Exploring rates of change and modes of evolution in blastozoan echinoderms

Over the past half-century, paleobiologists have advanced the estimation of phylogenetic relationships among fossil taxa to explore evolutionary patterns in deep time. This study employs phylogenetics, divergence time calculations, and character rate evolution within three blastozoan echinoderm clades: Diploporita, Eublastoidea, and Paracrinoidea. Utilizing Reversible Jump Markov Chain Monte Carlo (rjMCMC) and Fossilized Birth-Death (FBD) models, we investigated evolutionary rates through anatomical subunit partitioning. Results suggest similar rates among the three groups, though Paracrinoidea exhibits elevated rates in several anatomical subunits. The inferred trees largely agree with other recently published analyses and highlight the need to revise echinoderm taxonomy. We tested different clock models for each group and found that model choice had strong effects on resulting trees; our findings suggest that linked clocks had more support than unlinked clocks. These findings indicate..., Recent work suggests variation in rates of evolution of echinoderm traits (Novack-Gottshall et al. 2022). In prior work, it has been hypothesized that “functional” traits like feeding characters may evolve at faster rates than other traits, a hypothesis not limited to echinoderms (e.g., Foote 1995; Ciampaglio 2002; Smith and Hopkins 2015; Wright 2017), but seen in animals in general (Wagner 1995; Sánchez-Villagra and Williams 1998). The morphological diversity seen in blastozoan echinoderms has frequently hindered our abilities to establish homology amongst characters, let alone examine rates of evolution. However, with the development of echinoderm-specific homology schemes (Mooi and David 1997; Sumrall 2010) and the application of these schemes to many blastozoan groups, these questions of evolution questions can be addressed. Both homology schemes have strengths and weaknesses (Sumrall et al. 2023), but, because this particular study is focused on Paleozoic blastozoans, and the mode..., , # Data from: Exploring rates of change and modes of evolution in blastozoan echinoderms

[https://doi.org/10.5061/dryad.s7h44j1hg](https://doi.org/10.5061/dryad.s7h44j1hg)

## Description of the data and file structure

Models of Character Evolution

A core goal in this study is to examine if the reversible jump Markov Chain Monte Carlo (rjMCMC) algorithm can be used to efficiently compare different hypotheses about character evolution. Reversible Jump Markov Chain Monte Carlo (rjMCMC) is an adaptation of the MCMC algorithm that allows for the number of parameters to change throughout an analysis. In this type of analysis, the model itself is a random variable. For example, in Table S1, you will note that some skyline models have more categories than others. In the case of adding a category, this means (minimally) adding three additional parameters — a new speciation, extinction, and fossil sampling rate. In a traditional MCMC, the number of parameters cannot be varied in an analysis. T..., , **Changes after Nov 20, 2025:** 

The journal does not host supplemental figures and has requested us to upload them here (uploaded to Zenodo, not Dryad because Dryad datasets are published under the CC0 waiver; to apply the CC-BY license, supplemental data files are hosted on Zenodo)

近半个世纪以来，古生物学家不断推进化石类群间系统发育关系的估算工作，以探索深时演化模式。本研究针对双孔目（Diploporita）、真海果亚纲（Eublastoidea）与副海林檎亚纲（Paracrinoidea）三个芽体棘皮动物（blastozoan echinoderm）演化支，运用系统发育学、分化时间估算以及性状演化速率分析方法。本研究采用可逆跳跃马尔可夫链蒙特卡洛（Reversible Jump Markov Chain Monte Carlo，rjMCMC）与化石出生-死亡（Fossilized Birth-Death，FBD）模型，通过解剖亚单元分区的方式探究演化速率。结果显示，三个类群的演化速率整体相近，但副海林檎亚纲在多个解剖亚单元中呈现更高的演化速率。所推断的系统发育树与近期其他已发表的分析结果大体一致，同时指出修订棘皮动物分类学的必要性。我们针对每个类群测试了不同的分子钟模型，发现模型选择对最终生成的系统发育树具有显著影响；研究结果表明，关联式分子钟比非关联式分子钟获得了更高的支持度。上述发现表明……

近期研究显示棘皮动物性状的演化速率存在差异（Novack-Gottshall等，2022）。此前的研究提出假说认为，诸如取食性状这类"功能性"性状的演化速率可能快于其他性状，这一假说并非仅适用于棘皮动物（如Foote 1995；Ciampaglio 2002；Smith & Hopkins 2015；Wright 2017），而是在整个动物界中普遍存在（Wagner 1995；Sánchez-Villagra & Williams 1998）。芽体棘皮动物所展现的形态多样性长期以来阻碍了我们建立性状间同源性的工作，更遑论探究其演化速率。然而，随着针对棘皮动物的同源性框架的发展（Mooi & David 1997；Sumrall 2010），以及该框架在诸多芽体棘皮动物类群中的应用，这类演化相关问题终于得以解决。两类同源性框架各有优劣（Sumrall等，2023），但鉴于本研究聚焦于古生代芽体棘皮动物，且其演化模式……

# 数据来源：探索芽体棘皮动物的性状变化速率与演化模式
[https://doi.org/10.5061/dryad.s7h44j1hg]

## 数据与文件结构说明

### 性状演化模型
本研究的核心目标之一是验证可逆跳跃马尔可夫链蒙特卡洛（Reversible Jump Markov Chain Monte Carlo，rjMCMC）算法能否用于高效比较不同的性状演化假说。可逆跳跃马尔可夫链蒙特卡洛算法是马尔可夫链蒙特卡洛（MCMC）算法的改进版本，允许在分析过程中调整参数的数量。在此类分析中，模型本身即为随机变量。例如，在附表S1中，部分天际线模型包含的类别数量多于其他模型。当新增一个类别时，至少需要额外添加三个参数：新的物种形成速率、灭绝速率以及化石采样速率。而传统MCMC算法无法在分析过程中调整参数数量……

**2025年11月20日后的更新：**
由于期刊不支持补充图表的托管，我们应期刊要求将补充材料上传至本平台（补充材料上传至Zenodo而非Dryad，原因在于Dryad数据集采用CC0协议豁免；若需应用CC-BY许可，补充数据文件需托管于Zenodo）