Data from: Phylogenetic stability, tree shape, and character compatibility: a case study using early tetrapods

Phylogenetic tree shape varies as the evolutionary processes affecting a clade change over time. In this study, we examined an empirical phylogeny of fossil tetrapods during several time intervals, and studied how temporal constraints manifested in patterns of tree imbalance and character change. The results indicate that the impact of temporal constraints on tree shape is minimal and highlights the stability through time of the reference tetrapod phylogeny. Unexpected values of imbalance for Mississippian and Pennsylvanian time slices strongly support the hypothesis that the Carboniferous was a period of explosive tetrapod radiation. Several significant diversification shifts take place in the Mississippian and underpin increased terrestrialization among the earliest limbed vertebrates. Character incompatibility is relatively high at the beginning of tetrapod history, but quickly decreases to a relatively stable lower level, relative to a null distribution based on constant rates of character change. This implies that basal tetrapods had high, but declining, rates of homoplasy early in their evolutionary history, although the origin of Lissamphibia is an exception to this trend. The time slice approach is a powerful method of phylogenetic analysis and a useful tool for assessing the impact of combining extinct and extant taxa in phylogenetic analyses of large and speciose clades.系统发育树（phylogenetic tree）的形态会随作用于某一支系（clade）的演化进程随时间推移而改变。本研究针对多个时间间隔内的化石四足类（fossil tetrapods）经验性系统发育树（empirical phylogeny）展开分析，探究时间约束如何体现在系统发育树的不平衡性（tree imbalance）与性状演化（character change）模式之中。研究结果显示，时间约束对系统发育树形态的影响微乎其微，这凸显了所参考的四足类系统发育树随时间保持的稳定性。密西西比纪（Mississippian）与宾夕法尼亚纪（Pennsylvanian）时间切片的不平衡性数值异常偏高，有力支撑了“石炭纪（Carboniferous）是四足类爆发式辐射时期”这一假说。多项显著的多样化转变（diversification shift）发生于密西西比纪，为早期有肢脊椎动物（limbed vertebrates）陆生化（terrestrialization）程度的提升提供了依据。四足类演化早期的性状不相容性（character incompatibility）相对较高，但相较于基于恒定性状演化速率构建的零分布（null distribution），其数值会快速下降至相对稳定的较低水平。这表明基底四足类在演化早期的趋同演化（homoplasy）速率较高且呈下降趋势，不过滑体两栖类（Lissamphibia）的起源是这一趋势的例外。时间切片法（time slice approach）是一种高效的系统发育分析方法，同时也是评估在大型物种丰富支系（speciose clade）的系统发育分析中整合灭绝类群与现生类群所产生影响的实用工具。