DOI: 10.5061/dryad.b8gtht7pm
title: The postglacial history of Euphrasia micrantha in Scotland: evidence from genome skimming

description: The flora of northern Europe has been shaped by a complex history of
 glaciation, where species have recolonised from different refugia and
 spread via contrasting migration routes. Our understanding of plant
 phylogeography in northern Europe has been limited by the resolution of
 genetic markers that cannot detect subtle population structure arising
 from close or cryptic refugia. Here, we employ genome skimming to recover
 complete plastid genomes and partial nuclear ribosomal arrays in the
 widespread plant species Euphrasia micrantha. We focus on populations from
 Scotland, where cryptic and complex patterns of recent recolonisation may
 prove hard to resolve. Genome skimming from 145 individuals revealed a
 species specific plastid DNA lineage in Scotland and England, while two
 other genetic clusters were highly intermixed with co-occurring taxa.
 Within the distinct plastid DNA lineage we recover subtle genetic
 divergence corresponding to West-East differentiation. These findings
 suggest E. micrantha has recolonised from multiple distinct refugia,
 potentially including cryptic northern refugia.
description: # The postglacial history of *Euphrasia micrantha* in Scotland: evidence
 from genome skimming Dataset DOI:
 [10.5061/dryad.b8gtht7pm](10.5061/dryad.b8gtht7pm) ## Description of the
 data and file structure This dataset includes complete plastid genomes and
 partial nuclear ribosomal DNA (nrDNA) sequences obtained through genome
 skimming of 145 *Euphrasia* individuals. Leaf tissue was collected from
 field populations across Scotland and England, and total genomic DNA was
 extracted and sequenced using Illumina short-read technology. Reads were
 quality-filtered and organellar genomes were assembled bioinformatically
 to extract complete plastid sequences and nrDNA arrays. The dataset
 includes aligned sequence files, associated sample metadata (species ID,
 geographic origin), and phylogenetic trees inferred using maximum
 likelihood methods. These data were used to explore population structure
 and postglacial history in *Euphrasia micrantha*, with broader relevance
 for phylogeographic inference in selfing, polyploid plant species. ###
 Files and variables #### File: SupportingDataCodes.zip
 **Description:** This dataset is archived in a compressed folder titled
 `SupportingDataCodes.zip`, which contains two subfolders: #### Folder 1:
 `1_SeqAlignment` This folder includes all raw and processed sequence
 alignment files: ·       **`1_IndividualSequence.geneious`**: Geneious
 project file containing individual DNA sequences (both cpDNA and nrDNA)
 for *Euphrasia micrantha* and related taxa. *Format*: `.geneious`
 (proprietary Geneious format) *Content*: Raw unaligned sequences labeled
 with individual sample codes. ·       **`2_Alignment_cp_nrDNA.geneious`**:
 Geneious project file containing aligned plastid (cpDNA) and nuclear
 ribosomal (nrDNA) sequences used for downstream phylogenetic analyses.
 *Content*: Includes sequence alignments for all samples across both loci.
 ·       **`3_cpDNA_MIC.fasta`**: FASTA file containing cpDNA sequences for
 *E. micrantha* individuals only. *Format*: Standard FASTA; sequences
 labeled with sample codes (e.g., M1_1, M1_2, etc.). ·      
 **`4_nrDNA_MIC.fasta`**: FASTA file containing nrDNA sequences for *E.
 micrantha* individuals only. *Format*: Standard FASTA; same sample naming
 convention as above. #### Folder 2: `2_AnalysisFilesCodes` This folder
 includes files used for phylogenetic inference and the associated R script
 for downstream analysis and figure generation: ·      
 **`cpDNA.fasta.treefile`**: Newick-format tree file for cpDNA sequences.
 *Format*: `.treefile` output from IQ-TREE2, used for visualizing and
 comparing plastid phylogenies. ·       **`nrDNA.fasta.treefile`**:
 Newick-format tree file for nrDNA sequences. *Format*: `.treefile` output
 from IQ-TREE2, used for visualizing nuclear phylogenies. ·      
 **`Rscripts.R`**: R script file used to process alignment data, generate
 summary plots, build phylogenies, and compare plastid and nuclear datasets
 using phytools, ggtree etc. packages. #### **Variables & Notation**
 ·       Sample identifiers are consistently abbreviated (e.g., M1_1–M59_2
 for *E. micrantha* individuals). ·       All sequence data is unscaled and
 without units; genetic divergence is expressed in substitutions per site
 in tree output. ·       Missing data is notated as `-` in alignments or
 gaps in the tree matrices. No explicit “NA” values are present. ·      
 All metadata (species ID, sampling origin) is embedded in the
 supplementary table. ## Code/software The dataset can be viewed and
 analyzed using the following free and open-source software: ·      
 **Geneious Prime (for `.geneious` files)** While the `.geneious` files
 require Geneious Prime (commercial software), sequence alignments can also
 be exported and viewed in standard formats (e.g., FASTA) using tools like
 AliView or MEGA. ·       **IQ-TREE2 (v2.1.2 or later)** Used to perform
 maximum likelihood phylogenetic inference. Relevant commands and
 parameters are documented within the R script. ·       **R (v4.2.0 or
 later)** Used for all downstream visualization and statistical analysis.
 Required R packages include: o   `ape` o   `phytools` o   `ggtree` o  
 `adegenet` o   `stats` o   `ips` o   `msa` o   `Biostrings` o  
 `haplotypes` o   `pegas` o   `reshape2` o   `factoextra` o   `cluster` o  
 `marmap` o   `RColorBrewer` o   `dartR` o   `tibble` o   `poppr` o  
 `ggplot2` o   `dplyr` o   `ggpubr` ·       **R script: `Rscripts.R`** This
 script includes commands to: o   Import and manipulate tree files and
 sequence alignments. o   Generate figures (e.g., combined cpDNA/nrDNA
 phylogeny using `cophylo()`). o   Color sample clades and annotate
 results. o   Perform haplotype analysis and visualize regional patterns.
 Each step is documented in-line in the script, allowing reproduction of
 all analytical workflows presented in the manuscript: **“Postglacial
 expansion and divergence in *Euphrasia micrantha* revealed by genome
 skimming”** (*Plant Ecology & Diversity*,
 [https://doi.org/10.1080/17550874.2025.2519256](https://doi.org/10.1080/17550874.2025.2519256)) ## Access information Other publicly accessible locations of the data: * Data was derived from the following sources: *