Vanderpoorten A, Goffinet B
Institute of Botany, University of Liège, B22 Sart Tilman, B-4000 Liège, Belgium.
Syst Biol. 2006 Dec;55(6):957-71. doi: 10.1080/10635150601088995.
The evolution of species traits along a phylogeny can be examined through an increasing number of possible, but not necessarily complementary, approaches. In this paper, we assess whether deriving ancestral states of discrete morphological characters from a model whose parameters are (i) optimized by ML on a most likely tree; (II) optimized by ML onto each of a Bayesian sample of trees; and (III) sampled by a MCMC visiting the space of a Bayesian sample of trees affects the reconstruction of ancestral states in the moss genus Brachytheciastrum. In the first two methods, the choice of a single- or two-rate model and of a genetic distance (wherein branch lengths are used to determine the probabilities of change) or speciational (wherein changes are only driven by speciation events) model based upon a likelihood-ratio test strongly depended on the sampled trees. Despite these differences in model selection, reconstructions of ancestral character states were strongly correlated to each others across nodes, often at r > 0.9, for all the characters. The Bayesian approach of ancestral character state reconstruction offers, however, a series of advantages over the single-tree approach or the ML model optimization on a Bayesian sample of trees because it does not involve restricting model parameters prior to reconstructing ancestral states, but rather allows a range of model parameters and ancestral character states to be sampled according to their posterior probabilities. From the distribution of the latter, conclusions on trait evolution can be made in a more satisfactorily way than when a substantial part of the uncertainty of the results is obscured by the focus on a single set of model parameters and associated ancestral states. The reconstructions of ancestral character states in Brachytheciastrum reveal rampant parallel morphological evolution. Most species previously described based on phenetic grounds are thus resolved of polyphyletic origin. Species polyphylly has been increasingly reported among mosses, raising severe reservations regarding current species definition.
沿着系统发育树的物种性状进化可以通过越来越多可能但不一定互补的方法来研究。在本文中，我们评估了从一个模型推导离散形态特征的祖先状态是否会影响对短叶藓属祖先状态的重建，该模型的参数分别为：（i）在最可能的树上通过最大似然法（ML）进行优化；（ii）在贝叶斯树样本中的每棵树上通过最大似然法进行优化；（iii）通过马尔可夫链蒙特卡罗（MCMC）访问贝叶斯树样本空间进行采样。在前两种方法中，基于似然比检验选择单速率或双速率模型以及遗传距离模型（其中分支长度用于确定变化概率）或物种形成模型（其中变化仅由物种形成事件驱动）在很大程度上取决于所采样的树。尽管在模型选择上存在这些差异，但对于所有性状，跨节点的祖先性状状态重建彼此之间都具有很强的相关性，通常r>0.9。然而，祖先性状状态重建的贝叶斯方法相对于单树方法或在贝叶斯树样本上进行最大似然模型优化具有一系列优势，因为它在重建祖先状态之前不涉及限制模型参数，而是允许根据后验概率对一系列模型参数和祖先性状状态进行采样。从后者的分布中，可以比专注于单一组模型参数和相关祖先状态而掩盖结果很大一部分不确定性时，更令人满意地得出关于性状进化的结论。短叶藓属祖先性状状态的重建揭示了猖獗的平行形态进化。因此，大多数以前基于表型依据描述的物种被证明是多系起源的。苔藓中越来越多地报道了物种多系性，这引发了对当前物种定义的严重质疑。
