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Objective: Anti-drug antibodies (ADA) to anti-tumour necrosis factor (anti-TNF) therapy drive treatment loss of response. An association between intestinal microbial composition and response to anti-TNF therapy was noted. We therefore aimed to assess the implications of antibiotic treatments on ADA formation in patients with inflammatory bowel disease (IBD)., Design: We analysed data from the epi-IIRN (epidemiology group of the Israeli IBD research nucleus), a nationwide registry of all patients with IBD in Israel. We included all patients treated with anti-TNF who had available ADA levels. Survival analysis with drug use as time varying covariates were used to assess the association between antibiotic use and ADA development. Next, specific pathogen and germ-free C57BL mice were treated with respective antibiotics and challenged with infliximab. ADA were assessed after 14 days., Results: Among 1946 eligible patients, with a median follow-up of 651 days from initiation of therapy, 363 had positive ADA. Cox proportional hazard model demonstrated an increased risk of ADA development in patients who used cephalosporins (HR=1.97, 95% CI 1.58 to 2.44), or penicillins with β-lactamase inhibitors (penicillin-BLI, HR=1.4, 95% CI 1.13 to 1.74), whereas a reduced risk was noted in patients treated with macrolides (HR=0.38, 95% CI 0.16 to 0.86) or fluoroquinolones (HR=0.20, 95% CI 0.12 to 0.35). In mice exposed to infliximab, significantly increased ADA production was observed in cephalosporin as compared with macrolide pretreated mice. Germ-free mice produced no ADA., Conclusion: ADA production is associated with the microbial composition. The risk of ADA development during anti-TNF therapy can possibly be reduced by avoidance of cephalosporins and penicillin-BLIs, or by treatment with fluoroquinolones or macrolides., Competing Interests: Competing interests: YC received research grants, speaker and advisory fees from AbbVie; speaker and advisory fees from Janssen; grant, speaker and advisory fees from Takeda and consultancy fees from CytoReason. SSO received grant funding from Takeda, holds equity and receives consultancy fees from CytoReason. SG-V declares CytoReason advisory fees for last 3 years. RK received consultation fee, research grant, royalties or honorarium from Takeda and Pfizer. ID received consultation fee, research grant or honorarium from Janssen, AbbVie, Takeda, Pfizer, Roche/Genentech, Celgene/BMS, Arena, Neopharm, Gilead, Gallapagos, Celltrion, Ferring, Falk Pharma, MSD, DSM, Cambridge Healthcare, Sublimity, Sangamo, Nestle, Wild bio, Food Industries Association, Integran Holdings, Abbott, Altman Research, (© Author(s) (or their employer(s)) 2022. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)

We describe the genomic DNA diversity and divergence of the cyanobacterium Nostoc linckia from "Evolution Canyon," a microsite consisting of ecologically contrasting slopes, south-facing slope (SFS) and north-facing slope (NFS), at lower Nahal Oren, Mt. Carmel, Israel. The opposing slopes share their limestone lithology but vary greatly in their ecology, primarily because of different levels of solar radiation (which is six times higher on the SFS than on the NFS). The warm and xeric SFS displays a tropical African savanna, whereas the cool and mesic NFS displays a temperate South European Mediterranean live-oak maquis shrub forest. The cyanobacterium Nostoc linckia tested here is a sessile microorganism, growing as a carpet on rock surfaces and constantly exposed to environmental fluctuations of solar radiation, temperature, and desiccation. We demonstrate remarkable interslope and intraslope genetic divergence of the genome (including both coding and noncoding regions) of Nostoc linckia, by using 211 AFLP (amplified fragment length polymorphism) DNA molecular marker loci. Genetic polymorphism of N. linckia subpopulations on the ecologically harsher SFS was significantly (p <0.05) higher (p = 99.53%) than was that of the subpopulations on the climatically milder nfs (p = 85.78%). genetic polymorphism (p) and gene diversity (he) were significantly correlated with variables influencing aridity stress: solar radiation (sr) (rp = 0.956; p = 0.046), temperature (tm) (rp = 0.993; p = 0.0068), and day-night temperature difference (tdd) (rp = 0.975; p = 0.025). as in other tested organisms from "evolution canyon", but even more exceptionally because of its completely sedentary nature, we suggest that the climatically stressed sfs environment is responsible for this marked increase of genetic polymorphism, which is maintained by the combined evolutionary forces of diversifying and balancing selection. This could highlight the importance of ecological stress and selection in evolution and its remarkable effect on the genetic system across the prokaryotic genome. [ABSTRACT FROM AUTHOR]

Modern man-made environments, including urban, agricultural, and industrial environments, have complex ecological interactions among themselves and with the natural surroundings. Microbial source tracking (MST) offers advanced tools to resolve the host source of fecal contamination beyond indicator monitoring. This study was intended to assess karst spring susceptibilities to different fecal sources using MST quantitative PCR (qPCR) assays targeting human, bovine, and swine markers. It involved a dual-time monitoring frame: (i) monthly throughout the calendar year and (ii) daily during a rainfall event. Data integration was taken from both monthly and daily MST profile monitoring and improved identification of spring susceptibility to host fecal contamination; three springs located in close geographic proximity revealed different MST profiles. The Giach spring showed moderate fluctuations of MST marker quantities amid wet and dry samplings, while the Zuf spring had the highest rise of the GenBac3 marker during the wet event, which was mirrored in other markers as well. The revelation of human fecal contamination during the dry season not connected to incidents of raining leachates suggests a continuous and direct exposure to septic systems. Pigpens were identified in the watersheds of Zuf, Shefa, and Giach springs and on the border of the Gaaton spring watershed. Their impact was correlated with partial detection of the Pig-2-Bac marker in Gaaton spring, which was lower than detection levels in all three of the other springs. Ruminant and swine markers were detected intermittently, and their contamination potential during the wet samplings was exposed. These results emphasized the importance of sampling design to utilize the MST approach to delineate subtleties of fecal contamination in the environment., (Copyright © 2015, American Society for Microbiology. All Rights Reserved.)

A 3-year environmental and clinical Vibrio vulnificus survey using simple-sequence repeats typing shows that V. vulnificus biotype 3 constitutes approximately 21% of the bacterium population in tested aquaculture ponds as opposed to approximately 86% of clinical cases. Simple-sequence repeats proved to be a useful epidemiologic tool, providing information on the environmental source of the pathogen.

During the 11-year period from 1997 to 2007, 321 isolates of Listeria monocytogenes from sporadic cases of invasive listeriosis were reported to the national reference laboratory in Israel. Of these isolates, 113 (35%) were identified from perinatal cases, and 208 (65%) from non-perinatal cases. The prevalent serovars were 4b, 1/2b, 1/2a and 4c. Serovar 4b was identified in 80.5% of the perinatal isolates (P=0.0162), while the number of 1/2b and 1/2a strains increased in the > or = 60 years old group (P=0.0285). Resistance to tetracycline was found in eight 4b isolates. The seasonal distribution showed that 206 isolates (64.2%) were submitted during the hot season (May-October). The estimated morbidity for the study period was 4.4 per million. The incidence of invasive listeriosis was higher in the perinatal group (5.6/100 000), than in individuals aged > or = 60 years (1.5/100 000).

Vibrio cholerae is a natural inhabitant of aquatic ecosystems, yet its interactions within this habitat are poorly understood. Here we describe the current knowledge on the interaction of V. cholerae with one group of co-inhabitants, the chironomids. Chironomids, non-biting midges (Chironomidae, Diptera), are an abundant macroinvertebrate group encountered in freshwater aquatic habitats. As holometabolous insects, chironomids start life when their larvae hatch from eggs laid at the water/air interface; through various feeding strategies, the larvae grow and pupate to become short-lived, non-feeding, adult flying insects. The discovery of the connection between V. cholerae and chironomids was accidental. While working with Chironomus transavaalensis, we observed the disintegration of its egg masses and searched for a possible microbial agent. We identified V. cholerae as the primary cause of this phenomenon. Haemagglutinin/protease, a secreted extracellular enzyme, degraded the gelatinous matrix surrounding the eggs, enabling bacterial growth. Observation of chironomids in relation to V. cholerae continuously for 7 years in various types of water bodies in Israel, India, and Africa revealed that environmental V. cholerae adhere to egg-mass surfaces of various Chironomini ('bloodworms'). The flying adults' potential to serve as mechanical vectors of V. cholerae from one water body to another was established. This, in turn, suggested that these insects play a role in the ecology of V. cholerae and possibly take part in the dissemination of the pathogenic serogroups during, and especially between, epidemics.

The asymmetric bio-reduction of 4-chloro-acetoacetic-acid-ethyl-ester to the pharmaceutical building block (S)-4-chloro-3-hydroxybutanoate-ethyl-ester requires the utilization of an enantioselective robust biocatalyst. Some of the natural Saccharomyces cerevisiae strains, isolated from Mount Carmel National Park in Israel, were characterized as resistant to environmental stress. Nevertheless, these strains showed relatively low enantiomeric-excess (ee), while a laboratory strain, Y103, exhibited a selectivity of 98% ee. The enantioselective lab strain was crossed with the multi-stress resistant environmental isolate (93% ee) followed by backcross with Y103, to subsequently obtain a haploid offspring of backcross-1, exhibiting both high multi-stress resistance and high enantioselectivity (98% ee). Introducing osmotic (1 M NaCl), oxidative (0.6 mM H(2)O(2)) and thermal stress (44 degrees C) to growing cultures of the enantioselective parent, resulted in a decrease of 24-32% in specific activity, while the enantioselectivity of the stress-resistant parent decreased by 4-12% ee. Unlike its original parental strains, the new strain maintained constant specific activity and enantioselectivity when introduced to the various stress factors. This work shows that the classic introgression method, can serve as a viable approach for creating a robust enantioselective biocatalyst, designed for industrial production of chiral compounds.

Vibrio vulnificus is an opportunistic, highly invasive human pathogen with worldwide distribution. V. vulnificus strains are commonly divided into three biochemical groups (biotypes), most members of which are pathogenic. Simple sequence repeats (SSR) provide a source of high-level genomic polymorphism used in bacterial typing. Here, we describe the use of variations in mutable SSR loci for accurate and rapid genotyping of V. vulnificus. An in silico screen of the genomes of two V. vulnificus strains revealed thousands of SSR tracts. Twelve SSR with core motifs longer than 5 bp in a panel of 32 characterized and 56 other V. vulnificus isolates, including both clinical and environmental isolates from all three biotypes, were tested for polymorphism. All tested SSR were polymorphic, and diversity indices ranged from 0.17 to 0.90, allowing a high degree of discrimination among isolates (27 of 32 characterized isolates). Genetic analysis of the SSR data resulted in the clear distinction of isolates that belong to the highly virulent biotype 3 group. Despite the clonal nature of this new group, SSR analysis demonstrated high-level discriminatory power within the biotype 3 group, as opposed to other molecular methods that failed to differentiate these isolates. Thus, SSR are suitable for rapid typing and classification of V. vulnificus strains by high-throughput capillary electrophoresis methods. SSR (>/=5 bp) by their nature enable the identification of variations occurring on a small scale and, therefore, may provide new insights into the newly emerged biotype 3 group of V. vulnificus and may be used as an efficient tool in epidemiological studies.

The yeast S. cerevisiae is a central model organism in eukaryotic cell studies and a major component in many food and biotechnological industrial processes. However, the wide knowledge regarding genetics and molecular biology of S. cerevisiae is based on an extremely narrow range of strains. Studies of natural populations of S. cerevisiae, not associated with human activities or industrial fermentation environments, are very few. We isolated a panel of S. cerevisiae strains from a natural microsite, "Evolution Canyon" at Mount Carmel, Israel, and studied their genomic biodiversity. Analysis of 19 microsatellite loci revealed high allelic diversity and variation in ploidy level across the panel, from diploids to tetraploids, confirmed by flow cytometry. No significant differences were found in the level of microsatellite variation between strains derived from the major localities or microniches, whereas strains of different ploidy showed low similarity in allele content. Maximum genetic diversity was observed among diploids and minimum among triploids. Phylogenetic analysis revealed clonal, rather than sexual, structure of the triploid and tetraploid subpopulations. Viability tests in tetrad analysis also suggest that clonal reproduction may predominate in the polyploid subpopulations.

Israeli Holstein-Friesian dairy bulls were screened for restriction fragment length polymorphisms by hybridizing cloned DNA probes for bovine growth hormone, for chymosin, and for rat muscle beta-actin to restriction endonuclease-digested DNA immobilized on nitrocellulose filters. The population proved to be polymorphic at the growth hormone locus, with evidence consistent with the phenotypes being inherited in allelic fashion. A low level of polymorphism was also observed at one of the beta-actin gene family loci. The chymosin locus was monomorphic with the restriction enzymes utilized. The results illustrate the power of restriction fragment length polymorphism methodology in visualizing genetic variability in dairy cattle populations.

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. [ABSTRACT FROM AUTHOR]

Background: Species of the genus Aeromonas are native inhabitants of aquatic environments and have recently been considered emerging human pathogens. Although the gastrointestinal tract is by far the most common anatomic site from which aeromonads are recovered, their role as etiologic agents of bacterial diarrhea is still disputed. Aeromonas-associated diarrhea is a phenomenon occurring worldwide; however, the exact prevalence of Aeromonas infections on a global scale is unknown. Methodology/Principal Findings: The prevalence and virulence potential of Aeromonas in patients suffering from diarrhea in Israel was studied using molecular methods. 1,033 diarrheal stools were sampled between April and September 2010 and Aeromonas species were identified in 17 (∼2%) patients by sequencing the rpoD gene. Aeromonas species identity and abundance was: A. caviae (65%), A. veronii (29%) and Aeromonas taiwanensis (6%). This is the first clinical record of A. taiwanensis as a diarrheal causative since its recent discovery from a wound infection in a patient in Taiwan. Most of the patients (77%) from which Aeromonas species were isolated were negative for any other pathogens. The patients ranged from 1 to 92 years in age. Aeromonas isolates were found to possess different virulence-associated genes: ahpB (88%), pla/ lip/lipH3/apl-1 (71%), act/hlyA/aerA (35%), alt (18%), ast (6%), fla (65%), lafA (41%), TTSS ascV (12%), TTSS ascF-ascG (12%), TTSS-dependent ADP-ribosylating toxins aexU (41%) and aexT (6%) in various combinations. Most of the identified strains were resistant to beta-lactam antibiotics but susceptible to third-generation cephalosporin antibiotics. Conclusions: Aeromonas may be a causative agent of diarrhea in patients in Israel and therefore should be included in routine bacteriological screenings. [ABSTRACT FROM AUTHOR]

The mode of reproduction of the soil ascomycetous fungus Emericella nidulans of Israeli populations was studied using 15 microsatellite (simple sequence repeats or SSR) trinucleotide markers. The study was performed in three canyons: two located in the northern part of Israel (Mount Carmel and western Upper Galilee) and one in the southern Negev desert. In each canyon, E. nidulans strains were isolated from the opposite slopes and (in the desert canyon) the valley bottom. Testing the reproductive structure of the populations indicated the presence of sexuality in the northern population and predominant clonality in the desert population. The predominantly clonal character of the desert population of E. nidulans was explained by the assumption that for relevant multilocus systems of a fungus, only several haplotypes can survive in the rather constant, extremely stressful desert conditions. Additionally, the very low density of E. nidulans populations in the soil of the desert canyon, which reduces the probability of finding a sexual partner, might favour predominant clonality via selfing. Increasing sexuality in E. nidulans populations on the north-facing slopes of the northern canyons may be a result of biotic stress (pressure of competitive fungal species), due to the more mild ecological conditions in these canyons. [ABSTRACT FROM AUTHOR]

The article provides an overview of the evidence indicating the importance of the Evolution Canyon (EC) model in Israel for resolving many open problems in evolutionary biology. It discusses the rise and challenges of evolutionism, particularly Darwinian evolution. It also shows how microevolutionary studies across sharp boundaries can not only serve as a model for evolutionary analysis, but also point the way forward in evolutionary biology.

We examined the genetic diversity and divergence of Ricotia lunaria, a family relative species of Arabidopsis thaliana, sampled from 6 stations on 2 opposing slopes, the south-facing slope ("African" or AS) and north-facing slope ("European" or ES), separated on average by 200 m, at "Evolution Canyon," Lower Nahal Oren, Mount Carmel, Israel, along a transect presenting sharply differing microclimates. The density of R. lunaria populations was slope specific: a higher density and smaller plants were observed on the AS. In addition, the density was positively correlated with annual plant cover. The interslope and intraslope genetic diversities of R. lunara populations were examined using the amplified fragment length polymorphism (AFLP) technique with 5 primer pairs. Ricotia lunaria populations inhabiting the ES and AS differed, and among the 468 scored loci, 304 (65%) were polymorphic (at P ≥ 0.05 level). Polymorphism values obtained for AS and ES populations were similar (52% vs. 56%), but different loci were polymorphic in different populations; 40% of polymorphic loci were identical on both the ES and AS, 16% were polymorphic for the ES only, and 12% were polymorphic only for the AS. The AFLP results grouped the analyzed genotypes into 2 distinct clusters: one cluster included the plants belonging to the AS and the other included ES plants. The unbiased estimate of Nei genetic distances (D) indicated significantly higher interslope (D = 0.124 ± 0.011) than intraslope (D = 0.076 ± 0.015) differences (P < 0.001 in t-test). Correspondingly, mean intraslope gene flow was significantly higher than the interslope gene flow (2.9 ± 0.6 vs. 1.9 ± 0.2). Natural selection appears to adaptively diverge the plant ecotypes on the opposite slope, both phenotypically and genotypically. This includes significant divergence in flowering time likely to initiate incipient sympatric speciation. [ABSTRACT FROM AUTHOR]

Background: Natural populations of most organisms, especially unicellular microorganisms, are constantly exposed to harsh environmental factors which affect their growth. UV radiation is one of the most important physical parameters which influences yeast growth in nature. Here we used 46 natural strains of Saccharomyces cerevisiae isolated from several natural populations at the ''Evolution Canyon'' microsite (Nahal Oren, Mt. Carmel, Israel). The opposing slopes of this canyon share the same geology, soil, and macroclimate, but they differ in microclimatic conditions. The interslope differences in solar radiation (200%-800% more on the ''African'' slope) caused the development of two distinct biomes. The south-facing slope is sunnier and has xeric, savannoid ''African'' environment while the north-facing slope is represented by temperate, ''European'' forested environment. Here we studied the phenotypic response of the S. cerevisiae strains to UVA and UVC radiations and to methyl methanesulfonate (MMS) in order to evaluate the interslope effect on the strains' ability to withstand DNA-damaging agents. Methodology/Principal Findings: We exposed our strains to the different DNA-damaging agents and measured survival by counting colony forming units. The strains from the ''African'' slope were more resilient to both UVA and MMS than the strains from the ''European'' slope. In contrast, we found that there was almost no difference between strains (with similar ploidy) from the opposite slopes, in their sensitivity to UVC radiation. These results suggest that the ''African'' strains are more adapted to higher solar radiation than the ''European'' strains. We also found that the tetraploids strains were more tolerant to all DNA-damaging agents than their neighboring diploid strains, which suggest that high ploidy level might be a mechanism of adaptation to high solar radiation. Conclusions/Significance: Our results and the results of parallel studies with several other organisms, suggest that natural selection appears to select, at a microscale, for adaptive complexes that can tolerate the higher UV radiation on the ''African'' slope. [ABSTRACT FROM AUTHOR]

The "Evolution Canyon" model reveals evolution in action across life at a microscale involving biodiversity divergence, adaptation and incipient sympatric ecological speciation across life. The model highlights diverse taxa species richness, genomics, proteomics and phenomics phenomena by exploring genetic polymorphisms at protein and DNA levels and, recently, genome-wide gene expression and regulation. Genetic diversity and divergence reveal evolutionary dynamics of natural populations exposed to sharp-interslope, ecologically divergent, tropical and temperate microclimates on a xeric, tropical, "African" south-facing slope (AS) abutting with a mesic, temperate, "European" north-facing slope (ES) separated by 200 meters on average. Four "Evolution Canyons" (EC) are currently being investigated in Israel in the Carmel, Galilee, Negev, and Golan Mountains (EC I-IV), respectively. We identified 2,500 species in ECI (Carmel) from bacteria to mammals in an area of 7,000 m2. Local biodiversity patterns parallel global patterns. Higher terrestrial species richness was found on the AS. Aquatic species richness prevails on the ES. In 9 out of 14 (64%) model organisms across life, we identified a significantly higher genetic polymorphism on the more stressful AS. Likewise, in some model taxa, we found largely higher levels of mutation rates, gene conversion, recombination, DNA repair, genome size, small sequence repeats (SSRs), single nucleotide polymorphism (SNPs), retrotransposons, transposons, candidate gene diversity, and genome-wide gene expression and regulation on the more stressful AS. Remarkably, interslope incipient sympatric ecological speciation was found across life from bacteria to mammals. The "Evolution Canyon" model represents the Israeli ecological analogue of the Galapagos Islands. Microclimatic selection overrides gene flow and drift, and drives both interslope adaptive divergence and incipient sympatric ecological speciation at a microscale. The EC model could potentially highlight many mysteries of evolutionary biology including the genetic basis of adaptation and speciation, especially now with the rapid high-throughput techniques of whole genome analysis. [ABSTRACT FROM AUTHOR]

During 1996-1997, a new Vibrio vulnificus biotype 3, which caused severe soft tissue infection after fishbone injury, emerged in Israel. We conducted a follow-up study from 1998 through 2005 to assess changing trends, outcomes, and molecular relatedness of the implicated strains. A total of 132 cases (71% confirmed and 29% suspected) of V. vulnificus biotype 3 infection were found. Most infections (95%) were related to percutaneous fish exposure, mainly tilapia (83%) or common carp (13%). Bacteremia, altered immune status, and history of ischemic heart disease were identified as independent risk factors for death, which reached a prevalence of 7.6%. Pulsed-field gel electrophoresis patterns of strains from 1998 through 2005 and from 1996 through 1997 showed a high degree of homogeneity and were distinct from those of V. vulnificus biotype 1. Infections caused by V. vulnificus biotype 3 continue to affect the public's health in Israel. [ABSTRACT FROM AUTHOR]

The genes for the two respiratory proteins neuroglobin (Ngb) and cytoglobin (Cygb) in the subterranean Israeli mole rat Spalax carmeli have been sequenced and compared to other mammals including human. Coding regions of both Spalax genes are highly conserved on the nucleotide and amino acid level. The ratios of non-synonymous to synonymous nucleotide substitutions suggest strong purifying selection acting on Ngb and Cygb in all mammals. Thus, there appears to be no special sequence level adaptation in the two respiratory proteins within the hypoxia-tolerant mole rat. On the genomic level, Spalax Ngb and Cygb gene regions revealed the conserved 4-exon-3-intron structure and conserved CpG-rich islands in the 5' region. The Spalax Cygb gene promoter contains a conserved hypoxia-responsive transcription factor binding site, indicating a possible up-regulation of Cygb under oxygen deprivation. In Cygb intron 1, we observed a stretch of highly conserved putatively non-coding sequence of yet unknown (regulatory?) importance. In the Spalax Ngb gene, we note the presence of candidate hypoxia-responsive elements, which are not conserved in Ngb of hypoxia-sensitive mammals. Both globin gene regions harbor Spalax-specific simple sequence regions, which might be of adaptive value. We conclude that adaptations for hypoxia in mole rats are most likely to be found in regulatory functions rather than in protein structure. [ABSTRACT FROM AUTHOR]

Local microcosmic natural laboratories, dubbed "Evolution Canyon" (EC) models, reinforce studies of regional and global macrocosmic ecological theaters across life and unravel evolution in action. The EC model laboratories permit genomic, proteomic, and phenomic studies highlighting speciation and adaptation at a microscale. Critical transplant experiment tests can evaluate interslope differential fitness. Novel techniques of genetic mapping, sequence nucleotide polymorphisms (SNPs), and wide genome coding and noncoding expressions can unravel evolutionary dynamics. Finally, fundamental problems such as stress effects on nonrandom mutations, lateral transfers, splicing variations, sex, and social evolutions, and adaptive strategies of prokaryotes and eukaryotes are testable. We are studying four "Evolution Canyons" (EC I-IV) in the Carmel, Galilee, Negev, and Golan mountains. We've identified 2,500 species in EC I (Carmel) from bacteria to mammals in an area of 7,000 m. Higher terrestrial species richness was found on the more stressful tropical "African" slope (AS). Aquatic species richness was higher on the milder, temperate "European" slope (ES). In soil fungi we found interslope local and regional adaptive divergence in sex, melanism, and conidia. In nine out of 14 (64%) model organisms across life we identified largely higher genetic polymorphisms on the more stressful "African" slope. In some model species we found higher mutation rates, gene conversion, recombination, DNA repair, and larger genome size as well as interslope divergent micro-satellites, molecular polymorphisms, retrotransposons, and wide-genome gene expression on the more stressful AS. Remarkably, interslope incipient sympatric speciation was found across life. The "Evolution Canyon" model represents the Israeli ecological equivalent of the Galapagos Islands. Micro-climatic selection overrides drift and drives both interslope adaptive radiation and incipient sympatric speciation. The EC model could potentially highlight many mysteries of evolutionary biology. [ABSTRACT FROM AUTHOR]

This study focuses on the molecular features of three candidate behavioural genes in Drosophila melanogaster from the opposite slopes of Nahal Oren Canyon, Mount Carmel, Israel. These slopes display dramatic physical and biotic contrasts. Spatial variation of microclimatic conditions leads to adaptive differentiation and partial sexual isolation of populations, as suggested by our previous studies. The chosen candidate genes presumably contributing to genetic variation in sexual behaviour of Drosophila in the Canyon were desaturase, period, and no-on-transient A. These genes are known to include polymorphic repeated sequences, insertions/deletions, or nucleotide substitutions. The idea was that their polymorphism might be one of the determinants of behavioural peculiarities of flies derived from the opposite slopes. Indeed, interslope differences in the sequence encoding the (Thr-Gly) n repeat (exon 5) of the period gene were established, suggesting evolutionary functional importance. In particular, we unraveled variation in the length and composition of this region in different NFS (north-facing slope) and SFS (south-facing slope) lines. The ‘European’ allele ( n = 20) was a 2.6-fold more abundant on the NFS compared to the SFS. This predominance probably gives some advantages for flies inhabiting wet and less warm conditions of the NFS. We suggest that repeat length/composition may influence the functional features of flies, i.e. habitat choice, nonrandom mating, and temperature adaptation. A series of female single-mate-choice tests show that females derived from NFS distinguish between males with specific per alleles ( n = 17 vs. n = 20), as well as between males originated from the opposing slopes. Females from SFS were less discriminating and did not manifest significant deviation from random mating. [ABSTRACT FROM AUTHOR]

We examined diversity levels and patterns of 19 nuclear microsatellites and four chloroplast microsatellites in 275 genotypes of wild barleyHordeum spontaneum, in seven stations at the‘Evolution Canyon’ (EC) microsite, Lower Nahal Oren, Mt. Carmel, Israel. EC is sharply subdivided ecologically into a tropical savannoid,‘African’, xeric, south-facing slope (SFS) abutting the temperate, dense, liveoak, brushwood,‘European’, mesic, north-facing slope (NFS). We found the following. (i) 17 of 19 (89.5%) nuDNA simple sequence repeats (SSRs) were polymorphic across all seven subpopulations and three chDNA SSRs were polymorphic. (ii) A total of 216 nuDNA SSR alleles, with a maximum of 23 alleles in a nuclear locus, and ten chDNA SSRs, with a maximum of four alleles in a locus, were registered. (iii) There were striking and significant inter- and intraslope diversities, based on the 19 nuDNA SSRs, climaxing with a remarkable genetic distance between the mid-slope stations on opposite slopes (D A = 0.481), across a distance of 200 m. This genetic distance is as large as that between theH. spontaneumpopulations of Jerusalem and Sede Boqer, which are separated by 100 km (× 500 larger in transect length). (iv) Slope-unique alleles (103 = 45.6%) were higher on the‘European’ than on the‘African’ slope. Slope-specific (predominant) alleles (17) were equal on opposite slopes. (v) nuDNA SSR gene diversity was higher on the‘European’ slope and the opposite was found for the chDNA SSR. (vi) nuDNA SSR genic differentiation was very high between opposite slopes, withGst = 0.187; for chDNA SSR this value was 0.127. Our results are inexplicable by stochastic processes and suggest that: (i) microclimatic diversifying selection is the major evolutionary, fast-acting, interslope force, overriding migration and drift, and (ii) ecological stress can generate local, regional and global adaptive patterns, suggesting that natural selection is a major differentiating force of both coding and noncoding SSRs linking micro- and macroevolutionary processes. © 2005 The Linnean Society of London,Biological Journal of the Linnean Society, 2005,84, 205–224. [ABSTRACT FROM AUTHOR]

We analyzed the ecological-genomic diversity of microsatellites of wild barley, Hordeum spontaneum (C. Koch) Thell., at 18 loci in 306 individuals of 16 populations from Jordan across a southward transect of increasing aridity. The 18 microsatellites revealed a total of 249 alleles, with an average of 13.8 alleles per locus (range 3–29), with nonrandom distribution. The proportion of polymorphic loci per population averaged 0.91 (range 0.83–1.00); gene diversity, He, averaged 0.512 (range 0.38–0.651). We compared the number of alleles of the 18 loci to those found in Israel populations by Turpeinen et al.. Out of the 280 alleles, 138 (49.3%) were unique (i.e. occurred in only one of the countries). The percentage of unique alleles in Jordan and Israel populations was 43.0% and 17.9%, respectively, suggesting that Jordan is an important center of origin and diversity of wild barley. Estimates of mean gene diversity were highest in the populations collected near the Golan Heights, such as Shuni North, Shuni South and Jarash. Sixty nine percent of the microsatellite variation was partitioned within populations and 31% between populations. Associations between ecogeographical values and gene diversity were established for eight microsatellite loci. The cluster produced by simple sequence repeat (SSR) data is mostly coincidence with the result of the dendrogram of the Spalax ehrenbergi superspecies of subterranean mole rats in Jordan based on allozyme gene loci. The major soil type in the wild barley habitat of each ecological group was different. Stepwise multiple regression analysis indicated that the variance of gene diversity was explained by altitude (R2 = 0.362**). These observations suggest that microsatellites are at least partly adaptive and subject to natural selection. Electronic Supplementary Material is available if you access this article at http://dx.doi.org/10.1007/s00122-002-1029-7. On that page (frame on the left side), a link takes you directly to the supplementary material. [ABSTRACT FROM AUTHOR]

This study investigated allele size constraints and clustering, and genetic effects on microsatellite (simple sequence repeat, SSR) diversity at 28 loci comprising seven types of tandem repeated dinucleotide motifs in a natural population of wild emmer wheat, Triticum dicoccoides, from a shade vs sun microsite in Yehudiyya, northeast of the Sea of Galilee, Israel. It was found that allele distribution at SSR loci is clustered and constrained with lower or higher boundary. This may imply that SSR have functional significance and natural constraints. Genetic factors, involving genome, chromosome, motif, and locus significantly affected SSR diversity. Genome B appeared to have a larger average repeat number (ARN), but lower variance in repeat number (σ²ARN), and smaller number of alleles per locus than genome A. SSRs with compound motifs showed larger ARN than those with perfect motifs. The effects of replication slippage and recombinational effects (eg, unequal crossing over) on SSR diversity varied with SSR motifs. Ecological stresses (sun vs shade) may affect mutational mechanisms, influencing the level of SSR diversity by both processes. [ABSTRACT FROM AUTHOR]

Genetic diversity at 38 microsatellite (short sequence repeats (SSRs)) loci was studied in a sample of 54 plants representing a natural population of wild barley, Hordeum spontaneum, at the Neve Yaar microsite in Israel. Wild barley at the microsite was organized in a mosaic pattern over an area of 3180 m[sup 2] in the open Tabor oak forest, which was subdivided into four microniches: (i) sun–rock (11 genotypes), (ii) sun–soil (18 genotypes), (iii) shade–soil (11 genotypes), and (iv) shade–rock (14 genotypes). Fifty-four genotypes were tested for ecological–genetic microniche correlates. Analysis of 36 loci showed that allele distributions at SSR loci were nonrandom but structured by ecological stresses (climatic and edaphic). Sixteen (45.7%) of 35 polymorphic loci varied significantly (p < 0.05) in allele frequencies among the microniches. Significant genetic divergence and diversity were found among the four subpopulations. The soil and shade subpopulations showed higher genetic diversities at SSR loci than the rock and sun subpopulations, and the lowest genetic diversity was observed in the sun–rock subpopulation, in contrast with the previous allozyme and RAPD studies. On average, of 36 loci, 88.75% of the total genetic diversity exists within the four microniches, while 11.25% exists between the microniches. In a permutation test, G[sub ST] was lower for 4999 out of 5000 randomized data sets (p < 0.001) when compared with real data (0.1125). The highest genetic distance was between shade-soil and sun–rock (D = 0.222). Our results suggest that diversifying natural selection may act upon some regulatory regions, resulting in adaptive SSR divergence. Fixation of some loci (GMS61, GMS1, and EBMAC824) at a specific microniche seems to suggest directional selection. The pattern of other SSR loci suggests the operation of balancing selection. SSRs may be either direct targets of selection or markers of selected haplotypes (selective sweep).Key words: natural selection, genetic diversity, microsatellites, adaptation, Hordeum spontaneum, wild barley, microsite divergence.La diversité génétique au niveau de 38 locus microsatellites (SSR) a été examinée chez une collection de 54 plantes représentative d'une population naturelle de l'orge sauvage, Hordeum spontaneum, provenant du microsite Neve Yaar en Israël. L'orge sauvage se retrouve en mosaïque au sein d'une aire de 3180 m[sup 2] dans la forêt Tabor, une forêt ouverte de chênes, laquelle comprend quatre microniches : (i) soleil–roche (11 génotypes), (ii) soleil–sol (18 génotypes), (iii) ombre–sol (11 génotypes) et (iv) ombre–roche (14 génotypes). Cinquante-quatre génotypes ont été testés pour des corrélations écologiques-génétiques au sein des microniches. L'analyse de 36 locus a montré que la distribution des allèles aux locus SSR n'était pas aléatoire, mais plutôt structurée par les stress écologiques (climatiques et édaphiques). Chez seize (45,7 %) des 35 locus polymorphes, la fréquence allélique était significativement différente (p < 0,05) entre les microniches. Des divergences et des distances génétiques significatives ont été observées au sein des quatre sous-populations. Les sous-populations sol et ombre présentaient une plus grande diversité génétique aux locus SSR que les sous-populations roche et soleil. La plus faible diversité génétique a été observée chez la sous-population soleil-roche, contrairement à ce qui avait été noté lors de précédentes études à l'aide d'alloenzymes et de marqueurs RAPD. En moyenne pour les 36 locus, 88,75 % de la diversité génétique existait au sein des quatre microniches tandis que 11,25 % existait entre les microniches. Lors de permutations, la valeur G[sub ST] obtenue à l'aide de données randomisées était plus faible que les données réelles (0,1125) 4999 fois sur 5000 (p < 0,001). La plus grande distance génétique a été notée entre les sous-populations ombre–sol et soleil–roche (D = 0,222). Ces résultats suggèrent qu'une sélection naturelle induisant une diversification pourrait s'exercer sur certaines régions régulatrices entraînant une divergence adaptative au niveau des locus SSR. La fixation de certains locus (GMS61, GMS1 et EBMAC824) dans une microniche semble suggérer une sélection directionnelle. Dans d'autres cas, les données suggèrent une sélection équilibrante. Les locus SSR pourraient être des cibles immédiates de la sélection ou encore des marqueurs des haplotypes sélectionnés (une vague sélective, « selective sweep »).Mots clés : sélection naturelle, diversité génétique, microsatellites, adaptation, Hordeum spontaneum, orge sauvage, divergence au sein d'un microsite.[Traduit par la Rédaction] [ABSTRACT FROM AUTHOR]

Abstract Microsatellite diversity at 18 loci was analysed in 94 individual plants of 10 wild barley, Hordeum spontaneum (C. Koch) Thell., populations sampled from Israel across a southward transect of increasing aridity. Allelic distribution in populations was not distributed randomly. Estimates of mean gene diversity were highest in stressful arid-hot environments. Sixty-four per cent of the genetic variation was partitioned within populations and 36% between populations. Associations between ecogeographical variables and gene diversity, He, were established in nine microsatellite loci. By employing principle component analysis we reduced the number of ecogeographical variables to three principal components including water factors, temperature and geography. At three loci, stepwise multiple regression analysis explained significantly the gene diversity by a single principal component (water factors). Based on these observations it is suggested that simple sequence repeats are not necessarily biologically neutral. [ABSTRACT FROM AUTHOR]

Twenty eight microsatellite markers were used to analyze genetic divergence in tandem dinucleotide repeated DNA regions between two edaphic subpopulations of Triticum dicoccoides growing on the contrasting terra rossa and basalt soilsfrom a microsite at Tabigha, north of the Sea of Galilee, Israel. The terra rossa soil niche was drier and more stressful than the basalt throughout the growing season (November to May). Significant microsatellite divergence in allele distribution, repeat length, genetic diversity, and linkage disequilibria were found between emmer wheat from the two soil types over two short transects of 100 m each. Soil-specific and -unique alleles and linkage disequilibria were observed in the terra rossa and basalt subpopulations. A permutation test showed that the effects of random genetic drift were very low for the significant genetic diversity at microsatellite loci between the two subpopulations, suggesting that an adaptive molecular pattern derived by edaphic selection may act upon variation of the microsatellites. [ABSTRACT FROM AUTHOR]

Genetic diversity at 28 microsatellite loci was studied in a natural population of Triticum dicoccoides at the Ammiad microsite, north of the Sea of Galilee, Israel. This microsite was subdivided into four major habitats, North, Valley, Ridge and Karst, and further subdivided into nine subhabitats. The units thus defined showed strong and highly significant differentiation in ecological factors; in particular with respect to cover, proximity and height of rocks, and surface soil moisture after early rains. The results showed that allele distributions at microsatellite loci were nonrandom and associated with habitats. Significant genetic differentiation and variation in repeat number were found among subpopulations in the four major habitats and nine subhabitats. Habitat-specific and -unique alleles and linkage disequilibria were observed in the Karst subpopulation. The subpopulations dwelling in drier habitats and subhabitats showed higher genetic diversities at microsatellite loci. These results suggest that natural selection, presumably through aridity stress, acts upon microsatellite divergence predominantly on noncoding sequences, thereby contributing to differences in fitness. [ABSTRACT FROM AUTHOR]