Bayesian inference in phylogeny (English Wikipedia)

Analysis of information sources in references of the Wikipedia article "Bayesian inference in phylogeny" in English language version.

refsWebsite

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58nih.gov

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49doi.org

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16harvard.edu

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7semanticscholar.org

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4worldcat.org

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2jstor.org

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2handle.net

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1ohiolink.edu

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1nii.ac.jp

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1osti.gov

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1oup.com

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doi.org

Rannala, Bruce; Yang, Ziheng (September 1996). "Probability distribution of molecular evolutionary trees: A new method of phylogenetic inference". Journal of Molecular Evolution. 43 (3): 304–311. Bibcode:1996JMolE..43..304R. doi:10.1007/BF02338839. PMID 8703097. S2CID 8269826.
Yang, Z.; Rannala, B. (1 July 1997). "Bayesian phylogenetic inference using DNA sequences: a Markov Chain Monte Carlo Method". Molecular Biology and Evolution. 14 (7): 717–724. doi:10.1093/oxfordjournals.molbev.a025811. PMID 9214744.
Mau, Bob; Newton, Michael A.; Larget, Bret (March 1999). "Bayesian Phylogenetic Inference via Markov Chain Monte Carlo Methods". Biometrics. 55 (1): 1–12. doi:10.1111/j.0006-341x.1999.00001.x. JSTOR 2533889. PMID 11318142. S2CID 932887.
Li, Shuying; Pearl, Dennis K.; Doss, Hani (June 2000). "Phylogenetic Tree Construction Using Markov Chain Monte Carlo". Journal of the American Statistical Association. 95 (450): 493–508. doi:10.1080/01621459.2000.10474227. JSTOR 2669394. S2CID 122459537.
Huelsenbeck, J. P.; Ronquist, F. (1 August 2001). "MRBAYES: Bayesian inference of phylogenetic trees". Bioinformatics. 17 (8): 754–755. doi:10.1093/bioinformatics/17.8.754. PMID 11524383.
Laplace P (1774). "Mémoire sur la Probabilité des Causes par les Évenements". Mémoires de l'Académie Royale des Sciences. 6: 621–656. NAID 10010866843. English translation by Stigler SM (1986). "Memoir on the Probability of the Causes of Events". Statistical Science. 1 (3): 359–378. doi:10.1214/ss/1177013620.
Nascimento, Fabrícia F.; Reis, Mario dos; Yang, Ziheng (October 2017). "A biologist's guide to Bayesian phylogenetic analysis". Nature Ecology & Evolution. 1 (10): 1446–1454. Bibcode:2017NatEE...1.1446N. doi:10.1038/s41559-017-0280-x. PMC 5624502. PMID 28983516.
Hastings WK (April 1970). "Monte Carlo sampling methods using Markov chains and their applications". Biometrika. 57 (1): 97–109. Bibcode:1970Bimka..57...97H. doi:10.1093/biomet/57.1.97.
Metropolis N, Rosenbluth AW, Rosenbluth MN, Teller AH, Teller E (June 1953). "Equation of state calculations by fast computing machines". The Journal of Chemical Physics. 21 (6): 1087–92. Bibcode:1953JChPh..21.1087M. doi:10.1063/1.1699114. OSTI 4390578. S2CID 1046577.
Larget B, Simon DL (June 1999). "Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees". Molecular Biology and Evolution. 16 (6): 750–9. doi:10.1093/oxfordjournals.molbev.a026160.
Mau B, Newton MA, Larget B (March 1999). "Bayesian phylogenetic inference via Markov chain Monte Carlo methods". Biometrics. 55 (1): 1–12. doi:10.1111/j.0006-341x.1999.00001.x. PMID 11318142. S2CID 932887.
Felsenstein J (December 1978). "Cases in which parsimony or compatibility methods will be positively misleading". Systematic Zoology. 27 (4): 401–10. doi:10.1093/sysbio/27.4.401.
Castorani MC, Reed DC, Raimondi PT, Alberto F, Bell TW, Cavanaugh KC, et al. (January 2017). "Fluctuations in population fecundity drive variation in demographic connectivity and metapopulation dynamics". Proceedings. Biological Sciences. 284 (1847): 20162086. doi:10.1098/rspb.2016.2086. PMC 5310032. PMID 28123088.
O'Reilly JE, Puttick MN, Parry L, Tanner AR, Tarver JE, Fleming J, Pisani D, Donoghue PC (April 2016). "Bayesian methods outperform parsimony but at the expense of precision in the estimation of phylogeny from discrete morphological data". Biology Letters. 12 (4): 20160081. doi:10.1098/rsbl.2016.0081. PMC 4881353. PMID 27095266.
Goloboff PA, Torres A, Arias JS (2018). "Weighted parsimony outperforms other methods of phylogenetic inference under models appropriate for morphology". Cladistics. 34 (4): 407–437. doi:10.1111/cla.12205. hdl:11336/57822. ISSN 0748-3007. PMID 34649370.
Keating JN, Sansom RS, Sutton MD, Knight CG, Garwood RJ (February 2020). "Morphological phylogenetics evaluated using novel evolutionary simulations". Systematic Biology. 69 (5): 897–912. doi:10.1093/sysbio/syaa012. PMC 7440746. PMID 32073641.
Suzuki Y, Glazko GV, Nei M (December 2002). "Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics". Proceedings of the National Academy of Sciences of the United States of America. 99 (25): 16138–43. Bibcode:2002PNAS...9916138S. doi:10.1073/pnas.212646199. PMC 138578. PMID 12451182.
Alfaro ME, Zoller S, Lutzoni F (February 2003). "Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence". Molecular Biology and Evolution. 20 (2): 255–66. doi:10.1093/molbev/msg028. PMID 12598693.
Douady CJ, Delsuc F, Boucher Y, Doolittle WF, Douzery EJ (February 2003). "Comparison of Bayesian and maximum likelihood bootstrap measures of phylogenetic reliability". Molecular Biology and Evolution. 20 (2): 248–54. doi:10.1093/molbev/msg042. PMID 12598692.
García-Sandoval R (January 2014). "Why some clades have low bootstrap frequencies and high Bayesian posterior probabilities". Israel Journal of Ecology & Evolution. 60 (1): 41–4. Bibcode:2014IsJEE..60...41G. doi:10.1080/15659801.2014.937900.
Yang, Z. (18 April 2007). "Fair-Balance Paradox, Star-tree Paradox, and Bayesian Phylogenetics". Molecular Biology and Evolution. 24 (8): 1639–1655. doi:10.1093/molbev/msm081. PMID 17488737.
Yang, Ziheng; Zhu, Tianqi (20 February 2018). "Bayesian selection of misspecified models is overconfident and may cause spurious posterior probabilities for phylogenetic trees". Proceedings of the National Academy of Sciences. 115 (8): 1854–1859. Bibcode:2018PNAS..115.1854Y. doi:10.1073/pnas.1712673115. PMC 5828583. PMID 29432193.
Erixon P, Svennblad B, Britton T, Oxelman B (October 2003). "Reliability of Bayesian posterior probabilities and bootstrap frequencies in phylogenetics". Systematic Biology. 52 (5): 665–73. doi:10.1080/10635150390235485. PMID 14530133.
Huelsenbeck JP, Ronquist F (August 2001). "MRBAYES: Bayesian inference of phylogenetic trees". Bioinformatics. 17 (8). Oxford, England: 754–5. doi:10.1093/bioinformatics/17.8.754. PMID 11524383.
Maddison DR, Swofford DL, Maddison WP (December 1997). "NEXUS: an extensible file format for systematic information". Systematic Biology. 46 (4): 590–621. doi:10.1093/sysbio/46.4.590. PMID 11975335.
Yang Z (November 1993). "Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites". Molecular Biology and Evolution. 10 (6): 1396–401. doi:10.1093/oxfordjournals.molbev.a040082. PMID 8277861.
Ronquist F, Huelsenbeck JP (August 2003). "MrBayes 3: Bayesian phylogenetic inference under mixed models". Bioinformatics. 19 (12). Oxford, England: 1572–4. doi:10.1093/bioinformatics/btg180. PMID 12912839.
Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Höhna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP (May 2012). "MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space". Systematic Biology. 61 (3): 539–42. doi:10.1093/sysbio/sys029. PMC 3329765. PMID 22357727.
Drummond AJ, Suchard MA, Xie D, Rambaut A (August 2012). "Bayesian phylogenetics with BEAUti and the BEAST 1.7". Molecular Biology and Evolution. 29 (8): 1969–73. doi:10.1093/molbev/mss075. PMC 3408070. PMID 22367748.
Bouckaert R, Heled J, Kühnert D, Vaughan T, Wu CH, Xie D, Suchard MA, Rambaut A, Drummond AJ (April 2014). "BEAST 2: a software platform for Bayesian evolutionary analysis". PLOS Computational Biology. 10 (4): e1003537. Bibcode:2014PLSCB..10E3537B. doi:10.1371/journal.pcbi.1003537. PMC 3985171. PMID 24722319.
Lartillot N, Philippe H (June 2004). "A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process". Molecular Biology and Evolution. 21 (6): 1095–109. doi:10.1093/molbev/msh112. PMID 15014145.
Suchard MA, Redelings BD (August 2006). "BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny". Bioinformatics. 22 (16): 2047–8. doi:10.1093/bioinformatics/btl175. PMID 16679334.
Ané C, Larget B, Baum DA, Smith SD, Rokas A (February 2007). "Bayesian estimation of concordance among gene trees". Molecular Biology and Evolution. 24 (2): 412–26. doi:10.1093/molbev/msl170. PMID 17095535.
Wilson IJ, Weale ME, Balding DJ (June 2003). "Inferences from DNA data: population histories, evolutionary processes and forensic match probabilities". Journal of the Royal Statistical Society, Series A (Statistics in Society). 166 (2): 155–88. doi:10.1111/1467-985X.00264.
Pagel M, Meade A (June 2006). "Bayesian analysis of correlated evolution of discrete characters by reversible-jump Markov chain Monte Carlo". The American Naturalist. 167 (6): 808–25. Bibcode:2006ANat..167..808P. doi:10.1086/503444. PMID 16685633. S2CID 205984494.
Lord E, Leclercq M, Boc A, Diallo AB, Makarenkov V (2012). "Armadillo 1.1: an original workflow platform for designing and conducting phylogenetic analysis and simulations". PLOS ONE. 7 (1): e29903. Bibcode:2012PLoSO...729903L. doi:10.1371/journal.pone.0029903. PMC 3256230. PMID 22253821.
Milne I, Lindner D, Bayer M, Husmeier D, McGuire G, Marshall DF, Wright F (January 2009). "TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops". Bioinformatics. 25 (1): 126–7. doi:10.1093/bioinformatics/btn575. PMC 2638937. PMID 18984599.
Alonso R, Crawford AJ, Bermingham E (March 2012). "Molecular phylogeny of an endemic radiation of Cuban toads (Bufonidae: Peltophryne) based on mitochondrial and nuclear genes". Journal of Biogeography. 39 (3): 434–51. Bibcode:2012JBiog..39..434A. doi:10.1111/j.1365-2699.2011.02594.x. S2CID 4152245.
Antonelli A, Sanmartín I (October 2011). "Mass extinction, gradual cooling, or rapid radiation? Reconstructing the spatiotemporal evolution of the ancient angiosperm genus Hedyosmum (Chloranthaceae) using empirical and simulated approaches". Systematic Biology. 60 (5): 596–615. doi:10.1093/sysbio/syr062. hdl:10261/34829. PMID 21856636.
de Villemereuil P, Wells JA, Edwards RD, Blomberg SP (June 2012). "Bayesian models for comparative analysis integrating phylogenetic uncertainty". BMC Evolutionary Biology. 12 (1): 102. Bibcode:2012BMCEE..12..102V. doi:10.1186/1471-2148-12-102. PMC 3582467. PMID 22741602.
Ronquist F (September 2004). "Bayesian inference of character evolution". Trends in Ecology & Evolution. 19 (9): 475–81. doi:10.1016/j.tree.2004.07.002. PMID 16701310.
Schäffer S, Koblmüller S, Pfingstl T, Sturmbauer C, Krisper G (August 2010). "Ancestral state reconstruction reveals multiple independent evolution of diagnostic morphological characters in the "Higher Oribatida" (Acari), conflicting with current classification schemes". BMC Evolutionary Biology. 10 (1): 246. Bibcode:2010BMCEE..10..246S. doi:10.1186/1471-2148-10-246. PMC 2930640. PMID 20701742.
Filipowicz N, Renner SS (July 2012). "Brunfelsia (Solanaceae): a genus evenly divided between South America and radiations on Cuba and other Antillean islands". Molecular Phylogenetics and Evolution. 64 (1): 1–11. Bibcode:2012MolPE..64....1F. doi:10.1016/j.ympev.2012.02.026. PMID 22425729.
Bacon CD, Baker WJ, Simmons MP (May 2012). "Miocene dispersal drives island radiations in the palm tribe Trachycarpeae (Arecaceae)". Systematic Biology. 61 (3): 426–42. doi:10.1093/sysbio/syr123. PMID 22223444.
Särkinen T, Bohs L, Olmstead RG, Knapp S (September 2013). "A phylogenetic framework for evolutionary study of the nightshades (Solanaceae): a dated 1000-tip tree". BMC Evolutionary Biology. 13 (1): 214. Bibcode:2013BMCEE..13..214S. doi:10.1186/1471-2148-13-214. PMC 3850475. PMID 24283922.
Silvestro D, Schnitzler J, Liow LH, Antonelli A, Salamin N (May 2014). "Bayesian estimation of speciation and extinction from incomplete fossil occurrence data". Systematic Biology. 63 (3): 349–67. doi:10.1093/sysbio/syu006. PMC 4361715. PMID 24510972.
Lemey P, Rambaut A, Drummond AJ, Suchard MA (September 2009). "Bayesian phylogeography finds its roots". PLOS Computational Biology. 5 (9): e1000520. Bibcode:2009PLSCB...5E0520L. doi:10.1371/journal.pcbi.1000520. PMC 2740835. PMID 19779555.
Cybis G, Sinsheimer J, Bedford T, Mather A, Lemey P, Suchard MA (2015). "Assessing phenotypic correlation through the multivariate phylogenetic latent liability model". The Annals of Applied Statistics. 9 (2): 969–991. doi:10.1214/15-AOAS821. ISSN 1932-6157. PMC 4820077. PMID 27053974.
Tolkoff M, Alfaro M, Baele G, Lemey P, Suchard MA (2018). "Phylogenetic Factor Analysis". Systematic Biology. 67 (3): 384–399. doi:10.1093/sysbio/syx066. ISSN 1063-5157. PMC 5920329. PMID 28950376.

handle.net

hdl.handle.net

Goloboff PA, Torres A, Arias JS (2018). "Weighted parsimony outperforms other methods of phylogenetic inference under models appropriate for morphology". Cladistics. 34 (4): 407–437. doi:10.1111/cla.12205. hdl:11336/57822. ISSN 0748-3007. PMID 34649370.
Antonelli A, Sanmartín I (October 2011). "Mass extinction, gradual cooling, or rapid radiation? Reconstructing the spatiotemporal evolution of the ancient angiosperm genus Hedyosmum (Chloranthaceae) using empirical and simulated approaches". Systematic Biology. 60 (5): 596–615. doi:10.1093/sysbio/syr062. hdl:10261/34829. PMID 21856636.

harvard.edu

ui.adsabs.harvard.edu

Rannala, Bruce; Yang, Ziheng (September 1996). "Probability distribution of molecular evolutionary trees: A new method of phylogenetic inference". Journal of Molecular Evolution. 43 (3): 304–311. Bibcode:1996JMolE..43..304R. doi:10.1007/BF02338839. PMID 8703097. S2CID 8269826.
Nascimento, Fabrícia F.; Reis, Mario dos; Yang, Ziheng (October 2017). "A biologist's guide to Bayesian phylogenetic analysis". Nature Ecology & Evolution. 1 (10): 1446–1454. Bibcode:2017NatEE...1.1446N. doi:10.1038/s41559-017-0280-x. PMC 5624502. PMID 28983516.
Hastings WK (April 1970). "Monte Carlo sampling methods using Markov chains and their applications". Biometrika. 57 (1): 97–109. Bibcode:1970Bimka..57...97H. doi:10.1093/biomet/57.1.97.
Metropolis N, Rosenbluth AW, Rosenbluth MN, Teller AH, Teller E (June 1953). "Equation of state calculations by fast computing machines". The Journal of Chemical Physics. 21 (6): 1087–92. Bibcode:1953JChPh..21.1087M. doi:10.1063/1.1699114. OSTI 4390578. S2CID 1046577.
Suzuki Y, Glazko GV, Nei M (December 2002). "Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics". Proceedings of the National Academy of Sciences of the United States of America. 99 (25): 16138–43. Bibcode:2002PNAS...9916138S. doi:10.1073/pnas.212646199. PMC 138578. PMID 12451182.
García-Sandoval R (January 2014). "Why some clades have low bootstrap frequencies and high Bayesian posterior probabilities". Israel Journal of Ecology & Evolution. 60 (1): 41–4. Bibcode:2014IsJEE..60...41G. doi:10.1080/15659801.2014.937900.
Yang, Ziheng; Zhu, Tianqi (20 February 2018). "Bayesian selection of misspecified models is overconfident and may cause spurious posterior probabilities for phylogenetic trees". Proceedings of the National Academy of Sciences. 115 (8): 1854–1859. Bibcode:2018PNAS..115.1854Y. doi:10.1073/pnas.1712673115. PMC 5828583. PMID 29432193.
Bouckaert R, Heled J, Kühnert D, Vaughan T, Wu CH, Xie D, Suchard MA, Rambaut A, Drummond AJ (April 2014). "BEAST 2: a software platform for Bayesian evolutionary analysis". PLOS Computational Biology. 10 (4): e1003537. Bibcode:2014PLSCB..10E3537B. doi:10.1371/journal.pcbi.1003537. PMC 3985171. PMID 24722319.
Pagel M, Meade A (June 2006). "Bayesian analysis of correlated evolution of discrete characters by reversible-jump Markov chain Monte Carlo". The American Naturalist. 167 (6): 808–25. Bibcode:2006ANat..167..808P. doi:10.1086/503444. PMID 16685633. S2CID 205984494.
Lord E, Leclercq M, Boc A, Diallo AB, Makarenkov V (2012). "Armadillo 1.1: an original workflow platform for designing and conducting phylogenetic analysis and simulations". PLOS ONE. 7 (1): e29903. Bibcode:2012PLoSO...729903L. doi:10.1371/journal.pone.0029903. PMC 3256230. PMID 22253821.
Alonso R, Crawford AJ, Bermingham E (March 2012). "Molecular phylogeny of an endemic radiation of Cuban toads (Bufonidae: Peltophryne) based on mitochondrial and nuclear genes". Journal of Biogeography. 39 (3): 434–51. Bibcode:2012JBiog..39..434A. doi:10.1111/j.1365-2699.2011.02594.x. S2CID 4152245.
de Villemereuil P, Wells JA, Edwards RD, Blomberg SP (June 2012). "Bayesian models for comparative analysis integrating phylogenetic uncertainty". BMC Evolutionary Biology. 12 (1): 102. Bibcode:2012BMCEE..12..102V. doi:10.1186/1471-2148-12-102. PMC 3582467. PMID 22741602.
Schäffer S, Koblmüller S, Pfingstl T, Sturmbauer C, Krisper G (August 2010). "Ancestral state reconstruction reveals multiple independent evolution of diagnostic morphological characters in the "Higher Oribatida" (Acari), conflicting with current classification schemes". BMC Evolutionary Biology. 10 (1): 246. Bibcode:2010BMCEE..10..246S. doi:10.1186/1471-2148-10-246. PMC 2930640. PMID 20701742.
Filipowicz N, Renner SS (July 2012). "Brunfelsia (Solanaceae): a genus evenly divided between South America and radiations on Cuba and other Antillean islands". Molecular Phylogenetics and Evolution. 64 (1): 1–11. Bibcode:2012MolPE..64....1F. doi:10.1016/j.ympev.2012.02.026. PMID 22425729.
Särkinen T, Bohs L, Olmstead RG, Knapp S (September 2013). "A phylogenetic framework for evolutionary study of the nightshades (Solanaceae): a dated 1000-tip tree". BMC Evolutionary Biology. 13 (1): 214. Bibcode:2013BMCEE..13..214S. doi:10.1186/1471-2148-13-214. PMC 3850475. PMID 24283922.
Lemey P, Rambaut A, Drummond AJ, Suchard MA (September 2009). "Bayesian phylogeography finds its roots". PLOS Computational Biology. 5 (9): e1000520. Bibcode:2009PLSCB...5E0520L. doi:10.1371/journal.pcbi.1000520. PMC 2740835. PMID 19779555.

jstor.org

Mau, Bob; Newton, Michael A.; Larget, Bret (March 1999). "Bayesian Phylogenetic Inference via Markov Chain Monte Carlo Methods". Biometrics. 55 (1): 1–12. doi:10.1111/j.0006-341x.1999.00001.x. JSTOR 2533889. PMID 11318142. S2CID 932887.
Li, Shuying; Pearl, Dennis K.; Doss, Hani (June 2000). "Phylogenetic Tree Construction Using Markov Chain Monte Carlo". Journal of the American Statistical Association. 95 (450): 493–508. doi:10.1080/01621459.2000.10474227. JSTOR 2669394. S2CID 122459537.

nih.gov

pubmed.ncbi.nlm.nih.gov

Rannala, Bruce; Yang, Ziheng (September 1996). "Probability distribution of molecular evolutionary trees: A new method of phylogenetic inference". Journal of Molecular Evolution. 43 (3): 304–311. Bibcode:1996JMolE..43..304R. doi:10.1007/BF02338839. PMID 8703097. S2CID 8269826.
Yang, Z.; Rannala, B. (1 July 1997). "Bayesian phylogenetic inference using DNA sequences: a Markov Chain Monte Carlo Method". Molecular Biology and Evolution. 14 (7): 717–724. doi:10.1093/oxfordjournals.molbev.a025811. PMID 9214744.
Mau, Bob; Newton, Michael A.; Larget, Bret (March 1999). "Bayesian Phylogenetic Inference via Markov Chain Monte Carlo Methods". Biometrics. 55 (1): 1–12. doi:10.1111/j.0006-341x.1999.00001.x. JSTOR 2533889. PMID 11318142. S2CID 932887.
Huelsenbeck, J. P.; Ronquist, F. (1 August 2001). "MRBAYES: Bayesian inference of phylogenetic trees". Bioinformatics. 17 (8): 754–755. doi:10.1093/bioinformatics/17.8.754. PMID 11524383.
Nascimento, Fabrícia F.; Reis, Mario dos; Yang, Ziheng (October 2017). "A biologist's guide to Bayesian phylogenetic analysis". Nature Ecology & Evolution. 1 (10): 1446–1454. Bibcode:2017NatEE...1.1446N. doi:10.1038/s41559-017-0280-x. PMC 5624502. PMID 28983516.
Mau B, Newton MA, Larget B (March 1999). "Bayesian phylogenetic inference via Markov chain Monte Carlo methods". Biometrics. 55 (1): 1–12. doi:10.1111/j.0006-341x.1999.00001.x. PMID 11318142. S2CID 932887.
Castorani MC, Reed DC, Raimondi PT, Alberto F, Bell TW, Cavanaugh KC, et al. (January 2017). "Fluctuations in population fecundity drive variation in demographic connectivity and metapopulation dynamics". Proceedings. Biological Sciences. 284 (1847): 20162086. doi:10.1098/rspb.2016.2086. PMC 5310032. PMID 28123088.
O'Reilly JE, Puttick MN, Parry L, Tanner AR, Tarver JE, Fleming J, Pisani D, Donoghue PC (April 2016). "Bayesian methods outperform parsimony but at the expense of precision in the estimation of phylogeny from discrete morphological data". Biology Letters. 12 (4): 20160081. doi:10.1098/rsbl.2016.0081. PMC 4881353. PMID 27095266.
Goloboff PA, Torres A, Arias JS (2018). "Weighted parsimony outperforms other methods of phylogenetic inference under models appropriate for morphology". Cladistics. 34 (4): 407–437. doi:10.1111/cla.12205. hdl:11336/57822. ISSN 0748-3007. PMID 34649370.
Keating JN, Sansom RS, Sutton MD, Knight CG, Garwood RJ (February 2020). "Morphological phylogenetics evaluated using novel evolutionary simulations". Systematic Biology. 69 (5): 897–912. doi:10.1093/sysbio/syaa012. PMC 7440746. PMID 32073641.
Suzuki Y, Glazko GV, Nei M (December 2002). "Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics". Proceedings of the National Academy of Sciences of the United States of America. 99 (25): 16138–43. Bibcode:2002PNAS...9916138S. doi:10.1073/pnas.212646199. PMC 138578. PMID 12451182.
Alfaro ME, Zoller S, Lutzoni F (February 2003). "Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence". Molecular Biology and Evolution. 20 (2): 255–66. doi:10.1093/molbev/msg028. PMID 12598693.
Douady CJ, Delsuc F, Boucher Y, Doolittle WF, Douzery EJ (February 2003). "Comparison of Bayesian and maximum likelihood bootstrap measures of phylogenetic reliability". Molecular Biology and Evolution. 20 (2): 248–54. doi:10.1093/molbev/msg042. PMID 12598692.
Yang, Z. (18 April 2007). "Fair-Balance Paradox, Star-tree Paradox, and Bayesian Phylogenetics". Molecular Biology and Evolution. 24 (8): 1639–1655. doi:10.1093/molbev/msm081. PMID 17488737.
Yang, Ziheng; Zhu, Tianqi (20 February 2018). "Bayesian selection of misspecified models is overconfident and may cause spurious posterior probabilities for phylogenetic trees". Proceedings of the National Academy of Sciences. 115 (8): 1854–1859. Bibcode:2018PNAS..115.1854Y. doi:10.1073/pnas.1712673115. PMC 5828583. PMID 29432193.
Erixon P, Svennblad B, Britton T, Oxelman B (October 2003). "Reliability of Bayesian posterior probabilities and bootstrap frequencies in phylogenetics". Systematic Biology. 52 (5): 665–73. doi:10.1080/10635150390235485. PMID 14530133.
Huelsenbeck JP, Ronquist F (August 2001). "MRBAYES: Bayesian inference of phylogenetic trees". Bioinformatics. 17 (8). Oxford, England: 754–5. doi:10.1093/bioinformatics/17.8.754. PMID 11524383.
Maddison DR, Swofford DL, Maddison WP (December 1997). "NEXUS: an extensible file format for systematic information". Systematic Biology. 46 (4): 590–621. doi:10.1093/sysbio/46.4.590. PMID 11975335.
Yang Z (November 1993). "Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites". Molecular Biology and Evolution. 10 (6): 1396–401. doi:10.1093/oxfordjournals.molbev.a040082. PMID 8277861.
Ronquist F, Huelsenbeck JP (August 2003). "MrBayes 3: Bayesian phylogenetic inference under mixed models". Bioinformatics. 19 (12). Oxford, England: 1572–4. doi:10.1093/bioinformatics/btg180. PMID 12912839.
Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Höhna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP (May 2012). "MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space". Systematic Biology. 61 (3): 539–42. doi:10.1093/sysbio/sys029. PMC 3329765. PMID 22357727.
Drummond AJ, Suchard MA, Xie D, Rambaut A (August 2012). "Bayesian phylogenetics with BEAUti and the BEAST 1.7". Molecular Biology and Evolution. 29 (8): 1969–73. doi:10.1093/molbev/mss075. PMC 3408070. PMID 22367748.
Bouckaert R, Heled J, Kühnert D, Vaughan T, Wu CH, Xie D, Suchard MA, Rambaut A, Drummond AJ (April 2014). "BEAST 2: a software platform for Bayesian evolutionary analysis". PLOS Computational Biology. 10 (4): e1003537. Bibcode:2014PLSCB..10E3537B. doi:10.1371/journal.pcbi.1003537. PMC 3985171. PMID 24722319.
Lartillot N, Philippe H (June 2004). "A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process". Molecular Biology and Evolution. 21 (6): 1095–109. doi:10.1093/molbev/msh112. PMID 15014145.
Suchard MA, Redelings BD (August 2006). "BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny". Bioinformatics. 22 (16): 2047–8. doi:10.1093/bioinformatics/btl175. PMID 16679334.
Ané C, Larget B, Baum DA, Smith SD, Rokas A (February 2007). "Bayesian estimation of concordance among gene trees". Molecular Biology and Evolution. 24 (2): 412–26. doi:10.1093/molbev/msl170. PMID 17095535.
Pagel M, Meade A (June 2006). "Bayesian analysis of correlated evolution of discrete characters by reversible-jump Markov chain Monte Carlo". The American Naturalist. 167 (6): 808–25. Bibcode:2006ANat..167..808P. doi:10.1086/503444. PMID 16685633. S2CID 205984494.
Lord E, Leclercq M, Boc A, Diallo AB, Makarenkov V (2012). "Armadillo 1.1: an original workflow platform for designing and conducting phylogenetic analysis and simulations". PLOS ONE. 7 (1): e29903. Bibcode:2012PLoSO...729903L. doi:10.1371/journal.pone.0029903. PMC 3256230. PMID 22253821.
Milne I, Lindner D, Bayer M, Husmeier D, McGuire G, Marshall DF, Wright F (January 2009). "TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops". Bioinformatics. 25 (1): 126–7. doi:10.1093/bioinformatics/btn575. PMC 2638937. PMID 18984599.
Antonelli A, Sanmartín I (October 2011). "Mass extinction, gradual cooling, or rapid radiation? Reconstructing the spatiotemporal evolution of the ancient angiosperm genus Hedyosmum (Chloranthaceae) using empirical and simulated approaches". Systematic Biology. 60 (5): 596–615. doi:10.1093/sysbio/syr062. hdl:10261/34829. PMID 21856636.
de Villemereuil P, Wells JA, Edwards RD, Blomberg SP (June 2012). "Bayesian models for comparative analysis integrating phylogenetic uncertainty". BMC Evolutionary Biology. 12 (1): 102. Bibcode:2012BMCEE..12..102V. doi:10.1186/1471-2148-12-102. PMC 3582467. PMID 22741602.
Ronquist F (September 2004). "Bayesian inference of character evolution". Trends in Ecology & Evolution. 19 (9): 475–81. doi:10.1016/j.tree.2004.07.002. PMID 16701310.
Schäffer S, Koblmüller S, Pfingstl T, Sturmbauer C, Krisper G (August 2010). "Ancestral state reconstruction reveals multiple independent evolution of diagnostic morphological characters in the "Higher Oribatida" (Acari), conflicting with current classification schemes". BMC Evolutionary Biology. 10 (1): 246. Bibcode:2010BMCEE..10..246S. doi:10.1186/1471-2148-10-246. PMC 2930640. PMID 20701742.
Filipowicz N, Renner SS (July 2012). "Brunfelsia (Solanaceae): a genus evenly divided between South America and radiations on Cuba and other Antillean islands". Molecular Phylogenetics and Evolution. 64 (1): 1–11. Bibcode:2012MolPE..64....1F. doi:10.1016/j.ympev.2012.02.026. PMID 22425729.
Bacon CD, Baker WJ, Simmons MP (May 2012). "Miocene dispersal drives island radiations in the palm tribe Trachycarpeae (Arecaceae)". Systematic Biology. 61 (3): 426–42. doi:10.1093/sysbio/syr123. PMID 22223444.
Särkinen T, Bohs L, Olmstead RG, Knapp S (September 2013). "A phylogenetic framework for evolutionary study of the nightshades (Solanaceae): a dated 1000-tip tree". BMC Evolutionary Biology. 13 (1): 214. Bibcode:2013BMCEE..13..214S. doi:10.1186/1471-2148-13-214. PMC 3850475. PMID 24283922.
Silvestro D, Schnitzler J, Liow LH, Antonelli A, Salamin N (May 2014). "Bayesian estimation of speciation and extinction from incomplete fossil occurrence data". Systematic Biology. 63 (3): 349–67. doi:10.1093/sysbio/syu006. PMC 4361715. PMID 24510972.
Lemey P, Rambaut A, Drummond AJ, Suchard MA (September 2009). "Bayesian phylogeography finds its roots". PLOS Computational Biology. 5 (9): e1000520. Bibcode:2009PLSCB...5E0520L. doi:10.1371/journal.pcbi.1000520. PMC 2740835. PMID 19779555.
Cybis G, Sinsheimer J, Bedford T, Mather A, Lemey P, Suchard MA (2015). "Assessing phenotypic correlation through the multivariate phylogenetic latent liability model". The Annals of Applied Statistics. 9 (2): 969–991. doi:10.1214/15-AOAS821. ISSN 1932-6157. PMC 4820077. PMID 27053974.
Tolkoff M, Alfaro M, Baele G, Lemey P, Suchard MA (2018). "Phylogenetic Factor Analysis". Systematic Biology. 67 (3): 384–399. doi:10.1093/sysbio/syx066. ISSN 1063-5157. PMC 5920329. PMID 28950376.

ncbi.nlm.nih.gov

Nascimento, Fabrícia F.; Reis, Mario dos; Yang, Ziheng (October 2017). "A biologist's guide to Bayesian phylogenetic analysis". Nature Ecology & Evolution. 1 (10): 1446–1454. Bibcode:2017NatEE...1.1446N. doi:10.1038/s41559-017-0280-x. PMC 5624502. PMID 28983516.
Castorani MC, Reed DC, Raimondi PT, Alberto F, Bell TW, Cavanaugh KC, et al. (January 2017). "Fluctuations in population fecundity drive variation in demographic connectivity and metapopulation dynamics". Proceedings. Biological Sciences. 284 (1847): 20162086. doi:10.1098/rspb.2016.2086. PMC 5310032. PMID 28123088.
O'Reilly JE, Puttick MN, Parry L, Tanner AR, Tarver JE, Fleming J, Pisani D, Donoghue PC (April 2016). "Bayesian methods outperform parsimony but at the expense of precision in the estimation of phylogeny from discrete morphological data". Biology Letters. 12 (4): 20160081. doi:10.1098/rsbl.2016.0081. PMC 4881353. PMID 27095266.
Keating JN, Sansom RS, Sutton MD, Knight CG, Garwood RJ (February 2020). "Morphological phylogenetics evaluated using novel evolutionary simulations". Systematic Biology. 69 (5): 897–912. doi:10.1093/sysbio/syaa012. PMC 7440746. PMID 32073641.
Suzuki Y, Glazko GV, Nei M (December 2002). "Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics". Proceedings of the National Academy of Sciences of the United States of America. 99 (25): 16138–43. Bibcode:2002PNAS...9916138S. doi:10.1073/pnas.212646199. PMC 138578. PMID 12451182.
Yang, Ziheng; Zhu, Tianqi (20 February 2018). "Bayesian selection of misspecified models is overconfident and may cause spurious posterior probabilities for phylogenetic trees". Proceedings of the National Academy of Sciences. 115 (8): 1854–1859. Bibcode:2018PNAS..115.1854Y. doi:10.1073/pnas.1712673115. PMC 5828583. PMID 29432193.
Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Höhna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP (May 2012). "MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space". Systematic Biology. 61 (3): 539–42. doi:10.1093/sysbio/sys029. PMC 3329765. PMID 22357727.
Drummond AJ, Suchard MA, Xie D, Rambaut A (August 2012). "Bayesian phylogenetics with BEAUti and the BEAST 1.7". Molecular Biology and Evolution. 29 (8): 1969–73. doi:10.1093/molbev/mss075. PMC 3408070. PMID 22367748.
Bouckaert R, Heled J, Kühnert D, Vaughan T, Wu CH, Xie D, Suchard MA, Rambaut A, Drummond AJ (April 2014). "BEAST 2: a software platform for Bayesian evolutionary analysis". PLOS Computational Biology. 10 (4): e1003537. Bibcode:2014PLSCB..10E3537B. doi:10.1371/journal.pcbi.1003537. PMC 3985171. PMID 24722319.
Lord E, Leclercq M, Boc A, Diallo AB, Makarenkov V (2012). "Armadillo 1.1: an original workflow platform for designing and conducting phylogenetic analysis and simulations". PLOS ONE. 7 (1): e29903. Bibcode:2012PLoSO...729903L. doi:10.1371/journal.pone.0029903. PMC 3256230. PMID 22253821.
Milne I, Lindner D, Bayer M, Husmeier D, McGuire G, Marshall DF, Wright F (January 2009). "TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops". Bioinformatics. 25 (1): 126–7. doi:10.1093/bioinformatics/btn575. PMC 2638937. PMID 18984599.
de Villemereuil P, Wells JA, Edwards RD, Blomberg SP (June 2012). "Bayesian models for comparative analysis integrating phylogenetic uncertainty". BMC Evolutionary Biology. 12 (1): 102. Bibcode:2012BMCEE..12..102V. doi:10.1186/1471-2148-12-102. PMC 3582467. PMID 22741602.
Schäffer S, Koblmüller S, Pfingstl T, Sturmbauer C, Krisper G (August 2010). "Ancestral state reconstruction reveals multiple independent evolution of diagnostic morphological characters in the "Higher Oribatida" (Acari), conflicting with current classification schemes". BMC Evolutionary Biology. 10 (1): 246. Bibcode:2010BMCEE..10..246S. doi:10.1186/1471-2148-10-246. PMC 2930640. PMID 20701742.
Särkinen T, Bohs L, Olmstead RG, Knapp S (September 2013). "A phylogenetic framework for evolutionary study of the nightshades (Solanaceae): a dated 1000-tip tree". BMC Evolutionary Biology. 13 (1): 214. Bibcode:2013BMCEE..13..214S. doi:10.1186/1471-2148-13-214. PMC 3850475. PMID 24283922.
Silvestro D, Schnitzler J, Liow LH, Antonelli A, Salamin N (May 2014). "Bayesian estimation of speciation and extinction from incomplete fossil occurrence data". Systematic Biology. 63 (3): 349–67. doi:10.1093/sysbio/syu006. PMC 4361715. PMID 24510972.
Lemey P, Rambaut A, Drummond AJ, Suchard MA (September 2009). "Bayesian phylogeography finds its roots". PLOS Computational Biology. 5 (9): e1000520. Bibcode:2009PLSCB...5E0520L. doi:10.1371/journal.pcbi.1000520. PMC 2740835. PMID 19779555.
Cybis G, Sinsheimer J, Bedford T, Mather A, Lemey P, Suchard MA (2015). "Assessing phenotypic correlation through the multivariate phylogenetic latent liability model". The Annals of Applied Statistics. 9 (2): 969–991. doi:10.1214/15-AOAS821. ISSN 1932-6157. PMC 4820077. PMID 27053974.
Tolkoff M, Alfaro M, Baele G, Lemey P, Suchard MA (2018). "Phylogenetic Factor Analysis". Systematic Biology. 67 (3): 384–399. doi:10.1093/sysbio/syx066. ISSN 1063-5157. PMC 5920329. PMID 28950376.

nii.ac.jp

ci.nii.ac.jp

Laplace P (1774). "Mémoire sur la Probabilité des Causes par les Évenements". Mémoires de l'Académie Royale des Sciences. 6: 621–656. NAID 10010866843. English translation by Stigler SM (1986). "Memoir on the Probability of the Causes of Events". Statistical Science. 1 (3): 359–378. doi:10.1214/ss/1177013620.

ohiolink.edu

rave.ohiolink.edu

Li, Shuying; Pearl, Dennis K.; Doss, Hani (June 2000). "Phylogenetic Tree Construction Using Markov Chain Monte Carlo". Journal of the American Statistical Association. 95 (450): 493–508. doi:10.1080/01621459.2000.10474227. JSTOR 2669394. S2CID 122459537.

osti.gov

Metropolis N, Rosenbluth AW, Rosenbluth MN, Teller AH, Teller E (June 1953). "Equation of state calculations by fast computing machines". The Journal of Chemical Physics. 21 (6): 1087–92. Bibcode:1953JChPh..21.1087M. doi:10.1063/1.1699114. OSTI 4390578. S2CID 1046577.

oup.com

academic.oup.com

Tolkoff M, Alfaro M, Baele G, Lemey P, Suchard MA (2018). "Phylogenetic Factor Analysis". Systematic Biology. 67 (3): 384–399. doi:10.1093/sysbio/syx066. ISSN 1063-5157. PMC 5920329. PMID 28950376.

semanticscholar.org

api.semanticscholar.org

Rannala, Bruce; Yang, Ziheng (September 1996). "Probability distribution of molecular evolutionary trees: A new method of phylogenetic inference". Journal of Molecular Evolution. 43 (3): 304–311. Bibcode:1996JMolE..43..304R. doi:10.1007/BF02338839. PMID 8703097. S2CID 8269826.
Mau, Bob; Newton, Michael A.; Larget, Bret (March 1999). "Bayesian Phylogenetic Inference via Markov Chain Monte Carlo Methods". Biometrics. 55 (1): 1–12. doi:10.1111/j.0006-341x.1999.00001.x. JSTOR 2533889. PMID 11318142. S2CID 932887.
Li, Shuying; Pearl, Dennis K.; Doss, Hani (June 2000). "Phylogenetic Tree Construction Using Markov Chain Monte Carlo". Journal of the American Statistical Association. 95 (450): 493–508. doi:10.1080/01621459.2000.10474227. JSTOR 2669394. S2CID 122459537.
Metropolis N, Rosenbluth AW, Rosenbluth MN, Teller AH, Teller E (June 1953). "Equation of state calculations by fast computing machines". The Journal of Chemical Physics. 21 (6): 1087–92. Bibcode:1953JChPh..21.1087M. doi:10.1063/1.1699114. OSTI 4390578. S2CID 1046577.
Mau B, Newton MA, Larget B (March 1999). "Bayesian phylogenetic inference via Markov chain Monte Carlo methods". Biometrics. 55 (1): 1–12. doi:10.1111/j.0006-341x.1999.00001.x. PMID 11318142. S2CID 932887.
Pagel M, Meade A (June 2006). "Bayesian analysis of correlated evolution of discrete characters by reversible-jump Markov chain Monte Carlo". The American Naturalist. 167 (6): 808–25. Bibcode:2006ANat..167..808P. doi:10.1086/503444. PMID 16685633. S2CID 205984494.
Alonso R, Crawford AJ, Bermingham E (March 2012). "Molecular phylogeny of an endemic radiation of Cuban toads (Bufonidae: Peltophryne) based on mitochondrial and nuclear genes". Journal of Biogeography. 39 (3): 434–51. Bibcode:2012JBiog..39..434A. doi:10.1111/j.1365-2699.2011.02594.x. S2CID 4152245.

worldcat.org

search.worldcat.org

Geyer CJ (1991). "Markov chain Monte Carlo maximum likelihood.". In Keramidas EM, Kaufman SM (eds.). Computing Science and Statistics: Proceedings of the 23rd Symposium on the Interface. Fairfax Station: Interface Foundation. pp. 156–163. OCLC 26603816.
Goloboff PA, Torres A, Arias JS (2018). "Weighted parsimony outperforms other methods of phylogenetic inference under models appropriate for morphology". Cladistics. 34 (4): 407–437. doi:10.1111/cla.12205. hdl:11336/57822. ISSN 0748-3007. PMID 34649370.
Cybis G, Sinsheimer J, Bedford T, Mather A, Lemey P, Suchard MA (2015). "Assessing phenotypic correlation through the multivariate phylogenetic latent liability model". The Annals of Applied Statistics. 9 (2): 969–991. doi:10.1214/15-AOAS821. ISSN 1932-6157. PMC 4820077. PMID 27053974.
Tolkoff M, Alfaro M, Baele G, Lemey P, Suchard MA (2018). "Phylogenetic Factor Analysis". Systematic Biology. 67 (3): 384–399. doi:10.1093/sysbio/syx066. ISSN 1063-5157. PMC 5920329. PMID 28950376.