Lungless tadpoles breathe fresh air into hypotheses for tetrapod lung loss and trait regain

The environmental factors associated with adaptive trait loss and the extent to which lost traits can be regained have been subject to much speculation and debate in evolutionary biology. We use tadpole lungs to test if previously proposed environmental factors, such as a stream habitat, are associated with larval lung loss and whether lungs can be regained following loss. We assembled a dataset of lung presence for the larvae of 529 anurans, finding 28 instances of larval lung loss, and developed a methodological framework to test the evolutionary associations between lung loss, general habitat type, terrestriality, and stream specialization, finding strong support for the final two factors in adaptive lung loss. The likelihood of regain is thought to depend on whether developmental pathways are preserved over time; accordingly, we predicted larval lung loss to be highly reversible. And yet, we found that larval lungs were never regained, despite lungless tadpoles evolving to live in h..., This dataset includes a few different sources. Table 1 includes tadpole lung presence/absence data from a variety of sources listed in the table, including dissection, microCT scanning, and literature searches. Table 1 also includes tadpole habitat data from literature searches (citations embedded within the table). We also include BayesTraits command files and posterior outputs.
, , # Data from: Lungless tadpoles breathe fresh air into hypotheses for tetrapod lung loss and trait regain

[https://doi.org/10.5061/dryad.3tx95x6sk](https://doi.org/10.5061/dryad.3tx95x6sk)

## Description of the data and file structure

This data was collected for phylogenetic analysis of lung and habitat evolution in frog tadpoles. Missing data are represented as NAs.

### Files and variables

#### File: Supp_table_1.csv

**Description:** Data table used in all analyses

##### Variables

* sort: numeric identifier for sorting data by family
* Family: Taxonomic Family
* Subfamily: Taxonomic subfamily when relevant
* Genus: 
* Taxa:
* lung data source: Note on where lung data originated (dissection, literature, etc.)
* specimen numbers: Museum specimen identifier
* Tip in Portik et al. 2023: If different name is used in that tree, that alternative name is provided here.
* phylogeny notes: Notes for how and why alternative names were used.
* lung: binary lung status (0 = lungless, 1 = lun...,

在进化生物学领域，与适应性性状丢失相关的环境因素，以及丢失性状可被恢复的程度，长期以来引发了诸多推测与争论。本研究以蝌蚪肺为研究对象，检验此前提出的环境因素（如溪流生境）是否与幼体肺脏丢失相关，并探究肺脏在丢失后能否得以恢复。我们收集了529种无尾目（Anura）幼体的肺脏存在情况数据集，共发现28例幼体肺脏丢失案例；同时构建了一套方法学框架，用于检验肺脏丢失与整体生境类型、陆生性以及溪流特化之间的进化关联，结果为后两项因素在适应性肺脏丢失中的作用提供了强有力的支持证据。性状恢复的可能性通常取决于发育通路是否随时间得以保留；据此，我们曾预测幼体肺脏丢失具有高度可逆性。然而，尽管无肺蝌蚪已演化出适应特定生境的生存方式，我们却发现幼体肺脏从未实现恢复。本数据集整合了多类来源的数据。表1收录了表格中列明的多种来源的蝌蚪肺脏存在/缺失数据，涵盖解剖检测、微型计算机断层扫描（microCT）以及文献检索结果；同时表1还包含通过文献检索获取的蝌蚪生境数据（文献引用内嵌于表格中）。此外，本数据集还附带BayesTraits命令文件与后验输出结果。

数据集来源：《无肺蝌蚪的呼吸方式为四足动物肺脏丢失与性状恢复假说提供新证》[https://doi.org/10.5061/dryad.3tx95x6sk]

## 数据与文件结构说明
本数据集采集自针对蛙类蝌蚪肺脏与生境演化的系统发育分析研究，缺失数据以NAs表示。

### 文件与变量
#### 文件：Supp_table_1.csv
**描述**：所有分析所用的数据表格

#### 变量说明
* sort：用于按科对数据进行排序的数值标识符
* Family：分类学科名
* Subfamily：相关情况下的分类学亚科名
* Genus：属名
* Taxa：分类类群
* lung data source：肺脏数据来源说明（如解剖检测、文献检索等）
* specimen numbers：博物馆标本编号
* Portik等人2023年研究的系统发育树分支：若该树中使用了不同的物种名称，则在此处提供替代名称
* phylogeny notes：关于替代名称的使用方式与原因的注释说明
* lung：肺脏状态二分类变量（0代表无肺，1代表有肺，原文此处存在截断）