DOI: 10.5061/dryad.xd2547dt7
title: Genome-wide differentiation by geography not species in taxonomically complex eyebrights (Euphrasia)

description: 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 extensive gene flow between putative species is supported
 by a lack of species-specific SNPs or clear outlier loci. We anticipate a
 similar lack of association between genomic clusters and species
 identities may occur in other recent postglacial groups. Where new species
 emerge this is associated with a transition in mating system or novel
 ecological preferences.
description: # 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 applied additional filtering to remove all linked SNPs: * **unlink_DiploidDataset.vcf.gz**: Contains **6,016 SNPs**for the diploid dataset. * **unlink_AllTaxaDataset.vcf.gz**: Contains **5,220 SNPs**for the all taxa dataset. 3. **Analyses and R Scripts**: The majority of the analyses were performed in **R**. The following analyses are included, with corresponding R scripts provided: * **AMOVA** (Analysis of Molecular Variance) * **PCA** (Principal Component Analysis) * **DAPC** (Discriminant Analysis of Principal Components) * FastStructure plots and geographic maps for the pie plots  ### Files and variables #### File: DiploidDataset.vcf.gz **Description:** Contains **26,278 SNPs** for diploid dataset, with an average missing data per site of **11%**. #### File: unlink\_AllTaxaDataset.vcf.gz **Description:** Contains **5,220 SNPs**for the all taxa dataset. #### File: unlink\_DiploidDataset.vcf.gz **Description:** Contains **6,016 SNPs**for the diploid dataset. #### File: AllTaxaDataset.vcf.gz **Description:** Contains **19,666 SNPs** for all taxa dataset, with an average missing data per site of **19%**. #### Supplemental information file: SupTab1\_SampleInfo.xlsx **Description:** Contains two sheets: Samples_Info & Keyfile. Smaples_Info contains all the individual sample annotation information requires for the analyses. Keyfile link to the raw data (from NCBI, see below access information) in running TASSEL-GBS pipeline.  ## Code/software #### R script: 1\_AMOVA.R **Description:** Analysis of Molecular Variance #### R script: 2\_PCA.R **Description:** Principal Component Analysis #### R script: 3\_DAPC.R **Description:** Discriminant Analysis of Principal Components #### R script: 4\_Structure\&Maps.R **Description:** FastStructure plots and geographic maps for the pie plots ## Access information Data was derived from the following sources: * RAW data is on NCBI with the BioProject number: **PRJNA1125641**