Genome-wide differentiation by geography not species in taxonomically complex eyebrights (Euphrasia)

Most studies investigating the genomic nature of species differences anticipate monophyletic species with genome-wide differentiation. However, this may not be the case at the earliest stages of speciation where reproductive isolation is weak and homogenising gene flow blurs species boundaries. We investigate genomic differences between species in a postglacial radiation of eyebrights (Euphrasia), a taxonomically complex plant group with variation in ploidy and mating system. We use genotyping-by-sequencing and spatially-aware clustering methods to investigate genetic structure across 378 populations from 18 British and Irish Euphrasia species. We find only northern Scottish populations of the selfing heathland specialist E. micrantha demonstrate genome-wide divergence from other species. Instead of genetic clusters corresponding to species, all other clusters align with geographic regions, such as a genetic cluster on Shetland that includes ten tetraploid species. Recent divergence and..., , , # Genome-wide differentiation by geography not species in taxonomically complex eyebrights (Euphrasia)

[https://doi.org/10.5061/dryad.xd2547dt7](https://doi.org/10.5061/dryad.xd2547dt7)

## Description of the data and file structure

**Data Description and Analysis Details**

This paper includes two main datasets: the **“All Taxa Dataset”** and the **“Diploid Dataset”**, generated using specific filtering parameters as described below.

1. **Main Datasets**: 
* **AllTaxaDataset.vcf.gz**: Contains **19,666 SNPs** for all taxa dataset, with an average missing data per site of **19%**.
* **DiploidDataset.vcf.gz**: Contains **26,278 SNPs** for diploid dataset, with an average missing data per site of **11%**.
A total of **768 individuals** from **356 populations** were retained for downstream analyses.
* **SupTab1_SampleInfo.xlsx:** Contains all the annotation information for each sample. 
2. **Datasets for fastStructure**:
To meet the requirements of **fastStructure**, we...

大多数探究物种差异基因组本质的研究均假设单系物种具有全基因组分化。然而，在物种形成的最初阶段——此时生殖隔离较弱且同质化基因流模糊物种边界——情况可能并非如此。我们研究了小米草属（Euphrasia，俗称eyebrights）冰后期辐射类群中物种间的基因组差异；该植物类群分类学复杂，存在倍性和交配系统的变异。我们采用基因分型测序（genotyping-by-sequencing）和空间感知聚类方法，探究了来自不列颠及爱尔兰18个小米草属物种的378个种群的遗传结构。结果发现，仅自交型石南生境专化种E. micrantha的苏格兰北部种群表现出与其他物种的全基因组分化。与对应物种的遗传聚类不同，所有其他聚类均与地理区域一致，例如设得兰群岛的一个遗传聚类包含10个四倍体物种。近期分化及..., , , # 分类学复杂的小米草属（Euphrasia）中，基因组分化由地理而非物种决定

[https://doi.org/10.5061/dryad.xd2547dt7](https://doi.org/10.5061/dryad.xd2547dt7)

## 数据与文件结构描述

**数据描述与分析细节**

本研究包含两个主要数据集：**“全类群数据集（All Taxa Dataset）”** 和 **“二倍体数据集（Diploid Dataset）”**，二者均通过如下所述的特定过滤参数生成。

1. **主要数据集**：
* **AllTaxaDataset.vcf.gz**：包含全类群数据集的19,666个单核苷酸多态性（SNPs），每个位点的平均缺失数据率为19%。
* **DiploidDataset.vcf.gz**：包含二倍体数据集的26,278个单核苷酸多态性（SNPs），每个位点的平均缺失数据率为11%。共保留了来自356个种群的768个个体用于下游分析。
* **SupTab1_SampleInfo.xlsx**：包含每个样本的所有注释信息。
2. **用于fastStructure的数据集**：
为满足**fastStructure**的要求，我们...