<b>Early human selection of crops' wild progenitors explains the acquisitive physiology of modern cultivars</b>

The "DomesticationPhysion" folder consists of two subfolders:The "rawData" subfolder contains all the input (raw) data of the experimental dataset. This includes leaf‐level measurements of gas exchange, morphology and chemistry of each individual plant included in the experiment. The "compiledData" subfolder contains species-specific data on diverse life-history traits (woodiness, growth form, life cycle, and photosynthetic pathway), taken from different global databases and published literature. </p

DATA-MEC-09-0209.xls

Molecular and Phenotypic data for trees sampled in the field. Plant material: leaves of the current year. Excel file

Two dimensional PCA scatter plot for population differentiation.

<p>Principal Components was performed to analyze samples belonging to Tordesillas and Bogarra populations using MSAPs with significant epigenetic effect differentiating populations and propagated trees. Bogarra ramets are identified by squares and Tordesillas ramets by triangles. Propagated trees which ramets clustered together are highlighted with circles. First component (X axis) gathers 21.60% of the variation and second component (Y axis) 13.64.</p

<i>Pinus pinea</i> genome-wide methylation analysis based on MSAPs.

<p>Four different classes of MSAPs were identified depending on their cytosine methylation status and their polymorphic profile: Monomorphic Methylation Insensitive (MMI), Polymorphic Methylation Insensitive (PMI), Monomorphic Methylation Sensitive (MMS) and Polymorphic Methylation Sensitive (PMS). a): percentage of MSAP markers assigned to each class; b) fragment pattern associated with each class.</p

Quantification of cytosine methylation in all analyzed genotypes.

<p>Percentage of cytosine methylation and number of polymorphic fragments are provided for each genotype.</p

Epigenetic Variability in the Genetically Uniform Forest Tree Species <i>Pinus pinea</i> L

<div><p>There is an increasing interest in understanding the role of epigenetic variability in forest species and how it may contribute to their rapid adaptation to changing environments. In this study we have conducted a genome-wide analysis of cytosine methylation pattern in <i>Pinus pinea</i>, a species characterized by very low levels of genetic variation and a remarkable degree of phenotypic plasticity. DNA methylation profiles of different vegetatively propagated trees from representative natural Spanish populations of <i>P. pinea</i> were analyzed with the Methylation Sensitive Amplified Polymorphism (MSAP) technique. A high degree of cytosine methylation was detected (64.36% of all scored DNA fragments). Furthermore, high levels of epigenetic variation were observed among the studied individuals. This high epigenetic variation found in <i>P. pinea</i> contrasted with the lack of genetic variation based on Amplified Fragment Length Polymorphism (AFLP) data. In this manner, variable epigenetic markers clearly discriminate individuals and differentiates two well represented populations while the lack of genetic variation revealed with the AFLP markers fail to differentiate at both, individual or population levels. In addition, the use of different replicated trees allowed identifying common polymorphic methylation sensitive MSAP markers among replicates of a given propagated tree. This set of MSAPs allowed discrimination of the 70% of the analyzed trees.</p></div

Detailed isoschizomer-based analysis of Methylation Sensitive fragments (MS).

<p>Comparison of Methylation Sensitive (MS) fragments between <i>Eco</i>RI/<i>Hpa</i>II and <i>Eco</i>RI/<i>Msp</i>I profiles. PMS.- Polymorphic Methylation Sensitive fragments; MMS.- Monomorphic Methylation Sensitive fragments.</p

UPGM tree for genotype identification.

<p>Genetic similarity was calculated and bootstrapped UPGMA clustering was performed for genotype discrimination. Bootstrap computation percentages are shown over the different branches. Tree has been condensed a 25% and clones from the same genotype clustering together are labeled under the genotype code name for easier visualization.</p