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）的拓扑结构会随着作用于某一演化支（clade）的演化进程随时间推移而发生改变。本研究针对多个时间区间内的化石四足动物（fossil tetrapods）经验系统发育树展开分析，探究了时间约束如何体现在树的不平衡性（tree imbalance）与性状演化（character change）模式中。研究结果显示，时间约束对系统发育树拓扑结构的影响微乎其微，这也凸显了作为参照的四足动物系统发育树随时间推移所保持的稳定性。密西西比纪（Mississippian）与宾夕法尼亚纪（Pennsylvanian）时间切片（time slice）的不平衡性数值显著偏高，这一结果有力支撑了"石炭纪（Carboniferous）是四足动物爆发式辐射演化时期"的假说。密西西比纪期间发生了多次显著的演化辐射转移事件，这为早期有肢脊椎动物逐步增强的陆生适应（terrestrialization）奠定了基础。相较于基于恒定性状演化速率的零假设分布，四足动物演化早期的性状不相容性（character incompatibility）相对较高，但会快速下降至一个相对稳定的较低水平。这表明四足动物的基干类群在演化早期的趋同演化（homoplasy）速率较高，但呈逐步下降趋势，不过滑体两栖类（Lissamphibia）的起源是这一趋势的例外。时间切片法是一种极具效力的系统发育分析手段，同时也是评估"将灭绝类群与现生类群整合后，对大型物种丰富演化支开展系统发育分析所产生的影响"的实用工具。