一个适于最大似然法估计物种分化年代的进化速率平滑近似.PDFVIP

动物学报 　50 (4) :645 - 656 , 2004 A cta Zoologica S inica 　　　　　 　 A heuristic rate smoothing procedure for maximum likelihood esti mation of species divergence times Ziheng YAN G Department of Biolo gy , University College London , Darwin Building , Gower Street , London WC1 E 　6BT , England Abstract 　Estimation of species divergence times is wellknown to be sensitive to violation of the molecular clock assump tion (rate constancy over time) . However , the molecular clock is almost always violated in comparisons of distantly related species , such as different orders of mammals. Thus it is important to take into account different rates among lineages when divergence times are estimated. The maximum likelihood method provides a framework for accommodating rate variation and can naturally accommodate heterogeneous datasets from multiple loci and fossil calibrations at multiple nodes. Previous implementations of the likelihood method require the researcher to assign branches to different rate classes. In this paper , I implement a heuristic ratesmoothing algorithm ( the AHRS algorithm) to automate the assignment of branches to rate groups. The method combines features of previous likelihood , Bayesian and ratesmoothing methods. The likelihood algorithm is also improved to accommodate missing sequences at some loci in the combined analysis. The new al gorithms are applied to estimate the divergence times of Malagasy mouse lemurs using a dataset of mammalian mitochon drial genes and compared with previous likelihood and Bayesian Markov chain Monte Carlo analyses [ Acta Zoologica Sini ca 50 (4) : 645 - 656 , 2004 ]. Key words 　Rate smoothing , Molecular clock , Divergence times , Maximum likelihood , Combined