Quaternary dune carbonates from the Mediterranean Coast of Egypt: Petrography and diagenesis

Summary The Quaternary carbonates of the Mediterranean coast of Egypt between Alexandria and Salum appear as parallel limestone ridges rising up to 100 m above sea level. These ridges are dominated by dunal carbonates which differ not only in their primary composition but also by distinct grades of meteoric water diagenesis. Oolitic facies dominates the younger aeolianites of the first and second ridges. Bioclastic facies with abundant coralline algae, benthonic foraminifers, molluscs, echinoderms and intraclasts represents the major rock type in the older aeolianites. Features of meteoric water diagenesis include precipitation of increasing amounts of avoid-filling low Mg-calcite spar, dissolution of aragonite and stabilization of aragonite and high Mg-calcite to low Mg-calcite. Aeolianites below paleosol horizons contain abundant calcrete cements, micritized fossils and detrital grains which are commonly corroded and replaced by calcite. Three stages of progressive meteoric diagenesis are recognised in the Egyptian Quaternary aeolianites. In stage 1 minor precipitation of low Mg-calcite occurs at the grain boundaries. Stage 2 is marked by partial dissolution of aragonite, partial loss of high Mg-calcite and precipitation of low Mg-calcite in some pore spaces. In stage 3, most of the remaining pores are occluded by cementation. At the end of stage 3, Mg is removed from high Mg-calcite but some aragonite still persists. The early vadose cements are represented by miniscus, bridge and pendant cements. The phreatic cements were precipitated as bladed spar in the isopachous rims and equant spar in the intergranular and mouldic porosity. The late vadose cements are represented by micritic cements that were related to calcrete formation. Elemental behaviour during meteoric water diagenesis indicates that it leads to a gradual decrease in bulk Sr along with Na in progressively altered aeolianites. Mn distribution is controlled by the carbonate mineralogy (aragonite versus calcite) as well as the proximity of the aeolianites to the overlying paleosol horizons.     

Salt marsh vegetation of the Western Mediterranean desert of Egypt

The extensive salt marshes in the plains and depressions of the western Mediterranean desert of Egypt were classified into three habitat types: A with shallow water table and high salinity, B with relatively deep water table and high salinity, and C transitional habitats in which salinity and water table are no controlling factors. Fourteen vegetation types were distinguished, each dominated by one or two species.The dominating life forms are chamaephytes in sites of high salinity, and therophytes in sites of low salinity. Spatial and temporal variations in the standing crop biomass were pronounced. The accumulation of material started during spring and reached a maximum in autumn, when photosynthetic activity was maintained to account for transpiration losses.There was a general trend of increasing salinity and concentration of different ions from habitat type A to habitat type C through habitat type B. The periodical variation in the water table was insignificant, while a significant drop in salinity and the concentration of different ions was detected in spring, which was attributed to the diluting effect of rain water during that season.Most species exhibited clear distribution patterns and their a bundance varied significantly along gradients of different factors. Simple correlations between the compositional gradients or the distributional behaviour of species and salinity or the concentration of individual ions were generally low, while correlations with combinations of ions in the form of ratios (notably sodium and potassium adsorption ratos) were higher.During the early stages of succession the building up of soil and the decrease in salinity are the most important factors while at more advanced stages, soil texture and calcium carbonate content become more decisive.Nomenclature follows Täckholm (1974)     

Regional genetic differentiation among populations of Cladocora caespitosa in the Western Mediterranean

Cladocora caespitosa is the only reef-forming zooxanthellate scleractinian in the Mediterranean Sea. This endemic coral has suffered severe mortality events at different Mediterranean sites owing to anomalous summer heat waves related to global climate change. In this study, we assessed genetic structure and gene flow among four populations of this species in the Western Mediterranean Sea: Cape Palos (SE Spain), Cala Galdana (Balearic Islands), Columbretes Islands, and L’Ametlla (NE Spain). The results obtained from Bayesian approaches, F _ST statistics, and Bayesian analysis of migration rates suggest certain levels of genetic differentiation driven by high levels of self-recruitment, a fact that is supported by egg-retention mechanisms. Conversely, genetic connectivity among distant populations, even if generally low, seems to be related to sporadic dispersal events through regional surface currents linked to the spawning period that occurs at the end of summer-beginning of autumn. These features, together with a certain isolation of the Columbretes Islands, could explain the regional genetic differentiation found among populations. These results help to better understand population structure and connectivity of the species and will serve as an approach for further studies on different aspects of the biology and ecology of C. caespitosa.     

Genetic Identification of Western Mediterranean Sturgeons and its Implication for Conservation

To date, the only native sturgeon species in Western Europe was believed to be Acipenser sturio. However, this species is currently restricted to the Gironde River (Southern France), and it poses serious difficulties for rearing in captivity and for using in recovery programme. Furthermore, it has been questioned whether A. sturio is in fact the only species within the rivers of Western Europe, as A. naccarii, a species previously considered endemic of the Adriatic region, has been reported from the Iberian Peninsula in recent years. Here, we have used forensic techniques to obtain DNA from several museum specimens of sturgeons caught in the Spanish Guadalquivir River and in other European rivers. We analysed DNA sequences from these specimens for five genetic markers (three nuclear and two mitochondrial regions), which were subsequently compared with sequences obtained from A. sturioand A. naccarii. Our study demonstrates that A. naccarii coexists withA. sturio, from the Adriatic Sea to the Iberian Peninsula, a finding that could be taken into account in future sturgeon recovery programmes in Western Europe.     

Mutant allele frequencies and genetic distance relationships in domestic cat populations of lower Egypt and the eastern Mediterranean

Summary Gene frequency surveys conducted in Alexandria and Cairo reveal genetic profiles which are extensions of those that characterize the cat populations of European cities. For nine selected comparisons with Alexandria, regression analysis indicates that a linear function best describes the relationship between Nei's and Cavalli-Sforza's genetic distance indices and geographic distance.     

Genetic structure of continental and island populations of the Mediterranean endemic Cyclamen balearicum (Primulaceae)

Cyclamen balearicum is a self-compatible perennial herb endemic to the western Mediterranean Basin. This species occurs in five geographically isolated terrestrial islands in southern France and on four Balearic islands. In this study, we compare genetic variability and differentiation within and among 11 terrestrial island populations and 17 true island populations. Of nine readable enzyme loci, five were polymorphic in both terrestrial and true islands. F statistics showed a significant heterozygote deficiency in all populations, probably due to high levels of autonomous selfing, restricted gene flow, and subsequent genetic drift. Genetic diversity was higher in terrestrial islands than on the Balearic islands, suggesting that the Balearic islands were colonized when they were in contact with the continent. Population differentiation was greater among terrestrial islands (Fst = 0.417 and Gst = 0.344) than among true islands (Fst = 0.112 and Gst = 0.093). Furthermore, differentiation among populations on the Basses Cévennes terrestrial island was greater (Fst = 0.254) than among populations on the true island of Mallorca (Fst = 0.163). The greater genetic differentiation among terrestrial islands could have been caused by genetic bottlenecks associated with changes in climate and human land use that may have reduced population sizes more severely in terrestrial islands in southern France than on the Balearic islands.     

Spatial and temporal deforestation dynamics in protected and unprotected dry forests: a case study from Myanmar (Burma)

Tropical dry forests are more threatened, less protected and especially susceptible to deforestation. However, most deforestation research focuses on tropical rain forests. We analyzed spatial and temporal changes in land cover from 1972 through 2005 at Chatthin Wildlife Sanctuary (CWS), a tropical dry forest in Myanmar (Burma). CWS is one of the largest protected patches of tropical dry forest in Southeast Asia and supports over half the remaining wild population of the endangered Eld’s deer. Between 1973 and 2005, 62% of forest was lost at an annual rate of 1.86% in the area, while forest loss inside CWS was only 16% (0.45% annually). Based on trends found during our study period, dry forests outside CWS would not persist beyond 2019, while forests inside CWS would persist for at least another 100 years. Analysis of temporal deforestation patterns indicates the highest rate of loss occurred between 1992 and 2001. Conversion to agriculture, shifting agriculture, and flooding from a hydro-electric development were the main deforestation drivers. Fragmentation was also severe, halving the area of suitable Eld’s deer habitat between 1973 and 2001, and increasing its isolation. CWS protection efforts were effective in reducing deforestation rates, although deforestation effects extended up to 2 km into the sanctuary. Establishing new protected areas for dry forests and finding ways to mitigate human impacts on existing forests are both needed to protect remaining dry forests and the species they support.     

Conservation genetics of an endemic from the Mediterranean Basin: high genetic differentiation but no genetic diversity loss from the last populations of the Sicilian Grape Hyacinth Leopoldia gussonei

The Mediterranean Basin is a biodiversity hotspot, housing >11.000 narrowly endemic plant species, many of which are declining due to mass tourism and agricultural intensification. To investigate the genetic resource impacts of ongoing habitat loss and degradation, we characterized the genetic variation in the last known populations of Leopoldia gussonei, a self-compatible endangered Sicilian Grape Hyacinth numbering less than 3,000 remaining individuals, using AFLP. Results demonstrated significant genome-wide genetic differentiation among all extant populations (Φ_ST = 0.05–0.56), and genetic clustering according to geographic location. Gene diversity was fairly constant across population (mean H_E = 0.13) and was neither affected by current population size nor by spatial isolation. Vegetation analysis showed the presence of known invasive weeds in a quarter of the populations, but we found no relation between genetic diversity and plant community composition. The marked genetic differences among populations and the profusion of rare and private alleles indicate that any further population loss will lead to significant losses of genetic diversity. Conservation efforts should therefore focus on the preservation of all sites where L. gussonei still occurs, yet the deliberate introduction of diverse material into the smallest populations seems unneeded as clonality likely mitigated genetic drift effects thus far. More generally, our findings support the view that endemic plant species with a narrow ecological amplitude, as many specialists in Mediterranean coastal ecosystems, are highly genetically differentiated and that conservation of their genetic diversity requires preservation of most, if not all of their extant populations.     

Intracellular demography and the dynamics of Salmonella enterica infections

An understanding of within-host dynamics of pathogen interactions with eukaryotic cells can shape the development of effective preventive measures and drug regimes. Such investigations have been hampered by the difficulty of identifying and observing directly, within live tissues, the multiple key variables that underlay infection processes. Fluorescence microscopy data on intracellular distributions of Salmonella enterica serovar Typhimurium (S. Typhimurium) show that, while the number of infected cells increases with time, the distribution of bacteria between cells is stationary (though highly skewed). Here, we report a simple model framework for the intensity of intracellular infection that links the quasi-stationary distribution of bacteria to bacterial and cellular demography. This enables us to reject the hypothesis that the skewed distribution is generated by intrinsic cellular heterogeneities, and to derive specific predictions on the within-cell dynamics of Salmonella division and host-cell lysis. For within-cell pathogens in general, we show that within-cell dynamics have implications across pathogen dynamics, evolution, and control, and we develop novel generic guidelines for the design of antibacterial combination therapies and the management of antibiotic resistance.     

Vulnerability of Mediterranean Ecosystems to Long-Term Changes along the Coast of Israel

Although human activity is considered to be a major driving force affecting the distribution and dynamics of Mediterranean ecosystems, the full consequences of projected climate variability and relative sea-level changes on fragile coastal ecosystems for the next century are still unknown. It is unclear how these waterfront ecosystems can be sustained, as well as the services they provide, when relative sea-level rise and global warming are expected to exert even greater pressures in the near future (drought, habitat degradation and accelerated shoreline retreat). Haifa Bay, northern Israel, has recorded a landward sea invasion, with a maximum sea penetration 4,000 years ago, during an important period of urban development and climate instability. Here, we examine the cumulative pressure of climate shifts and relative sea-level changes in order to investigate the patterns and mechanisms behind forest replacement by an open-steppe. We provide a first comprehensive and integrative study for the southern Levant that shows that (i) human impact, through urbanization, has been the main driver behind ecological erosion in the past 4,000 years; (ii) climate pressures have reinforced this impact; and (iii) local coastal changes have played a decisive role in eroding ecosystem resilience. These three parameters, which have closely interacted during the last 4,000 years in Haifa Bay, clearly indicate that for an efficient management of the coastal habitats, anthropogenic pressures linked to urban development must be reduced in order to mitigate the predicted effects of Global Change.     

A phenomenological approach to the simulation of metabolism and proliferation dynamics of large tumour cell populations

A major goal of modern computational biology is to simulate the collective behaviour of large cell populations starting from the intricate web of molecular interactions occurring at the microscopic level. In this paper we describe a simplified model of cell metabolism, growth and proliferation, suitable for inclusion in a multicell simulator, now under development (Chignola R and Milotti E 2004 Physica A 338 261-6). Nutrients regulate the proliferation dynamics of tumour cells which adapt their behaviour to respond to changes in the biochemical composition of the environment. This modelling of nutrient metabolism and cell cycle at a mesoscopic scale level leads to a continuous flow of information between the two disparate spatiotemporal scales of molecular and cellular dynamics that can be simulated with modern computers and tested experimentally.     

Conservation unit allows assessing vulnerability and setting conservation priorities for a Mediterranean endemic plant within the context of extreme urbanization

Current biodiversity patterns are a temporary state in a continuum of ecological and evolutionary changes. Conservation policies must incorporate this dynamic to ensure the long-term conservation of biodiversity which is particularly challenging in a context of extreme urbanization. An original approach, rarely used for plant conservation, is to define conservation units to set conservation priorities within species by combining ecological and evolutionary divergences. In the Maritime Alps (southern France), the ecological and evolutionary divergences between the populations of Acis nicaeensis has allowed us the determination of conservation units of this endemic plant threatened by severe urbanization and land-use changes. Phylogeographical data (cpDNA haplotype) were considered as a proxy for evolutionary legacy, and ecological data (multivariate analysis of habitat) were used as a proxy for ecological distinctiveness. Our goal was to explore the potential of this approach to assess vulnerability and set conservation priorities for narrow endemic species in the context of conflict between biodiversity and human activities. The results highlight five different conservation units within A. nicaeensis distribution. Genetic and ecological divergences are present at fine-scale. This pattern is highly endangered by urbanisation. This study highlights the vulnerability of conservation units near the coast whose originality and restricted distribution call for rapid conservation management to avoid the loss of species evolutionary and ecological distinctiveness.     

Circulation of endemic type 2 vaccine-derived poliovirus in Egypt from 1983 to 1993

From 1988 to 1993, 30 cases of poliomyelitis associated with poliovirus type 2 were found in seven governorates of Egypt. Because many of the cases were geographically and temporally clustered and because the case isolates differed antigenically from the vaccine strain, it was initially assumed that the cases signaled the continued circulation of wild type 2 poliovirus. However, comparison of sequences encoding the major capsid protein, VP1 (903 nucleotides), revealed that the isolates were related (93 to 97% nucleotide sequence identity) to the Sabin type 2 oral poliovirus vaccine (OPV) strain and unrelated (<82% nucleotide sequence identity) to the wild type 2 polioviruses previously indigenous to Egypt (last known isolate: 1979) or to any contemporary wild type 2 polioviruses found elsewhere. The rate and pattern of VP1 divergence among the circulating vaccine-derived poliovirus (cVDPV) isolates suggested that all lineages were derived from a single OPV infection that occurred around 1983 and that progeny from the initiating infection circulated for approximately a decade within Egypt along several independent chains of transmission. Complete genomic sequences of an early (1988) and a late (1993) cVDPV isolate revealed that their 5' untranslated region (5' UTR) and noncapsid- 3' UTR sequences were derived from other species C enteroviruses. Circulation of type 2 cVDPVs occurred at a time of low OPV coverage in the affected communities and ceased when OPV coverage rates increased. The potential for cVDPVs to circulate in populations with low immunity to poliovirus has important implications for current and future strategies to eradicate polio worldwide.     

Stochastic demography and population dynamics in the red kangaroo Macropus rufus

1.  Many organisms inhabit strongly fluctuating environments but their demography and population dynamics are often analysed using deterministic models and elasticity analysis, where elasticity is defined as the proportional change in population growth rate caused by a proportional change in a vital rate. Deterministic analyses may not necessarily be informative because large variation in a vital rate with a small deterministic elasticity may affect the population growth rate more than a small change in a less variable vital rate having high deterministic elasticity.
2.  We analyse a stochastic environment model of the red kangaroo ( Macropus rufus ), a species inhabiting an environment characterized by unpredictable and highly variable rainfall, and calculate the elasticity of the stochastic growth rate with respect to the mean and variability in vital rates.
3.  Juvenile survival is the most variable vital rate but a proportional change in the mean adult survival rate has a much stronger effect on the stochastic growth rate.
4.  Even if changes in average rainfall have a larger impact on population growth rate, increased variability in rainfall may still be important also in long-lived species. The elasticity with respect to the standard deviation of rainfall is comparable to the mean elasticities of all vital rates but the survival in age class 3 because increased variation in rainfall affects both the mean and variability of vital rates.
5.  Red kangaroos are harvested and, under the current rainfall pattern, an annual harvest fraction of c . 20% would yield a stochastic growth rate about unity. However, if average rainfall drops by more than c . 10%, any level of harvesting may be unsustainable, emphasizing the need for integrating climate change predictions in population management and increase our understanding of how environmental stochasticity translates into population growth rate.     

Identification and conservation of remnant genetic resources of brown trout in relict populations from Western Mediterranean streams

Brown trout is a cold-adapted freshwater species with restricted distribution to headwater streams in rivers of the South European peninsulas, where populations are highly vulnerable because Mediterranean regions are highly sensitive to the global climatic warming. Moreover, these populations are endangered due to the introgressive hybridization with cultured stocks. Individuals from six remnant populations in Western Mediterranean rivers were sequenced for the complete mitochondrial DNA control region and genotyped for 11 nuclear markers. Three different brown trout lineages were present in the studied region. Significant genetic divergence was observed among locations and a strong effect of genetic drift was suggested. An important stocking impact (close to 25%) was detected in the zone. Significant correlations between mitochondrial-based rates of hatchery introgression and water flow variation suggested a higher impact of stocked females in unstable habitats. In spite of hatchery introgression, all populations remained highly differentiated, suggesting that native genetic resources are still abundant. However, climatic predictions indicated that suitable habitats for the species in these rivers will be reduced and hence trout populations are highly endangered and vulnerable. Thus, management policies should take into account these predictions to design upstream refuge areas to protect remnant native trout in the region.