Ekman Stefan, Andersen Heidi L, Wedin Mats
Museum of Evolution, Evolutionary Biology Centre, Uppsala University, Norbyvägen 16, Uppsala, Sweden.
Syst Biol. 2008 Feb;57(1):141-56. doi: 10.1080/10635150801910451.
Ancestral state reconstructions of morphological or ecological traits on molecular phylogenies are becoming increasingly frequent. They rely on constancy of character state change rates over trees, a correlation between neutral genetic change and phenotypic change, as well as on adequate likelihood models and (for Bayesian methods) prior distributions. This investigation explored the outcomes of a variety of methods for reconstructing discrete ancestral state in the ascus apex of the Lecanorales, a group containing the majority of lichen-forming ascomycetes. Evolution of this character complex has been highly controversial in lichen systematics for more than two decades. The phylogeny was estimated using Bayesian Markov chain Monte Carlo inference on DNA sequence alignments of three genes (small subunit of the mitochondrial rDNA, large subunit of the nuclear rDNA, and largest subunit of RNA polymerase II). We designed a novel method for assessing the suitable number of discrete gamma categories, which relies on the effect on phylogeny estimates rather than on likelihoods. Ancestral state reconstructions were performed using maximum parsimony and maximum likelihood on a posterior tree sample as well as two fully Bayesian methods. Resulting reconstructions were often strikingly different depending on the method used; different methods often assign high confidence to different states at a given node. The two fully Bayesian methods disagree about the most probable reconstruction in about half of the nodes, even when similar likelihood models and similar priors are used. We suggest that similar studies should use several methods, awaiting an improved understanding of the statistical properties of the methods. A Lecanora-type ascus may have been ancestral in the Lecanorales. State transformations counts, obtained using stochastic mapping, indicate that the number of state changes is 12 to 24, which is considerably greater than the minimum three changes needed to explain the four observed ascus apex types. Apparently, the ascus in the Lecanorales is far more apt to change than has been recognized. Phylogeny corresponds well with morphology, although it partly contradicts currently used delimitations of the Crocyniaceae, Haematommataceae, Lecanoraceae, Megalariaceae, Mycoblastaceae, Pilocarpaceae, Psoraceae, Ramalinaceae, Scoliciosporaceae, and Squamarinaceae.
在分子系统发育树上对形态或生态性状进行祖先状态重建的情况越来越普遍。它们依赖于性状状态变化率在树上的恒定性、中性遗传变化与表型变化之间的相关性，以及适当的似然模型和（对于贝叶斯方法）先验分布。本研究探讨了多种用于重建茶渍目子囊顶端离散祖先状态的方法的结果，茶渍目包含了大多数形成地衣的子囊菌。在二十多年里，这个性状复合体的进化在地衣系统学中一直极具争议。系统发育是通过对三个基因（线粒体rDNA的小亚基、核rDNA的大亚基和RNA聚合酶II的最大亚基）的DNA序列比对，使用贝叶斯马尔可夫链蒙特卡罗推断法来估计的。我们设计了一种评估离散伽马类别合适数量的新方法，该方法依赖于对系统发育估计的影响而非似然性。祖先状态重建是在一个后验树样本上使用最大简约法和最大似然法以及两种完全贝叶斯方法进行的。根据所使用的方法不同，得到的重建结果往往差异显著；不同方法通常会对给定节点的不同状态赋予高置信度。即使使用相似的似然模型和相似的先验，这两种完全贝叶斯方法在大约一半的节点上对于最可能的重建结果也存在分歧。我们建议类似的研究应该使用多种方法，等待对这些方法的统计特性有更深入的理解。茶渍型子囊可能是茶渍目的祖先类型。使用随机映射获得的状态转变计数表明，状态变化的数量为12到24次，这远大于解释四种观察到的子囊顶端类型所需的最少三次变化。显然，茶渍目的子囊比人们所认识到的更容易发生变化。系统发育与形态学吻合得很好，尽管它部分地与目前对叉丝壳科、血盘菌科、茶渍科、大孢衣科、拟盘菌科、皮果衣科、皱盘衣科、挂钟衣科、糙孢衣科和鳞盘衣科的划分相矛盾。
