DOI: 10.5061/dryad.gb5mkkwmg
title: Data from: Altai Mountains – cradle of hybrids and introgressants: A case study in <em>Veronica</em> subg. <em>Pseudolysimachium</em> (Plantaginaceae)

description: Mountains form a diverse mosaic of microhabitats over small distances
 created by changes in climate, soil, and water availability. A key to
 adaptation of plants to such microhabitats is genetic variation; however,
 natural accumulation of genetic variation through mutation is slow and
 often not sufficient alone. Adaptive introgression via hybridization is an
 alternative to generate genetic variation. Here, we investigate
 hybridization and discuss its adaptive role
 in Veronica subg. Pseudolysimachium at
 their Altai Mountains distribution. To support our hypotheses of frequent
 hybridization, we genotyped thousands of SNPs for 233 individuals from 10
 species and 7 putative hybrids previously described based on morphology.
 We employed Bayesian and likelihood statistical models and supported our
 results by morphometric analysis and genomic in situ
 hybridization (GISH). The results suggest that almost all the individuals
 of the putative hybrids are of F1 type. The GISH investigation in one case
 strongly supports homoploid hybridization (origin of
 V. ×schmakovii from V. longifolia and V. porphyriana. Divergence times of Altai Veronica species are estimated to be within 1–2 million years ago with high probability of gene flow over that time. Our results also demonstrate that the direction of gene flow is mainly from the locally endemic V. porphyriana. We hypothesize that the large Siberian plains and topographically diverse foreland of the Altai Mountains provide an ideal setting for hybridization with the potential for adaptive introgression of alleles conferring tolerance to cooler climates, to the lowland species migrating into the Altai Mountains.
description: We used GBS-SNP-CROP to generate polyploid-aware bi-allelic SNPs
 (Melo & al., 2016). GBS-SNP-CROP is explicitly designed for sample
 sets including individuals of varying ploidy levels and has the potential
 to genotype bi-allelic SNPs and exclude the multi-allelic variants by
 imposing a population-level allele frequency filter via a user-defined
 Alternative Allele Strength parameter. For each potential SNP position,
 this parameter considers the total read depth, across the whole
 population, of all four bases, from primary (the allele with the highest
 depth at that position) to quaternary (the allele with the lowest depth).
 A potential SNP is retained for further downstream analysis if and only if
 it is strongly bi-allelic. The GBS-SNP-CROP workflow first processes the
 raw GBS data to exclude the sequences with noise/bad quality; secondly
 builds a mock reference (if reference genome is unavailable); maps the
 high-quality reads to generate standardized alignment files; and lastly,
 calls the SNPs. The pipeline has seven Perl scripts utilizing VSEARCH and
 PEAR for clustering and merging of pair-end reads respectively (Zhang
 & al., 2014; Rognes & al., 2016). To make a mock reference
 we used only the diploid individuals (confirmed by flow cytometry) with a
 high number of reads after quality filtering (suppl. Table S1). At the end
 we got a total of 233,987 SNPs with 99.9999% confidence, which means
 0.000001 error rate and Alternative Allele Strength parameter 0.90. For
 phylogeny estimation we used all these 233,987 SNPs with 75% missing data
 allowance before the post-processing step in VCFtools v.3.0. For STRUCTURE
 analyses, we only used the unlinked bi-allelic SNPs allowing every SNP to
 be present again in at least 75% of the individuals with minor allele
 frequency equal to 0.05 utilizing VCFtools (Danecek & al.,
 2011).
description: # Data from: Altai Mountains – cradle of hybrids and introgressants: A
 case study in *Veronica* subg. *Pseudolysimachium* (Plantaginaceae) The
 dataset comprises: Phylogenetic alignments (.phy files) used for tree
 reconstruction and evolutionary inference. Variant call format file (.vcf)
 containing SNP data recoded for population genetic analyses. Structure
 input file (.str) formatted for Bayesian clustering and admixture
 analysis. These files were derived from high-throughput sequencing of 1148
 loci across multiple individuals. The data support findings of reticulate
 evolution and complex genetic relationships among taxa in this
 biodiversity hotspot.