贝叶斯法

貝葉氏譜系分析（Bayesian inference of phylogeny）是根據已知的先驗機率推導後驗機率的似然函數，進而去預測最可能的系譜樹。隨著電腦計算速度的演進以及马尔科夫-蒙特卡洛法的演進，貝葉氏譜系分析越來越受重視和應用。贝叶斯推断時常應用於分子系統發生學以及系統分類學。

貝葉氏譜系分析
分類演化生物学
子分類分子系統發生學
最佳搜索條件贝叶斯推断

分析軟體列表

下表列出最常用的系譜分析軟體，有些不只使用貝葉氏譜系分析。

軟體描述方法作者網址
Armadillo Workflow PlatformWorkflow platform dedicated to phylogenetic and general bioinformatic analysisInference of phylogenetic trees using Distance, Maximum Likelihood, Maximum Parsimony, Bayesian methods and related workflowsE. Lord, M. Leclercq, A. Boc, A.B. Diallo and V. Makarenkov [1]https://web.archive.org/web/20161024081942/http://www.bioinfo.uqam.ca/armadillo/.
Bali-PhySimultaneous Bayesian inference of alignment and phylogenyBayesian inference, alignment as well as tree searchM.A. Suchard, B. D. Redelings [2]http://www.bali-phy.org （页面存档备份，存于）
BATWINGBayesian Analysis of Trees With Internal Node GenerationBayesian inference, demographic history, population splitsI. J. Wilson, D. Weale, D.Balding [3]http://www.maths.abdn.ac.uk/˜ijw%5B%5D
Bayes PhylogeniesBayesian inference of trees using Markov Chain Monte Carlo methodsBayesian inference, multiple models, mixture model (auto-partitioning)M. Pagel, A. Meade [4]http://www.evolution.rdg.ac.uk/BayesPhy.html （页面存档备份，存于）
PhyloBayes / PhyloBayes MPIBayesian Monte Carlo Markov Chain (MCMC) sampler for phylogenetic reconstruction.Non-parametric methods for modeling among-site variation in nucleotide or amino-acid propensities.N. Lartillot, N. Rodrigue, D. Stubbs, J. Richer [5]https://web.archive.org/web/20181218053945/http://www.phylobayes.org/
BEASTBayesian Evolutionary Analysis Sampling TreesBayesian inference, relaxed molecular clock, demographic historyA. J. Drummond, A. Rambaut & M. A. Suchard [6]http://beast.bio.ed.ac.uk （页面存档备份，存于）
BUCKyBayesian concordance of gene treesBayesian concordance using modified greedy consensus of unrooted quartetsC. Ané, B. Larget, D.A. Baum, S.D. Smith, A. Rokas and B. Larget, S.K. Kotha, C.N. Dewey, C. Ané [7]http://www.stat.wisc.edu/~ane/bucky/ （页面存档备份，存于）
Geneious (MrBayes plugin)Geneious provides genome and proteome research toolsNeighbor-joining, UPGMA, MrBayes plugin, PHYML plugin, RAxML plugin, FastTree plugin, GARLi plugin, PAUP* PluginA. J. Drummond,M.Suchard,V.Lefort et al.http://www.geneious.com （页面存档备份，存于）
TOPALiPhylogenetic inferencePhylogenetic model selection, Bayesian analysis and Maximum Likelihood phylogenetic tree estimation, detection of sites under positive selection, and recombination breakpoint location analysisI.Milne, D.Lindner, et al.[8]http://www.topali.org （页面存档备份，存于）

應用

貝葉氏譜系分析在分子系統發生學上具有相當廣泛的應用，包含：

BEAST以分子時鐘分析法（molecular clock analysis）得出的系譜樹。圓餅圖表示的是利用貝葉氏二元MCMC分析（BBM）所推斷的祖源。
  • 系統發生學預測[9][10]
  • 預測及評估未明祖源[11]
  • 祖徵演化[12][13]
  • 祖源地域推論[14]
  • 分子測年分析[15][16]
  • 物種多樣化和滅絕的動力學模型[17]
  • 傳染病擴散模型[18]

參考文獻
  1. Lord, E., Leclercq, M., Boc, A., Diallo, A.B., Makarenkov, V. 2012. Armadillo 1.1: An Original Workflow Platform for Designing and Conducting Phylogenetic Analysis and Simulations. PLoS ONE 7(1): e29903. doi:10.1371/journal.pone.0029903
  2. Suchard, M.A. and Redelings, B.D. 2006. BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny, Bioinformatics. 22:2047-2048
  3. Wilson, I., Weale, D. and Balding, M. 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: 155-188
  4. Pagel, M. and Meade, A. 2006. Bayesian analysis of correlated evolution of discrete characters by reversible-jump Markov chain Monte Carlo. American Naturalist, 167, 808-825
  5. Lartillot N., Philippe H. 2004. A Bayesian Mixture Model for Across-Site Heterogeneities in the Amino-Acid Replacement Process. Molecular Biology and Evolution 21(6):1095-1109
  6. Drummond, A.J., Rambaut, A. 2007. Beast: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol. 7:214
  7. Ané, C., Larget, B., Baum, D.A.,Smith, S.D., Rokas, A. 2007. Bayesian estimation of concordance among gene trees. Molecular Biology and Evolution 24(2), 412-426
  8. Milne, I., Lindner, D., Bayer, M., Husmeier, D., McGuire, G., Marshall, D.F. and Wright, F. 2008. TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops. Bioinformatics 25 (1), 126-127
  9. Alonso, R., Crawford, A.J. & Bermingham, E. 2011. Molecular phylogeny of an endemic radiation of Cuban toads (Bufonidae: Peltophryne) based on mitochondrial and nuclear genes. Journal of Biogeography 39 (3): 434-451
  10. Antonelli, A., Sanmart.n, I. 2011. Mass Extinction, Gradual Cooling, or Rapid Radiation? Reconstructing the Spatiotemporal Evolution of the Ancient Angiosperm Genus Hedyosmum (Chloranthaceae) Using Empirical and Simulated Approaches. Syst. Biol. 60(5):596–615
  11. de Villemereuil, P.,Wells, J.A., Edwards, R.D. and Blomberg, S.P. 2012. Bayesian Phylogeography Finds Its Roots BMC Evolutionary Biology 12:102
  12. Ronquist, F. 2004. Bayesian inference of character Evolution. Trends in Ecology and Evolution 19 No.9: 475-481
  13. Schäffer , S., Koblmüller, S., Pfingstl, T., Sturmbauer, C., Krisper, G. 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 10:246
  14. Filipowicz, N., Renner, S. 2012. Brunfelsia (Solanaceae): A genus evenly divided between South America and radiations on Cuba and other Antillean islands. Molecular Phylogenetics and Evolution 64: 1-11
  15. Bacon, C.D., Baker, W.J., Simmons, M.P. 2012a. Miocene dispersal drives island radiations in the palm tribe Trachycarpeae (Arecaceae). Systematic Biology 61: 426–442
  16. Särkinen, T., Bohs, L., Olmstead,R.G. and Knapp, S. 2013. A phylogenetic framework for evolutionary study of the nightshades (Solanaceae): a dated 1000-tip tree. BMC Evolutionary Biology. 13:214
  17. Silvestro, D., Schnitzler, J., Liow, L.H., Antonelli, A., Salamin, N. 2014. Bayesian Estimation of Speciation and Extinction from Incomplete Fossil Occurrence Data. Syst. Biol. 63(3):349–367
  18. Lemey, P., Rambaut, A., Drummond, A.J., Suchard, M.A. 2009. Bayesian Phylogeography Finds Its Roots. PLoS Comput Biol 5(9): e1000520

外部連結

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