Exploring new dating approaches for parasites: The worldwide Apodanthaceae (Cucurbitales) as an example
Exploring new dating approaches for parasites: The worldwide Apodanthaceae (Cucurbitales) as an example
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DOI：
10.1016/j.ympev.2014.07.005
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发表时间：
2014-11-01
影响因子：
4.1
通讯作者：
Renner, Susanne S.
中科院分区：
文献类型：
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作者：
Bellot, Sidonie;Renner, Susanne S.
全寄生植物的基因树通常表现出明显较长的分支长度比光合最近的亲戚。这种替代率的跳跃使得很难推断寄生虫的绝对发散时间。另一个问题是寄生虫分支往往缺乏化石记录。使用Apodanthaceae的核和线粒体DNA序列，Apodanthaceae是生活在豆科和杨柳科内部的一个世界性的体内寄生虫家族，我们比较了几种测年方法：（i）用外群化石校准的不相关对数正态（UCLN）模型，（ii）作为UCLN模型中的最大年龄的宿主谱系的年龄，（iii）用户指定的本地时钟，以及（iv）外群化石校准的随机本地时钟（RLC），其具有关于允许的速率变化的数量的变化的先验概率（RLCu和RLCp模型），这是从未被探索过的变量。最后确定的物种包括该科的所有10个物种，其中3个在澳大利亚，1个在伊朗，1个在非洲，其余的在美洲。所有的时钟模型推断一个剧烈的跳跃率之间的非寄生外类群和Apodanthaceae，但由于它们分布的速率异质性不同，它们导致不同的年龄估计。贝叶斯因子使用路径和垫脚石抽样表明，RLCp模型拟合差，而对于matR，拓扑无约束RLCu和UCLN模型没有显着差异，18 S，UCLN模型是首选。在同样拟合良好的模型下，Apodanthaceae似乎是一个相对较老的分支，茎龄在65 - 81万年之间，Apodanthes与Pilostyles的分歧在36 - 57万年前，澳大利亚分支的冠龄在8-18万年前。在我们的研究系统中，宿主年龄校准没有产生良好的约束结果，但他们可能会更好地工作在其他寄生虫分支。对于小数据集，即使使用复杂的模型也可以达到统计收敛，随机本地时钟应该被探索作为唯一依赖UCLN时钟的替代方案。(C)2014爱思唯尔公司All rights reserved.
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 mitochondria] 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 81 my, the divergence of Apodanthes from Pilostyles between 36 and 57 my ago, and the crown age of the Australian clade 8-18 my 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. (C) 2014 Elsevier Inc. All rights reserved.