DOI: 10.5061/dryad.xgxd254ts
title: Data from: The impact of Pleistocene glacial cycles on the evolutionary diversification of the arctic-alpine <em>Silene acaulis</em> species complex

description: Arctic-alpine species are highly sensitive to long-term temperature
 changes and associated glacial cycles due to their occurrence in cold
 environments to which they are adapted and spatially restricted.
 Unravelling their evolutionary responses to past climatic fluctuations can
 provide new insights into their diversification. In this study, we
 investigated the evolutionary history of the Silene acaulis species
 complex and how it was shaped by past glacial cycles. We assembled the
 first high-quality reference genome for S. acaulis and analyzed reduced
 representation sequencing data from 955 individuals spanning 132
 populations across the Holarctic distribution range of these arctic-alpine
 cushion plants. We identified five evolutionary lineages and assessed
 their phylogeographical structure in relation to current subspecies
 classifications, refugia, and historic migration patterns. Phylogenetic
 dating revealed that lineage divergence largely coincided with repeated
 phases of glacial cooling over the last two million years and was driven
 by isolation in glacial refugia. Secondary contact in glacial refugia or
 during interglacial expansions promoted hybridization and further shaped
 the distribution of genetic diversity across the species complex. Adaptive
 divergence among sympatric genetic groups in the European Alps highlights
 the contribution of niche specialization to intraspecific divergence, with
 evidence for ecotype differentiation in response to a combination of
 edaphic and climatic factors. The S. acaulis species complex has an
 intricate evolutionary history, shaped by glacial cycles in the Late
 Pleistocene that have driven lineage diversification, secondary contact
 and ecotype formation. Our study underscores the significance of glacial
 cycles in shaping genetic diversity in arctic-alpine plant species and
 improves our understanding of how arctic-alpine species have responded to
 past climate fluctuations.
description: ### *README file associated with the study:* **Glacial cycles and adaptive
 divergence characterize the evolutionary history of the arctic-alpine**
 ***Silene acaulis*** **species complex** --- ## Summary This dataset
 includes: * Functional annotation of the *Silene acaulis* reference
 genome\ (NCBI BioProject: PRJNA1267970) * SNP datasets derived from ddRAD
 sequencing aligned to the reference genome * Input and output files for
 phylogenetic analysis using SNAPPER in BEAST --- ### Functional annotation
 of the reference genome (eggNOG-mapper output files) *
 `SilAcau_F_GE_1.1.anno.eggnog.emapper.annotations.xlsx`\ *Functional
 annotation of haplotype 1, *“-” = missing / not available data *
 `SilAcau_F_GE_1.2.anno.eggnog.emapper.annotations.xlsx`\ *Functional
 annotation of haplotype 2, *“-” = missing / not available data
 Variable description for .xlsx files (retrieved from
 [GitHub](https://github.com/eggnogdb/eggnog-mapper/wiki/eggNOG-mapper-v2.1.5-to-v2.1.13#user-content-Output_files)): *Search hit fields* * query * seed_ortholog * evalue * score *Orthologous Groups fields* * eggNOG_OGs * a comma-separated, clade depth-sorted (broadest to narrowest), list of Orthologous Groups (OGs) identified for this query. Note that each OG is represented in the following format: OG@tax_id|tax_name - max_annot_lvl * tax_id|tax_name of the level of widest OG used to retrieve orthologs for annotations. * COG_cat * COG category of the narrowest OG with a valid one. - Description * Description of the narrowest OG with a valid one. *Transferred annotations fields* * Preferred_name * GOs * EC * KEGG_ko * KEGG_Pathway * KEGG_Module * KEGG_Reaction * KEGG_rclass * BRITE * KEGG_TC * CAZy * BiGG_Reaction * PFAMs --- ### SNP datasets * `Complete_SNP_set.vcf`\ *Filtered SNPs from all 955 individuals in the study* * `Core_SNP_set.vcf`\ *Filtered SNPs excluding* S. acaulis *subsp.* cenisia *(892 individuals)* * `Phylogeny_48_ind.vcf`\ *SNPs from 48 individuals representing all five evolutionary lineages and the admixed group* * `Phylogeny_48_ind_LD.vcf`\ *LD-pruned SNPs from the same 48 individuals as in* *`Phylogeny_48_ind.vcf`* * `Phylogeny_40_ind.vcf`\ *SNPs from 40 individuals representing all five evolutionary lineages* * `Phylogeny_40_ind_LD.vcf`\ *LD-pruned SNPs from the same 40 individuals as in* *`Phylogeny_40_ind.vcf`* --- ### Phylogenetic analysis files (SNAPPER in BEAST) * `Silene_snapper.xml`\ *BEAST input file for SNAPPER analysis (based on* *`Phylogeny_40_ind_LD.vcf`)* * `Silene_snapper.trees`\ *Posterior distribution of species trees* * `Silene_snapper_HPD.tre`\ *Maximum clade credibility tree with mean divergence times, 95 % HPD intervals, and posterior support values* ---