DOI: 10.5061/dryad.0p2ngf26b
title: Evolution of the Sabulina verna group (Caryophyllaceae) in Europe: A deep split, followed by secondary contacts, multiple allopolyploidization and colonization of challenging substrates

description: One of the major goals of contemporary evolutionary biology is to
 elucidate the relative roles of allopatric and ecological differentiation
 and polyploidy in speciation. In this study, we address the taxonomically
 intricate Sabulina verna group, which has a disjunct Arctic–alpine
 postglacial range in Europe and occupies a broad range of ecological
 niches, including substrates toxic to plants. Using genome-wide ddRAD
 sequencing combined with morphometric analyses based on extensive sampling
 of 111 natural populations, we aimed to disentangle internal evolutionary
 relationships and examine their correspondence with the pronounced edaphic
 and ploidy diversity within the group. We identified two spatially
 distinct groups of diploids: a widespread Arctic–alpine group and a
 spatially restricted yet diverse Balkan group. Most tetraploids exhibited
 a considerably admixed ancestry derived from both these groups, suggesting
 their allopolyploid origin. Four genetic clusters in congruence with
 geography and mostly supported by morphological traits were recognized in
 the diploid Arctic–alpine group. Tetraploids are split into two distinct
 and geographically vicariant groups, indicating their repeated polytopic
 origin. Furthermore, our results also revealed at least five-fold parallel
 colonization of toxic substrates (serpentine and metalliferous),
 altogether demonstrating a complex interaction between geography,
 challenging substrates, and polyploidy in the evolution of the group.
 Finally, we propose a new taxonomic treatment of this intricate complex.
description: # Evolution of the Sabulina verna group (Caryophyllaceae) in Europe: a
 deep split, followed by secondary contacts, multiple allopolyploidization
 and colonization of challenging substrates ## V.Lipanova 10.8.2023 --- In
 this study, we address the taxonomically intricate *Sabulina verna* group,
 which has a disjunct Arcticalpine postglacial range in Europe and occupies
 a broad range of ecological niches, including substrates toxic to plants.
 Using genome-wide ddRAD sequencing combined with morphometric analyses
 based on extensive sampling of 111 natural populations, we aimed to
 disentangle internal evolutionary relationships and examine their
 correspondence with the pronounced edaphic and ploidy diversity within the
 group. ## Description of the data and file structure ### vcf file of 111
 populations of Sabulina verna
 fylo_var.join.vcf.filtered.snp_sagout.hardfilteredMQ20.DP6.var.biallelic.permiss0.5_sel_var.vcf.gz filtration pipeline: 1. hard filtering (according to reccomanded thresholds by GATK) bcftools filter -i 'FS&lt;60.0 && SOR&lt;3 && MQ&gt;20.0 && MQRankSum&gt;-12.5 && QD&gt;2.0 && ReadPosRankSum&gt;-8.0' -Oz fylo_var.join.vcf.filtered.snp_sagout.vcf.gz -o fylo_var.join.vcf.filtered.snp_sagout.hardfilteredMQ20.vcf.gz bcftools view -H fylo_var.join.vcf.filtered.snp_sagout.hardfilteredMQ20.vcf.gz | wc -l #135 350 2. filter variants only with read depth (DP) &gt; 6 bcftools view -i 'AVG(FMT/DP)&gt;6' -Oz fylo_var.join.vcf.filtered.snp_sagout.hardfilteredMQ20.vcf.gz -o fylo_var.join.vcf.filtered.snp_sagout.hardfilteredMQ20.DP6.vcf.gz bcftools view -H fylo_var.join.vcf.filtered.snp_sagout.hardfilteredMQ20.DP6.vcf.gz | wc -l #49 728 3. remove multiallelic SNPs and monomorphic SNPs bcftools filter -e 'AC==0 || AC==AN' fylo_var.join.vcf.filtered.snp_sagout.hardfilteredMQ20.DP6.vcf.gz | bcftools view -m2 -M2 -v snps -Oz -o fylo_var.join.vcf.filtered.snp_sagout.hardfilteredMQ20.DP6.var.biallelic.vcf.gz bcftools view -H fylo_var.join.vcf.filtered.snp_sagout.hardfilteredMQ20.DP6.var.biallelic.vcf.gz | wc -l #37 821 4. Remove variants with a high amount of missing genotypes bcftools filter -e 'F_MISSING &gt; 0.5' -Oz fylo_var.join.vcf.filtered.snp_sagout.hardfilteredMQ20.DP6.var.biallelic.vcf.gz -o fylo_var.join.vcf.filtered.snp_sagout.hardfilteredMQ20.DP6.var.biallelic.permiss0.5.vcf.gz bcftools view -H fylo_var.join.vcf.filtered.snp_sagout.hardfilteredMQ20.DP6.var.biallelic.permiss0.5.vcf.gz | wc -l #34 613 (14.18%) missing data check bcftools stats -s - fylo_var.join.vcf.filtered.snp_sagout.hardfilteredMQ20.DP6.var.biallelic.permiss0.5.vcf.gz &gt; bcftools_stats_fylo_var.join.vcf.filtered.snp_sagout.hardfilteredMQ20.DP6.var.biallelic.permiss0.5.txt 5. remove individuals &gt; 0.5 missing genotypes, individuals with average DP&lt;4 and multiple individuals within one population (with the lowest coverage) bcftools view -s ^M_cae_152_07,M_pau_031_0J,M_aut_156_02,M_at1_111_04,M_at1_118_06,M_at1_119_04,M_at1_121_07,M_cae_029_0E,M_cae_029_0B,M_cae_060_07,M_cae_060_09,M_cae_062_03,M_cae_063_10,M_cae_063_13,M_cae_064_08,M_cae_064_13,M_cae_074_03,M_cae_074_09,M_cae_075_07,M_cae_075_09,M_cae_076_12,M_cae_076_04,M_cor_151_03,M_cor_151_06,M_ger_095_01,M_ger_096_02,M_ger_096_06,M_ger_126_01,M_ger_126_05,M_ger_127_01,M_ger_127_08,M_ger_128_01,M_ger_128_02,M_ger_129_06,M_ger_140_0C,M_ger_140_0D,M_sme_153_01,M_sme_153_04,M_sme_154_01,M_sme_154_11,M_sme_155_02,M_tyA_093_07,M_ver_077_06,M_ver_077_12,M_ver_142_08 -Oz fylo_var.join.vcf.filtered.snp_sagout.hardfilteredMQ20.DP6.var.biallelic.permiss0.5.vcf.gz -o fylo_var.join.vcf.filtered.snp_sagout.hardfilteredMQ20.DP6.var.biallelic.permiss0.5_sel.vcf.gz 13.26% missing data 6. after removing the individuals remove again multiallelic SNPs and monomorphic SNPs bcftools filter -e 'AC==0 || AC==AN' fylo_var.join.vcf.filtered.snp_sagout.hardfilteredMQ20.DP6.var.biallelic.permiss0.5_sel.vcf.gz | bcftools view -m2 -M2 -v snps -Oz -o fylo_var.join.vcf.filtered.snp_sagout.hardfilteredMQ20.DP6.var.biallelic.permiss0.5_sel_var.vcf.gz bcftools view -H fylo_var.join.vcf.filtered.snp_sagout.hardfilteredMQ20.DP6.var.biallelic.permiss0.5_sel_var.vcf.gz | wc -l #31225 final check bcftools stats -s - fylo_var.join.vcf.filtered.snp_sagout.hardfilteredMQ20.DP6.var.biallelic.permiss0.5_sel_var.vcf.gz &gt; bcftools_stats_fylo_var.join.vcf.filtered.snp_sagout.hardfilteredMQ20.DP6.var.biallelic.permiss0.5_sel_var.txt ## Sharing/Access information Manuscript submitted to Molecular Phylogenetics and Evolution; links to GenBank for fastq files available in the manuscript.