Smedmark Jenny E E, Swenson Ulf, Anderberg Arne A
Department of Phanerogamic Botany, Swedish Museum of Natural History, P.O. Box 50007, SE-104 05 Stockholm, Sweden.
Mol Phylogenet Evol. 2006 Jun;39(3):706-21. doi: 10.1016/j.ympev.2006.01.018. Epub 2006 Feb 21.
We used Bayesian phylogenetic analysis of 5 kb of chloroplast DNA data from 68 Sapotaceae species to clarify phylogenetic relationships within Sapotoideae, one of the two major clades within Sapotaceae. Variation in substitution rates through time was shown to be a very important aspect of molecular evolution for this data set. Relative rates tests indicated that changes in overall rate have taken place in several lineages during the history of the group and Bayes factors strongly supported a covarion model, which allows the rate of a site to vary over time, over commonly used models that only allow rates to vary across sites. Rate variation over time was actually found to be a more important model component than rate variation across sites. The covarion model was originally developed for coding gene sequences and has so far only been tested for this type of data. The fact that it performed so well with the present data set, consisting mainly of data from noncoding spacer regions, suggests that it deserves a wider consideration in model based phylogenetic inference. Repeatability of phylogenetic results was very difficult to obtain with the more parameter rich models, and analyses with identical settings often supported different topologies. Overparameterization may be the reason why the MCMC did not sample from the posterior distribution in these cases. The problem could, however, be overcome by using less parameter rich evolutionary models, and adjusting the MCMC settings. The phylogenetic results showed that two taxa, previously thought to belong in Sapotoideae, are not part of this group. Eberhardtia aurata is the sister of the two major Sapotaceae clades, Chrysophylloideae and Sapotoideae, and Neohemsleya usambarensis belongs in Chrysophylloideae. Within Sapotoideae two clades, Sideroxyleae and Sapoteae, were strongly supported. Bayesian analysis of the character history of some floral morphological traits showed that the ancestral type of flower in Sapotoideae may have been characterized by floral parts (sepals, petals, stamens, and staminodes) in single whorls of five, entire corolla lobes, and seeds with an adaxial hilum.
我们对68种山榄科植物的5 kb叶绿体DNA数据进行了贝叶斯系统发育分析，以阐明山榄亚科内的系统发育关系，山榄亚科是山榄科两个主要分支之一。结果表明，随着时间推移替换率的变化是该数据集分子进化的一个非常重要的方面。相对速率检验表明，在该类群的历史中，几个谱系的总体速率发生了变化，贝叶斯因子强烈支持协变模型，该模型允许位点的速率随时间变化，优于仅允许速率在位点间变化的常用模型。实际上，随时间的速率变化是比位点间速率变化更重要的模型组成部分。协变模型最初是为编码基因序列开发的，迄今为止仅针对此类数据进行过测试。它在主要由非编码间隔区数据组成的当前数据集中表现如此出色，这一事实表明它在基于模型的系统发育推断中值得更广泛的考虑。使用参数更丰富的模型很难获得系统发育结果的可重复性，相同设置的分析往往支持不同的拓扑结构。过度参数化可能是在这些情况下MCMC未从后验分布中抽样的原因。然而，通过使用参数较少的进化模型并调整MCMC设置，可以克服这个问题。系统发育结果表明，之前认为属于山榄亚科的两个类群并非该类群的一部分。金黄坚木是山榄科两个主要分支，金叶树亚科和山榄亚科的姊妹类群，而乌桑巴拉新亥姆木属于金叶树亚科。在山榄亚科内，两个分支，铁青树族和铁线子族，得到了有力支持。对一些花部形态特征的性状历史进行贝叶斯分析表明，山榄亚科花的原始类型可能具有以下特征：花部（萼片、花瓣、雄蕊和退化雄蕊）呈单轮五枚、花冠裂片全缘、种子具近轴种脐。
