SNP-revealed genetic diversity in wild emmer wheat correlates with ecological factors

Abstract Background Patterns of genetic diversity between and within natural plant populations and their driving forces are of great interest in evolutionary biology. However, few studies have been performed on the genetic structure and population divergence in wild emmer wheat using a large number of EST-related single nucleotide polymorphism (SNP) markers. Results In the present study, twenty-five natural wild emmer wheat populations representing a wide range of ecological conditions in Israel and Turkey were used. Genetic diversity and genetic structure were investigated using over 1,000 SNP markers. A moderate level of genetic diversity was detected due to the biallelic property of SNP markers. Clustering based on Bayesian model showed that grouping pattern is related to the geographical distribution of the wild emmer wheat. However, genetic differentiation between populations was not necessarily dependent on the geographical distances. A total of 33 outlier loci under positive selection were identified using a F ST -outlier method. Significant correlations between loci and ecogeographical factors were observed. Conclusions Natural selection appears to play a major role in generating adaptive structures in wild emmer wheat. SNP markers are appropriate for detecting selectively-channeled adaptive genetic diversity in natural populations of wild emmer wheat. This adaptive genetic diversity is significantly associated with ecological factors

Scorpion Biodiversity and Interslope Divergence at “Evolution Canyon”, Lower Nahal Oren Microsite, Mt. Carmel, Israel

BACKGROUND: Local natural laboratories, designated by us as the "Evolution Canyon" model, are excellent tools to study regional and global ecological dynamics across life. They present abiotic and biotic contrasts locally, permitting the pursuit of observations and experiments across diverse taxa sharing sharp microecological subdivisions. Higher solar radiation received by the "African savannah-like" south-facing slopes (AS) in canyons north of the equator than by the opposite "European maquis-like" north-facing slopes (ES) is associated with higher abiotic stress. Scorpions are a suitable taxon to study interslope biodiversity differences, associated with the differences in abiotic factors (climate, drought), due to their ability to adapt to dry environments. METHODOLOGY/PRINCIPAL FINDINGS: Scorpions were studied by the turning stone method and by UV light methods. The pattern observed in scorpions was contrasted with similar patterns in several other taxa at the same place. As expected, the AS proved to be significantly more speciose regarding scorpions, paralleling the interslope patterns in taxa such as lizards and snakes, butterflies (Rhopalocera), beetles (families Tenebrionidae, Dermestidae, Chrysomelidae), and grasshoppers (Orthoptera). CONCLUSIONS/SIGNIFICANCE: Our results support an earlier conclusion stating that the homogenizing effects of migration and stochasticity are not able to eliminate the interslope intra- and interspecific differences in biodiversity despite an interslope distance of only 100 m at the "EC" valley bottom. In our opinion, the interslope microclimate selection, driven mainly by differences in insolance, could be the primary factor responsible for the observed interslope pattern

Circadian Genes in a Blind Subterranean Mammal III: Molecular Cloning and Circadian Regulation of Cryptochrome Genes in the Blind Subterranean Mole Rat, Spalax Ehrenbergi Superspecies

The blind subterranean mole rat superspecies Spalax ehrenbergi is an extreme example of mammalian adaptation to life underground. Though this rodent is totally visually blind, harboring a drastically degenerated subcutaneous rudimentary eye, its daily activity rhythm is entrainable to LD cycles. This indicates that it confers light information to the clock, as has been previously shown by the authors in behavioral studies as well as by molecular analyses of its Clock/MOP3 and its three Per genes. The Cryptochrome (Cry) genes found in animals and plants act both as photoreceptors and as essential components of the negative feedback mechanism of the biological clock. To further understand the circadian system of this unique mammal, the authors cloned and characterized the open reading frame of Spalax Cry1 and Cry2. The Spalax CRY1 protein is significantly closer to the human homolog than to the mice one, in contrast to the evolutionary expectations. They have found two isoforms of Cry2 in Spalax, which differ in their 5’ end of the open reading frame and defined their expression in Spalax populations. They found a large and significant excess of heterozygotes of sCry2 (sCry2L/S genotype). Both sCry1 and sCry2 mRNAs were found in the SCN, the eye, the harderian gland, as well as in a wide range of peripheral tissues. Their expression pattern under different LD conditions has also been analyzed. As was already shown for other circadian genes, despite being blind and living in darkness, the Cry genes of Spalax behave in a similar, though not identical, pattern as in sighted animals. Once again, the results indicate that the uniquely hypertrophied harderian gland of Spalax plays a key role in its circadian system

Adaptive evolution of benzoxazinoids in wild emmer wheat, Triticum dicoccoides, at "Evolution Canyon", Mount Carmel, Israel.

"Evolution Canyon" (ECI) at Lower Nahal Oren, Mount Carmel, Israel, is an optimal natural microscale model for unraveling evolution-in-action, highlighting the evolutionary processes of biodiversity evolution, adaptation, and incipient sympatric speciation. A major model organism in ECI is the tetraploid wild emmer wheat, Triticum dicoccoides (TD), the progenitor of cultivated emmer and durum wheat. TD displays dramatic interslope adaptive evolutionary divergence on the tropical, savannoid-hot and dry south-facing, "African" slope (AS), and on the temperate, forested, cool and humid, north-facing, "European" slope (ES), separated on average by 250 m. From the perspective of chemical evolution and metabolomics, it is important to unravel interslope divergence in biologically relevant secondary metabolites between the abutting slope populations. Here, in TD we examined hydroxamic acid (Hx), which is a family of secondary cereal metabolites, and plays a major role in defending the plant against fungi, insects and weeds.Our examination revealed that higher concentrations of DIBOA and DIMBOA were found in seedlings growing in the same greenhouse from seeds collected from the cool and humid forested ES, whereas the seedlings of seeds collected from the savannoid AS (both in root and shoot tissues), showed no DIMBOA. Remarkably, only DIBOA appears in both shoots and roots of the AS seedlings. It rises to a peak and then decreases in both organs and in seedlings from both slopes. The DIMBOA, which appears only in the ES seedlings, rises to a peak and decreases in the shoot, but increased and remained in a plateau in the root, till the end of the experiment.The results suggest stronger genetic resistance of defense compounds DIBOA and DIMBOA against biotic stresses (fungi and other pathogens) by ES seedlings. However, AS seedlings responded earlier but were to the same biotic stresses. The genetic difference found in AS seedlings was caused by the main adaptive selection in AS, which was against climatic, abiotic stresses, and was weaker, or not at all, against biotic stresses. The distinct genetic interslope differences appear important and is very significant and are elaborated in the discussion

Additional file 2: Table S2. of Putative adaptive inter-slope divergence of transposon frequency in fruit flies (Drosophila melanogaster) at “Evolution Canyon”, Mount Carmel, Israel

TE frequency estimates in stations NFS6 and SFS2 and in each slope. The line separeites between the adaptive families (above line) and the neutral families (below line). The data is also included in Table 3. (DOC 60 kb

“Evolution Canyon” I (ECI) at Lower Nahal Oren, Mount Carmel, Israel.

<p><b>(A)</b> Cross section of “Evolution Canyon” showing the savannoid "African" slope (AS) = south-facing slope (SFS), and the opposite shady, forested "European" slope (ES) = north-facing slope (NFS). (B) Air view of ECI with the forested NFS = ES and the savanoid SFS = AS, with the 7 experimental stations where the <i>T</i>. <i>dicoccoides</i> was sampled, indicated by the numbers 1–7 (from ref. 7, private picture of Prof. E. Nevo).</p

Variation in the amounts of Bx (DIBOA and DIMBOA) in <i>T</i>. <i>dicoccoides</i> seedlings (nmol/mg FW) grown in Sapir greenhouse from seeds collected on the opposing slopes, AS and ES, of “Evolution Canyon”.

<p>The measurements were separately done in shoots and roots of each seedling. Each average, standard error and median appearing in the table were calculated from 7 replications of the measuring at the same time. The replications appear in a separate column in the table. When the first 4 replications had 0 Bx, we terminated this analysis and assumed that the 3 unmeasured replications are also zero. Mean +/- Standard error values of the 7 replications measured each time, and Median values of the replications. Abbreviations: AS = African slope, ES = European slope, Bx = Benzoxazinoid. Glc = Glucosidase, Fw = Fresh Weight, nmol. = Nano mole, Rep. (or R.) = Replicates. Note: Each replication in the table is the result of measuring a mixture of 3 seedlings from the same genotype in order to receive more reliable amounts.</p