A total evidence approach justifies taxonomic splitting of the endangered Pecos Gambusia into three species

Gambusia nobilis is a federally Endangered species found across a fragmented distribution within the Pecos River Drainage of Texas and New Mexico, USA. Drought, human water usage, and potential hybridization and competition with introduced congeners threaten species persistence. Therefore, a population genomics study was conducted to provide critical information for conservation planning. Unsupervised clustering suggested hierarchical structure, with a primary K =3, and deep divergences were detected among samples grouped into the Leon Creek watershed, the Toyah Creek watershed, and water bodies within the Bitter Lake National Wildlife Refuge (F’ST = 0.55–0.76 for putatively neutral data). Phylogenetic analyses showed three distinct clades corresponding to these groups, with split times estimated to be in the last 50,000 years. Subsequent morphological analyses detected differences among the three groups, including male colour pattern in life, and the number of caudal-fin rays in both s..., Sample collection
Fin clips or voucher specimens of Gambusia nobilis sensu lato were collected between 2020–2024, from twelve discrete sampling sites within the Pecos River drainage (Rio Grande basin) of Texas and New Mexico. This included three springs (Diamond Y Head Pool, HEAD; Karges, KGS; and Euphrasia, EU) within the Leon Creek watershed (LC) in Pecos County, Texas; three springs (San Solomon; SS, Phantom Lake; PL, and East Sandia; ES) within the Toyah Creek watershed (TC) in Jeff Davis and Reeves counties, Texas; and six sites within the Bitter Lake watershed and a series of geographically proximate sinkholes in greater Chaves County, New Mexico (NM). Sites in LC are not directly connected, though HEAD and KGS are only separated by ~ 0.3 km and connected intermittently. Sites in TC are not connected and separated by an average of 8.9 km. Sites in New Mexico included the Bitter Lake National Wildlife Refuge (BLNWR), a section of Bitter Creek north of the refuge (BC), and four sink..., # A total evidence approach justifies taxonomic splitting of the endangered Pecos Gambusia into three species

Dataset DOI: [10.5061/dryad.jsxksn0nf](10.5061/dryad.jsxksn0nf)

## Description of the data and file structure

The Variant Call Format (vcf) files provided are gzipped files consisting of double digest restriction site associated DNA (ddRAD) sequenced samples mapped to *Gambusia affinis* genome (Genbank # GCF_019740435) and single nucleotide polymorphisms (SNPs) called using a modified version of dDocent. A metadata text file is also included to describe the catch locations and species identities. Please refer to the vcf file format for fields within the vcf file ([https://samtools.github.io/hts-specs/VCFv4.2.pdf](https://samtools.github.io/hts-specs/VCFv4.2.pdf))

### Files and variables

#### File: SNP.TRS.QC.recode.vcf.gz

**Description:** The full dataset consists of 395 samples with 356 unique individuals and their duplicates across 870,332 SNPs. These individuals are fro...,

高贵食蚊鱼（Gambusia nobilis）是美国联邦列级濒危物种，分布于美国德克萨斯州与新墨西哥州的佩科斯河流域（Pecos River Drainage），其栖息地理呈碎片化状态。干旱、人类水资源利用活动，以及与引入的同属物种可能存在的杂交与竞争，均威胁着该物种的种群存续。为此，本研究开展了种群基因组学分析，以期为物种保护规划提供关键科学依据。无监督聚类（unsupervised clustering）分析显示其存在层级式遗传结构，最优聚类数K=3；在归为莱昂溪流域（Leon Creek watershed）、托亚溪流域（Toyah Creek watershed）以及苦湖国家野生动物保护区（Bitter Lake National Wildlife Refuge）内水体的样本之间，检测到了显著的遗传分化（假定中性位点的F’ST值为0.55~0.76）。系统发育分析（phylogenetic analyses）显示存在三个对应的独立演化支（clades），其分化时间（split times）估算均发生在近5万年以内。后续的形态学分析（morphological analyses）也发现了这三个类群之间的差异，包括活体雄性的体色模式，以及尾鳍鳍条（caudal-fin rays）数目等[原文截断]。

## 样本采集
2020年至2024年间，研究团队于美国德克萨斯州与新墨西哥州的佩科斯河流域（格兰德河（Rio Grande）流域）内的12个独立采样点，采集了广义高贵食蚊鱼（Gambusia nobilis sensu lato）的鳍组织剪样（fin clips）或凭证标本（voucher specimens）。其中包括位于德克萨斯州佩科斯县莱昂溪流域（LC）内的3处泉眼：戴蒙德Y泉主池（Diamond Y Head Pool，缩写HEAD）、卡格斯泉（Karges，KGS）以及欧弗拉西亚泉（Euphrasia，EU）；位于德克萨斯州杰佛逊戴维斯县与里夫斯县托亚溪流域（TC）内的3处泉眼：圣所罗门泉（San Solomon，SS）、幻影湖泉（Phantom Lake，PL）以及东桑迪亚泉（East Sandia，ES）；以及位于新墨西哥州查韦斯县更大范围内的苦湖流域与一系列邻近落水洞（sinkholes）的6处采样点。莱昂溪流域内的采样点之间并无直接连通，不过HEAD与KGS两泉间距仅约0.3公里，仅存在间歇性连通。托亚溪流域内的采样点彼此互不连通，平均间距达8.9公里。新墨西哥州的采样点包括苦湖国家野生动物保护区（BLNWR）、保护区北侧的苦溪河段（BC）以及四处落水洞[原文截断]。

# 综合证据法（total evidence approach）支持将濒危佩科斯食蚊鱼划分为三个独立物种
数据集DOI: [10.5061/dryad.jsxksn0nf](10.5061/dryad.jsxksn0nf)

## 数据与文件结构说明
本研究提供的变异检测格式（Variant Call Format, VCF）文件为gzip压缩文件（gzipped files），包含以双酶切限制性位点关联DNA测序（double digest restriction site associated DNA, ddRAD）获得的样本，这些样本比对至食蚊鱼（Gambusia affinis）参考基因组（GenBank登录号：GCF_019740435），并使用修改版dDocent软件调用单核苷酸多态性（Single Nucleotide Polymorphism, SNP）位点。此外还附带一份元数据（metadata）文本文件，用于说明采样点位与物种鉴定信息。关于VCF文件内的字段信息，请参考VCF v4.2格式规范：[https://samtools.github.io/hts-specs/VCFv4.2.pdf](https://samtools.github.io/hts-specs/VCFv4.2.pdf)

### 文件与变量
#### 文件：SNP.TRS.QC.recode.vcf.gz
**描述：** 本完整数据集包含395个样本，对应356个独特个体及其重复样本，涵盖870,332个SNP位点。这些个体来自[原文截断]