SSR data

This file contains SSR data of 20 populations, 10 plants per population, and data for 15 SSR. It includes some characteristics of the population, see abbreviations in ReadMe file. SSR’s are phi051, phi115, phi015, phi033, phi053, phi072, phi093, phi024, phi085, phi034, phi121, phi029, phi073, phi96342, phi109275. See publication for details. Data of each plant are in two consecutive rows. Missing data is coded as -

La Charente

18 novembre 18831883/11/18 (A12,N5114)-1883/11/18.Appartient à l’ensemble documentaire : PoitouCh

Comparison of mean annual temperature and mean annual precipitation among occurrences of <i>Q. palmeri</i>.

<p>The black dot represents the <i>Q. palmeri</i> at the Jurupa Mountains site. The Jurupa site is outside the one-tailed 95% confidence interval for both variables.</p

Cross-sections of <i>Q. palmeri</i> stems.

<p>Ring counts were made from high-resolution images of cross sections of each stem. Scale is in millimeters. Example stem sections, from left to right: Jurupa Mountains, Aguanga, Garner Valley.</p

Map of the studied population of <i>Q. palmeri</i>.

<p>White dots and ‘X’s represent known occurrences of <i>Q. palmeri</i> throughout California; the red ‘X’ in the insert represents the location of the Jurupa population. Percentiles are the two-tailed probability of suitability given 19 bioclimatic parameters.</p

Overlap with domestication candidate genes.

<p>(a) Patterns of expression shown as a proportion of genes differentially expressed between EH and MA conditions that are also differentially expressed between maize and teosinte. Monte Carlo re-sampling of DE genes in teosinte (b, c) and maize (d, e) for enrichment in genes showing <i>cis</i>-regulated differential expression between maize and teosinte (b, d) or evidence of selection during domestication (c, e). Maize and teosinte differential expression data are from Lemmon <i>et al</i>. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0184202#pone.0184202.ref019" target="_blank">19</a>], and selected gene lists are from Hufford <i>et al</i>. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0184202#pone.0184202.ref017" target="_blank">17</a>].</p

The potential role of genetic assimilation during maize domestication

<div><p>Domestication research has largely focused on identification of morphological and genetic differences between extant populations of crops and their wild relatives. Little attention has been paid to the potential effects of environment despite substantial known changes in climate from the time of domestication to modern day. In recent research, the exposure of teosinte (i.e., wild maize) to environments similar to the time of domestication, resulted in a plastic induction of domesticated phenotypes in teosinte. These results suggest that early agriculturalists may have selected for genetic mechanisms that cemented domestication phenotypes initially induced by a plastic response of teosinte to environment, a process known as genetic assimilation. To better understand this phenomenon and the potential role of environment in maize domestication, we examined differential gene expression in maize (<i>Zea mays</i> ssp. <i>mays</i>) and teosinte (<i>Zea mays</i> ssp. <i>parviglumis</i>) between past and present conditions. We identified a gene set of over 2000 loci showing a change in expression across environmental conditions in teosinte and invariance in maize. In fact, overall we observed both greater plasticity in gene expression and more substantial changes in co-expressionnal networks in teosinte across environments when compared to maize. While these results suggest genetic assimilation played at least some role in domestication, genes showing expression patterns consistent with assimilation are not significantly enriched for previously identified domestication candidates, indicating assimilation did not have a genome-wide effect.</p></div

Box plot of the coefficient of variation.

<p>Genes not differentially expressed are shown in gray, maize-specific DE genes in blue, and teosinte-specific DE genes in red. The significance of the Mann-Whitney U test is as shown with **<0.01, ***<0.001.</p

Module preservation in co-expression analysis.

<p>WGCNA preservation scores for teosinte (a.) and maize (b.) modules across early Holocene and modern ambient environmental conditions. Modules with scores below 2 (blue dashed line) have no preservation across conditions, those between 2 and 10 (green dashed line) are moderately preserved, and those above 10 are highly preserved.</p

Correction: Transposable Elements Contribute to Activation of Maize Genes in Response to Abiotic Stress

<p>Correction: Transposable Elements Contribute to Activation of Maize Genes in Response to Abiotic Stress</p