European Slope Research Articles

Genome-wide analysis revisits incipient sympatric and allopatric speciation in a beetle

Abstract The grain beetle, Oryzaephilus surinamensis, is a widespread species distributed in the wild and in granaries. Our earlier extensive biological studies indicated that the beetle shows incipient sympatric speciation (SS) in the wild at Evolution Canyon I (EC-I), Israel, and allopatric speciation, in a granary. Here we provide genome-wide evidence supporting our adaptive evolution scenario involving two models of speciation, SS in the wild, and allopatric in the granary. The EC-I microsite is a hot spot of SS across life from bacteria to mammals caused by the sharp opposite microclimates. The tropical hot, dry and savannoid biome dubbed the “African” slope (AS), sharply contrasts with the opposite temperate, cool, humid, and forested biome on the European” slope (ES), separated by only ~250 meters. The third allopatric granary population is 26 km north of EC-I. The granary population showed larger genomic, morphological, and behavioral distances, smaller genome size, more unique transposable elements, and reproductive isolation, displaying faster genomic divergence than between the wild populations at EC-I. The incipient SS of the wild populations, and the speciation of the granary population are reinforced by the substantial genomic divergence among the three beetle populations, supporting again the evolutionary scenario of incipient SS with gene flow at EC-I, and allopatric speciation in the granary population. We propose additional studies in Israel, the Mediterranean basin, and worldwide, to negate alternative explanations, based on a broader sampling and analysis.

Soil translocation at “Evolution Canyon” I (Mount Carmel, Israel) reveals the importance of microclimatic variation for structuring soil microfungal communities

An experimental study involving the translocation of soil from the south-facing, tropical, savannoid, “African” slope (AS) to the north-facing, temperate, forested “European” slope (ES), 250 m apart, and vice versa, was performed at “Evolution Canyon”, Mount Carmel, Israel. The purpose of the study was to explore whether the new microclimatic conditions would affect community structure of culturable fungi. The translocation of soil from the AS to the ES significantly decreased the abundance of xeric and thermotolerant components of microfungal communities – melanin-containing fungi and Aspergillus spp. Simultaneously, the mesic component – Penicillium spp, increased in the abundance. The translocation also caused substantial increases in abundance of fast-growing mycoparasitic Clonostachys rosea and Trichoderma koningii, which are known to produce toxic secondary metabolites and grow over other fungi in culture. High abundance of these species apparently caused the significant decrease in species richness in the AS-to-ES translocated communities and made these communities more similar to the native ES communities as the cluster analysis revealed. Notably, the translocation from the xeric south-facing AS to the temperate north-facing ES caused more substantial changes in the microfungal communities as compared to the opposite soil translocation. The results of the study clearly indicated that translocation of the soil to the opposite slopes of “Evolution Canyon” had changed the community structure of microfungal communities, and these changes were apparently driven by variation in environmental conditions.

Adaptive evolution of benzoxazinoids in wild emmer wheat, Triticum dicoccoides, at "Evolution Canyon", Mount 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 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.ResultsOur 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.Conculsions/SignificanceThe 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.

Sympatric speciation of spiny mice, Acomys, unfolded transcriptomically at Evolution Canyon, Israel

Spiny mice, Acomys cahirinus, colonized Israel 30,000 y ago from dry tropical Africa and inhabited rocky habitats across Israel. Earlier, we had shown by mtDNA that A. cahirinus incipiently sympatrically speciates at Evolution Canyon I (EC I) in Mount Carmel, Israel because of microclimatic interslope divergence. The EC I microsite consists of a dry and hot savannoid "African" slope (AS) and an abutting humid and cool-forested "European" slope (ES). Here, we substantiate incipient SS in A. cahirinus at EC I based on the entire transcriptome, showing that multiple slope-specific adaptive complexes across the transcriptome result in two divergent clusters. Tajima's D distribution of the abutting Acomys interslope populations shows that the ES population is under stronger positive selection, whereas the AS population is under balancing selection, harboring higher genetic polymorphisms. Considerable sites of the two populations were differentiated with a coefficient of FST = 0.25-0.75. Remarkably, 24 and 37 putatively adaptively selected genes were detected in the AS and ES populations, respectively. The AS genes involved DNA repair, growth arrest, neural cell differentiation, and heat-shock proteins adapting to the local AS stresses of high solar radiation, drought, and high temperature. In contrast, the ES genes involved high ATP associated with energetics stress. The sharp ecological interslope divergence led to strong slope-specific selection overruling the interslope gene flow. Earlier tests suggested slope-specific mate choice. Habitat interslope-adaptive selection across the transcriptome and mate choice substantiate sympatric speciation (SS), suggesting its prevalence at EC I and commonality in nature.

Putative adaptive inter-slope divergence of transposon frequency in fruit flies (Drosophila melanogaster) at "Evolution Canyon", Mount Carmel, Israel.

BackgroundThe current analysis of transposon elements (TE) in Drosophila melanogaster at Evolution Canyon, (EC), Israel, is based on data and analysis done by our collaborators (Drs. J. Gonzalez, J. Martinez and W. Makalowski, this issue). They estimated the frequencies of 28 TEs (transposon elements) in fruit flies (D. melanogaster) from the ecologically tropic, hot, and dry south-facing slope (SFS) or “African” slope (AS) of EC and compared it with the TE frequencies on the temperate-cool and humid north-facing slope (NFS) or “European” slope (ES), separated, on average, by 250 m. The flies were sampled from two stations on each slope. We received their results, including the frequencies of each TE on each slope, and the probabilities of the statistical analyses (G-tests) of each TE separately. We continued the analysis of the inter-slope differences of the frequencies of the TEs, and based our different conclusions on that analysis and on the difference between micro (=EC) and macro (2000 km.) comparisons [Gonzalez et al. 2015 doi:10.1186/s13062-015-0075-4].ResultsOur collaborators based all their conclusions on the non-significant results of each of the individual tests of the 28 TEs. We analysed also the distribution of the TE differences between the slopes, based on their results. Thirteen TEs were more frequent on the SFS, 11 were more frequent on the NFS, and four had equal frequencies. Because of the equalizing effect of the ongoing migration, only small and temporary differences between the slopes (0 – 0.06) were regarded by us as random fluctuations (drift). Three TEs were intermediate (0.08-0.09) and await additional research. The 11 TEs with large frequency differences (0.12 – 0.22) were regarded by us as putative adaptive TEs, because the equalizing power of ongoing migration will eliminate random large differences. Five of them were higher on the SFS and six were higher on the NFS. Gaps in the distribution of the differences distinguished between the large and small differences. The large gap among the 11 TEs favored on the NFS was significant and supports our rejection of drift as the only explanation of the distribution of the slope differences. The gaps in the distribution of the differences separated the putative TEs with strong enough selection from those TEs that couldn't overrule the migration.The results are compared and contrasted with the directional effect of the frequencies of the same TEs in the study of global climatic comparisons across thousands of kilometers. From the 11 putative adaptive TEs in the local “Evolution Canyon,” six differentiate in the same direction as in the continental comparisons and four in the opposite direction. One TE, FBti0019144, differentiated in EC in the same direction as in Australia and in the opposite direction to that of North America.ConclusionsWe presume that the major divergent evolutionary driving force at the local EC microsite is natural selection overruling gene flow. Therefore, after we rejected drift as an explanation of all the large slope differences, we regarded them as putatively adaptive. In order to substantiate the individual TE adaptation, we need to increase the sample sizes and reveal the significant adaptive TEs.The comparison of local and global studies show only partial similarity in the adaptation of the TEs, because of the dryness of the ecologically tropical climate in EC, in contrast to the wet tropical climate in the global compared climates. Moreover, adaptation of a TE may be expressed only in part of the time and specific localities.ReviewersReviewed by Eugene Koonin, Limsoon Wong and Fyodor Kondrashov. For the full reviews, please go to the Reviewers’ comments section.Electronic supplementary materialThe online version of this article (doi:10.1186/s13062-015-0074-5) contains supplementary material, which is available to authorized users.

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.MethodsWe 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.ResultsIn 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/SignificanceRemarkable 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.

Sympatric incipient speciation of spiny miceAcomysat “Evolution Canyon,” Israel

Does the paucity of empirical evidence of sympatric speciation in nature reflect reality, despite theoretical support? Or is it due to inappropriate searches in nature with overly restrictive assumptions and an incorrect null hypothesis? Spiny mice, Acomys, described here at Evolution Canyon (EC) incipiently and sympatrically speciate owing to microclimatic interslope divergence. The opposite slopes at EC vary dramatically, physically and biotically, representing the dry and hot south-facing slope savannoid-African continent ["African" slope (AS)], abutting with the north-facing slope forested south-European continent ["European" slope (ES)]. African-originated spiny mice, of the Acomys cahirinus complex, colonized Israel 30,000 y ago based on fossils. Genotypically, we showed significantly higher genetic diversity of mtDNA and amplified fragment length polymorphism of Acomys on the AS compared with the ES. This is also true regionally across Israel. In complete mtDNA, 25% of the haplotypes at EC were slope-biased. Phenotypically, the opposite slope's populations also showed adaptive morphology, physiology, and behavior divergence paralleling regional populations across Israel. Preliminary tests indicate slope-specific mate choices. Colonization of Acomys at the EC first occurred on the AS and then moved to the ES. Strong slope-specific natural selection (both positive and negative) overrules low interslope gene flow. Both habitat slope selection and mate choices suggest ongoing incipient sympatric speciation. We conclude that Acomys at the EC is ecologically and genetically adaptively, incipiently, sympatrically speciating on the ES owing to adaptive microclimatic natural selection.

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 342bp 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 342bp 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".

Spiny Mice Modulate Eumelanin to Pheomelanin Ratio to Achieve Cryptic Coloration in “Evolution Canyon,” Israel

BackgroundCoat coloration in mammals is an explicit adaptation through natural selection. Camouflaging with the environment is the foremost evolutionary drive in explaining overall coloration. Decades of enquiries on this topic have been limited to repetitive coat color measurements to correlate the morphs with background/habitat blending. This led to an overwhelming endorsement of concealing coloration as a local phenotypic adaptation in animals, primarily rodents to evade predators. However, most such studies overlooked how rodents actually achieve such cryptic coloration. Cryptic coloration could be attained only through optimization between the yellow- to brown-colored “pheomelanin” and gray to black-colored “eumelanin” in the hairs. However, no study has explored this conjecture yet. “Evolution Canyon” (EC) in Israel is a natural microscale laboratory where the relationship between organism and environment can be explored. EC is comprised of an “African” slope (AS), which exhibits a yellow-brownish background habitat, and a “European” slope (ES), exhibiting a dark grayish habitat; both slopes harbor spiny mice (Acomys cahirinus). Here, we examine how hair melanin content of spiny mice living in the opposing slopes of EC evolves toward blending with their respective background habitat.Methodology/Principal FindingsWe measured hair-melanin (both eumelanin and pheomelanin) contents of 30 spiny mice from the EC using high-performance liquid chromatography (HPLC) that detects specific degradation products of eumelanin and pheomelanin. The melanin pattern of A. cahirinus approximates the background color of the slope on which they dwell. Pheomelanin is slightly (insignificantly) higher in individuals found on the AS to match the brownish background, whereas individuals of the ES had significantly greater eumelanin content to mimic the dark grayish background. This is further substantiated by a significantly higher eumelanin and pheomelanin ratio on the ES than on the AS.Conclusion/SignificanceIt appears that rodents adaptively modulate eumelanin and pheomelanin contents to achieve cryptic coloration in contrasting habitats even at a microscale.

Adaptive Melanin Response of the Soil Fungus Aspergillus niger to UV Radiation Stress at “Evolution Canyon”, Mount Carmel, Israel

BackgroundAdaptation is an evolutionary process in which traits in a population are tailored by natural selection to better meet the challenges presented by the local environment. The major discussion relating to natural selection concerns the portraying of the cause and effect relationship between a presumably adaptive trait and selection agents generating it. Therefore, it is necessary to identify trait(s) that evolve in direct response to selection, enhancing the organism's fitness. “Evolution Canyon” (EC) in Israel mirrors a microcosmic evolutionary system across life and is ideal to study natural selection and local adaptation under sharply, microclimatically divergent environments. The south-facing, tropical, sunny and xeric “African” slope (AS) receives 200%–800% higher solar radiation than the north-facing, temperate, shady and mesic “European” slope (ES), 200 meters apart. Thus, solar ultraviolet radiation (UVR) is a major selection agent in EC influencing the organism-environment interaction. Melanin is a trait postulated to have evolved for UV-screening in microorganisms. Here we investigate the cause and effect relationship between differential UVR on the opposing slopes of EC and the conidial melanin concentration of the filamentous soil fungus Aspergillus niger. We test the working hypothesis that the AS strains exhibit higher melanin content than strains from the ES resulting in higher UV resistance.Methodology/Principal FindingsWe measured conidial melanin concentration of 80 strains from the EC using a spectrophotometer. The results indicated that mean conidial melanin concentration of AS strains were threefold higher than ES strains and the former resisted UVA irradiation better than the latter. Comparisons of melanin in the conidia of A. niger strains from sunny and shady microniches on the predominantly sunny AS and predominantly shady ES indicated that shady conditions on the AS have no influence on the selection on melanin; in contrast, the sunny strains from the ES displayed higher melanin concentrations.Conclusions/SignificanceWe conclude that melanin in A. niger is an adaptive trait against UVR generated by natural selection.

"Evolution Canyon": A Microcosm of Life's Evolution Focusing on Adaptation and Speciation

Local microcosmic natural laboratories, dubbed "Evolution Canyon" (EC) models, reinforce studies of regional and global macrocosmic ecological theaters across life and unravelevolution 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.

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.