Collaborative Research: Integrating Phylogenomics with the Fossil Record: Sea Urchins as a Model Clade for Macroevolutionary Research

带刺的球形海胆是海带森林和珊瑚礁中常见的标志性海洋动物，它们通常是藻类和其他生物的主要消费者。相比之下，沙美元是非常扁平的海胆，通常生活在沙质海底，通过从沉积物中挑选微小的食物颗粒来觅食。多种证据表明，这两个种群是密切相关的，它们的祖先的身体形态和生态环境与现代海胆大致相似。这表明在进化路径上有一个显著的对比：虽然一些谱系在数亿年里几乎没有改变，但其他谱系却发生了巨大的变化。确定这些不同轨迹背后的机制对于理解产生和维持生物多样性的过程是必要的。然而，这样做需要精确地重建发生在很久以前的事件，并整合基因组、形态学和古生物学信息。该项目将这些有魅力的动物作为研究进化变化的模型，包括本科生研究项目、教师研讨会和公共博物馆的展览。该项目的重点是开发系统基因组资源，以提高我们对活海胆、沙美元和盟友（统称为棘足类动物）之间进化关系的认识。考虑到该分支的杰出化石记录，这些数据将与形态学和地层信息结合使用全证据测年方法，允许所有主要的现存和化石棘足类动物谱系被放置在一个共同的、经过时间校准的生命树中。利用系统发育的比较方法，该项目将揭示与不规则棘球蚴和沙美元起源相关的进化过程，这是身体计划创新的两个主要事件。分析将依赖于一个大型的类棘球蚴体测量数据集来探索进化速度和模块化的变化，并将这些指标的变化与已知的发展创新和生态专业化事件联系起来。生态、发育和形态特征对物种形成和灭绝动力学的贡献将使用状态依赖的多样化模型进行评估。最后，基于本体论的祖先状态重建将有助于确定砂元形态的独立起源（和损失）的数量，以及这些事件的相对时间。通过结合系统基因组学和系统发育古生物学的最新发展，本项目将把棘足类动物作为宏观进化研究的一个模式分支。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

Spine-covered, globular sea urchins are iconic marine animals common in kelp forests and coral reefs, where they are often the main consumers of algae and other organisms. By contrast, sand dollars are extremely flattened urchins that generally live buried in sandy seafloors, feeding by picking tiny particles of food from the sediment. Multiple lines of evidence suggest these two groups are closely related, originating from an ancestor whose body form and ecology were broadly similar to those of modern sea urchins. This suggests a striking contrast in evolutionary pathways: while some lineages have barely changed over hundreds of millions of years, others have innovated dramatically. Identifying the mechanisms that underlie these different trajectories is necessary to understand the processes generating and maintaining biological diversity. However, doing so requires accurate reconstructions of events that took place in the deep past, and integrating genomic, morphological, and paleontological information. The project highlights these charismatic animals as models for studying evolutionary change in a variety of outreach modes including undergraduate research programs, teacher workshops, and displays in public museums.The project focuses on developing phylogenomic resources to improve our knowledge of evolutionary relationships among living sea urchins, sand dollars and allies (collectively known as echinoids). Given the clade’s outstanding fossil record, these data will be combined with morphological and stratigraphic information using a total-evidence dating approach, allowing all major lineages of living and fossil echinoids to be placed in a common, time-calibrated tree of life. Using phylogenetic comparative methods, the project will reveal evolutionary processes associated with the origins of both irregular echinoids and sand dollars, two major events in body-plan innovation. Analyses will rely on a large-scale dataset of echinoid body measurements to explore changes in evolutionary rate and modularity, and correlate shifts in these metrics with known events of developmental innovation and ecological specialization. The contributions of ecological, developmental and morphological traits to speciation and extinction dynamics will be assessed using state-dependent models of diversification. Finally, ontology-informed ancestral state reconstructions will help identify the number of independent origins (and losses) of the sand dollar morphotype, as well as the relative timing of these events. By combining recent developments in phylogenomics and phylogenetic paleobiology, this project will establish echinoids as a model clade in macroevolutionary research.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.