DOI: 10.5061/dryad.7wm37pvvm
title: Data from: Adaptation of perennial flowering phenology across the European range of Arabis alpina

description: Perennial Arabis alpina has a wide geographic distribution and is adapted
 to local environments. However, the traits that underlie adaptation are
 unknown. Flowering phenology is an adaptive trait in other species, but
 its geographic variation has not been systematically studied in herbaceous
 perennials. Accessions of A. alpina were collected across the European
 range. Their flowering behavior was tested in controlled conditions, in
 experimental common-garden plantations at native sites and in-situ in
 natural populations. Also, genetic diversity within and among populations
 was examined. French Alpine and Scandinavian accessions varied in timing
 and duration of flowering. By contrast, in controlled conditions and
 in-situ, all Spanish accessions were obligate vernalization-requiring with
 a short duration of flowering. Nevertheless, Spanish populations were as
 genetically diverse as French Alpine populations and more so than
 Scandinavian populations. Furthermore, perpetual flowering 1, a mutant
 that shows no vernalization requirement and a long duration of flowering,
 showed higher mortality and poorer performance than local accessions at
 Spanish experimental sites. We propose that in this perennial species, the
 vernalization requirement and short duration of flowering are under
 selection in Spain as a strategy to survive exposure to longer, warmer
 growing seasons.
description: Genotyping
 and whole-genome sequencing Genetic variation and
 differentiation of <em>A. alpina</em> populations were
 analyzed with genotype and whole-genome sequence data. First, DNA was
 extracted from fresh leaves of 31 individuals from 9 populations
 representing Spanish, French Alpine and Scandinavian populations (using
 Qiagen DNeasy Plant Maxi Kit, Qiagen) and whole genomes were sequenced on
 an Illumina HiSeq2000 at the Max Planck Genome Centre Cologne and at
 FASTERIS sequencing service in Switzerland (www.fasteris.com).
 From these sequences, 35788 unambiguous biallelic SNPs were identified
 (details in Supporting Information). A subset of 253 widely spread,
 intergenic SNPs was used for genotyping on a Custom GoldenGate SNP-panel.
 The SNP set was chosen to be informative across the entire sampled
 geographic range and/or within regions and populations. Then, 892
 accessions were genotyped using DNA extracted from leaf material collected
 <em>in-situ </em>(Supporting Information). These accessions
 include: i) a range-wide collection; ii) an evenly subsampled set of 50
 accessions from each of three populations from each of the three main
 regions; iii) a total of 187 Spanish accessions from 10 populations to
 analyze in detail population structure in Spain.  In
 addition, genetic variation was analyzed genome-wide on an evenly
 subsampled set of the whole genome sequences, comprising eight individuals
 from two populations in both Spain and the French Alps, and eleven
 individuals from four populations in Scandinavia, for a total of 27
 individuals. Average coverage for these samples varied between 7.2X and
 23.1X (mean across samples = 15.9X). Phenotyping
 experiments Flowering and
 fitness traits were scored by phenotyping plants in controlled greenhouse
 conditions and at experimental sites established within or next to native
 populations of <em>A. alpina</em>. Some traits were also
 scored <em>in situ</em>. Details are given in Supporting
 Information.  Greenhouse
 experiments Flowering
 behavior was scored under greenhouse conditions following two different
 experimental treatments. i) Experiment without vernalization: Plants were
 grown under long days (LD: 16h/8h day/night cycle, 22°/16°C) and scored
 for flowering traits twice a week, for 26 to 51 weeks after germination
 across four replicates of the experiment (Table S1) ii) Experiment with
 vernalization: Plants were grown in long days for 6 weeks, then vernalized
 for about 14 weeks (short days, SD: 8h/16h day/night cycle, 4°C), and then
 transferred back into LD and scored for 19 weeks. In each experiment, most
 natural populations were represented by at least 20 maternal families and
 at least 8 siblings per family, except experiment 4 in which smaller
 family sizes were used (Table S1). As controls, the reference accession
 <em>Pajares </em>from Spain and the early-flowering
 <em>pep1-1</em> mutant were used in all experiments. All
 plants were randomized in all experiments. Experimental
 sites    Flowering
 behavior and fitness of plants grown at experimental sites were scored in
 Spain, the French Alps and Scandinavia, close to or within native
 populations, and in Germany outside the natural range. Plants were
 pre-grown in small plugs for about 4 weeks in a greenhouse to ensure high
 establishment success. The seedlings were then transplanted into natural
 soil at the experimental sites in spring. Apart from watering on the first
 few days after planting, the plants grew under natural environmental
 conditions and in native soil, and they were scored at the end of the
 growing season the year of plantation and the following year. Each
 population was represented by about 20 maternal families and 10 siblings
 per family (Table S1). As controls, we used the reference accession
 <em>Pajares</em> from Spain and the early-flowering
 <em>pep1-1</em> mutant. The individuals were planted in a
 randomized block design. Observations
 <em>in-situ</em> Plants in
 natural populations were labelled, photographed and scored for various
 traits 2-5 times per year over several years. To estimate the duration of
 flowering the photographic documentation was evaluated for a period of
 five years (Supporting Information). Phenotypic
 traits For flowering
 behavior under controlled greenhouse conditions, the following traits were
 scored: i) the onset of flowering without vernalization, which was the
 time between germination and appearance of the first open flower, ii) the
 onset of flowering after vernalization, which was the time from the end of
 the vernalization treatment to the appearance of the first open flower,
 iii) the duration of flowering after vernalization, which was the time
 between appearance of the first and the last open flower and iv) the
 proportion of flowering plants, which was the proportion of plants that
 produced visible open flowers. Plants were assigned to three categories
 for the onset of flowering without vernalization: “Early-onset” plants
 flowered within four months of germination (this reflects the average
 snow-free period in the Scandinavian and French Alpine habitats).
 “Late-onset” plants required more than four months from germination to
 flowering. “Not flowering” plants produced no open flowers without
 vernalization during the experiment (up to 51 weeks). At
 experimental sites, we scored survival, as the percentage of surviving
 plants, and the proportion of flowering plants, inferred by the proportion
 of plants bearing siliques. Scoring was done at the end of the growing
 season the year of plantation and the following year. At the Spanish site
 we additionally scored the number of rosettes for vegetative performance,
 and the average number of siliques as an indication of fecundity and
 fitness (Supporting Information). In natural
 populations (<em>in-situ</em>) individual plants were labeled,
 visited 2-5 times per year, photographed and scored for whether or not
 they were flowering. The proportion of plants showing an extended
 (perpetual) flowering duration was estimated at the end of the growing
 season, typically late September to early October. Weather
 data Air temperature was measured with
 logging intervals ≤ 45 minutes by sensors installed about 20 cm above the
 soil surface in a subset of the natural populations and at all
 experimental sites. Records were standardized to hourly means from which
 daily means were calculated. Periods of snow coverage were estimated based
 on oscillations ≤ 1°C in daily temperature, indicating that the sensor was
 covered by snow. The growing season was defined as the number of days
 between the midpoints of the first and last snow-free, 5-day period with
 mean temperature &gt; 5°C, following the definition of (Sletvold
 & Agren, 2015). Temperature data were analyzed
 using custom made scripts and the R-package ‘seas’ (Toews<em> et
 al.</em>, 2007). Precipitation data was obtained from public weather
 stations near the field sites. 
description: # Adaptation of perennial flowering phenology across the European range of
 Arabis alpina Jörg Wunder,
 Andrea Fulgione, Per Toräng, Stefan Wötzel, Michel Herzog, José Ramón
 Obeso, Yiannis Kourmpetis, Roeland van Ham, Thomas Odong, Marco Bink, Ulla
 Kemi, Jon Ågren and George Coupland ## Description of the data and file
 structure Across data files, missing data is encoded as "NA" or
 "NaN". When this is the case, the data value is unavailable and
 the scripts in "Code/Software" are designed to exclude these
 missing data from some analyses. ### Genotype data:
 SNPs_and_flanking_sequences_Wunder_etAl.txt: 253 widely spread, intergenic
 SNPs used for genotyping on a Custom GoldenGate SNP-panel. The SNP set was
 chosen to be informative across the entire sampled geographic range and/or
 within regions and populations. * Genomic position * Sequence of the SNP
 and of the flanking region genotypes_Wunder_etAl.xlsx: Genotypes at the
 253 SNPs of the accessions used in this study. DNA was extracted from leaf
 material collected in-situ (Supporting Information). These accessions
 include: i) a range-wide collection; ii) an evenly subsampled set of 50
 accessions from each of three populations from each of the three main
 regions; iii) a total of 187 Spanish accessions from 10 populations to
 analyze in detail population structure in Spain. * Accession name * Region
 of origin * Population or location of origin * SNPs
 snp_matrix_wg.txt.b.gz: Matrix of segregating and non-segregating sites
 for the 27 whole genome sequences. Decompress with: bgzip -cd ${filename}
 &gt; ${decompressed_file} * Chromosome * Position * Reference genotype *
 Genotypes ### Phenotype data:
 flowering_behavior_greenhouse_no_vernalization_Wunder_etAl.txt: Flowering
 behavior was scored under greenhouse conditions with no vernalisation.
 Plants were grown under long days (LD: 16h/8h day/night cycle, 22°/16°C)
 and scored for flowering traits twice a week, for 26 to 51 weeks after
 germination across four replicates of the experiment (Table S1) * Counter
 * Year of the Experiment * Subsets * Priority * Region of origin * Country
 of origin * Accession ID * population of origin * Family ID * Individual
 genotype * Flowering time after germination (days) * Flowering time after
 germination until the end of the experiment (days) * Flowering time after
 germination until the end of the shortest experiment (days, until 209
 days) * Flowering early (0/1) * Flowering-late (0/1) * Flowering binomial
 (0/1) flowering_behavior_greenhouse_with_vernalization_Wunder_etAl.txt:
 Flowering behavior was scored under greenhouse conditions with
 vernalisation. Plants were grown in long days for 6 weeks, then vernalised
 for about 14 weeks (short days, SD: 8h/16h day/night cycle, 4°C), and then
 transferred back into LD and scored for 19 weeks. * Counter * Priority *
 Region of origin * Accession ID * Population of origin * Family ID *
 Individual genotype * Flowering time after germination (days) * Flowering
 time after germination excluding vernalization time (days) * Flowering
 time after germination excluding vernalization time plus 14 days (days) *
 Flowering time after shift from vernalization to long-days (days) *
 Flowering binomial (0/1) * Flowering duration (days) * Flowering at the
 end of the experiment (0/1)
 survival_and_flowering_at_experimental_sites_Wunder_etAl.txt: Flowering
 behavior and fitness of plants grown at experimental sites were scored in
 Spain, the French Alps and Scandinavia, close to or within native
 populations, and in Germany outside the natural range. * Counter * Year of
 plantation * Experimental site * Country of origin * Accession ID *
 Population of origin * Family ID * Individual genotype * Plants alive in
 2011 (0/1) * Flowering binomial in 2011 (0/1) * Plants alive in 2012 (0/1)
 * Flowering binomial in 2012 (0/1)
 vegetative_and_reproductive_performance_in_Spain_Wunder_etAl.txt: At the
 Spanish experimental site we scored survival, as the percentage of
 surviving plants, the average number of siliques as an indication of
 fecundity and fitness, the number of rosettes for vegetative performance,
 and the proportion of flowering plants, inferred by the proportion of
 plants bearing siliques (Supporting Information). Scoring was done at the
 end of the growing season the year of plantation and the following year. *
 Priority * Accession ID * Population of origin * Family ID * Individual
 genotype * Alive in 2010 (0/1) * Alive in 2011 (0/1) * Alive in 2012 (0/1)
 * Flowering in 2010 (0/1) * Flowering in 2011 (0/1) * Flowering in 2012
 (0/1) * Silique number in 2010 * Rosette number in 2010 * Diameter in 2010
 (cm) * Silique number in 2010 * Total siliques in 2010 * Rosette number in
 2011 * Diameter in 2011 (cm) * Total siliques in 2011 * Silique number in
 2012 * Rosette number in 2012 * Diameter in 2012 * Total siliques in 2012
 * Overall total number of siliques ### Weather data: Yearly course of
 temperature at different populations: E1_2010-2013.txt,
 E3-11_2010-2013.txt, E3-3H_2010-2013.txt, E4_2010-2013.txt,
 F1a_2011-2013.txt, F1b_2012-2013.txt, F1ex_2010-2013.txt,
 F2_2010-2013.txt, S1_2010-2013.txt, S4_2010-2013.txt, S5_2010-2013.txt *
 Date * Time * Air temperature (degrees) * Soil temperature (degrees)
 Precipitation_France-VdArene.txt: Yearly course of precipitation near the
 experimental sites in the French Alps * Year * Month
 Precipitation_Spain-Leitariegos.txt: Yearly course of precipitation near
 the experimental sites in Spain * Year * Month
 Precipitation_Sweden-Katterjakk.txt: Yearly course of precipitation near
 the experimental sites in Scandinavia * Year * Month ## Code/Software The
 code used for plotting figures and computing statistics in the paper is
 in: code_flowering_behaviour_A.alpina.tar.gz