, McLean and G, McVean (2013). ‘Integrating genealogical and dynamical modelling to infer escape and reversion rates in HIV epitopes’. In: Proceedings of the Royal Society B: Biological Sciences 280.1762, art. 2013.0696 (pages 69, 75).
Pamilo, P and M, Nei (1988). ‘Relationships between gene trees and species trees’. In: Molecular Biology and Evolution 5.5, pp. 568–83 (pages 41, 116).
Penny, D, BJ, McComish, MA, Charleston and MD, Hendy (2001). ‘Mathematical elegance with biochemical realism: the covarion model of molecular evolution’. In: Journal of Molecular Evolution 53.6, pp. 711–723 (page 57).
Pereira, L, F, Freitas, V, Fernandes, et al. (2009). ‘The diversity present in 5140 human mitochondrial genomes’. In: American Journal of Human Genetics 84.5, pp. 628–640 (page 102).
Popinga, A, TG, Vaughan, T, Stadler and AJ, Drummond (2015). ‘Inferring epidemiological dynamics with Bayesion coalescent inference: the merits of deterministic and Stochastic models’. In: Genetics 199.2, pp. 595–607 (page 36).
Posada, D (2008). ‘jModelTest: phylogenetic model averaging’. In: Molecular Biology and Evolution 25.7, pp. 1253–1256 (page 145).
Posada, D and KA, Crandall (1998). ‘Modeltest: testing the model of DNA substitution.’In: Bioinformatics 14.9, pp. 817–818 (page 145).
Procter, JB, J, Thompson, I, Letunic, et al. (2010). ‘Visualization of multiple alignments, phylogenies and gene family evolution’. In: Nature Methods 7, S16–S25 (page 156).
Pybus, OG and A, Rambaut (2002). ‘GENIE: estimating demographic history from molecular phylogenies’. In: Bioinformatics 18.10, pp. 1404–1405 (page 29).
Pybus, OG and A, Rambaut (2009). ‘Evolutionary analysis of the dynamics of viral infectious disease’. In: Nature Reviews Genetics 10.8, pp. 540–550 (pages 8, 75).
Pybus, OG, A, Rambaut and PH, Harvey (2000). ‘An integrated framework for the inference of viral population history from reconstructed genealogies’. In: Genetics 155, pp. 1429–1437 (pages 29, 32).
Pybus, OG, MA, Charleston, S, Gupta, et al. (2001). ‘The epidemic behavior of the hepatitis C virus’.In: Science 292, pp. 2323–2325 (page 29).
Pybus, OG, AJ, Drummond, T, Nakano, BH, Robertson and A, Rambaut (2003). ‘The epidemiology and iatrogenic transmission of hepatitis C virus in Egypt: a Bayesian coalescent approach’. In: Molecular Biology and Evolution 20.3, pp. 381–387 (pages 29, 32, 106).
Pybus, OG, E, Barnes, R, Taggest, et al. (2009). ‘Genetic history of hepatitis C virus in East Asia’. In: Journal of Virology 83.2, pp. 1071–1082 (page 33).
Pybus, OG, MA, Suchard, P, Lemey, et al. (2012). ‘Unifying the spatial epidemiology and molecular evolution of emerging epidemics’. In: Proceedings of the National Academy of Sciences USA 109.37, pp. 15 066–15 071 (page 135).
Pyron, RA (2011). ‘Divergence time estimation using fossils as terminal taxa and the origins of Lissamphibia’.In: Systematic Biology, syr047 (page 57).
Rabosky, D (2007). ‘Likelihood methods for detecting temporal shifts in diversification rates’. In: Evolution 60.6, pp. 1152–1164 (page 39).
Raftery, AE and SM, Lewis (1992). ‘[Practical Markov chain Monte Carlo]: comment: one long run with diagnostics: implementation strategies for Markov chain Monte Carlo’. In: Statistical Science 7.4, pp. 493–497 (page 140).
Raftery, A, M, Newton, J, Satagopan and P, Krivitsky (2007). ‘Estimating the integrated likelihood via posterior simulation using the harmonic mean identity’. In: Bayesian statistics. Ed. by JM, Bernardo, MJ, Bayarri, JO, Berger et al. Vol. 8. Oxford: Oxford University Press, pp. 1–45 (page 18).
Rambaut, A (2000). ‘Estimating the rate of molecular evolution: incorporating noncontemporaneous sequences into maximum likelihood phylogenies’. In: Bioinformatics 16, pp. 395–399 (pages 31, 66).
Rambaut, A (2010). Path-O-Gen: temporal signal investigation tool. Version 1.3 (page 149).
Rambaut, A and AJ, Drummond (2014). Tracer v1.6http://tree.bio.ed.ac.uk/software/tracer/ (pages 130, 137).
Rannala, B and Z, Yang (1996). ‘Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference’. In: Journal of Molecular Evolution 43, pp. 304–311 (page 160).
Rannala, B and Z, Yang (2007). ‘Inferring speciation times under an episodic molecular clock’. In: Systematic Biology 56.3, pp. 453–466 (pages 62, 63).
Rasmussen, DA, O, Ratmann and K, Koelle (2011). ‘Inference for nonlinear epidemiological models using genealogies and time series’. In: PLoS Computational Biology 7.8, e1002136 (page 75).
Redelings, BD and MA, Suchard (2005). ‘Joint Bayesian estimation of alignment and phylogeny’. In: Systematic Biology 54.3, pp. 401–418 (pages 4, 9, 99, 137).
Redelings, BD and MA, Suchard (2007). ‘Incorporating indel information into phylogeny estimation for rapidly emerging pathogens’. In: BMC Evolutionary Biology 7, art. 40 (page 99).
Reid, NM, SM, Hird, JM, Brown, et al. (2013). ‘Poor fit to the multispecies coalescent is widely detectable in empirical data’. In: Systematic Biology, syt057 (page 116).
Richard, GF and F, Pâques (2000). ‘Mini- and microsatellite expansions: the recombination connection’. In: EMBO Report 1.2, pp. 122–126 (page 52).
Robinson, D and LR, Foulds (1981). ‘Comparison of phylogenetic trees’. In: Mathematical Biosciences 53.1, pp. 131–147 (page 161).
Rodrigo, AG and J, Felsenstein (1999). ‘Coalescent approaches to HIV population genetics’. In: The evolution of HIV. Ed. by KA, Crandall. Baltimore, MD: Johns Hopkins University Press, pp. 233–272 (pages 31, 33).
Rodrigo, AG, EG, Shpaer, EL, Delwart, et al. (1999). ‘Coalescent estimates of HIV-1 generation time in vivo’. In: Proceedings of the National Academy Sciences USA 96.5, pp. 2187–2191 (page 31).
Rodrigue, N, H, Philippe and N, Lartillot (2008). ‘Uniformization for sampling realizations of Markov processes: applications to Bayesian implementations of codon substitution models’. In: Bioinformatics 24.1, pp. 56–62 (page 72).
Romero-Severson, E, H, Skar, I, Bulla, J, Albert and T, Leitner (2014). ‘Timing and order of transmission events is not directly reflected in a pathogen phylogeny’. In: Molecular Biology and Evolution 31.9, pp. 2472–2482 (page 41).
Ronquist, F and JP, Huelsenbeck (2003). ‘MrBayes 3: Bayesian phylogenetic inference under mixed models’. In: Bioinformatics 19.12, pp. 1572–1574 (page 23).
Ronquist, F, M, Teslenko, P van der, Mask, et al. (2012a). ‘MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space’. In: Systematic Biology 61.3, pp. 539–542 (page 74).
Ronquist, F, S, Klopfstein, L, Vilhelmsen, et al. (2012b). ‘A total-evidence approach to dating with fossils, applied to the early radiation of the Hymenoptera’. In: Systematic Biology 61.6, pp. 973–999 (pages 65, 66).
Rosenberg, MS (2009). Sequence alignment: methods, models, concepts, and strategies. Berkeley, CA: University of California Press (page 8).
Rosenberg, M, S, Subramanian and S, Kumar (2003). ‘Patterns of transitional mutation biases within and among mammalian genomes’. In: Molecular Biology and Evolution 20.6, pp. 988– 993 (pages 84, 102).
Roure, B, D, Baurain and H, Philippe (2013). ‘Impact of missing data on phylogenies inferred from empirical phylogenomic data sets’. In: Molecular Biology and Evolution 30.1, pp. 197–214 (page 99).
Sanmartín, I, P van der, Mark and F, Ronquist (2008). ‘Inferring dispersal: a Bayesian approach to phylogeny-based island biogeography, with special reference to the Canary Islands’. In: Journal of Biogeography 35.3, pp. 428–449 (page 68).
Sarich, VM and AC, Wilson (1967). ‘Immunological time scale for hominid evolution’. In: Science 158, pp. 1200–1203 (pages 58, 60).
Sato, A, C, O'hUigin, F, Figueroa, et al. (1999). ‘Phylogeny of Darwin's finches as revealed by mtDNA sequences’. In: Proceedings of the National Academy of Sciences USA 96, pp. 5101– 5106 (page 116).
Seo, TK, JL, Thorne, M, Hasegawa and H, Kishino (2002). ‘A viral sampling design for testing the molecular clock and for estimating evolutionary rates and divergence times’. In: Bioinformatics 18.1, pp. 115–123 (page 7).
Shankarappa, R, JB, Margolick, SJ, Gange, et al. (1999). ‘Consistent viral evolutionary changes associated with the disease progression of human immunodeficiency virus type 1 infection’. In: Journal of Virology 73, pp. 10489–10502 (page 31).
Shapiro, B, AJ, Drummond, A, Rambaut, et al. (2004). ‘Rise and fall of the Beringian steppe bison.’ In: Science 306, pp. 1561–1565 (pages 66, 129).
Shapiro, B, A, Rambaut and AJ, Drummond (2006). ‘Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences’. In: Molecular Biology and Evolution 23.1, pp. 7–9 (pages 100, 104, 146).
Silva, E de, N, Ferguson and C, Fraser (2012). ‘Inferring pandemic growth rates from sequence data’. In: Journal of the Royal Society Interface 9.73, pp. 1797–1808 (pages 97, 132).
Sjödin, P, I, Kaj, S, Krone, M, Lascoux and M, Nordborg (2005). ‘On the meaning and existence of an effective population size’. In: Genetics 169.2, pp. 1061–1070 (page 29).
Slatkin, M (1991). ‘Inbreeding coefficients and coalescence times’. In: Genetic Research 58.2, pp. 167–175 (page 29).
Slatkin, M and WP, Maddison (1989). ‘A cladistic measure of gene flow inferred from the phylogenies of alleles’. In: Genetics 123.3, pp. 603–613 (page 68).
Smith, BJ (2007). ‘boa: an R package for MCMC output convergence assessment and posterior inference’. In: Journal of Statistical Software 21.11, pp. 1–37 (page 140).
Smith, GP (1976). ‘Evolution of repeated DNA sequences by unequal crossover’. In: Science 191, pp. 528–535 (page 52).
Smith, SA and MJ, Donoghue (2008). ‘Rates of molecular evolution are linked to life history in flowering plants’. In: Science 322, pp. 86–89 (page 96).
Stadler, T (2009). ‘On incomplete sampling under birth–death models and connections to the sampling-based coalescent’. In: Journal of Theoretical Biology 261.1, pp. 58–66 (pages 38, 108).
Stadler, T (2010). ‘Sampling-through-time in birth–death trees’. In: Journal of Theoretical Biology 267.3, pp. 396–404 (pages 36, 40, 75).
Stadler, T (2011). ‘Mammalian phylogeny reveals recent diversification rate shifts’. In: Proceedings of the National Academy of Sciences USA 108.15, pp. 6187–6192 (page 39).
Stadler, T (2013a). ‘Recovering speciation and extinction dynamics based on phylogenies’. In: Journal of Evolutionary Biology 26.6, pp. 1203–1219 (page 39).
Stadler, T (2013b). ‘How can we improve accuracy of macroevolutionary rate estimates?’ In: Systematic Biology 62.2, pp. 321–329 (pages 37, 38).
Stadler, T and S, Bonhoeffer (2013). ‘Uncovering epidemiological dynamics in heterogeneous host populations using phylogenetic methods’. In: Philosophical Transactions of the Royal Society B: Biological Sciences 368. 1614 (pages 40, 70, 73, 75).
Stadler, T, R, Kouyos, V von, Wyl, et al. (2012). ‘Estimating the basic reproductive number from viral sequence data’. In: Molecular Biology and Evolution 29, pp. 347–357 (page 40).
Stadler, T, D, Kühnert, S, Bonhoeffer and AJ, Drummond (2013). ‘Birth–death skyline plot reveals temporal changes of epidemic spread in HIV and HCV’. In: Proceedings of the National Academy of Sciences USA 110.1, pp. 228–233 (pages 39, 40, 75, 108, 130, 132).
Stadler, T, TG, Vaughan, A, Gavruskin, et al. (2015). ‘How well can the exponential-growth coalescent approximate constant rate birth–death population dynamics?’ In: Proceedings of the Royal Society B: Biological Sciences, in press (pages 36, 38).
Stan Development Team (2014). Stan: A C++ Library for probability and sampling. Version 2.4 (page 156).
Steel, M (2005). ‘Should phylogenetic models be trying to “fit an elephant”?’ In: Trends in Genetics 21.6, pp. 307–309 (page 149).
Steel, M and A, Mooers (2010). ‘The expected length of pendant and interior edges of a Yule tree’. In: Applied Mathematics Letters 23.11, pp. 1315–1319 (page 110).
Stephens, M and P, Donnelly (2000). ‘Inference in molecular population genetics’. In: Journal of the Royal Statistical Society. Series B, 62.4, pp. 605–655 (page 31).
Stewart, WJ (1994). Introduction to the numerical solution of Markov chains. Vol. 41. Princeton, NJ: Princeton University Press (pages 12, 45).
Stockham, C, LS, Wang and T, Warnow (2002). ‘Statistically based postprocessing of phylogenetic analysis by clustering’. In: Bioinformatics 18.suppl 1, S285–S293 (page 161).
Strimmer, K and OG, Pybus (2001). ‘Exploring the demographic history of DNA sequences using the generalized skyline plot’. In: Molecular Biology and Evolution 18.12, pp. 2298–2305 (page 32).
Suchard, MA and A, Rambaut (2009). ‘Many-core algorithms for statistical phylogenetics’. In: Bioinformatics 25.11, pp. 1370–1376 (pages 71, 114).
Suchard, MA and BD, Redelings (2006). ‘BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny’. In: Bioinformatics 22.16, pp. 2047–2048 (pages 9, 99).
Suchard, MA, RE, Weiss and JS, Sinsheimer (2001). ‘Bayesian selection of continuous-time Markov chain evolutionary models’. In: Molecular Biology and Evolution 18, pp. 1001–1013 (page 147).
Suchard, MA, RE, Weiss and JS, Sinsheimer (2003). ‘Testing a molecular clock without an outgroup: derivations of induced priors on branch length restrictions in a Bayesian framework’. In: Systematic Biology 52, pp. 48–54 (page 99).
Sullivan, J and DL, Swofford (2001). ‘Should we use model-based methods for phylogenetic inference when we known that assumptions about among-site rate variation and nucleotide substitution pattern are violated?’ In: Systematic Biology 50, pp. 723–729 (page 54).
Sullivan, J, DL, Swofford and GJ, Naylor (1999). ‘The effect of taxon sampling on estimating rate heterogeneity parameters of maximum-likelihood models’. In: Molecular Biology and Evolution 16, pp. 1347–1356 (page 54).
Swofford, DL (2003). PAUP*: phylogenetic analysis using parsimony (* and other methods). Version 4. Sunderland, MA: Sinauer Associates (page 68).
Tajima, F (1983). ‘Evolutionary relationship of DNA sequences in finite populations’. In: Genetics 105.2, pp. 437–460 (pages 29, 43).
Tajima, F (1989). ‘DNA polymorphism in a subdivided population: the expected number of segregating sites in the two-subpopulation model’. In: Genetics 123.1, pp. 229–240 (page 29).
Takahata, N (1989). ‘Gene genealogy in three related populations: consistency probability between gene and population trees’. In: Genetics 122.4, pp. 957–966 (page 29).
Tamura, K and M, Nei (1993). ‘Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees’. In: Molecular Biology and Evolution 10, pp. 512–526 (page 103).
Teixeira, S, EA, Serrão and S, Arnaud-Haond (2012). ‘Panmixia in a fragmented and unstable environment: the hydrothermal shrimp Rimicaris exoculata disperses extensively along the mid-Atlantic Ridge’. In: PloS One 7.6, e38521 (page 133).
Thorne, JL and H, Kishino (2002). ‘Divergence time and evolutionary rate estimation with multilocus data.’ In: Systematic Biology 51.5, pp. 689–702 (page 62).
Thorne, JL, H, Kishino and IS, Painter (1998). ‘Estimating the rate of evolution of the rate of molecular evolution’. In: Molecular Biology and Evolution 15.12, pp. 1647–1657 (page 62).
Vaughan, TG and AJ, Drummond (2013). ‘A stochastic simulator of birth–death master equations with application to phylodynamics’. In: Molecular Biology and Evolution 30.6, pp. 1480–1493 (pages 43, 138).
Vaughan, TG, D, Kühnert, A, Popinga, D, Welch and AJ, Drummond (2014). ‘Efficient Bayesian inference under the structured coalescent’. In: Bioinformatics, btu201 (pages 14, 71, 72).
Vijaykrishna, D, GJ, Smith, OG, Pybus, et al. (2011). ‘Long-term evolution and transmission dynamics of swine influenza A virus’. In: Nature 473.7348, pp. 519–522 (page 129).
Volz, EM (2012). ‘Complex population dynamics and the coalescent under neutrality’. In: Genetics 190.1, pp. 187–201 (pages 35, 69, 75).
Volz, EM, SL, Kosakovsky Pond, MJ, Ward, AJ, Leigh Brown and SDW, Frost (2009). ‘Phylodynamics of infectious disease epidemics’. In: Genetics 183.4, pp. 1421–1430 (page 75).
Volz, EM, K, Koelle and T, Bedford (2013). ‘Viral phylodynamics’. In: PLoS Computational Biology 9.3, e1002947 (pages 8, 75).
Waddell, P and D, Penny (1996). ‘Evolutionary trees of apes and humans from DNA sequences’. In: Handbook of symbolic evolution. Ed. by AJ, Lock and CR, Peters. Oxford: Clarendon Press, pp. 53–73 (page 54).
Wakeley, J and O, Sargsyan (2009). ‘Extensions of the coalescent effective population size’. In: Genetics 181.1, pp. 341–345 (page 29).
Wallace, R, H, HoDac, R, Lathrop and W, Fitch (2007). ‘A statistical phylogeography of influenza A H5N1’. In: Proceedings of the National Academy of Sciences USA 104.11, pp. 4473–4478 (page 68).
Welch, D (2011). ‘Is network clustering detectable in transmission trees?’ In: Viruses 3.6, pp. 659–676 (page 75).
Whidden, C, I, Matsen and A, Frederick (2014). ‘Quantifying MCMC exploration of phylogenetic tree space’. In: arXiv preprint arXiv:1405.2120 (pages 150, 156).
Wiens, JJ and DS, Moen (2008). ‘Missing data and the accuracy of Bayesian phylogenetics’. In: Journal of Systematics and Evolution 46.3, pp. 307–314 (page 99).
Wilson, AC and VM, Sarich (1969). ‘A molecular time scale for human evolution’. In: Proceedings of the National Academy of Sciences USA 63.4, pp. 1088–1093 (page 60).
Wilson, IJ and DJ, Balding (1998). ‘Genealogical inference from microsatellite data’. In: Genetics 150.1, pp. 499–510 (page 14).
Wolinsky, S, B, Korber, A, Neumann, et al. (1996). ‘Adaptive evolution of human immunodeficiency virus type-1 during the natural course of infection’. In: Science 272, pp. 537–542 (page 31).
Wong, KM, MA, Suchard and JP, Huelsenbeck (2008). ‘Alignment uncertainty and genomic analysis’. In: Science 319, pp. 473–476 (page 9).
Worobey, M, M, Gemmel, DE, Teuwen, et al. (2008). ‘Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960’. In: Nature 455.7213, pp. 661–664 (page 32).
Worobey, M, P, Telfer, S, Souquière, et al. (2010). ‘Island biogeography reveals the deep history of SIV’. In: Science 329, p. 1487 (page 129).
Wright, S (1931). ‘Evolution inMendelian populations’. In: Genetics 16.2, pp. 97–159 (page 28).
Wu, CH and AJ, Drummond (2011). ‘Joint inference of microsatellite mutation models, population history and genealogies using transdimensional Markov chain Monte Carlo’. In: Genetics 188.1, pp. 151–164 (pages 17, 52).
Wu, CH, MA, Suchard and AJ, Drummond (2013). ‘Bayesian selection of nucleotide substitution models and their site assignments’. In: Molecular Biology and Evolution 30.3, pp. 669–688 (pages 17, 57, 100, 145).
Xie, W, P, Lewis, Y, Fan, L, Kuo and M, Chen (2011). ‘Improving marginal likelihood estimation for Bayesian phylogenetic model selection’. In: Systematic Biology 60, pp. 150–160 (pages 19, 136, 137).
Yang, Z (1994). ‘Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods’. In: Journal of Molecular Evolution 39.3, pp. 306–314 (pages 54, 103).
Yang, Z and B, Rannala (1997). ‘Bayesian phylogenetic inference using DNA sequences: a Markov chain Monte Carlo method’. In: Molecular Biology and Evolution 14.7, pp. 717–724 (pages 14, 37, 108).
Yang, Z and B, Rannala (2006). ‘Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds’. In: Molecular Biology and Evolution 23.1, pp. 212–226 (page 66).
Yang, Z and A, Yoder (1999). ‘Estimation of the transition/transversion rate bias and species sampling’. In: Journal of Molecular Evolution 48.3, pp. 274–283 (page 102).
Yang, Z, N, Goldman and A, Friday (1995). ‘Maximum likelihood trees from DNA sequences: a peculiar statistical estimation problem’. In: Systematic Biology 44.3, pp. 384–399 (page 146).
Yang, Z, R, Nielsen, N, Goldman and A, Pedersen (2000). ‘Codon-substitution models for heterogeneous selection pressure at amino acid sites’. In: Genetics 155.1, pp. 431–449 (page 111).
Yoder, A and Z, Yang (2000). ‘Estimation of primate speciation dates using local molecular clocks’. In: Molecular Biology and Evolution 17.7, pp. 1081–1090 (page 63).
Ypma, RJF, WM van, Ballegooijen and J, Wallinga (2013). ‘Relating phylogenetic trees to transmission trees of infectious disease outbreaks’. In: Genetics 195.3, pp. 1055–1062 (page 43).
Yu, Y, C, Than, JH, Degnan and L, Nakhleh (2011). ‘Coalescent histories on phylogenetic networks and detection of hybridization despite incomplete lineage sorting’. In: Systematic Biology 60.2, pp. 138–149 (page 120).
Yule, G (1924). ‘A mathematical theory of evolution based on the conclusions of Dr. J.C.Willis’. In: Philosophical Transactions of the Royal Society B: Biological Sciences 213, pp. 21–87 (pages 36, 38).
