Shifts in species and phylogenetic diversity between sapling and tree communities indicate negative density dependence in a lowland rain forest

1. As trees in a given cohort progress through ontogeny, many individuals die. This risk of mortality is unevenly distributed across species because of many processes such as habitat filtering, interspecific competition and negative density dependence. Here, we predict and test the patterns that such ecological processes should inscribe on both species and phylogenetic diversity as plants recruit from saplings to the canopy. 2. We compared species and phylogenetic diversity of sapling and tree communities at two sites in French Guiana. We surveyed 2084 adult trees in four 1-ha tree plots and 943 saplings in sixteen 16-m2 subplots nested within the tree plots. Species diversity was measured using Fisher's alpha (species richness) and Simpson's index (species evenness). Phylogenetic diversity was measured using Faith's phylogenetic diversity (phylogenetic richness) and Rao's quadratic entropy index (phylogenetic evenness). The phylogenetic diversity indices were inferred using four phylogenetic hypotheses: two based on rbcLa plastid DNA sequences obtained from the inventoried individuals with different branch lengths, a global phylogeny available from the Angiosperm Phylogeny Group, and a combination of both. 3. Taxonomic identification of the saplings was performed by combining morphological and DNA barcoding techniques using three plant DNA barcodes (psbA-trnH, rpoC1 and rbcLa). DNA barcoding enabled us to increase species assignment and to assign unidentified saplings to molecular operational taxonomic units. 4. Species richness was similar between saplings and trees, but in about half of our comparisons, species evenness was higher in trees than in saplings. This suggests that negative density dependence plays an important role during the sapling-to-tree transition. 5. Phylogenetic richness increased between saplings and trees in about half of the comparisons. Phylogenetic evenness increased significantly between saplings and trees in a few cases (4 out of 16) and only with the most resolved phylogeny. These results suggest that negative density dependence operates largely independently of the phylogenetic structure of communities. 6. Synthesis. By contrasting species richness and evenness across size classes, we suggest that negative density dependence drives shifts in composition during the sapling-to-tree transition. In addition, we found little evidence for a change in phylogenetic diversity across age classes, suggesting that the observed patterns are not phylogenetically constrained.

Biotic and abiotic variables show little redundancy in explaining tree species distributions

Abiotic factors such as climate and soil determine the species fundamental niche, which is further constrained by biotic interactions such as interspecific competition. To parameterize this realized niche, species distribution models (SDMs) most often relate species occurrence data to abiotic variables, but few SDM studies include biotic predictors to help explain species distributions. Therefore, most predictions of species distributions under future climates assume implicitly that biotic interactions remain constant or exert only minor influence on large-scale spatial distributions, which is also largely expected for species with high competitive ability. We examined the extent to which variance explained by SDMs can be attributed to abiotic or biotic predictors and how this depends on species traits. We fit generalized linear models for 11 common tree species in Switzerland using three different sets of predictor variables: biotic, abiotic, and the combination of both sets. We used variance partitioning to estimate the proportion of the variance explained by biotic and abiotic predictors, jointly and independently. Inclusion of biotic predictors improved the SDMs substantially. The joint contribution of biotic and abiotic predictors to explained deviance was relatively small (similar to 9%) compared to the contribution of each predictor set individually (similar to 20% each), indicating that the additional information on the realized niche brought by adding other species as predictors was largely independent of the abiotic (topo-climatic) predictors. The influence of biotic predictors was relatively high for species preferably growing under low disturbance and low abiotic stress, species with long seed dispersal distances, species with high shade tolerance as juveniles and adults, and species that occur frequently and are dominant across the landscape. The influence of biotic variables on SDM performance indicates that community composition and other local biotic factors or abiotic processes not included in the abiotic predictors strongly influence prediction of species distributions. Improved prediction of species' potential distributions in future climates and communities may assist strategies for sustainable forest management.

New grass phylogeny resolves deep evolutionary relationships and discovers C4 origins.

• Grasses rank among the world's most ecologically and economically important plants. Repeated evolution of the C(4) syndrome has made photosynthesis highly efficient in many grasses, inspiring intensive efforts to engineer the pathway into C(3) crops. However, comparative biology has been of limited use to this endeavor because of uncertainty in the number and phylogenetic placement of C(4) origins. • We built the most comprehensive and robust molecular phylogeny for grasses to date, expanding sampling efforts of a previous working group from 62 to 531 taxa, emphasizing the C(4)-rich PACMAD (Panicoideae, Arundinoideae, Chloridoideae, Micrairoideae, Aristidoideae and Danthonioideae) clade. Our final matrix comprises c. 5700 bp and is > 93% complete. • For the first time, we present strong support for relationships among all the major grass lineages. Several new C(4) lineages are identified, and previously inferred origins confirmed. C(3)/C(4) evolutionary transitions have been highly asymmetrical, with 22-24 inferred origins of the C(4) pathway and only one potential reversal. • Our backbone tree clarifies major outstanding systematic questions and highlights C(3) and C(4) sister taxa for comparative studies. Two lineages have emerged as hotbeds of C(4) evolution. Future work in these lineages will be instrumental in understanding the evolution of this complex trait.

Trophic resource partitioning and competition between the two sibling bat species Myotis myotis and Myotis blythii

1. Niche theory predicts that the stable coexistence of species within a guild should be associated, if resources are limited, with a mechanism of resource partitioning. Using extensive data on diets, the present study attempts: (i) to test the hypothesis that, in sympatry, the interspecific overlap between the trophic niches of the sibling bat species Myotis myotis and M. blythii-which coexist intimately in their roosts-is effectively lower than the two intraspecific overlaps; (ii) to assess the role played by interspecific competition in resource partitioning through the study of trophic niche displacement between several sympatric and allopatric populations. 2. Diets were determined by the analysis of faecal samples collected in the field from individual bats captured in various geographical areas. Trophic niche overlaps were calculated monthly for all possible intraspecific and interspecific pairs of individuals from sympatric populations. Niche breadth was estimated from: (i) every faecal sample; (ii) all the faecal samples collected per month in a given population (geographical area). 3. In every population, the bulk of the diets of M. myotis and M. blythii consisted of, respectively, terrestrial (e.g. carabid beetles) and grass-dwelling (mostly bush crickets) prey. All intraspecific trophic niche overlaps were significantly greater than the interspecific one, except in Switzerland in May when both species exploited mass concentrations of cockchafers, a non-limiting food source. This clearcut partitioning of resources may allow the stable, intimate coexistence observed under sympatric conditions. 4. Relative proportions of ground-and grass-dwelling prey, as well as niche breadths (either individual or population), did not differ significantly between sympatry and allopatry, showing that, under allopatric conditions, niche expansion does not take place. This suggests that active interspecific competition is not the underlying mechanism responsible for the niche partitioning which is currently observed between M. myotis and M. blythii.

Tree cover at fine and coarse spatial grains interacts with shade tolerance to shape plant species distributions across the Alps

The role of competition for light among plants has long been recognized at local scales, but its potential importance for plant species' distribution at larger spatial scales has largely been ignored. Tree cover acts as a modulator of local abiotic conditions, notably by reducing light availability below the canopy and thus the performance of species that are not adapted to low-light conditions. However, this local effect may propagate to coarser spatial grains. Using 6,935 vegetation plots located across the European Alps, we fit Generalized Linear Models (GLM) for the distribution of 960 herbs and shrubs species to assess the effect of tree cover at both plot and landscape grain sizes (~ 10-m and 1-km, respectively). We ran four models with different combinations of variables (climate, soil and tree cover) for each species at both spatial grains. We used partial regressions to evaluate the independent effects of plot- and landscape-scale tree cover on plant communities. Finally, the effects on species' elevational range limits were assessed by simulating a removal experiment comparing the species' distribution under high and low tree cover. Accounting for tree cover improved model performance, with shade-tolerant species increasing their probability of presence at high tree cover whereas shade-intolerant species showed the opposite pattern. The tree cover effect occurred consistently at both plot and landscape spatial grains, albeit strongest at the former. Importantly, tree cover at the two grain sizes had partially independent effects on plot-scale plant communities, suggesting that the effects may be transmitted to coarser grains through meta-community dynamics. At high tree cover, shade-intolerant species exhibited elevational range contractions, especially at their upper limit, whereas shade-tolerant species showed elevational range expansions at both limits. Our findings suggest that the range shifts for herb and shrub species may be modulated by tree cover dynamics.

The role of clade competition in the diversification of North American canids.

The history of biodiversity is characterized by a continual replacement of branches in the tree of life. The rise and demise of these branches (clades) are ultimately determined by changes in speciation and extinction rates, often interpreted as a response to varying abiotic and biotic factors. However, understanding the relative importance of these factors remains a major challenge in evolutionary biology. Here we analyze the rich North American fossil record of the dog family Canidae and of other carnivores to tease apart the roles of competition, body size evolution, and climate change on the sequential replacement of three canid subfamilies (two of which have gone extinct). We develop a novel Bayesian analytic framework to show that competition from multiple carnivore clades successively drove the demise and replacement of the two extinct canid subfamilies by increasing their extinction rates and suppressing their speciation. Competitive effects have likely come from ecologically similar species from both canid and felid clades. These results imply that competition among entire clades, generally considered a rare process, can play a more substantial role than climate change and body size evolution in determining the sequential rise and decline of clades.

Oligocene CO2 decline promoted C4 photosynthesis in grasses.

C4 photosynthesis is an adaptation derived from the more common C3 photosynthetic pathway that confers a higher productivity under warm temperature and low atmospheric CO2 concentration [1, 2]. C4 evolution has been seen as a consequence of past atmospheric CO2 decline, such as the abrupt CO2 fall 32-25 million years ago (Mya) [3-6]. This relationship has never been tested rigorously, mainly because of a lack of accurate estimates of divergence times for the different C4 lineages [3]. In this study, we inferred a large phylogenetic tree for the grass family and estimated, through Bayesian molecular dating, the ages of the 17 to 18 independent grass C4 lineages. The first transition from C3 to C4 photosynthesis occurred in the Chloridoideae subfamily, 32.0-25.0 Mya. The link between CO2 decrease and transition to C4 photosynthesis was tested by a novel maximum likelihood approach. We showed that the model incorporating the atmospheric CO2 levels was significantly better than the null model, supporting the importance of CO2 decline on C4 photosynthesis evolvability. This finding is relevant for understanding the origin of C4 photosynthesis in grasses, which is one of the most successful ecological and evolutionary innovations in plant history.

Predicting positive food challenges in children sensitised to peanuts/tree nuts.

BACKGROUND: Children with atopic diseases in early life are frequently found with positive IgE tests to peanuts/tree nuts without a history of previous ingestion. We aimed to identify risk factors for reactions to nuts at first introduction. METHODS: A retrospective case-note and database analysis was performed. Recruitment criteria were: patients aged 3-16 yr who had a standardized food challenge to peanut and/or tree nuts due to sensitisation to the peanut/tree nut (positive spIgE or SPT) without previous consumption. A detailed assessment was performed of factors relating to food challenge outcome with univariate and multivariate logistic regression analysis. RESULTS: There were 98 food challenges (47 peanut, 51 tree nut) with 29 positive, 67 negative and 2 inconclusive outcomes. A positive maternal history of allergy and a specific IgE >5 kU/l were strongly associated with a significantly increased risk of a positive food challenge (OR 3.73; 95% CI 1.31-10.59; p = 0.013 and OR 3.35; 95% CI 1.23-9.11; p = 0.007, respectively). Adjusting for age, a three year-old with these criteria has a 67% probability of a positive challenge. There was no significant association between types of peanut/tree nut, other food allergies, atopic conditions or severity of previous food reactions and positive challenges. CONCLUSIONS: We have demonstrated an association between the presence of maternal atopic history and a specific IgE >5 kU/l, with a significant increase in the likelihood of a positive food challenge. Although requiring further prospective validation these easily identifiable components should be considered when deciding the need for a challenge.

A concentric analysis of the impact of urbanization on the threatened European tree frog in an agricultural landscape

Pond-breeding amphibians are affected by site-specific factors and regional and landscape-scale patterns of land use. Recent anthropogenic landscape modifications (drainage, agriculture intensification, larger road networks, and increased traffic) affect species by reducing the suitable habitat area and fragmenting remaining populations. Using a robust concentric approach based on permutation tests, we evaluated the impact of recent landscape changes on the presence of the endangered European tree frog (Hyla arborea.) in wetlands. We analyzed the frequency of 1 traffic and 14 land-use indices at 20 circular ranges (from 100-m up to 2-km radii) around 76 ponds identified in western Switzerland. Urban areas and road surfaces had a strong adverse effect on tree frog presence even at relatively great distances (from 100 m up to 1 km). When traffic measurements were considered instead of road surfaces, the effect increased, suggesting a negative impact due to a vehicle-induced effect. Altogether, our results indicate that urbanization and traffic must be taken into account when pond creation is an option in conservation management plans, as is the case for the European tree frog in western Switzerland. We conclude that our easy-to-use and robust concentric method of analysis can successfully assist managers in identifying potential sites for pond creation, where probability of the presence of tree frogs is maximized.

A stepwise protocol to coat aAPC beads prevents out-competition of anti-CD3 mAb and consequent experimental artefacts.

Artificial antigen-presenting cells (aAPC) are widely used for both clinical and basic research applications, as cell-based or bead-based scaffolds, combining immune synapse components of interest. Adequate and controlled preparation of aAPCs is crucial for subsequent immunoassays. We reveal that certain proteins such as activatory anti-CD3 antibody can be out-competed by other proteins (e.g. inhibitory receptor ligands such as PDL1:Fc) during the coating of aAPC beads, under the usually performed coating procedures. This may be misleading, as we found that decreased CD8 T cell activity was not due to inhibitory receptor triggering but rather because of unexpectedly low anti-CD3 antibody density on the beads upon co-incubation with inhibitory receptor ligands. We propose an optimized protocol, and emphasize the need to quality-control the coating of proteins on aAPC beads prior to their use in immunoassays.