Adaptive microclimatic structural and expressional dehydrin 1 evolution in wild barley, Hordeum spontaneum, at 'Evolution Canyon', Mount Carmel, Israel

'Evolution Canyon' (ECI) at Lower Nahal Oren, Mount Carmel, Israel, is an optimal natural microscale model for unravelling evolution in action highlighting the twin evolutionary processes of adaptation and speciation. A major model organism in ECI is wild barley, Hordeum spontaneum , the progenitor of cultivated barley, which displays dramatic interslope adaptive and speciational divergence on the 'African' dry slope (AS) and the 'European' humid slope (ES), separated on average by 200 m. Here we examined interslope single nucleotide polymorphism (SNP) sequences and the expression diversity of the drought resistant dehydrin 1 gene ( Dhn1 ) between the opposite slopes. We analysed 47 plants (genotypes), 4–10 individuals in each of seven stations (populations) in an area of 7000 m², for Dhn1 sequence diversity located in the 5' upstream flanking region of the gene. We found significant levels of Dhn1 genic diversity represented by 29 haplotypes, derived from 45 SNPs in a total of 708 bp sites. Most of the haplotypes, 25 out of 29 (= 86.2%), were represented by one genotype; hence, unique to one population. Only a single haplotype was common to both slopes. Genetic divergence of sequence and haplotype diversity was generally and significantly different among the populations and slopes. Nucleotide diversity was higher on the AS, whereas haplotype diversity was higher on the ES. Interslope divergence was significantly higher than intraslope divergence. The applied Tajima D rejected neutrality of the SNP diversity. The Dhn1 expression under dehydration indicated interslope divergent expression between AS and ES genotypes, reinforcing Dhn1 associated with drought resistance of wild barley at 'Evolution Canyon'. These results are inexplicable by mutation, gene flow, or chance effects, and support adaptive natural microclimatic selection as the major evolutionary divergent driving force.     

Growth and asymmetry of soil microfungal colonies from "Evolution Canyon," Lower Nahal Oren, Mount Carmel, Israel

Background

Fluctuating asymmetry is a contentious indicator of stress in populations of animals and plants. Nevertheless, it is a measure of developmental noise, typically obtained by measuring asymmetry across an individual organism''s left-right axis of symmetry. These individual, signed asymmetries are symmetrically distributed around a mean of zero. Fluctuating asymmetry, however, has rarely been studied in microorganisms, and never in fungi.

Objective and Methods

We examined colony growth and random phenotypic variation of five soil microfungal species isolated from the opposing slopes of “Evolution Canyon,” Mount Carmel, Israel. This canyon provides an opportunity to study diverse taxa inhabiting a single microsite, under different kinds and intensities of abiotic and biotic stress. The south-facing “African” slope of “Evolution Canyon” is xeric, warm, and tropical. It is only 200 m, on average, from the north-facing “European” slope, which is mesic, cool, and temperate. Five fungal species inhabiting both the south-facing “African” slope, and the north-facing “European” slope of the canyon were grown under controlled laboratory conditions, where we measured the fluctuating radial asymmetry and sizes of their colonies.

Results

Different species displayed different amounts of radial asymmetry (and colony size). Moreover, there were highly significant slope by species interactions for size, and marginally significant ones for fluctuating asymmetry. There were no universal differences (i.e., across all species) in radial asymmetry and colony size between strains from “African” and “European” slopes, but colonies of Clonostachys rosea from the “African” slope were more asymmetric than those from the “European” slope.

Conclusions and Significance

Our study suggests that fluctuating radial asymmetry has potential as an indicator of random phenotypic variation and stress in soil microfungi. Interaction of slope and species for both growth rate and asymmetry of microfungi in a common environment is evidence of genetic differences between the “African” and “European” slopes of “Evolution Canyon.”     

Microsatellite analysis of Drosophila melanogaster populations along a microclimatic contrast at lower Nahel Oren canyon, Mount Carmel, Israel

Drosophila melanogaster populations collected at the south-facing slope (SFS) and north-facing slope (NFS) of lower Nahel Oren canyon, Mount Carmel, Israel display significant differences in survival and longevity at temperature, drought, and starvation stresses. Furthermore, significant assortative mating was previously observed between populations of the two slopes. We used a set of 48 microsatellite markers to analyze patterns of genetic differentiation between D. melanogaster populations from both slopes and D. simulans. Consistent with previous reports, we found D. simulans to be well differentiated from D. melanogaster. Genetic differentiation between SFS and NFS D. melanogaster populations was low (F(ST) = 0.0012). Also a tree of individuals based on the proportion of shared alleles and a model-based clustering method provided no evidence for population substructuring.     

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.     

Desiccation resistance and mating behaviour in laboratory populations of Drosophila simulans originating from the opposing slopes of Lower Nahal Oren (Israel)

Lower Nahal Oren in Northern Israel, often referred to as 'Evolution Canyon', has been proposed as a microscale model site for ecological evolution. However, conflicting stress resistance and mating assay results contribute to controversy over the Nahal Oren model. In this study, we further tested the Nahal Oren model, while extending its focus from Drosophila melanogaster to its sister species, Drosophila simulans. Using fly populations derived from the opposing canyon slopes and acclimated to laboratory conditions for 11-22 generations, we did not find a significant slope effect on desiccation resistance (P = 0.96) or body metabolic fuel content (P > 0.43), which would indicate a genetic basis for adaptation to local resource limitation. Multiple-choice mating assays (47-48% homotypic couples in two replicate populations) did not indicate divergence from a random mating pattern between north- and south-facing slope flies. In conclusion, our findings do not support divergence of D. simulans populations across Lower Nahal Oren.     

Lower Paleolithic hominin ecology at the fringe of the desert: Faunal remains from Bizat Ruhama and Nahal Hesi, Northern Negev, Israel

The Southern Levant is a pivotal area for the study of hominin paleoecology during the Lower Paleolithic, because of its location on the out-of-Africa dispersal route and its significant ecological diversity. Important information has been gained by archaeofaunal studies, which usually reveal that exploitation of diverse Mediterranean environments with woodlands, marshes and lake margins, represents a dominant subsistence strategy for Lower Paleolithic hominins. Here, we present new taxonomic and taphonomic data from two sites in the southern coastal plain of the Southern Levant, at the fringe of the Negev Desert: Bizat Ruhama (Early Pleistocene) and Nahal Hesi (Middle Pleistocene). The sites preserve anthropogenic faunas, with the former signaling a marrow-exploitation strategy, perhaps related to scavenging from carnivore kills, and the latter showing evidence for primary access to fleshed ungulate carcasses. The species composition of these Northern Negev sites is unique for the Levantine Lower Paleolithic in that these sites lack typical woodland and riparian species, probably indicating an open, relatively uniform environment with patchy water sources and trees, much like this semiarid region today. Bizat Ruhama and Nahal Hesi are among the only Levantine Lower Paleolithic faunas associated with such a setting, thereby widening the known spectrum of environments exploited by hominins in the region. It is suggested that the two sites, coupled with the nearby Late Pleistocene evidence, reflect a largely stable semiarid environment on the northwestern fringe of the Negev Desert throughout much of the Pleistocene.     

Feeding behaviour of silver carp Hypophthalmichthys molitrix Val. and its impact on the food web in Lake Kinneret,Israel

Two series of plankton samples, collected in different parts of the Ivory Coast, are examined for their rotifer content. Seventy-one taxa are identified to species level, some of which are present in different forms. Seventeen taxa are new to the Ivory Coast, three are new to Africa. Ecological and distributional notes are given. The correct spelling of Brachionus quadridentatus f. melhemi is discussed.     

Fluctuating Helical Asymmetry and Morphology of Snails (Gastropoda) in Divergent Microhabitats at 'Evolution Canyons I and II,' Israel

Background

Developmental instability of shelled gastropods is measured as deviations from a perfect equiangular (logarithmic) spiral. We studied six species of gastropods at ‘Evolution Canyons I and II’ in Carmel and the Galilee Mountains, Israel, respectively. The xeric, south-facing, ‘African’ slopes and the mesic, north-facing, ‘European’ slopes have dramatically different microclimates and plant communities. Moreover, ‘Evolution Canyon II’ receives more rainfall than ‘Evolution Canyon I.’

Methodology/Principal Findings

We examined fluctuating asymmetry, rate of whorl expansion, shell height, and number of rotations of the body suture in six species of terrestrial snails from the two ‘Evolution Canyons.’ The xeric ‘African’ slope should be more stressful to land snails than the ‘European’ slope, and ‘Evolution Canyon I’ should be more stressful than ‘Evolution Canyon II.’ Only Eopolita protensa jebusitica showed marginally significant differences in fluctuating helical asymmetry between the two slopes. Contrary to expectations, asymmetry was marginally greater on the ‘European’ slope. Shells of Levantina spiriplana caesareana at ‘Evolution Canyon I,’ were smaller and more asymmetric than those at ‘Evolution Canyon II.’ Moreover, shell height and number of rotations of the suture were greater on the north-facing slopes of both canyons.

Conclusions/Significance

Our data is consistent with a trade-off between drought resistance and thermoregulation in snails; Levantina was significantly smaller on the ‘African’ slope, for increasing surface area and thermoregulation, while Eopolita was larger on the ‘African’ slope, for reducing water evaporation. In addition, ‘Evolution Canyon I’ was more stressful than Evolution Canyon II’ for Levantina.     

Fish fauna and environments of the Pilcomayo-Paraguay basins in Formosa,Argentina

The ichthyofauna from subtropical (East) and tropical (West) areas in the Formosa province (Northern Argentina) is analyzed. An up-to-date list of fishes is provided, including 18 new reports for environments associated with the Pilcomayo and Paraguay rivers, considering the detailed distribution of the fishes. Dominant families in terms of number of species are Characidae, Pimelodidae, Loricariidae and Curimatidae. Percentage of individuals (about 5000 examined) were 66% for characoids and 25% for siluriforms, with less than 10% for other groups. Comparisons were made with other South American environments. Most frequent species were Psellogrammus kennedyi, Astyanax bimaculatus, Gymnocorymbus ternetzi, Hoplosternum thoracatum and Cichlasoma portalegrense. The predominant type of environment sampled, of small size and shallow depth, with extensive plant cover, and temporal level variations, explains the dominance of the above groups. This interpretation is supported by independent studies. Diversity values ranged between 0.71 and 3.92. A marked reduction in number of species from East to West was observed (79 and 41 species respectively, 31 shared). No species of Gymnotidae, Hemiodidae, Characidiidae, Trichomycteridae, Lebiasinidae nor Aspredinidae were captured in the West. The higher number of species in eastern environments is considered to be due to the influence of the Paraguay river and the complex hydrology of the area. Other factors, both historical and ecological are considered. A correlation between total phosphorous content in the water and fish richness is also suggested. Water chemistry is compared with near by environments. Sites studied showed pH values from 6.14 to 7.5. The dissolved solid contents ranged from 51.8 to 474.3 mg 1^–1, within the hypohaline level. Ionic composition differed somewhat between East and West, water in the East being mainly hypocalcic, as in the Paraguay river. Conductivity was rather variable and Secchi disk values similar to those in the Parana river.     

Parallel microgeographic patterns of genetic diversity and divergence revealed by allozyme, RAPD, and microsatellites in Triticum dicoccoides at Ammiad, Israel

The levels of genetic diversity were compared by means of 35 allozyme, 60 RAPD, and 25 microsatellite (SSR) markers for 75–175 individuals of tetraploid wild emmer wheat (Triticum dicoccoides) collected in 1993 from a microgeographic microsite, Ammiad, north of the Sea of Galilee, Israel. This microsite included four major habitats, which showed highly significant differentiation in ecological factors, in particular with respect to rock cover, proximity and height, and surface soil moisture in the early growing season of T. dicoccoides. Higher within-subpopulation genetic diversity was found in the primarily non-coding DNA regions (RAPD and SSR) rather than in the protein-coding (allozymes) regions. However, much larger gene differentiation (G _ST) among the subpopulations was observed in the protein-coding allozymes than in the RAPDs and SSRs. Larger genetic distance was found at SSR loci, followed by allozyme and RAPD loci. The subpopulations in drier habitats tend to have higher allozyme, RAPD and SSR diversities (He), the relatively wet Karst subpopulation showed only about half He of the other relatively drier habitats. The subpopulations with larger difference of soil moisture between habitats tend to show larger genetic distances at allozyme, RAPD and SSR loci. These results suggest that climatic selection through aridity stress may be an important factor acting on both structural protein-coding and presumably partly regulatory non-coding DNA regions, resulting in microscale adaptive patterns, although hitchhiking and random drift may also intervene. These results have profound implications for genetic conservation both in situ and ex situ.     

Diet of wild chimpanzees (Pan troglodytes verus) at Mt. Assirik,Senegal: I. Composition

The composition of the diet of a savanna-living population of wild chimpanzees (Pan troglodytes verus) at Mt. Assirik in Senegal is presented. The study site had a prolonged dry season, high temperatures, and vegetation dominated by grasses. Data came from direct observation, fecal specimens, and feeding traces; thus, strict criteria for acceptance of the indirect data were specified. Composition of diet was given in terms of species and family of prey, parts eaten, life-form, type of habitat, and criteria for inclusion. Forty-three species of plants with 60 parts were eaten; mostly fruits, from trees, in woodland. Nine species of animal prey were eaten, mostly social insects. An additional 41 species of plants with 53 parts were classed as likely to be eaten by chimpanzees, mostly on the grounds of their being eaten by sympatric anthropoids. Overall, the diet of the apes at Mt. Assirik resembles that of this species elsewhere in Africa, but the size of the dietary repertoire seems small and the proportion of low-quality foodstuffs high. The latter are mostly time-consuming to collect or tedious to obtain or process, and include underground storage organs.     

Evidence for habitual use of fire at the end of the Lower Paleolithic: site-formation processes at Qesem Cave, Israel

The Amudian (late Lower Paleolithic) site of Qesem Cave in Israel represents one of the earliest examples of habitual use of fire by middle Pleistocene hominids. The Paleolithic layers in this cave were studied using a suite of mineralogical and chemical techniques and a contextual sedimentological analysis (i.e., micromorphology). We show that the lower ca. 3m of the stratigraphic sequence are dominated by clastic sediments deposited within a closed karstic environment. The deposits were formed by small-scale, concentrated mud slurries (infiltrated terra rosa soil) and debris flows. A few intervening lenses of mostly in situ burnt remains were also identified. The main part of the upper ca. 4.5 m consists of anthropogenic sediment with only moderate amounts of clastic geogenic inputs. The deposits are strongly cemented with calcite that precipitated from dripping water. The anthropogenic component is characterized by completely combusted, mostly reworked wood ash with only rare remnants of charred material. Micromorphological and isotopic evidence indicates recrystallization of the wood ash. Large quantities of burnt bone, defined by a combination of microscopic and macroscopic criteria, and moderately heated soil lumps are closely associated with the wood-ash remains. The frequent presence of microscopic calcified rootlets indicates that the upper sequence formed in the vicinity of the former cave entrance. Burnt remains in the sediments are associated with systematic blade production and faunas that are dominated by the remains of fallow deer. Use-wear damage on blades and blade tools in conjunction with numerous cut marks on bones indicate an emphasis on butchering and prey-defleshing activities in the vicinity of fireplaces.     

Colony growth rates of microfungal isolates from the north and south facing slopes of Evolution Canyon, Mount Carmel, Israel, after irradiation at 10(6) rads 60Co

Species of microfungi were isolated from both the north facing slope (NFS) and the south facing slope (SFS) of Evolution Canyon, Mount Carmel, Israel. They were examined for growth rates before and after exposure to 10(6) rads of cobalt 60 irradiation. Above 10(6) rads all growth ceased after 1 day following exposure.     

Archaeological horizons and fluvial processes at the Lower Paleolithic open-air site of Revadim (Israel)

In this paper we present new data pertaining to the paleo-landscape characteristics at the Acheulian site of Revadim, on the southern coastal plain of Israel. Sedimentological, isotopic, granulometric and micromorphological studies showed that the archaeological remains accumulated in an active fluvial environment where channel action, overbank flooding and episodic inundation occurred. Measurements of total organic matter and its carbon isotopic composition indicate that the hominin activity at the site started at a period of relatively drier conditions, which coincided with erosion of the preceding soil sequence. This process led to the formation of a gently-undulating topography, as reconstructed by a GIS model. Later deposition documents relatively wetter conditions, as indicated by carbon isotopic composition. Formation processes identified at the site include fluvial processes, inundation episodes that resulted in anaerobic conditions and formation of oxide nodules, as well as small-scale bioturbation and later infiltration of carbonate-rich solutions that resulted in the formation of calcite nodules and crusts. The combination of micro-habitats created favorable conditions that repeatedly drew hominins to the area, as seen by a series of super-imposed archaeological horizons. This study shows that site-specific paleo-landscape reconstructions should play an important role in understanding regional variation among hominin occupations and in extrapolating long-term behavioral patterns during the Middle Pleistocene.     

Types, levels and patterns of low-copy DNA sequence divergence, and phylogenetic implications, for Gossypium genome types

To explore types, levels and patterns of genetic divergence among diploid Gossypium (cotton) genomes, 780 cDNA, genomic DNA and simple sequence repeat (SSR) loci were re-sequenced in Gossypium herbaceum (A1 genome), G. arboreum (A2), G. raimondii (D5), G. trilobum (D8), G. sturtianum (C1) and an outgroup, Gossypioides kirkii. Divergence among these genomes ranged from 7.32 polymorphic base pairs per 100 between G. kirkii and G. herbaceum (A1) to only 1.44 between G. herbaceum (A1) and G. arboreum (A2). SSR loci are least conserved with 12.71 polymorphic base pairs and 3.77 polymorphic sites per 100 base pairs, whereas expressed sequence tags are most conserved with 3.96 polymorphic base pairs and 2.06 sites. SSR loci also exhibit the highest percentage of 'extended polymorphisms' (spanning multiple consecutive nucleotides). The A genome lineage was particularly rapidly evolving, with the D genome also showing accelerated evolution relative to the C genome. Unexpected asymmetry in mutation rates was found, with much more transition than transversion mutation in the D genome after its divergence from a common ancestor shared with the A genome. This large quantity of orthologous DNA sequence strongly supports a phylogeny in which A-C divergence is more recent than A-D divergence, a subject that is of much importance in view of A-D polyploid formation being key to the evolution of the most productive and finest-quality cottons. Loci that are monomorphic within A or D genome types, but polymorphic between genome types, may be of practical importance for identifying locus-specific DNA markers in tetraploid cottons including leading cultivars.     

Rates of genomic divergence in humans,chimpanzees and their lice

The rate of DNA mutation and divergence is highly variable across the tree of life. However, the reasons underlying this variation are not well understood. Comparing the rates of genetic changes between hosts and parasite lineages that diverged at the same time is one way to begin to understand differences in genetic mutation and substitution rates. Such studies have indicated that the rate of genetic divergence in parasites is often faster than that of their hosts when comparing single genes. However, the variation in this relative rate of molecular evolution across different genes in the genome is unknown. We compared the rate of DNA sequence divergence between humans, chimpanzees and their ectoparasitic lice for 1534 protein-coding genes across their genomes. The rate of DNA substitution in these orthologous genes was on average 14 times faster for lice than for humans and chimpanzees. In addition, these rates were positively correlated across genes. Because this correlation only occurred for substitutions that changed the amino acid, this pattern is probably produced by similar functional constraints across the same genes in humans, chimpanzees and their ectoparasites.     

Hymenopterous parasitoids of bark beetles [Scolytidae] in Israel: Host relation,host plant,abundance and seasonal history

Twenty six species of parasitoids were recorded from 15 species of bark beetles in Israel. Parasitoids were collected from infested cut branches of broadleaves and trap-trees of pine and cypress. Most of the parasitoids are oligophagous and range fromEcphylus caudatus, a monophagous species exclusive toHypoborus ficus, toHeydenia pretiosa, which develops on 11 species.Scleroderma domesticus, Agrilocida ferrieri andEupelmus nearurozonus are occasional parasitoids of bark beetles.Cephalonomia hypobori, Israelius carthami, S. domesticus, Entedon ergias, Cerocephala eccoptogasteri andRoptocerus xylophagorum are cryptoparasitoids and search for their host in the galleries. Known parasitoids are listed from 15 tree genera belonging to 8 botanical families. A typical range for the common parasitoids is presented with within-tree distribution of pine parasitoids. Relatively monophagous species are usually dominant parasitoids in a specific beetle population, whereas relatively polyphagous parasitoids vary in abundance among different host populations.Calosota spp., 2Eurytoma spp. andDendrosoter hartigii are usually present in small numbers. Information concerning the seasonal history of the parasitoids suggests that the major species may raise about 5 to 7 annual generations. Contribution from the Agricultural Research Organization, Bet Dagan, Israel N^o 1331-E, 1984 series     

Chromosomal diversification of diploid number,heterochromatin and rDNAs in two species of Phanaeus beetles (Scarabaeidae,Scarabaeinae)

The genus Phanaeus is included in the tribe Phanaeini, one of the most diverse tribes within the subfamily Scarabaeinae in terms of chromosomal characteristics. However, so far the species of this genus were not studied with differential cytogenetic techniques, limiting any inference of the probable mechanisms responsible for this diversity. In this work, several techniques were applied with the aim of cytogenetically characterizing two Phanaeus species. The karyotype found for Phanaeus (Notiophanaeus) chalcomelas was 2n = 12, neo-XY, and that of P. (N.) splendidulus was 2n = 20, Xy_p, considered primitive for the family Scarabaeidae. The chromosomes of both species showed a high amount of constitutive heterochromatin (CH), with blocks rich in base pairs GC (CMA₃⁺). Moreover, in P. (N.) chalcomelas the marks revealed by C-banding and fluorochrome staining were different in size, showing CH variability. Sites of 18S ribosomal DNA (rDNA) were identified in one autosomal pair of P. (N.) chalcomelas and in five autosomal pairs of P. (N.) splendidulus. On the other hand, only one autosomal pair exhibited 5S rDNA sequences in these species. The results suggest that the karyotype differentiation of the Phanaeus species studied here involved pericentric inversions and centric fusions, as well as mechanisms related to amplification and dispersion of CH and rDNA sequences.     

Tempo and mode of evolutionary divergence in modern and Holocene Vancouver Island marmots (Marmota vancouverensis) (Mammalia, Rodentia)

Marmota vancouverensis is the only insular species among the 14 species of marmots. The evolutionary history of this species is unresolved. Although M. vancouverensis is strongly differentiated in osteological and other morphological characters, its low genetic divergence suggests recent evolution from an ancestral continental species. We used geometric morphometric techniques to assess the morphology of hemimandibles from 239 modern M. vancouverensis , Marmota caligata , Marmota flaviventris , Marmota olympus and 30 Holocene (9435–735 cal. yr bp) subfossil M. vancouverensis . Our results confirm that the mandible of M. vancouverensis is strongly differentiated in shape from continental marmot species, but similar in size to its mainland sister species M. caligata . Temporal variation in size and shape over the past 2500 years among allochronic samples of M. vancouverensis was minimal suggesting that the morphological divergence of this species occurred in a period of rapid change following its isolation from mainland populations in the late Pleistocene. Selection pressures associated with environmental changes and founder effects and genetic drift resulting from population bottlenecks created by population declines and habitat fragmentation are hypothesized as factors contributing to the morphological divergence of this species.