Dating the molecular clock in fungi - how close are we?
Dating the molecular clock in fungi - how close are we?
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DOI：
10.1016/j.fbr.2010.03.001
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发表时间：
2010-02-01
影响因子：
6
通讯作者：
Taylor, John W.
中科院分区：
文献类型：
--
作者：
Berbee, Mary L.;Taylor, John W.
真菌进化与板块构造运动、古生态学以及动植物进化的结合需要一个分子钟。尽管分子钟可能并不完美，但它们提供了将分子变化转换为地质时间的方法。时钟之间的关系，地理，化石，和替代率的变化，沿着与不确定性纳入时钟估计是这个评论的主题。这篇评论是及时的，因为对于数亿年量级的更深层次的分歧，对起源年龄的估计正受益于越来越准确的有机体遗传学和越来越现实的分子进化模型。利用贝叶斯方法允许复杂的假设节点年龄和分子进化，我们使用的程序BEAST应用一个宽松的对数正态时钟分析的数据集，包括50个位点的26个类群。在由此产生的树，分支与化石校准的节点显示出更显着的替代率变化比分支节点缺乏校准。作为这一结果的逻辑延伸，我们怀疑，未检测到的速率变化的未校准的部分的树是戏剧性的校准部分，强调化石校准的重要性。幸运的是，新的和有趣的真菌化石正在被发现，我们回顾了一些新的发现，证实了重要类群的古老起源。为了帮助评估哪些化石可能有助于限制节点的年龄，我们选择了被认为是其分支的早期成员的化石，并使用核糖体或蛋白质编码基因序列替换率来计算化石年龄和预期的谱系年龄是否一致。当化石的年龄和谱系的预期年龄重合时，化石在分子钟分析中限制节点年龄方面将特别有用。(C)2010年英国真菌学会。由爱思唯尔有限公司出版。保留所有权利。
Integration of fungal evolution with the dates of plate tectonic movements, paleoecology, and the evolution of plants and animals requires a molecular clock. Imperfect though they may be, molecular clocks provide the means to convert molecular change into geological time. The relationships among clocks, phylogeography, fossils, and substitution rate variation, along with incorporation of uncertainty into clock estimates are the topics for this commentary. This commentary is timely because, for deeper divergences on the order of hundreds of millions of years, estimates of age of origin are benefiting from increasingly accurate organismal phylogenies and increasingly realistic models of molecular evolution. Taking advantage of Bayesian approaches permitting complex assumptions about node ages and molecular evolution, we used the program BEAST to apply a relaxed lognormal clock analysis to a data set comprising 50 loci for 26 taxa. In the resulting tree, branches associated with nodes calibrated by fossils showed more dramatic substitution rate variation than branches at nodes lacking calibration. As a logical extension of this result, we suspect that undetected rate variation in the uncalibrated parts of the tree is as dramatic as in the calibrated sections, underscoring the importance of fossil calibration. Fortunately, new and interesting fungal fossils are being discovered and we review some of the new discoveries that confirm the ancient origin of important taxa. To help evaluate which fossils might be useful for constraining the ages of nodes, we selected fossils thought to be early members of their clades and used ribosomal or protein-coding gene sequence substitution rates to calculate whether fossil age and expected lineage age coincide. Where ages of a fossil and the expected age of a lineage do coincide, the fossils will be particularly useful in constraining node ages in molecular clock analyses. (C) 2010 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.