Patterns of genetic diversity in the critically endangered Central American river turtle: human influence since the Mayan age?

We conducted a phylogeographic analysis of the strictly aquatic and critically endangered Central American river turtle, Dermatemys mawii, as part of a conservation management program for the species. We sampled 238 individuals from 15 different localities throughout the species range. Using sequence fragments from the mtDNA Cyt b and ND4 genes, we identified 16 different haplotypes. Overall, our results reveal a signal of phylogeographic structure throughout the range, which appears to have been secondarily blurred by extensive gene flow. Notably, this also applies to genetic structuring across three major hydrological basins that pose biogeographic breaks in other aquatic taxa. Divergence times of mtDNA haplotypes in D. mawii suggest that the main lineages split in the Pliocene–Pleistocene (3.73–0.227 MA) and demographic tests indicate that the species has undergone drastic demographic size fluctuations since this time period. One ancient haplotype (1D) was found to exhibit sequence divergence of up to 2% from other haplogroups. Divergence of this magnitude is indicative of species level differentiation in other turtle genera. Haplotype 1D was found in only two localities, Sarstun and Salinas, but specimens with other haplotypes were also found in those localities. It is not known whether the individuals with the 1D haplotype interbreed with non-1D individuals. Our results suggest that human activity, such as harvesting and long distance transport of animals, may have influenced the current patterns of genetic diversity. For more than 2000 years, D. mawii has been consumed by people from Middle American cultures, and the archeological record contains strong evidence that the Mayans transported animals between villages and far away from their natural distribution range. Therefore, the large-scale pattern of haplotype sharing even across hydrological barriers, the observed low haplotype diversity in some populations and the contemporary absence of a pronounced phylogeographic pattern is likely due to a combination of population expansions, gene flow, extensive human-mediated-movements and recent bottlenecks resulting from over-harvesting.     

The relative importance for plant invasiveness of trait means, and their plasticity and integration in a multivariate framework

? Functional traits, their plasticity and their integration in a phenotype have profound impacts on plant performance. We developed structural equation models (SEMs) to evaluate their relative contribution to promote invasiveness in plants along resource gradients. ? We compared 20 invasive-native phylogenetically and ecologically related pairs. SEMs included one morphological (root-to-shoot ratio (R/S)) and one physiological (photosynthesis nitrogen-use efficiency (PNUE)) trait, their plasticities in response to nutrient and light variation, and phenotypic integration among 31 traits. Additionally, these components were related to two fitness estimators, biomass and survival. ? The relative contributions of traits, plasticity and integration were similar in invasive and native species. Trait means were more important than plasticity and integration for fitness. Invasive species showed higher fitness than natives because: they had lower R/S and higher PNUE values across gradients; their higher PNUE plasticity positively influenced biomass and thus survival; and they offset more the cases where plasticity and integration had a negative direct effect on fitness. ? Our results suggest that invasiveness is promoted by higher values in the fitness hierarchy -- trait means are more important than trait plasticity, and plasticity is similar to integration -- rather than by a specific combination of the three components of the functional strategy.     

Manipulation of male attractiveness induces rapid changes in avian maternal yolk androgen deposition

Avian eggs contain maternal androgens that may adjust offspringdevelopment to environmental conditions. We review evidenceand functional explanations for the relationship between androgenconcentrations in avian eggs and male attractiveness. Experimentalstudies in captive birds show generally positive relationships,but results from correlational and experimental field studiesare less consistent, perhaps because they lack a within-femaledesign to control for confounding between-female variation.We analyzed the effect of male attractiveness on yolk levelsof maternal androgens in a wild bird, using a correlationaland experimental approach with a within-female design. We manipulatedthe sexually selected UV coloration of the crown feathers ofmale blue tits (Cyanistes caeruleus) after their female hadlaid the second egg and measured the subsequent effect on androgenconcentrations (testosterone and androstenedione) in the fifth,seventh, and ninth eggs relative to that in the second egg.Levels of testosterone, but not androstenedione, in eggs 5 and7 were higher for control (attractive) than for UV-reduced (unattractive)males. This effect disappeared in the ninth egg, coincidingwith the recovery of UV coloration after manipulation. Thissuggests that females are capable of rapid adjustments of testosteronedeposition in response to changes in their mate's ornamentalplumage. However, androgen concentrations in the second eggand pretreatment male crown coloration were not correlated.Possibly, the combination of relatively small variation in UVcoloration before treatment and the influence of unknown confoundingvariables in the correlative approach resulted in insufficientstatistical power to detect such a correlation.     

Ubiquitous late competence genes in Bacillus species indicate the presence of functional DNA uptake machineries

Natural competence for genetic transformation, i.e. the ability to take up DNA and stably integrate it in the genome, has so far only been observed in the bacterial kingdom (both in Gram-negative and Gram-positive species) and may contribute to survival under adverse growth conditions. Bacillus subtilis , the model organism for the Bacillus genus, possesses a well-characterized competence machinery. Phylogenetic analysis of several genome sequences of different Bacillus species reveals the presence of many, but not all genes potentially involved in competence and its regulation. The recent demonstration of functional DNA uptake by B. cereus supports the significance of our genome analyses and shows that the ability for functional DNA uptake might be widespread among Bacilli .     

The Hyperpolarizing Region of the Current-Voltage Curve in Frog Skin

Excitability (action potential and refractory period) has been described by A. Finkelstein in the depolarizing region of the current-voltage (I-V) curve of the isolated frog skin. Recently Fishman and Macey interpreted this phenomenon as a consequence of a region with negative resistance that confers to the I-V curve an N shape. We have studied the I-V relation of the isolated frog skin in the hyperpolarizing region with a current-ramp system. It was found that in Na₂SO₄ Ringer's, the resistance continuously increases in the hyperpolarizing direction. When hyperpolarization reaches 300 mv an electrical breakdown occurs, occasionally followed by a region of negative resistance. In NaCl Ringer's the breakdown was also found although the I-V relation was reasonably linear. Unidirectional Na⁺ outflux was measured at different levels of voltage clamping across the skin and with different Na⁺ concentrations in the solutions. The Na⁺ outflux was found to be relatively independent of these parameters. Based on these results a Na⁺ rectifying structure is postulated. An electrical model for active Na⁺ transport including a diode and an oscillator is proposed. The effects of CO₂, nitrogen, amiloride, and ouabain on the I-V relation are described.     

Environmental determinants of woody and herbaceous riparian vegetation patterns in a semi-arid mediterranean basin

What environmental variables determine riparian vegetation patterns? Are there differences between woody and herbaceous species? To answer these questions, we first explored the composition and richness patterns of both riparian woody and herbaceous species in a semi-arid mediterranean basin. Then, we assessed the environmental factors (climate, geology, topography, hydrogeomorphology and land use) that best explain these patterns. We used the following methodological approaches: clustering analyses, distance-based linear models, generalised linear models and hierarchical partitioning procedures. Valley shape, drought duration, river habitat heterogeneity, water conductivity and agricultural land use were the most important variables explaining variation in species composition for both groups. Woody riparian richness was mainly influenced by flow conditions and valley shape, whereas herbaceous one was more dependent on substrate features. Thus, although some differences in the importance of individual variables were observed, we found a notable congruence in the composition and species richness of both groups and also in the main types of variables explaining these patterns (hydrogeomorphology and land use, especially agriculture). Our results show that both communities could be treated in a holistic way, since they respond similarly to the strong natural and anthropogenic environmental gradients present in mediterranean basins.     

Monoclonal antibodies can affect complement deposition on the capsule of the pathogenic fungus Cryptococcus neoformans by both classical pathway activation and steric hindrance

The capsule of the human pathogenic fungus Cryptococcus neoformans presents the immune system with a formidable problem for phagocytosis. Capsule-mediated activation of the alternative complement (C) pathway results in component 3 (particularly, C3) binding to the capsule near the cell wall surface. Hence, for cells with large capsule, C3 cannot interact with the complement receptor (CR) and is not opsonic. However, C activation in either immune serum or in the presence of monoclonal antibody (mAb) to capsular polysaccharide localizes C3 to the capsular edge. When C. neoformans cells were coated with both C and antibody (Ab) opsonins, Ab bound first and promoted C3 deposition at the edge of the capsule. The mechanism for the Ab-mediated change in C3 localization to the capsule edge involved both classical C pathway activation and steric hindrance preventing C3 penetration into the capsule. The change in C3 localization changed the mode of phagocytosis in macrophages, such that localizing C3 at the edge of the capsule allowed phagocytosis through C3-CR3 and C3-CR4 interactions, which did not occur in serum without Ab. These findings reveal a new mechanism of Ab action whereby Abs affect the location of C3 and its interaction with its receptor in macrophages depending on the immunoglobulin concentration.     

Genome-wide analysis of signatures of selection in populations of African honey bees (Apis mellifera) using new web-based tools

Background

With the development of inexpensive, high-throughput sequencing technologies, it has become feasible to examine questions related to population genetics and molecular evolution of non-model species in their ecological contexts on a genome-wide scale. Here, we employed a newly developed suite of integrated, web-based programs to examine population dynamics and signatures of selection across the genome using several well-established tests, including F_ST, pN/pS, and McDonald-Kreitman. We applied these techniques to study populations of honey bees (Apis mellifera) in East Africa. In Kenya, there are several described A. mellifera subspecies, which are thought to be localized to distinct ecological regions.

Results

We performed whole genome sequencing of 11 worker honey bees from apiaries distributed throughout Kenya and identified 3.6 million putative single-nucleotide polymorphisms. The dense coverage allowed us to apply several computational procedures to study population structure and the evolutionary relationships among the populations, and to detect signs of adaptive evolution across the genome. While there is considerable gene flow among the sampled populations, there are clear distinctions between populations from the northern desert region and those from the temperate, savannah region. We identified several genes showing population genetic patterns consistent with positive selection within African bee populations, and between these populations and European A. mellifera or Asian Apis florea.

Conclusions

These results lay the groundwork for future studies of adaptive ecological evolution in honey bees, and demonstrate the use of new, freely available web-based tools and workflows (http://usegalaxy.org/r/kenyanbee) that can be applied to any model system with genomic information.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1712-0) contains supplementary material, which is available to authorized users.     

An easy NMR method to study the formation of parallel β-sheets in peptide aggregates

There is currently great interest in the study of peptide aggregation by -sheet formation because of its relevance in pathological states or in the design of self-assembling systems of technological interest. NMR studies of -sheet aggregates are difficult because of their long correlation times and spectral degeneracy. In this communication we demonstrate the combination of a semiselective TOCSY-NOESY experiment with partial deuterium exchange of labile protons to assign inter-molecular NOE cross peaks and prove the presence of a soluble parallel -sheet in fast exchange with monomeric Ac-ASTTTNYT-NH₂ (Ac-T-NH₂) in solution.