Reticulated origin of domesticated emmer wheat supports a dynamic model for the emergence of agriculture in the fertile crescent

We used supernetworks with datasets of nuclear gene sequences and novel markers detecting retrotransposon insertions in ribosomal DNA loci to reassess the evolutionary relationships among tetraploid wheats. We show that domesticated emmer has a reticulated genetic ancestry, sharing phylogenetic signals with wild populations from all parts of the wild range. The extent of the genetic reticulation cannot be explained by post-domestication gene flow between cultivated emmer and wild plants, and the phylogenetic relationships among tetraploid wheats are incompatible with simple linear descent of the domesticates from a single wild population. A more parsimonious explanation of the data is that domesticated emmer originates from a hybridized population of different wild lineages. The observed diversity and reticulation patterns indicate that wild emmer evolved in the southern Levant, and that the wild emmer populations in south-eastern Turkey and the Zagros Mountains are relatively recent reticulate descendants of a subset of the Levantine wild populations. Based on our results we propose a new model for the emergence of domesticated emmer. During a pre-domestication period, diverse wild populations were collected from a large area west of the Euphrates and cultivated in mixed stands. Within these cultivated stands, hybridization gave rise to lineages displaying reticulated genealogical relationships with their ancestral populations. Gradual movement of early farmers out of the Levant introduced the pre-domesticated reticulated lineages to the northern and eastern parts of the Fertile Crescent, giving rise to the local wild populations but also facilitating fixation of domestication traits. Our model is consistent with the protracted and dispersed transition to agriculture indicated by the archaeobotanical evidence, and also with previous genetic data affiliating domesticated emmer with the wild populations in southeast Turkey. Unlike other protracted models, we assume that humans played an intuitive role throughout the process.Natural Environment Research Council [NE/E015948/1]; Slovak Research and Development Agency [APVV-0661-10, APVV-0197-10]info:eu-repo/semantics/publishedVersio

Measuring procedure of experimental data acquisition and data evaluation of acoustic emission in rock disintegration

The paper describes the results of measurements of acoustic signal arising in rock disintegration on the drilling standof the Institute of Geotechnics SAS in Košice. The acoustic signal was registered with sonometer Mediator 2238. Registrationand processing of the acoustic signal is solved as a part of the research grant task within the basic research of the rock disintegrationby drilling

Filtered supernetworks constructed from multiple nuclear gene sequences

<p><b>[38]</b>. (A) Full dataset composed of 21 partial trees, and (B) a reduced dataset containing only the 15 rooted partial trees, for sequences from wild emmer (28 accessions, dots color coded according to region, <i>N/A</i>, location not available), domesticated emmer (12 accessions, red dots) and <i>durum</i> wheat (20 accessions, purple dots). Individual nodes may contain multiple samples. The geographic locations of the wild emmer accessions are indicated in accordance with <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0081955#pone-0081955-g004" target="_blank">Figure 4</a>. The outgroup comprises the <i>T. timopheevii</i> accessions.</p

Supernetwork of combined retrotransposon data.

<p>Network nodes containing samples are marked by black dots. The geographic locations of the wild emmer accessions are indicated next to the corresponding nodes as follows: <i>SW</i> (green), southern Levant (Israel, Lebanon, Jordan, SW Syria); <i>NW</i> (dark blue), northwest (western part of the Syria–Turkey border, here approximated as 'Gaziantep region'); <i>NE</i> (light blue), northeast (vicinity of Karaca Dağ); <i>SE</i> (orange), southeast (parts of Iraq and Iran). Domesticated emmer is found in the nodes within the grey background areas. Cluster A includes all but two free-threshing samples (22) together with <i>dicoccum</i> accessions from Ethiopia (6), Turkey (5), Oman (2), India (2), Slovakia (2), former Yugoslavia (1), Morocco (1), Palestine (1) and Germany (1). Cluster B includes four <i>dicoccum</i> samples (Palestine, Morocco, Turkey and Scandinavia). Cluster C includes all Iranian <i>dicoccum</i> (15) and <i>T. ispahanicum</i> (8) accessions, <i>dicoccum</i> samples from Turkey (8), Russia (4), Spain (3), Italy (2), Hungary (2), Palestine (2), Jordan (2), Germany (2), Switzerland (1), Armenia (1), Georgia (1), Ukraine (1), Belarus (1), Romania (1), Serbia (1), Israel (1), Morocco (1), Eritrea (1), Uzbekistan (1), and two free-threshing samples. The outgroup comprises the <i>T. timopheevii</i> accessions.</p

Virtual gel of the retrotransposon insertions detected in the 5S arrays.

<p>Accessions are identified by the codes given in Table A in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0081955#pone.0081955.s001" target="_blank">File S1</a>. All <i>T.timopheevii</i> accessions displayed the same profile marked here as <i>T.ti</i>. Pink and orange arrows indicate insertions detected only in wild and domesticated tetraploid wheats, respectively. Combinations absent in wild populations but frequent in domesticated accessions are highlighted with a pink background. Accessions for which 5.8S-<i>Jeli</i> sequences were obtained are color-coded in the same way as the node outer circles in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0081955#pone-0081955-g002" target="_blank">Figure 2</a>.</p

PCR system for detection of LTR retrotransposon insertions in the 5S and 5.8S rDNA loci.

<p>The example shown is for detection of a Jeli insertion in a 5S array. Primer P1 is specific for the distal region of the LTR, and primers P2-P5 anneal at different positions with the 5S gene. Depending on its orientation, a Jeli sequence is detected by PCRs with primer combinations P1-P2 and P1-P3, or P1-P4 and P1-P5. Two different PCRs are carried out for each detection to reduce false-positive results. A similar strategy is used to detect other types of LTR retrotransposon and to identify insertions adjacent to 5.8S genes.</p

MJ network constructed from 5.8S-<i>Jeli</i> sequence data.

<p>Node sizes are proportional to the number of accessions displaying that allele, and the edge lengths are proportional to the number of substitutions between pairs of allele sequences. The taxonomic content of each node is indicated as a pie chart. The color coding of the outer circle of each node relates to the symbols used for different groups of accessions in Figure A in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0081955#pone.0081955.s001" target="_blank">File S1</a>.</p

Correction: Heritable heading time variation in wheat lines with the same number of Ppd-B1 gene copies.

[This corrects the article DOI: 10.1371/journal.pone.0183745.]

Heritable heading time variation in wheat lines with the same number of Ppd-B1 gene copies.

The ability of plants to identify an optimal flowering time is critical for ensuring the production of viable seeds. The main environmental factors that influence the flowering time include the ambient temperature and day length. In wheat, the ability to assess the day length is controlled by photoperiod (Ppd) genes. Due to its allohexaploid nature, bread wheat carries the following three Ppd-1 genes: Ppd-A1, Ppd-B1 and Ppd-D1. While photoperiod (in)sensitivity controlled by Ppd-A1 and Ppd-D1 is mainly determined by sequence changes in the promoter region, the impact of the Ppd-B1 alleles on the heading time has been linked to changes in the copy numbers (and possibly their methylation status) and sequence changes in the promoter region. Here, we report that plants with the same number of Ppd-B1 copies may have different heading times. Differences were observed among F7 lines derived from crossing two spring hexaploid wheat varieties. Several lines carrying three copies of Ppd-B1 headed 16 days later than other plants in the population with the same number of gene copies. This effect was associated with changes in the gene expression level and methylation of the Ppd-B1 gene