Phylogenomic and paleontological data constitute complementary resources for unravelling the phylogenetic relationships and divergence times of lineages, yet few studies have attempted to fully integrate them. Several unique properties of echinoids (sea urchins) make them especially useful for such synthetizing approaches, including a remarkable fossil record that can be incorporated into explicit phylogenetic hypotheses. We revisit the phylogeny of crown group Echinoidea using a total-evidence dating approach that combines the largest phylogenomic dataset for the clade, a large-scale morphological matrix with a dense fossil sampling, and a novel compendium of tip and node age constraints. To this end, we develop a novel method for subsampling phylogenomic datasets that selects loci with high phylogenetic signal, low systematic biases and enhanced clock-like behavior. Our results demonstrate that combining different data sources increases topological accuracy and helps resolve conflicts between molecular and morphological data. Notably, we present a new hypothesis for the origin of sand dollars, and restructure the relationships between stem and crown echinoids in a way that implies a long stretch of undiscovered evolutionary history of the crown group in the late Paleozoic. Our efforts help bridge the gap between phylogenomics and phylogenetic paleontology, providing a model example of the benefits of combining the two.

中文翻译：

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结合系统基因组学和古生物学数据的海胆总证据年代系统发育

系统发育和古生物学数据构成了揭示谱系系统发育关系和分化时间的互补资源，但很少有研究试图将它们完全整合。海胆类动物（海胆）的几个独特特性使它们对这种合成方法特别有用，包​​括可以纳入明确的系统发育假设的非凡化石记录。我们使用全证据定年方法重新审视冠群 Echinoidea 的系统发育，该方法结合了最大的进化枝系统发育数据集、具有密集化石采样的大规模形态矩阵以及尖端和节点年龄限制的新纲要。为此，我们开发了一种对系统发育数据集进行二次采样的新方法，该方法选择具有高系统发育信号的基因座，低系统偏差和增强的类似时钟的行为。我们的结果表明，结合不同的数据源可以提高拓扑准确性，并有助于解决分子和形态数据之间的冲突。值得注意的是，我们提出了一个关于沙元起源的新假说，并以暗示晚古生代冠群长期未被发现的进化历史的方式重构了茎和冠海鞘之间的关系。我们的努力帮助弥合了系统基因组学和系统发育古生物学之间的差距，提供了将两者结合起来的好处的典型例子。我们提出了一个关于沙元起源的新假设，并以暗示晚古生代冠群长期未被发现的进化历史的方式重构了茎和冠海胆之间的关系。我们的努力帮助弥合了系统基因组学和系统发育古生物学之间的差距，提供了将两者结合起来的好处的典型例子。我们提出了一个关于沙元起源的新假设，并以暗示晚古生代冠群长期未被发现的进化历史的方式重构了茎和冠海胆之间的关系。我们的努力帮助弥合了系统基因组学和系统发育古生物学之间的差距，提供了将两者结合起来的好处的典型例子。