Low-dimensional trade-offs fail to explain richness and structure in species-rich plant communities

Mathematical models and ecological theory suggest that low-dimensional life history trade-offs (i.e. negative correlation between two life history traits such as competition vs. colonisation) may potentially explain the maintenance of species diversity and community structure. In the absence of trade-offs, we would expect communities to be dominated by ‘super-types’ characterised by mainly positive trait expressions. However, it has proven difficult to find strong empirical evidence for such trade-offs in species-rich communities. We developed a spatially explicit, rule-based and individual-based stochastic model to explore the importance of low-dimensional trade-offs. This model simulates the community dynamics of 288 virtual plant functional types (PFTs), each of which is described by seven life history traits. We consider trait combinations that fit into the trade-off concept, as well as super-types with little or no energy constraints or resource limitations, and weak PFTs, which do not exploit resources efficiently. The model is parameterised using data from a fire-prone, species-rich Mediterranean-type shrubland in southwestern Australia. We performed an exclusion experiment, where we sequentially removed the strongest PFT in the simulation and studied the remaining communities. We analysed the impact of traits on performance of PFTs in the exclusion experiment with standard and boosted regression trees. Regression tree analysis of the simulation results showed that the trade-off concept is necessary for PFT viability in the case of weak trait expression combinations such as low seed production or small seeds. However, species richness and diversity can be high despite the presence of super-types. Furthermore, the exclusion of super-types does not necessarily lead to a large increase in PFT richness and diversity. We conclude that low-dimensional trade-offs do not provide explanations for multi-species co-existence contrary to the prediction of many conceptual models.     

Opposing effects of the angiopoietins on the thrombin-induced permeability of human pulmonary microvascular endothelial cells

Background

Angiopoietin-2 (Ang-2) is associated with lung injury in ALI/ARDS. As endothelial activation by thrombin plays a role in the permeability of acute lung injury and Ang-2 may modulate the kinetics of thrombin-induced permeability by impairing the organization of vascular endothelial (VE-)cadherin, and affecting small Rho GTPases in human pulmonary microvascular endothelial cells (HPMVECs), we hypothesized that Ang-2 acts as a sensitizer of thrombin-induced hyperpermeability of HPMVECs, opposed by Ang-1.

Methodology/Principal Findings

Permeability was assessed by measuring macromolecule passage and transendothelial electrical resistance (TEER). Angiopoietins did not affect basal permeability. Nevertheless, they had opposing effects on the thrombin-induced permeability, in particular in the initial phase. Ang-2 enhanced the initial permeability increase (passage, P = 0.010; TEER, P = 0.021) in parallel with impairment of VE-cadherin organization without affecting VE-cadherin Tyr685 phosphorylation or increasing RhoA activity. Ang-2 also increased intercellular gap formation. Ang-1 preincubation increased Rac1 activity, enforced the VE-cadherin organization, reduced the initial thrombin-induced permeability (TEER, P = 0.027), while Rac1 activity simultaneously normalized, and reduced RhoA activity at 15 min thrombin exposure (P = 0.039), but not at earlier time points. The simultaneous presence of Ang-2 largely prevented the effect of Ang-1 on TEER and macromolecule passage.

Conclusions/Significance

Ang-1 attenuated thrombin-induced permeability, which involved initial Rac1 activation-enforced cell-cell junctions, and later RhoA inhibition. In addition to antagonizing Ang-1, Ang-2 had also a direct effect itself. Ang-2 sensitized the initial thrombin-induced permeability accompanied by destabilization of VE-cadherin junctions and increased gap formation, in the absence of increased RhoA activity.     

Endotoxemia decreases matching of regional blood flow and O2 delivery to O2 uptake in the porcine left ventricle

Heterogeneity of regional coronary blood flow is caused in part by heterogeneity in O(2) demand in the normal heart. We investigated whether myocardial O(2) supply/demand mismatching is associated with the myocardial depression of sepsis. Regional blood flow (microspheres) and O(2) uptake ([(13)C]acetate infusion and analysis of resultant NMR spectra) were measured in about nine contiguous tissue samples from the left ventricle (LV) in each heart. Endotoxemic pigs (n = 9) showed hypotension at unchanged cardiac output with a fall in LV stroke work and first derivative of LV pressure relative to controls (n = 4). Global coronary blood flow and O(2) delivery were maintained. Lactate accumulated in arterial blood, but net lactate extraction across the coronary bed was unchanged during endotoxemia. When LV O(2) uptake based on blood gas versus NMR data were compared, the correlation was 0.73 (P = 0.007). While stable over time in controls, regional blood flows were strongly redistributed during endotoxin shock, with overall flow heterogeneity unchanged. A stronger redistribution of blood flow with endotoxin was associated with a larger fall in LV function parameters. Moreover, the correlation of regional O(2) delivery to uptake fell from r = 0.73 (P < 0.001) in control to r = 0.18 (P = 0.25, P = 0.009 vs. control) in endotoxemic hearts. The results suggest a redistribution of LV regional coronary blood flow during endotoxin shock in pigs, with regional O(2) delivery mismatched to O(2) demand. Mismatching may underlie, at least in part, the myocardial depression of sepsis.     

An efficient approach to the deployment of complex open source information systems

Complex open source information systems are usually implemented as component-based software to inherit the available functionality of existing software packages developed by third parties. Consequently, the deployment of these systems not only requires the installation of operating system, application framework and the configuration of services but also needs to resolve the dependencies among components. The problem becomes more challenging when the application must be installed and used on different platforms such as Linux and Windows. To address this, an efficient approach using the virtualization technology is suggested and discussed in this paper. The approach has been applied in our project to deploy a web-based integrated information system in molecular genetics labs. It is a low-cost solution to benefit both software developers and end-users.     

Molecular phylogeny of the spiny lobster genus Palinurus (Decapoda: Palinuridae) with hypotheses on speciation in the NE Atlantic/Mediterranean and SW Indian Ocean

Sequence data derived from the mitochondrial DNA 16S rRNA and COI genes were used to determine the phylogenetic relationships among six Palinurus spiny lobster species. Three species (P. charlestoni, P. elephas, and P. mauritanicus) occur in the northeastern Atlantic/Mediterranean, and the others (P. barbarae, P. delagoae and P. gilchristi) inhabit the southwestern Indian Ocean. Parsimony and model based phylogenetics strongly supported the monophyly of the genus. A combined parsimony analysis based on 1001bp and 274 parsimony informative characters recovered the most resolved phylogeny with >70% bootstrap support for associations among species. The Atlantic P. charlestoni consistently clusters nested within the Indian Ocean clade, and the mtDNA sequence divergence between the two most distant species is 8.24%. If the northward collision of Africa with Eurasia in the Miocene caused the final physical separation between the Atlantic and Indian Ocean taxa, then the Palinurus mtDNA (COI and 16S combined) evolved no faster than 0.18% (lower bound) to 0.36% (upper bound) per lineage per million years. The six extant species occur in the pathways of the North Atlantic and South Indian Ocean gyres, and hypotheses on their radiation are developed relative to the strengthening of boundary currents in the Miocene and life history traits congruent with survival in strong ocean currents.     

Polytrichum strictum as a Nurse-Plant in Peatland Restoration

Polytrichum strictum is a pioneer plant frequently found on bare peat substrate after perturbations (fire, peat extraction). Can this moss facilitate the return of Sphagnum species or other boreal plants after disturbances? Field surveys of abandoned peatlands after peat extraction revealed that Sphagnum was always found in association with P. strictum carpets. We conducted field experiments in abandoned peatlands and showed that P. strictum carpets were able to keep Sphagnum fragments more humid than bare peat but only when the P. strictum carpets were not totally bone dry. In general, daytime temperatures beneath P. strictum carpets and fragments were reduced during the day and increased during the night compared to bare peat. Polytrichum strictum carpets acted as a seed trap, retaining more artificial seeds than bare peat. Polytrichum strictum can be a nurse‐plant: after 16 months, vascular plants transplanted in the P. strictum carpet were healthier than the ones planted on bare peat. The use of P. strictum as a nurse‐plant in boreal forest or peatland restoration is recommended for sites prone to frost heaving and with harsh microclimatic conditions.     

First report of Phytopythium vexans causing the “Avocado sadness” in Michoacan,Mexico

Mexico is the main producer, consumer and exporter of avocado in the world, being Michoacan the main producer state contributing more than 80% of the national production. There are phytopathogens that decimate the production causing the death of the tree. Root samples were collected in avocado trees that showed the characteristic symptomatology of the disease known as avocado sadness, the sampling was carried out in four of the main avocado producing towns, in the state of Michoacan, Mexico. The isolation consisted in sowing root tissue in Petri dishes with V8^®-PARPH culture medium, subsequently they were identified morphologically and for species level it was determined by molecular biology, with the PCR-ITS technique. Pathogenicity tests were performed in triplicate with avocado seedlings with more than six leaves. After 24 hours, the inoculated plants expressed decay in the apical part, after 120 hours the leaves showed yellowing and after 15 days there was a generalized wilt on the stem and leaves, re-isolating the phytopathogen Phytopythium vexans. This study confirms the first report of the oomycete P. vexans affecting avocado trees in the most important producing region of the Mexican Republic.     

High diversity at PRDM9 in chimpanzees and bonobos

Background

The PRDM9 locus in mammals has increasingly attracted research attention due to its role in mediating chromosomal recombination and possible involvement in hybrid sterility and hence speciation processes. The aim of this study was to characterize sequence variation at the PRDM9 locus in a sample of our closest living relatives, the chimpanzees and bonobos.

Methodology/Principal Findings

PRDM9 contains a highly variable and repetitive zinc finger array. We amplified this domain using long-range PCR and determined the DNA sequences using conventional Sanger sequencing. From 17 chimpanzees representing three subspecies and five bonobos we obtained a total of 12 alleles differing at the nucleotide level. Based on a data set consisting of our data and recently published Pan PRDM9 sequences, we found that at the subspecies level, diversity levels did not differ among chimpanzee subspecies or between chimpanzee subspecies and bonobos. In contrast, the sample of chimpanzees harbors significantly more diversity at PRDM9 than samples of humans. Pan PRDM9 shows signs of rapid evolution including no alleles or ZnFs in common with humans as well as signals of positive selection in the residues responsible for DNA binding.

Conclusions and Significance

The high number of alleles specific to the genus Pan, signs of positive selection in the DNA binding residues, and reported lack of conservation of recombination hotspots between chimpanzees and humans suggest that PRDM9 could be active in hotspot recruitment in the genus Pan. Chimpanzees and bonobos are considered separate species and do not have overlapping ranges in the wild, making the presence of shared alleles at the amino acid level between the chimpanzee and bonobo species interesting in view of the hypothesis that PRDM9 plays a universal role in interspecific hybrid sterility.