Bellot Sidonie, Renner Susanne S
Systematic Botany and Mycology, University of Munich (LMU), Menzinger Str. 67, 80638 Munich, Germany.
Systematic Botany and Mycology, University of Munich (LMU), Menzinger Str. 67, 80638 Munich, Germany.
Mol Phylogenet Evol. 2014 Nov;80:1-10. doi: 10.1016/j.ympev.2014.07.005. Epub 2014 Jul 22.
Gene trees of holoparasitic plants usually show distinctly longer branch lengths than seen in photosynthetic closest relatives. Such substitution rate jumps have made it difficult to infer the absolute divergence times of parasites. An additional problem is that parasite clades often lack a fossil record. Using nuclear and mitochondrial DNA sequences of Apodanthaceae, a worldwide family of endoparasites living inside Fabaceae and Salicaceae, we compared several dating approaches: (i) an uncorrelated lognormal (UCLN) model calibrated with outgroup fossils, (ii) ages of host lineages as a maximal age in an UCLN model, (iii) user-assigned local clocks, and (iv) outgroup-fossil-calibrated random local clocks (RLC) with varying prior probabilities on the number of permitted rate changes (RLCu and RLCp models), a variable that has never been explored. The resulting dated phylogenies include all 10 species of the family, three in Australia, one in Iran, one in Africa, and the remainder in the Americas. All clock models infer a drastic rate jump between nonparasitic outgroups and Apodanthaceae, but since they distribute the rate heterogeneity differently, they result in much-different age estimates. Bayes factors using path and stepping-stone sampling indicated that the RLCp model fit poorly, while for matR, topologically unconstrained RLCu and UCLN models did not differ significantly and for 18S, the UCLN model was preferred. Under the equally well fitting models, the Apodanthaceae appear to be a relatively old clade, with a stem age falling between 65 and 81my, the divergence of Apodanthes from Pilostyles between 36 and 57my ago, and the crown age of the Australian clade 8-18my ago. In our study system, host-age calibrations did not yield well-constrained results, but they may work better in other parasite clades. For small data sets where statistical convergence can be reached even with complex models, random local clocks should be explored as an alternative to the exclusive reliance on UCLN clocks.
全寄生植物的基因树通常显示出比其光合近缘种明显更长的分支长度。这种替代率的跃升使得推断寄生虫的绝对分化时间变得困难。另一个问题是寄生虫类群往往缺乏化石记录。利用寄生在豆科和杨柳科植物体内的全球内寄生植物科——无柄花科的核DNA和线粒体DNA序列，我们比较了几种定年方法：（i）用外类群化石校准的不相关对数正态（UCLN）模型；（ii）宿主谱系的年龄作为UCLN模型中的最大年龄；（iii）用户指定的局部时钟；以及（iv）外类群化石校准的随机局部时钟（RLC），在允许的速率变化数量上具有不同的先验概率（RLCu和RLCp模型），这是一个从未被探索过的变量。由此得到的定年系统发育树包括该科的所有10个物种，其中3种在澳大利亚，1种在伊朗，1种在非洲，其余在美洲。所有时钟模型都推断非寄生外类群和无柄花科之间存在急剧的速率跃升，但由于它们对速率异质性的分布不同，导致年龄估计差异很大。使用路径和踏脚石抽样的贝叶斯因子表明RLCp模型拟合不佳，而对于matR基因，拓扑无约束的RLCu和UCLN模型没有显著差异，对于18S基因，UCLN模型更受青睐。在拟合效果同样好的模型下，无柄花科似乎是一个相对古老的类群，其茎年龄在6500万至8100万年前，无柄花属与柱柄寄生属的分化在3600万至5700万年前，澳大利亚类群的冠年龄在800万至1800万年前。在我们的研究系统中，宿主年龄校准没有产生约束良好的结果，但它们在其他寄生虫类群中可能效果更好。对于即使使用复杂模型也能达到统计收敛的小数据集，应探索随机局部时钟作为唯一依赖UCLN时钟的替代方法。
