Shifting speciation mode and biogeographic patterns during the Late Ordovician (Sandbian-Katian) in Laurentian brachiopods (Atrypida, Anazygidae)

The Late Ordovician was a period of substantial environmental change. The co-evolution of Earth systems changes involving tectonic uplift, eustasy, and biotic changes are recorded in the Late Ordovician in Laurentia. In this study, species of the brachiopod family Anazygidae within the genera Zygospira and Catazyga were analyzed to assess dispersal pathways among eight sedimentary basins. Stochastic analysis applied to a Bayesian phylogeny (Anazygidae_tree.tre) through BioGeoBEARS facilitated estimation of speciation events including episodes of vicariance and basin-to-basin dispersal events (Anazygidae_geoareas.data) within the clade. Three algorithms were implemented and compared (BioGeoBEARS_code.R). Dispersal-extinction-cladogenesis (DEC) + jump dispersal parameter was the best supported model. For suggestions, advice, or requests related to the code and how to re-run our results, please contact me at [e-mail]. 
Results (b_AICc_table.csv) indicate that Anazygidae o..., , # Shifting speciation mode and biogeographic patterns during the Late Ordovician (Sandbian-Katian) in Laurentian brachiopods (Atrypida, Anazygidae)

Dataset DOI: [10.5061/dryad.d51c5b0fs](10.5061/dryad.d51c5b0fs)

## Description of the data and file structure

### Files and variables

#### File: BioGeoBEARS\_code.R

**Description:** R code used in R 4.3.0 with original (Matzke, 2013) and adapted comments

#### File: Anazygidae\_geoareas.data

**Description:** Anazygidae_geoareas.data is the file used in the R script. It's a .txt file saved as .data.

The first line contains the number of analyzed taxa (20), the number of total geographic areas (8), and the initial letters for each studied geographic area. Presence/absence of the taxa in a given geographic area is given by 0 (absence) or 1 (presence).

O = Scoto-Avalonia; W= Western Mid-Continent; U= Upper Mississippi Valley; E= Eastern Canada; F= Proximal Foreland basin; N= Northern Appalachian Basin; S= Southern Appalachian Basin; a...,

晚奥陶世是一段发生显著环境变革的地质时期。涉及构造隆升、海平面变化与生物更替的地球系统协同演化过程，均在劳伦大陆的晚奥陶世地层中留有记录。本研究针对腕足类Anazygidae科（Anazygidae）下Zygospira属（Zygospira）与Catazyga属（Catazyga）的物种展开分析，以厘清8个沉积盆地间的生物扩散路径。本研究通过BioGeoBEARS工具对基于贝叶斯法构建的系统发育树（Anazygidae_tree.tre）开展随机分析，以此估算该演化支内的成种事件，包括分隔演化事件与跨盆地扩散事件（相关数据存储于Anazygidae_geoareas.data文件）。本研究共设置三种算法开展对比分析，相关代码存储于BioGeoBEARS_code.R文件中。扩散-灭绝-分支演化模型（Dispersal-extinction-cladogenesis，DEC）结合跳跃扩散参数的方案为最优拟合模型。若需获取代码相关建议或复现研究结果的相关协助，请通过邮箱[e-mail]与作者联系。研究结果存储于b_AICc_table.csv文件中，相关内容涉及Anazygidae类群……，研究主题为：《劳伦大陆腕足类（Atrypida目、Anazygidae科）晚奥陶世（桑比阶-凯迪阶）的成种模式转变与生物地理格局》。

数据集DOI：10.5061/dryad.d51c5b0fs

## 数据与文件结构说明

### 文件与变量说明

#### 文件：BioGeoBEARS_code.R
**文件说明：** 本文件为基于R 4.3.0环境运行的R脚本，包含原始注释（Matzke, 2013）与自定义修改注释。

#### 文件：Anazygidae_geoareas.data
**文件说明：** 该文件为R脚本中使用的数据源文件，本质为以.data格式存储的纯文本文件（.txt）。

文件首行依次记录分析类群数（20）、总地理区域数（8）以及各研究地理区域的首字母缩写。类群在对应地理区域的存在与否以0（不存在）或1（存在）标识。

其中O代表斯科托阿瓦隆尼亚（Scoto-Avalonia）；W代表中大陆西部（Western Mid-Continent）；U代表密西西比河上游河谷（Upper Mississippi Valley）；E代表加拿大东部（Eastern Canada）；F代表近前陆盆地（Proximal Foreland basin）；N代表阿巴拉契亚北部盆地（Northern Appalachian Basin）；S代表阿巴拉契亚南部盆地（Southern Appalachian Basin）；其余缩写未完整标注。