Data from: Accelerated rate of molecular evolution for vittarioid ferns is strong and not due to selection

Molecular evolutionary rate heterogeneity—the violation of a molecular clock—is a prominent feature of many phylogenetic datasets. It has particular importance to systematists not only because of its biological implications, but also for its practical effects on our ability to infer and date evolutionary events. Here we show, using both maximum likelihood and Bayesian approaches, that a remarkably strong increase in substitution rate in the vittarioid ferns is consistent across the nuclear and plastid genomes. Contrary to some expectations, this rate increase is not due to selective forces; the vittarioids bear no signature of the change in the relative strengths of selection and drift that one would expect if the rate increase was caused by altered fixation rates. Instead, the substitution rate increase appears to stem from an elevated supply of mutations, perhaps limited to the vittarioid ancestral branch. This generalized rate increase is accompanied by extensive fine-scale heterogeneity in rates across loci, genomes, and taxa. Our analyses demonstrate the power and flexibility of trait-free investigations of rate heterogeneity within a model selection framework, emphasize the importance of explicit tests for signatures of selection prior to invoking selection-related or demography-based explanations for patterns of rate variation, and illustrate some unexpected nuances in the behavior of relaxed clock methods for modeling rate heterogeneity, with implications for our ability to confidently date divergence events. In addition, our data provide strong support for the monophylly of Adiantum, and for the position of Calciphilopteris in the cheilanthoid ferns, two relationships for which convincing support was previously lacking.分子进化速率异质性——即分子钟（molecular clock）的偏离——是诸多系统发育数据集（phylogenetic datasets）的典型特征。其对系统分类学家尤为关键，不仅因其承载着重要的生物学内涵，更因其对我们推断与定年进化事件的能力存在实际影响。本研究通过最大似然（maximum likelihood）与贝叶斯（Bayesian）两种分析范式，证实书带蕨类（vittarioid ferns）的核苷酸替换速率存在显著提升，且这一现象在核基因组与质体基因组中均保持一致。与部分学界预期相悖，该替换速率提升并非由选择压力（selective forces）驱动：若速率提升源于固定速率的改变，则理论上应伴随选择与遗传漂变（genetic drift）相对强度的变化信号，但书带蕨类并无此类特征。取而代之的是，替换速率的提升似乎源于突变（mutations）供给量的增加，且这一效应可能仅局限于书带蕨类的祖先分支。这种普遍性的速率提升，同时伴随基因座（loci）、基因组以及类群（taxa）间广泛存在的精细尺度速率异质性。本研究的分析结果证明了在模型选择框架（model selection framework）下开展无性状速率异质性研究的效力与灵活性，强调在针对速率变异模式援引选择相关或基于种群动态（demography）的解释前，需先对选择信号开展明确检验的重要性，并阐明了用于模拟速率异质性的宽松钟模型方法（relaxed clock methods）在行为特征上的一些意外细微之处，这对我们准确可靠地定年分化事件（divergence events）的能力具有重要启示。此外，本研究的数据为铁线蕨属（Adiantum）的单系性（monophyly），以及嗜钙蕨属（Calciphilopteris）在碎米蕨类（cheilanthoid ferns）中的系统位置提供了强有力的支持——此前这两类群的系统发育关系均缺乏令人信服的证据。