An estimation of the floristic richness of Bolivia’s Andean dry valleys

We estimate plant species richness of Bolivian Andean dry valleys applying the species/genus ratio of Compositae to all reported genera for those regions. The results suggest the existence of around 1500 species in the Bolivian dry valleys (12.6% more than the species recorded). A brief biogeographical analysis of our results suggests that the use of species/genus ratio of Compositae to estimate the size of the flora in Bolivian Andean dry valleys should be considered with caution, since the central Andes are geologically very young, and explosive speciation processes have taken place only in some taxa (mainly in Bromeliaceae and Cactaceae). We offer some evidence pointing to the possibility that the Andean dry valleys may possess many more species than suggested by the Compositae species/genus ratio. We discuss the implications of our estimation for conservation of the Andean dry valleys, which only represent 0.7% of the protected area of Bolivia.     

Conformational changes of yeast plasma membrane H(+)-ATPase during activation by glucose: role of threonine-912 in the carboxy-terminal tail

Yeast Pma1 H(+)-ATPase, which belongs to the P-type family of cation-transporting ATPases, is activated up to 10-fold by growth on glucose, and indirect evidence has linked the activation to Ser/Thr phosphorylation within the C-terminal tail. We have now used limited trypsinolysis to map glucose-induced conformational changes throughout the 100 kDa ATPase. In the wild-type enzyme, trypsin cleaves first at Lys-28 and Arg-73 in the extended N-terminal segment (sites T1 and T2); subsequent cleavages occur at Arg-271 between the A domain and M3 (site T3) and at Lys-749 or Lys-754 in the M6-M7 cytoplasmic loop (site T4). Activation by glucose leads to a striking increase in trypsin sensitivity. At the C-terminal end of the protein, the Arg- and Lys-rich tail is shielded from trypsin in membranes from glucose-starved cells (GS) but becomes accessible in membranes from glucose-metabolizing cells (GM). In the presence of orthovanadate, Lys-174 at the boundary between M2 and the A domain also becomes open to cleavage in GM but not GS samples (site T5). Significantly, this global conformational change can be suppressed by mutations at Thr-912, a consensus phosphorylation site near the C-terminus. Substitution by Ala at position 912 leads to a GS-like (trypsin-resistant) state, while substitution by Asp leads to a GM-like (trypsin-sensitive) state. Thus, the present results help to dissect the intramolecular movements that result in glucose activation.     

Process‐based functions for seed retention on animals: a test of improved descriptions of dispersal using multiple data sets

Studies of external seed transport on animals usually assume that the probability of detachment is constant, so that seed retention should show a simple exponential relationship with time. This assumption has not been tested explicitly, and may lead to inaccurate representation of long distance seed dispersal by animals. We test the assumption by comparing the fit to empirical data of simple, two‐parameter functions. Fifty‐two data sets were obtained from five published studies, describing seed retention of 32 plant species on sheep, cattle, deer, goats and mice. Model selection suggested a simple exponential function was adequate for data sets in which seed retention was followed for short periods ( <48 h). The data gathered over longer periods (49–219 days) were best described by the power exponential function, a form of the stretched exponential which allows a changing dropping rate. In these cases the power exponential showed that seed dropping rate decreased with time, suggesting that seeds vary in attachment, with some seeds becoming deeply buried or wound up in the animal's coat. Comparison of fitted parameters across all the data sets also confirmed that seeds with adhesive structures have lower dropping rates than those without. We conclude that the seed dropping rate often changes with time during external transport on animals and that the power exponential is an effective function to describe this change. We advise that, to analyse seed dropping rates adequately, retention should be measured over reasonable time periods – until most seeds are dropped – and both the simple and power exponential functions should be fitted to the resulting data. To increase its utility, we provide functions describing the seed dropping rate and the dispersal kernel resulting from the power exponential relationship.     

Seasonality provokes a shift of thermal preferences in a temperate lizard,but altitude does not

1. We compared the mean, limits and breadth of the preferred thermal range (PTR) of two Iberian populations of the lizard Psammodromus algirus separated by 700 m altitude in May and July.     

Rapid identification and interpretation of gene–environment associations using the new R.SamBada landscape genomics pipeline

sam βada is a genome–environment association software, designed to search for signatures of local adaptation. However, pre‐ and postprocessing of data can be labour‐intensive, preventing wider uptake of the method. We have now developed R.SamBada, an r ‐package providing a pipeline for landscape genomic analysis based on sam βada , spanning from the retrieval of environmental conditions at sampling locations to gene annotation using the Ensembl genome browser. As a result, R.SamBada standardizes the landscape genomics pipeline and eases the search for candidate genes of local adaptation, enhancing reproducibility of landscape genomic studies. The efficiency and power of the pipeline is illustrated using two examples: sheep populations from Morocco with no evident population structure and Lidia cattle from Spain displaying population substructuring. In both cases, R.SamBada enabled rapid identification and interpretation of candidate genes, which are further discussed in the light of local adaptation. The package is available in the r CRAN package repository and on GitHub (github.com/SolangeD/R.SamBada).     

The Antibiotic Dosage of Fastest Resistance Evolution: Gene Amplifications Underpinning the Inverted-U

To determine the dosage at which antibiotic resistance evolution is most rapid, we treated Escherichia coli in vitro, deploying the antibiotic erythromycin at dosages ranging from zero to high. Adaptation was fastest just below erythromycin’s minimal inhibitory concentration (MIC) and genotype-phenotype correlations determined from whole genome sequencing revealed the molecular basis: simultaneous selection for copy number variation in three resistance mechanisms which exhibited an “inverted-U” pattern of dose-dependence, as did several insertion sequences and an integron. Many genes did not conform to this pattern, however, reflecting changes in selection as dose increased: putative media adaptation polymorphisms at zero antibiotic dosage gave way to drug target (ribosomal RNA operon) amplification at mid dosages whereas prophage-mediated drug efflux amplifications dominated at the highest dosages. All treatments exhibited E. coli increases in the copy number of efflux operons acrAB and emrE at rates that correlated with increases in population density. For strains where the inverted-U was no longer observed following the genetic manipulation of acrAB, it could be recovered by prolonging the antibiotic treatment at subMIC dosages.     

Diversity, abundance or rare species as a target for the conservation of mammalian carnivores: a case study in Southern Spain

Management goals in protected areas and/or communities usually include diversity as one of the most valuable and confident criteria. Nevertheless, the use of diversity and related indices as a means of evaluating successful management practices could produce conflicting results. Here we report a case study in one of the most important European protected areas. After 6 years of intensive conservation management of the Don~ana National Park, the general abundance and numbers of the target single-species conservation plan (the Iberian lynx) increased, although carnivore community diversity and evenness decreased. This was a result of a disproportionate increase of an oportunistic native species, the red fox. We propose the combined use of diversity, richness and evenness indices when monitoring management practices such as those reported here.