Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, 3er Circuito de Ciudad Universitaria, Del. Coyoacán, México D.F. 04510, México.
Syst Biol. 2010 Jul;59(4):384-99. doi: 10.1093/sysbio/syq027. Epub 2010 Jun 10.
Long branches are potentially problematic in molecular dating because they can encompass a vast number of combinations of substitution rate and time. A long branch is suspected to have biased molecular clock estimates of the age of flowering plants (angiosperms) to be much older than their earliest fossils. This study explores the effect of the long branch subtending angiosperms in molecular dating and how different relaxed clocks react to it. Fossil angiosperm relatives, identified through a combined morphological and molecular phylogenetic analysis for living and fossil seed plants, were used to break the long angiosperm stem branch. Nucleotide sequences of angiosperm fossil relatives were simulated using a phylogeny and model parameters from living taxa and incorporated in molecular dating. Three relaxed clocks, which implement among-lineage rate heterogeneity differently, were used: penalized likelihood (using 2 different rate smoothing optimization criteria), a Bayesian rate-autocorrelated method, and a Bayesian uncorrelated method. Different clocks provided highly correlated ages across the tree. Breaking the angiosperm stem branch did not result in major age differences, except for a few sensitive nodes. Breaking the angiosperm stem branch resulted in a substantially younger age for crown angiosperms only with 1 of the 4 methods, but, nevertheless, the obtained age is considerably older than the oldest angiosperm fossils. The origin of crown angiosperms is estimated between the Upper Triassic and the early Permian. The difficulty in estimating crown angiosperm age probably lies in a combination of intrinsic and extrinsic complicating factors, including substantial molecular rate heterogeneity among lineages and through time. A more adequate molecular dating approach might combine moderate background rate heterogeneity with large changes in rate at particular points in the tree.
长枝在分子年代学中可能是一个问题，因为它们可以包含大量的替代率和时间的组合。长枝被怀疑会使分子钟对开花植物（被子植物）的年龄估计比其最早的化石要老得多。本研究探讨了长枝支撑的被子植物在分子年代学中的作用，以及不同的松弛时钟对其的反应。通过对活种子植物和化石种子植物的形态学和分子系统发育分析，确定了被子植物的化石亲缘关系，用于打破长枝的分支。利用活分类群的系统发育和模型参数，模拟了被子植物化石亲缘关系的核苷酸序列，并将其纳入分子年代学。使用了三种不同的松弛时钟，它们以不同的方式实现了谱系间速率异质性：惩罚似然法（使用 2 种不同的速率平滑优化标准）、贝叶斯速率自相关方法和贝叶斯不相关方法。不同的时钟在整个树中提供了高度相关的年龄。打破被子植物的主干分支并没有导致主要的年龄差异，除了一些敏感节点。只有在 4 种方法中的 1 种方法中，打破被子植物的主干分支才会导致冠部被子植物的年龄显著变年轻，但得到的年龄仍然比最古老的被子植物化石要老得多。冠部被子植物的起源估计在晚三叠世到早二叠世之间。估计冠部被子植物年龄的困难可能在于内在和外在的复杂因素的结合，包括谱系间和随时间的实质性分子速率异质性。更合适的分子年代学方法可能将适度的背景速率异质性与树中特定点的速率大变化相结合。
