Adaptive microclimatic evolution of the dehydrin 6 gene in wild barley at ��Evolution Canyon��, Israel

Dehydrins are one of the major stress-induced gene families, and the expression of dehydrin 6 (Dhn6) is strictly related to drought in barley. In order to investigate how the evolution of the Dhn6 gene is associated with adaptation to environmental changes, we examined 48 genotypes of wild barley, Hordeum spontaneum, from "Evolution Canyon" at Mount Carmel, Israel. The Dhn6 sequences of the 48 genotypes were identified, and a recent insertion of 342?bp at 5'UTR was found in the sequences of 11 genotypes. Both nucleotide and haplotype diversity of single nucleotide polymorphism in Dhn6 coding regions were higher on the AS ("African" slope or dry slope) than on the ES ("European" slope or humid slope), and the applied Tajima D and Fu-Li test rejected neutrality of SNP diversity. Expression analysis indicated that the 342?bp insertion at 5'UTR was associated with the earlier up-regulation of Dhn6 after dehydration. The genetic divergence of amino acids sequences indicated significant positive selection of Dhn6 among the wild barley populations. The diversity of Dhn6 in microclimatic divergence slopes suggested that Dhn6 has been subjected to natural selection and adaptively associated with drought resistance of wild barley at "Evolution Canyon".     

Microgeographic genome size differentiation of the carob tree, Ceratonia siliqua, at 'Evolution Canyon', Israel

BACKGROUND AND AIMS: We tested whether the local differences in genome size recorded earlier in the wild barley, Hordeum spontaneum, at 'Evolution Canyon', Mount Carmel, Israel, can also be found in other organisms. As a model species for our test we chose the evergreen carob tree, Ceratonia siliqua. METHODS: Genome size was measured by means of DAPI flow cytometry. KEY RESULTS: In adults, significantly more DNA was recorded in trees growing on the more illuminated, warmer, drier, microclimatically more fluctuating 'African' south-facing slope than in trees on the opposite, less illuminated, cooler and more humid, 'European' north-facing slope in spite of an interslope distance of only 100 m at the canyon bottom and 400 m at the top. The amount of DNA was significantly negatively correlated with leaf length and tree circumference. In seedlings, interslope differences in the amount of genome DNA were not found. In addition, the first cases of triploidy and tetraploidy were found in C. siliqua. CONCLUSIONS: The data on C. siliqua at 'Evolution Canyon' showed that local variability in the C-value exists in this species and that ecological stress might be a strong evolutionary driving force in shaping the amount of DNA.     

Population genetic response to microsite ecological stress in wild barley, Hordeum spontaneum

Genetic diversity was studied in six subpopulations (a total of 60 individuals) of wild barley, Hordeum spontaneum , the progenitor of cultivated barley, sampled from six stations located along a transect of 300 m across the two opposing slopes of 'Evolution Canyon', a Mediterranean microsite at Lower Nahal Oren, Mt Carmel. The two opposing slopes are separated by between 100 and 400 m and designated SFS (South-Facing Slope) and NFS (North-Facing Slope) with each having three equidistant test stations. The SFS, which receives up to 300% more solar radiation, is drier, ecologically more heterogeneous, fluctuating, and more stressful than the NFS. Analysis of 12 RAPD primers, representing a total of 51 putative loci, revealed a significant inter- and intraslope variation in RAPD band polymorphism. A significantly higher proportion of polymorphic RAPD loci was found amongst the subpopulations on the SFS (mean P = 0.909) than on the NFS (mean P = 0.682), on the basis of the presence and absence of 22 strong bands. Polymorphism generally increased upwards from the bottom to the top of the SFS (0.636, 0.773, 0.955) and NFS (0.409, 0.500, 0.545), respectively. Gametic phase disequilibria estimates, D, revealed SFS and NFS unique predominant combinations which sharply differentiated the two slopes and indicated that there is differential interslope selection favouring slope-specific multilocus combinations of alleles, or blocks of genes over tens to hundreds of meters. This suggests that selection overrides migration. RAPD polymorphism appears to parallel allozyme diversity which is climatically adaptive and driven by natural selection in the same subpopulations at the microsite.     

Adaptive spatiotemporal distribution of soil microfungi in 'Evolution Canyon' II, Lower Nahal Keziv, western Upper Galilee, Israel

We describe and interpret spatiotemporal micromycete community structure and adaptive complexes in contrasting xeric and mesic microclimates in the soils of 'Evolution Canyon' II, Lower Nahal Keziv, western Upper Galilee, Israel. A total of 192 species from 60 genera belonging to Zygomycota (nine species), Ascomycota (13 species), and mitosporic fungi (170 species) were isolated. The fungal communities on the south-facing, xeric, 'African' slope (AS) demonstrated significantly greater diversity than on the north-facing, mesic, 'European' slope (ES) and the valley bottom (VB). Seasonally, winter slope communities were less heterogeneous. Forest localities on the ES and the VB in all seasons and the shady localities on the AS in the winter were overwhelmingly dominated by mesophilic Penicillium species. The sunny locality on the AS was characterized by a dominance of melanin-containing micromycetes that was most pronounced in the summer and by high occurrence and abundance of thermotolerant and thermophilic Aspergillus and Fusarium species. Ascomycetes and zygomycetes were the minor components in all local mycobiota studied; sexual ascomycetes, being stress-selected fungi, were more than ten times more abundant in the soil of the AS than in that of the ES, with the peak of abundance in the sunny summer community. The results demonstrated a microscale adaptive spatiotemporal inter- and intraslope divergence in soil mycobiota structure. Microclimatic natural selection appears to be the major factor affecting soil fungus diversity patterns.  © 2003 The Linnean Society of London . Biological Journal of the Linnean Society , 2003, 78, 527–539.     

Soil microfungal communities of 'Evolution Canyons' in Israel – extreme differences on a regional scale

On a regional scale, we compared the local adaptive patterns of soil mycobiota revealed in four 'Evolution Canyons' located in the northern and southern parts of Israel. These microsites were chosen according to the framework of the Institute of Evolution, University of Haifa programme, focusing on the effect of interslope environmental divergence on biodiversity patterns. The comparative analysis demonstrated remarkable differences in spatiotemporal structure of the microfungal communities and their biodiversity level (species richness, heterogeneity and equitability). In the desert 'Evolution Canyon', stress-selected, slow-reproducing, dark-coloured species with large, multicelled conidia were dominant. At the same time, in the forest localities of the northern canyons, as well as in the agriculturally disturbed locality with soil degradation, ruderal-selected, fast-reproducing Penicillium species predominated. Environmental natural selection appeared to be the major factor affecting adaptive diversity patterns of soil microfungi in the studied area.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 93 , 157–163.     

Natural Selection Causes Adaptive Genetic Resistance in Wild Emmer Wheat against Powdery Mildew at “Evolution Canyon” Microsite,Mt. Carmel,Israel

Background

“Evolution Canyon” (ECI) at Lower Nahal Oren, Mount Carmel, Israel, is an optimal natural microscale model for unraveling evolution in action highlighting the basic evolutionary processes of adaptation and speciation. A major model organism in ECI is wild emmer, Triticum dicoccoides, the progenitor of cultivated wheat, which displays dramatic interslope adaptive and speciational divergence on the tropical-xeric “African” slope (AS) and the temperate-mesic “European” slope (ES), separated on average by 250 m.

Methods

We examined 278 single sequence repeats (SSRs) and the phenotype diversity of the resistance to powdery mildew between the opposite slopes. Furthermore, 18 phenotypes on the AS and 20 phenotypes on the ES, were inoculated by both Bgt E09 and a mixture of powdery mildew races.

Results

In the experiment of genetic diversity, very little polymorphism was identified intra-slope in the accessions from both the AS or ES. By contrast, 148 pairs of SSR primers (53.23%) amplified polymorphic products between the phenotypes of AS and ES. There are some differences between the two wild emmer wheat genomes and the inter-slope SSR polymorphic products between genome A and B. Interestingly, all wild emmer types growing on the south-facing slope (SFS=AS) were susceptible to a composite of Blumeria graminis, while the ones growing on the north-facing slope (NFS=ES) were highly resistant to Blumeria graminis at both seedling and adult stages.

Conclusion/Significance

Remarkable inter-slope evolutionary divergent processes occur in wild emmer wheat, T. dicoccoides at EC I, despite the shot average distance of 250 meters. The AS, a dry and hot slope, did not develop resistance to powdery mildew, whereas the ES, a cool and humid slope, did develop resistance since the disease stress was strong there. This is a remarkable demonstration in host-pathogen interaction on how resistance develops when stress causes an adaptive result at a micro-scale distance.     

Differential expression of dehydrin genes in wild barley, Hordeum spontaneum, associated with resistance to water deficit

Dehydrin gene (Dhn) expression is associated with plant response to dehydration. The aim of the present study was to investigate the association of differential expression of Dhn genes (Dhn 1, 3, 5, 6, and 9) with drought tolerance found in wild barley (Hordeum spontaneum). Tolerant and sensitive genotypes were identified from Israeli (Tabigha microsite) and Jordanian (Jarash and Waddi Hassa) populations (based on scoring of water loss rate of 390 genotypes). The five Dhn genes were up‐regulated by dehydration in resistant and sensitive wild barley genotypes. Notably, differences between resistant and sensitive genotypes were detected, mainly in the expression of Dhn1 and Dhn6 genes, depending on the duration of dehydration stress. Dhn1 tended to react earlier (after 3 h) and higher (12 h and 24 h) in resistant compared to sensitive genotypes. The level of expression of Dhn6 was significantly higher in the resistant genotypes at the earlier stages after stress. However, after 12 and 24 h Dhn6 expression was relatively higher in sensitive genotypes. The present results may indicate that these genes have some functional role in the dehydration tolerance in wild barley. The authors suggest that the observed differences of Dhn expression in wild barley, originating from different micro‐ and macro ecogeographic locations, may be the result of adaptive edaphic and climatic selective pressures.     

Gastropod biodiversity at the 'Evolution Canyon' microsite, lower Nahal Oren, Mount Carmel, Israel

Twenty-six species of gastropods (terrestrial, shell-bearing snails and slugs) were recorded at the 'Evolution Canyon' microsite, lower Nahal Oren, Mount Carmel, Israel. Twenty-five species were recorded at the temperate, mesic north-facing slope (NFS) and 20 species at the xeric south-facing slope (SFS). Out of these species, six were NFS specific ( Pilorcula raymondi hebraica , Euchondrus septemdentatus , Monacha crispulata , Pyramidula rupestris hierosolymitana , Truncatellina haasi , and Vitrea contracta ) and one was SFS specific ( Prolimax eustrictus ). The interslope difference was probably partly due to missing forest species at the SFS in comparison with the NFS. Twenty-two species were Levantine endemics (84.6%) and four species were more widely distributed in the Palaearctic region (15.4%). The Levantine species are inhabitants of the mesic and mainly mountainous regions, but four species ( Granopupa granum , Calaxis hierosolymarum , Cecilioides acicula , and Helix engaddensis ) also penetrate the deserts. Seven species ( Buliminus labrosus , H. engaddensis , Levantina spiriplana caesareana , Metafruticicola fourousi , Monacha syriaca , Sphincterochila cariosa , and Xeropicta vestalis joppensis ) were significantly more abundant on the SFS than on the NFS. The local physical microclimatic sharp divergence leads to gastropod adaptive interslope biotic divergence caused by natural selection.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 93 , 147–155.     

Characterizing genic and nongenic molecular markers: comparison of microsatellites and SNPs

The implications of transitioning to single nucleotide polymorphism (SNPs) from microsatellite markers (MSs) have been investigated in a number of population genetics studies, but the effect of genomic location on the amount of information each type of marker reveals has not been explored in detail. We developed novel SNP markers flanking 1 kb regions of 13 genic (within gene or <1 kb away from gene) and 13 nongenic (>10 kb from annotated gene) MSs in the threespine stickleback genome to obtain comparable data for both types of markers. We analysed patterns of genetic diversity and divergence on various geographic scales after converting the SNP loci within each genomic region into haplotypes. Marker type (SNP haplotype or MS) and location (genic or nongenic) significantly affected most estimates of population diversity and divergence. Between‐lineage divergence was significantly higher in SNP haplotypes (genic and nongenic), however, within‐lineage divergence was similar between marker types. Most divergence and diversity measures were uncorrelated between markers, except for population differentiation which was correlated between MSs and SNP haplotypes (both genic and nongenic). Broad‐scale population structure and assignment were similarly resolved by both marker types, however, only the MSs were able to delimit fine‐scale population structuring, particularly when genic and nongenic markers were combined. These results demonstrate that estimates of genetic variability and differentiation among populations can be strongly influenced by marker type, their genomic location in relation to genes and by the interaction of these two factors. This highlights the importance of having an awareness of the inherent strengths and limitations associated with different molecular tools to select the most appropriate methods for accurately addressing various ecological and evolutionary questions.     

Detection and quantification of Paenibacillus polymyxa in the rhizosphere of wild barley (Hordeum spontaneum) with real-time PCR

Aim:  To detect and quantify the plant drought tolerance enhancing bacterium Paenibacillus polymyxa in a collection of 160 Hordeum spontaneum rhizosphere samples at the 'Evolution Canyon' ('EC'), Israel.
Methods and Results:  PCR primers and a FAM-TAMRA probe (6-carboxyfluorescein, 6-carboxy-tetramethyl-rhodamine) targeting 16S rRNA genes were designed and used to detect and quantify the target strain. Two commercial kits, Bio101 Fast Spin and Mo Bio Ultra Clean Soil DNA, were tested for DNA isolation from the rhizosphere and surrounding soil. Population densities of P. polymyxa were studied in the rhizosphere of wild barley and surrounding soil from the contrasting climatic slopes at the 'EC' using the real-time PCR and culture based methods.
Conclusion:  Paenibacillus polymyxa is one of the best established species in wild barley rhizosphere at the 'EC' slopes. With the real-time PCR assay we are able to detect 1 pg of DNA per PCR corresponding to 100 cells per ml. The results at the 'EC' correlate well to bacterial estimations by culture based methods.
Significance and Impact of the Study:  Significantly higher P. polymyxa cell number was detected in the rhizosphere of arid 'African' microclimate indicating possible role of adaptive co-evolution with plants.     

Rapid upregulation ofDehyrin3 andDehydrin4 in response to dehydration is a characteristic of drought-tolerant genotypes in barley

The identification of molecular markers and marker-aided selection are essential to the efficient breeding of drought-tolerant plants. However, because that characteristic is controlled by many quantitative trait loci, such markers that can screen and trace desirable barley genotypes in a segregating population or germplasm have not yet been determined. Relative water content has been used to estimate drought tolerance in plants because it is highly correlated with the drought index of yield. To develop reliable gene-specific markers for identifying tolerant versus susceptible genotypes, we performed suppression subtractive hybridization to identify candidate genes. We used two domestic barley cultivars, one having the highest RWC (drought-tolerant ‘Chalbori’) and the other having the lowest (drought-susceptible ‘Daebaekbori’). In response to dehydration at the early seedling stage, rapid upregulation ofDehydrin3 (Dhn3) andDhn4 occurred in the drought-tolerant genotypes, but not in the susceptible ones. Similar results were obtained with mature plants growing under frequent drought stress in the greenhouse. In addition,Dhn3 andDhn4 conferred higher drought tolerance when they were over-expressed in transgenicArabidopsis. Thus, in addition to using assessments of RWC, we propose thatDhn3 andDhn4 expressions can serve as drought-induced gene-specific markers to determine drought-tolerant barley genotypes at the seedling stage.     

Genome size microscale divergence of <Emphasis Type="Italic">Cyclamen persicum</Emphasis> in Evolution Canyon,Israel

Using DAPI flow cytometry, we examined genome size divergence of the Persian violet, Cyclamen persicum (Primulaceae) (2n=48) on close opposite slopes of Evolution Canyon (EC), Mt. Carmel, Israel. The range of genome size variation detected among measured cyclamens was 6.41% in relation to the smallest measured DNA content. Our data on C. persicum at EC showed that local variability in the 2C-value exists. Significantly less DNA was recorded in plants growing in one station of the African savannah-like south-facing slope (AS) but not in the remaining two stations of the same slope. We were not able to reject the null hypothesis that there are no significant interslope differences in the genome size between the temperate European garrigue-like north-facing slope (ES) and the drier AS. In spite of the nonsignificant interslope trend for the higher genome size in C. persicum, the data-fusion (meta-analysis) test using correlations between C-values in C. persicum, and earlier studied carob tree (Ceratonia siliqua), trifoil (Lotus peregrinus) and a beetle (Oryzaephilus surinamensis) and their distribution along the aridity gradient indicates a positive relationship between drought and genome size at the microsite.     

Effects of introgression and recombination on haplotype structure and linkage disequilibrium surrounding a locus encoding Bymovirus resistance in barley

We present a detailed analysis of linkage disequilibrium (LD) in the physical and genetic context of the barley gene Hv-eIF4E, which confers resistance to the barley yellow mosaic virus (BYMV) complex. Eighty-three SNPs distributed over 132 kb of Hv-eIF4E and six additional fragments genetically mapped to its flanking region were used to derive haplotypes from 131 accessions. Three haplogroups were recognized, discriminating between the alleles rym4 and rym5, which each encode for a spectrum of resistance to BYMV. With increasing map distance, haplotypes of susceptible genotypes displayed diverse patterns driven mainly by recombination, whereas haplotype diversity within the subgroups of resistant genotypes was limited. We conclude that the breakdown of LD within 1 cM of the resistance gene was generated mainly by susceptible genotypes. Despite the LD decay, a significant association between haplotype and resistance to BYMV was detected up to a distance of 5.5 cM from the resistance gene. The LD pattern and the haplotype structure of the target chromosomal region are the result of interplay between low recombination and recent breeding history.     

Haplotype diversity in the endosperm specific β-amylase gene Bmy1 of cultivated barley (Hordeum vulgare L.)

Five single nucleotide polymorphism (SNP) sites corresponding to substitutions in the protein sequence of the β-amylase gene Bmy1 at amino acid (AA) positions 115, 165, 233, 347 and 430 were genotyped in 493 cultivated barley accessions by Pyrosequencing and a CAPS assay. A total of 6 different haplotypes for the Bmy1 gene were discovered of which 4 haplotypes were identified as previously described alleles Bmy1-Sd1, Bmy1-Sd2L, Bmy1-Sd2H and Bmy1-Sd3, while 2 haplotypes were new. A broad spectrum of haplotypes was found in spring barleys, while the winter barleys were dominated by the newly described haplotype Bmy1-Sd4. Individual haplotype frequencies varied between the geographic regions.Three pairs of SNP loci within the gene showed highly significant (P<0.0001) elevated values of linkage disequilibrium (LD) with r ² > 0.6. In the European and Asian subpopulations different loci were in linkage disequilibrium due to the differences in haplotype frequency distributions. By applying LD data to select haplotype tagging SNPs, three SNP sites corresponding to AA positions 115, 233 and 347 were identified that allowed to discriminate 4 haplotypes and to capture 91.6% of the available diversity by distinguishing 452 out of 493 accessions. In a subset of 2-rowed German spring barley varieties 4 SNPs and 2 haplotypes had a significant association with the malting quality parameter final attenuation limit which is related to the total amylolytic enzymatic activity.     

Carbon source utilization patterns of Bacillus simplex ecotypes do not reflect their adaptation to ecologically divergent slopes in 'Evolution Canyon', Israel

The 'Evolution Canyons' I and II in Israel are model habitats to study adaptation and speciation of bacteria in the environment. These canyons represent similar ecological replicates, separated by 40 km, with a strongly sun-exposed and hot 'African' south-facing slope (SFS) vs. a cooler and mesic-lush 'European' north-facing slope (NFS). Previously, among 131 Bacillus simplex isolates, distinct genetic lineages (ecotypes), each specific for either SFS or NFS, were identified, suggesting a temperature-driven slope-specific adaptation. Here, we asked whether the ecological heterogeneity of SFS vs. NFS also affected carbon utilization abilities, as determined using the Biolog assay. Contrary to expectation, a correlation between substrate utilization patterns and the ecological origin of strains was not found. Rather, the patterns split according to the two major phylogenetic lineages each of which contain SFS and NFS ecotypes. We conclude that traits related to the general energy metabolism, as far as assessed here, are neither shaped by the major abiotic features of 'Evolution Canyon', namely solar radiation, temperature, and drought, nor by the soil characteristics. We further conclude that some traits diverge rather neutrally from each other, whereas other, more environmentally related traits are shaped by natural selection and show evolutionary convergence.     

An exceptionally high nucleotide and haplotype diversity and a signature of positive selection for the eIF4E resistance gene in barley are revealed by allele mining and phylogenetic analyses of natural populations

In barley, the eukaryotic translation initiation factor 4E (eIF4E) gene situated on chromosome 3H is recognized as an important source of resistance to the bymoviruses Barley yellow mosaic virus and Barley mild mosaic virus. In modern barley cultivars, two recessive eIF4E alleles, rym4 and rym5, confer different isolate-specific resistances. In this study, the sequence of eIF4E was analysed in 1090 barley landraces and noncurrent cultivars originating from 84 countries. An exceptionally high nucleotide diversity was evident in the coding sequence of eIF4E but not in either the adjacent MCT-1 gene or the sequence-related eIF(iso)4E gene situated on chromosome 1H. Surprisingly, all nucleotide polymorphisms detected in the coding sequence of eIF4E resulted in amino acid changes. A total of 47 eIF4E haplotypes were identified, and phylogenetic analysis using maximum likelihood provided evidence of strong positive selection acting on this barley gene. The majority of eIF4E haplotypes were found to be specific to distinct geographic regions. Furthermore, the eI4FE haplotype diversity (uh) was found to be considerably higher in East Asia, whereas SNP genotyping identified a comparatively low degree of genome-wide genetic diversity in 16 of 17 tested accessions (each carrying a different eIF4E haplotype) from this same region. In addition, selection statistic calculations using coalescent simulations showed evidence of non-neutral variation for eIF4E in several geographic regions, including East Asia, the region with a long history of the bymovirus-induced yellow mosaic disease. Together these findings suggest that eIF4E may play a role in barley adaptation to local habitats.     

Haplotype characterization and markers at the barley Mlo powdery mildew resistance locus as tools for marker-assisted selection.

Recessive mlo alleles of the barley Mlo gene confer resistance to almost all known isolates of the powdery mildew fungal pathogen targeting barley (Hordeum vulgare). To characterize haplotypes present in the Mlo chromosomal region of cultivated Mlo and mlo barley genotypes, we conducted a polymorphism search in 3 predicted low-copy sequence regions adjacent to the Mlo gene by examining a sample of 4 Mlo and 3 mlo cultivars. Eight single-nucleotide polymorphisms (SNPs) and 1 insertion-deletion (indel) were detected, and easy to use PCR-based markers were developed for typing the SNPs. The PCR markers were used to characterize a collection of 46 Mlo and 25 mlo barley cultivars, identifying 3 distinct mlo-11 haplotypes, 1 mlo-9 haplotype, and 4 Mlo haplotypes. We summarized the haplotype and marker information obtained here and in a previous study to help breeders identify strategies for mlo marker-assisted selection. The ability of the markers to identify mlo-resistant genotypes in segregating populations was demonstrated using 2 resistance-characterized F2 populations derived by 3-way crosses.     

Haplotype structure at seven barley genes: relevance to gene pool bottlenecks, phylogeny of ear type and site of barley domestication

Archaeological remains indicate that the origin of western agriculture occurred in a brief period about 10,500 years ago in a region of the Middle East known as the Fertile Crescent, where the wild progenitors of several key agricultural cereal species are endemic. Domestication entailed the appearance of agronomic traits such as seed size and threshability. For a representative sample of 20 domesticated barley (Hordeum vulgare) lines, including 13 two-rowed and 7 six-rowed varieties, we determined the haplotypes at seven loci-Adh2, Adh3, Amy1, Dhn9, GAPDH, PEPC and WAXY encompassing 5,616 bases per line-and compared them to the haplotypes at the same loci for 25 wild forms (Hordeum spontaneum) collected within and outside the Fertile Crescent. In comparisons of wild versus domesticated barley, the number of haplotypes (70 vs. 17), average nucleotide diversity, pi, (0.0077 vs. 0.0028), and Watterson's theta at silent sites (0.0104 vs. 0.0028) was reduced in domesticated lines. Two loci, Amy1 and PEPC, were monomorphic in domesticated lines; Amy1 and GAPDH produced significant values of Tajima's D. At GAPDH, pi was slightly higher in domesticated than wild forms, due to divergent high-frequency haplotypes; for the remaining six loci, 87% of nucleotide diversity has been lost in the domesticated forms. Bottlenecks acting on neutrally evolving loci either during the domestication process, during subsequent breeding, or both, are sufficient to account for reduced diversity and the results of Tajima's test, without the need to evoke selection at these loci. Phylogenetic networks data uncover distinct wild and domesticated barley genotypes and suggest that barley may have been domesticated in the Jordan valley. Because, based on AFLP data, the domesticated Turkish cultivars had a genetic basis as large as that present in large germplasm collections, all comparisons provided in this paper are of general value more than being restricted to the Turkish barley germplasm.     

Adaptive evolution of α-amylase genes in wild barley (Hordeum spontaneum) on micro and macro scales

Alpha-amylases play essential roles in germination, and the malting and brewing processes, by hydrolyzing starch granules present in the endosperm of barley.Hordeum spontaneum C. Koch, the progenitor of cultivated barley that harbors rich genetic diversity, was collected from seven different environments. To investigate the influence of microclimatic ecological divergence on α-amylase, single nucleotide polymorphisms (SNPs) in amy genes from these populations were determined. A total of 16 and 17 SNPs were detected in the coding sequences of amy1 and amy2, respectively, from the seven wild barley populations. Among these SNPs, three in amy1-2 and nine in amy2-2 were significantly associated with ecological factors. The genetic divergence of amy sequences was significantly different among the populations. Natural microclimatic selection was apparently the major evolutionary driving force causing interslope divergence and adaptive evolution of these genes. The genetic variation in amy1-2 and amy2-2 was at least partly ecologically determined in these populations, representing adaptive patterns generated by natural selection. The SNPs were apparently generated by natural selection in climatic environmental patterns at both the micro (“Evolution Canyon”) and macro (across Israel, Galilee, and Negev) scales.