Dryad_121231

Seed size data of experimental crosses of Arabidopsis lyrata (column headings: experiment number, maternal population, abbreviation of maternal population, multilocus outcrossing rate tm, cross type, number of parental cross combinations, mean seed-surface area (sideview, in mm2))

Temperature-Stress Resistance and Tolerance along a Latitudinal Cline in North American <i>Arabidopsis lyrata</i>

<div><p>The study of latitudinal gradients can yield important insights into adaptation to temperature stress. Two strategies are available: resistance by limiting damage, or tolerance by reducing the fitness consequences of damage. Here we studied latitudinal variation in resistance and tolerance to frost and heat and tested the prediction of a trade-off between the two strategies and their costliness. We raised plants of replicate maternal seed families from eight populations of North American <i>Arabidopsis lyrata</i> collected along a latitudinal gradient in climate chambers and exposed them repeatedly to either frost or heat stress, while a set of control plants grew under standard conditions. When control plants reached maximum rosette size, leaf samples were exposed to frost and heat stress, and electrolyte leakage (PEL) was measured and treated as an estimate of resistance. Difference in maximum rosette size between stressed and control plants was used as an estimate of tolerance. Northern populations were more frost resistant, and less heat resistant and less heat tolerant, but—unexpectedly—they were also less frost tolerant. Negative genetic correlations between resistance and tolerance to the same and different thermal stress were generally not significant, indicating only weak trade-offs. However, tolerance to frost was consistently accompanied by small size under control conditions, which may explain the non-adaptive latitudinal pattern for frost tolerance. Our results suggest that adaptation to frost and heat is not constrained by trade-offs between them. But the cost of frost tolerance in terms of plant size reduction may be important for the limits of species distributions and climate niches.</p></div

Results of hierarchical mixed model analysis testing the effect of block, ancestral cluster, latitude, treatment and the interaction between the latter two on percentage electrolyte leakage (PEL), three parameters describing plant growth (asymptotic size, scale parameter and mid-point of growth x_mid), and the number of leaves of <i>Arabidopsis lyrata</i> plants (<i>N</i> = 384, 194, 193, 193, 194).

<p>The table shows <i>F</i> values; the last two rows show <i>t</i> values for contrasts between pairs of treatments. Statistics for the random effects are not shown. Significance is indicated in bold:</p><p>⁽*⁾<i>P</i> < 0.1,</p><p>*<i>P</i> < 0.05,</p><p>***<i>P</i> < 0.001</p><p>Results of hierarchical mixed model analysis testing the effect of block, ancestral cluster, latitude, treatment and the interaction between the latter two on percentage electrolyte leakage (PEL), three parameters describing plant growth (asymptotic size, scale parameter and mid-point of growth x_mid), and the number of leaves of <i>Arabidopsis lyrata</i> plants (<i>N</i> = 384, 194, 193, 193, 194).</p

Locations of the nine North American <i>Arabidopsis lyrata</i> populations included in this study.

<p>The grey shading indicates the approximate distribution of the species based on herbarium records, regional botanical lists, personal communication with local botanists, and our own field experience. The actual distribution is highly fragmented. The eastern and western regions represent distinct ancestral genetic clusters [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0131808#pone.0131808.ref023" target="_blank">23</a>].</p

Latitude of origin of <i>Arabidopsis lyrata</i> plants differing in electrolyte leakage (a), asymptotic size (b), resistance to frost and heat based on electrolyte leakage (c), and tolerance to frost and heat based on asymptotic size (d).

<p>Symbols depict population means based on family means and one-/two-sided bars indicate standard errors. Regression lines on panels a and b represent the significant or close to significant latitude-by-treatment interaction, regression lines on panels c and d represent significant latitude effect. For statistics see Tables <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0131808#pone.0131808.t001" target="_blank">1</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0131808#pone.0131808.t002" target="_blank">2</a>. Data for heat tolerance and frost resistance had been corrected for ancestral cluster.</p

allData_121010

txt file with population-cross type means and standard errors of a common garden study on Arabidopsis lyrata with the following columns: oberservationNo, population, site, expectedHeterozygosity, localDensity [m-2], multilocusOutcrossingRate (tm), crossType, multiplicative performance I (MPI), multiplicative performance II (MPII), seedLength [mm], germination (binary), infection 2009 (binary), time to flowering 2009 [days], pedicels 2009 (binary), fruits 2009 (binary), pollenNumber per flower 2009, pollenSize 2009 [um], time to flowering 2010 [days], noPedicels to 2010, noFruits to 2010, noPedicels to 2012, noFruits to 2012

Comparison of SNP numbers and frequency estimate accuracy revealed by Pool-seq and by GBS.

<p>Columns report: library/lane identity (population A or B, estimation of sequencing depth per individual in Pool-seq, and software used to detect SNPs of Pool-seq data set), number of SNPs detected by GBS (SNP_GBS) and Pool-seq (SNP_Pool-seq), overlapping number of SNPs detected (SNP_both), concordance correlation coefficient (CCC) with lower and upper 95% confidence limit (LCL; UCL) of CCC, the mean of the absolute difference in SNP frequency estimates of the two methods (|Δf|), false negative rate (FN rate), that is, the fraction of SNPs called by GBS but not by Pool-seq, and their mean minor allele frequency (FN MAF).</p

Tables_A2-A4_Paccard_et_al_2016_AmNat

Tables A2-A4. A2: R-code; A3: Houle’s I and heritability for all trait-population-treatment combinations; A4: G-Matrix for all population-treatment combinations

DRYAD - All traits raw data_140912

Trait values of replicates of 14 isolates of each of nine Rhynchosporium commune populations. The eight quantitative traits studied were: growth rate at 12°C, growth rate at 18°C, growth rate at 22°C, fungicide resistance, melanization, spore size, spore number, and virulence

Validation of Pooled Whole-Genome Re-Sequencing in <i>Arabidopsis lyrata</i>

<div><p>Sequencing pooled DNA of multiple individuals from a population instead of sequencing individuals separately has become popular due to its cost-effectiveness and simple wet-lab protocol, although some criticism of this approach remains. Here we validated a protocol for pooled whole-genome re-sequencing (Pool-seq) of <i>Arabidopsis lyrata</i> libraries prepared with low amounts of DNA (1.6 ng per individual). The validation was based on comparing single nucleotide polymorphism (SNP) frequencies obtained by pooling with those obtained by individual-based Genotyping By Sequencing (GBS). Furthermore, we investigated the effect of sample number, sequencing depth per individual and variant caller on population SNP frequency estimates. For Pool-seq data, we compared frequency estimates from two SNP callers, VarScan and Snape; the former employs a frequentist SNP calling approach while the latter uses a Bayesian approach. Results revealed concordance correlation coefficients well above 0.8, confirming that Pool-seq is a valid method for acquiring population-level SNP frequency data. Higher accuracy was achieved by pooling more samples (25 compared to 14) and working with higher sequencing depth (4.1× per individual compared to 1.4× per individual), which increased the concordance correlation coefficient to 0.955. The Bayesian-based SNP caller produced somewhat higher concordance correlation coefficients, particularly at low sequencing depth. We recommend pooling at least 25 individuals combined with sequencing at a depth of 100× to produce satisfactory frequency estimates for common SNPs (minor allele frequency above 0.05).</p></div