Macroecological patterns of species and genetic diversity in vascular plants of the Mediterranean basin

Aim We address the question of whether broad scale biogeographical structure of species diversity (SD) matches that of genetic diversity (GD) of vascular plants. Location The Mediterranean basin. Methods We normalized vascular plant species richness (SD) estimates per country using the Med‐Checklist taxonomic database. We used a linear regression analysis to correlate normalized country estimates with country longitudinal position. We also compiled published and geo‐referenced within‐population GD data for tree species, which had populations in the Mediterranean. We normalized GD estimates for each population across species. Again, we used a linear regression analysis to correlate GD with population longitudinal position. We then compared the populations’ geographical and bioclimatic trends for GD with Last Glacial Maximum (LGM) palaeo‐climate data and the species current ecological requirements. Results The eastern Mediterranean and the coast of former Yugoslavia had higher SD than other regions. There was no overall spatial structure of SD in the Mediterranean, whereas there was an east–west trend of decreasing GD. This trend for GD tended to covary with an east–west warm/wet–cold/dry trend detected during the LGM. Low elevation xerothermic pine species displayed significantly less GD than higher elevation mesothermic or mountain pine species. Main conclusions We suggest that LGM climate may have significantly shaped the current longitudinal and altitudinal patterns of GD we observed in woody taxa across the Mediterranean, although it did not affect comparable SD patterns. In particular, colder LGM summer temperatures in the western Mediterranean may have reduced population sizes significantly more than in the eastern Mediterranean. As plant species richness and GD did not covary, SD and GD may not be used as surrogates of one another in the Mediterranean basin. As they contain comparatively less GD, conservation priorities in the Mediterranean should focus on hot spots of endemism and Western Mediterranean populations and species.     

Tracking the ice: Subterranean harvestmen distribution matches ancient glacier margins

Biogeographic studies often underline the role of glacial dynamism during Pleistocene (1.806–0.011 Mya) in shaping the distribution of subterranean species. Accordingly, it is presumed that present‐day distribution of most specialized cold‐adapted (cryophilic) cave‐dwelling species should bear the signatures of past climatic events. To test this idea, we modelled the distribution of specialized cold‐adapted subterranean alpine harvestmen (Arachnida: Opiliones: Ischyropsalididae: Ischyropsalis). We found that the distance from the glacier margins during Last Glacial Maximum (LGM; about 22,000 years ago) was the most important predictor of their present‐day distribution. In particular, the peak in the probability of occurrence of alpine subterranean Ischyropsalis was found to be in close proximity to the LGM glacier, with a sharp drop at a distance of 30 km from the ice margin. In light of the role played by past climatic events in determining the species current range, we briefly discuss their biogeographic history and the role played by glacial refugia dynamics in determining the current distribution of these species. We argue that low dispersal harvestmen such as our model species can be used as biological indicators for tracking past glaciations and other similar biogeographic events.     

Race Profiling and Molecular Diversity Analysis of Fusarium oxysporum f.sp. ciceris Causing Wilt in Chickpea

Seventy isolates of Fusarium oxysporum f.sp. ciceris (Foc) causing chickpea wilt representing 13 states and four crop cultivation zones of India were analysed for their virulence and genetic diversity. The isolates of the pathogen showed high variability in causing wilt incidence on a new set of differential cultivars of chickpea, namely C104, JG74, CPS1, BG212, WR315, KWR108, GPF2, DCP92‐3, Chaffa and JG62. New differential cultivars for each race were identified, and based on differential responses, the isolates were characterized into eight races of the pathogen. The same set of isolates was used for molecular characterization with four different molecular markers, namely random amplified polymorphic DNA, universal rice primers, simple sequence repeats and intersimple sequence repeats. All the four sets of markers gave 100% polymorphism. Unweighted paired group method with arithmetic average analysis grouped the isolates into eight categories at genetic similarities ranging from 37 to 40%. The molecular groups partially corresponded to the states of origin/chickpea‐growing region of the isolates as well as races of the pathogen characterized in this study. The majority of southern, northern and central Indian populations representing specific races of the pathogen were grouped separately into distinct clusters along with some other isolates, indicating the existence of variability in population predominated by a single race of the pathogen. The present race profiling for the Indian population of the pathogen and its distribution pattern is entirely new. The knowledge generated in this study could be utilized in resistance breeding programme. The existence of more than one race, predominated by a single one, in a chickpea cultivation zone as supported by the present molecular findings is also a new information.     

An information-theoretic approach to evaluating the size and temperature dependence of metabolic rate

The effects of body mass and temperature on metabolic rate (MR) are among the most widely examined physiological relationships. Recently, these relationships have been incorporated into the metabolic theory of ecology (MTE) that links the ecology of populations, communities and ecosystems to the MR of individual organisms. The fundamental equation of MTE derives the relation between mass and MR using first principles and predicts the temperature dependence of MR based on biochemical kinetics. It is a deliberately simple, zeroth-order approximation that represents a baseline against which variation in real biological systems can be examined. In the present study, we evaluate the fundamental equation of MTE against other more parameter-rich models for MR using an information-theoretic approach to penalize the inclusion of additional parameters. Using a comparative database of MR measurements for 1359 species, from 11 groups ranging from prokaryotes to mammals, and spanning 16 orders of magnitude in mass and a 59°C range in body temperature, we show that differences between taxa in the mass and temperature dependence of MR are sufficiently large as to be retained in the best model for MR despite the requirement for estimation of 22 more parameters than the fundamental equation of MTE.     

In silico strategy to rationally engineer metabolite production: A case study for threonine in Escherichia coli

Genetic engineering of metabolic pathways is a standard strategy to increase the production of metabolites of economic interest. However, such flux increases could very likely lead to undesirable changes in metabolite concentrations, producing deleterious perturbations on other cellular processes. These negative effects could be avoided by implementing a balanced increase of enzyme concentrations according to the Universal Method [Kacser and Acerenza (1993) Eur J Biochem 216:361–367]. Exact application of the method usually requires modification of many reactions, which is difficult to achieve in practice. Here, improvement of threonine production via pyruvate kinase deletion in Escherichia coli is used as a case study to demonstrate a partial application of the Universal Method, which includes performing sensitivity analysis. Our analysis predicts that manipulating a few reactions is sufficient to obtain an important increase in threonine production without major perturbations of metabolite concentrations. Biotechnol. Bioeng. 2009;103: 609–620. © 2009 Wiley Periodicals, Inc.     

A new set of universal de novo sequencing primers for extensive coverage of noncoding chloroplast DNA: new opportunities for phylogenetic studies and cpSSR discovery

We present a new set of universal de novo sequencing primers targeting noncoding chloroplast DNA. The set of 107 polymerase chain reaction (PCR) primers span approximately 86% of the noncoding nucleotides in the large single copy region of Nicotiana tabacum, Oryza sativa and the orchid Phalaenopsis aphrodite. PCR tests confirmed the primers are effective in a wide range of monocots and dicots. More than 19.5 kb of cpDNA sequence was obtained across representative orchid genera with up to 82 chloroplast simple sequence repeats (cpSSRs) detected per genus. This primer set will facilitate both phylogenetic studies and rapid discovery of cpSSRs for plants, such as orchids, where there are limited genomic resources.     

Methodology for using a universal primer to label amplified DNA segments for molecular analysis

Detection of human DNA polymorphisms using high throughput methods often relies on generating a labeled DNA fraament which is generated by PCR using sequence-specific primers with an end labeled tag to detect a variant. The disadvantage of the synthesis of an end-labeled, sequence-specific primer to assay each DNA variant lies in the costs and time consume. In this report, we have demonstrated a methodology that can generate labeled DNA fragments using a labeled universal primer instead of requiring sequence-specific primers for each DNA variant.     

Dreams, Art and Virtual Worldmaking

This paper examines the possible role of dreams and other forms of virtual worldmaking (chiefly fictions) in forming and maintaining our adaptive systems. I posit no exclusive function for the dream. Rather, I treat it a an extension of fiction's preoccupation with our daily concerns, desires and fears. I suggest that narratives help us to enlarge and revise our perceptual and response systems, not by offering us moral or ethical propositions to live by but by increasing certain skills in our mental organization. Departing from John Paulos' idea that fictions and mathematics (narratives and numbers) work in similar ways, I further examine the role that probability ratios might play in dreams, despite the seeming bizarreness of many dreams. The overall idea is that narratives of all sorts are one cognitive means, among many, by which we accumulate sums of knowledge and expectation, and maintain and revise our notions of what goes with what in human experience. I also look briefly at fictional archetypes (Oedipus, Orestes/Hamlet, etc.) and universal dreams (falling, being lost or attacked, etc.) as master plots in our probability systems.     

Global terrestrial carbon storage and uncertainties in its temperature sensitivity examined with a simple model

The future of the land carbon sink is a significant uncertainty in global change projections. Here, key controls on global terrestrial carbon storage are examined using a simple model of vegetation and soil. Equilibrium solutions are derived as a function of atmospheric CO₂ and global temperature, these environmental variables are then linked in an idealized global change trajectory, and the lag between the dynamic and equilibrium solutions is derived for different linear rates of increase in atmospheric CO₂. Terrestrial carbon storage is departing significantly from equilibrium because CO₂ and temperature are increasing on a similar timescale to ecosystem change, and the lag is found to be proportional to the rate of forcing. Thus peak sizes of the land carbon sink, and any future land carbon source, are proportional to the rate of increase of CO₂. A switch from a land carbon sink to a source occurs at a higher CO₂ and temperature under more rapid forcing. The effects of parameter uncertainty in temperature sensitivities of photosynthesis, plant respiration and soil respiration, and structural uncertainty through the effect of fixing the ratio of plant respiration to photosynthesis are explored. In each case, the CO₂ fertilization effect on photosynthesis is constrained to reproduce the 1990 atmospheric CO₂ concentration within a closed global model. New literature compilations are presented for the temperature sensitivities of plant and soil respiration. A lower limit, Q₁₀=1.29, for soil respiration significantly increases future land carbon storage. An upper limit, Q₁₀=3.63, for soil respiration underpredicts the increase in carbon storage since the Last Glacial Maximum. Fixing the ratio of plant respiration to photosynthesis (R/P) at 0.5 generates the largest and most persistent land carbon sink, followed by the weakest land carbon source.