Abstract: Deforestation-reinforced by illegal logging-is a serious problem in many tropical regions and causes pervasive environmental and economic damage. Existing laws that intend to reduce illegal logging need efficient, fraud resistant control methods. We developed a genetic reference database for Jatoba (Hymenaea courbaril), an important, high value timber species from the Neotropics. The data set can be used for controls on declarations of wood origin. Samples from 308 Hymenaea trees from 12 locations in Brazil, Bolivia, Peru, and French Guiana have been collected and genotyped on 10 nuclear microsatellites (nSSRs), 13 chloroplast SNPs (cpSNP), and 1 chloroplast indel marker. The chloroplast gene markers have been developed using Illumina DNA sequencing. Bayesian cluster analysis divided the individuals based on the nSSRs into 8 genetic groups. Using self-assignment tests, the power of the genetic reference database to judge on declarations on the location has been tested for 3 different assignment methods. We observed a strong genetic differentiation among locations leading to high and reliable self-assignment rates for the locations between 50% to 100% (average of 88%). Although all 3 assignment methods came up with similar mean self-assignment rates, there were differences for some locations linked to the level of genetic diversity, differentiation, and heterozygosity. Our results show that the nuclear and chloroplast gene markers are effective to be used for a genetic certification system and can provide national and international authorities with a robust tool to confirm legality of timber. © 2018 The American Genetic Association. All rights reserved.

Abstract: Reflex bleeding is an effective defensive mechanism against predators. When attacked, some insects emit hemolymph, which coagulates, quickly entangling their aggressor. Bleeding occurs at weak intersegmental membranes or through dedicated organs, which can be associated or not with glandular cells. Here, we describe the behavior and morphological structures involved in reflex bleeding in the larvae of the ladybird, Diomus thoracicus, which are intranidal parasites of the ant Wasmannia auropunctata. The larvae are tolerated by the ants thanks to odor mimicry, but some rare aggressive ant behaviors were observed that trigger reflex bleeding both at a pair of thoracic tubercles and a pair of posterodorsal abdominal humps. No glandular structure was found in association with these emission points, which suggests that the material emitted was hemolymph only. A 3D reconstruction suggested that reflex bleeding seems to be controlled by muscles whose contraction increases the internal hydrostatic pressure and pushes the hemolymph into a funnel-like structure with an opening to the outside. In D. thoracicus, the morphological structures involved in reflex bleeding are among the most complex and prominent described to date. © 2017 Elsevier Ltd

Abstract: Tropical forests shelter an unparalleled biological diversity. The relative influence of environmental selection (i.e., abiotic conditions, biotic interactions) and stochastic?distance-dependent neutral processes (i.e., demography, dispersal) in shaping communities has been extensively studied for various organisms, but has rarely been explored across a large range of body sizes, in particular in soil environments. We built a detailed census of the whole soil biota in a 12-ha tropical forest plot using soil DNA metabarcoding. We show that the distribution of 19 taxonomic groups (ranging from microbes to mesofauna) is primarily stochastic, suggesting that neutral processes are prominent drivers of the assembly of these communities at this scale. We also identify aluminium, topography and plant species identity as weak, yet significant drivers of soil richness and community composition of bacteria, protists and to a lesser extent fungi. Finally, we show that body size, which determines the scale at which an organism perceives its environment, predicted the community assembly across taxonomic groups, with soil mesofauna assemblages being more stochastic than microbial ones. These results suggest that the relative contribution of neutral processes and environmental selection to community assembly directly depends on body size. Body size is hence an important determinant of community assembly rules at the scale of the ecological community in tropical soils and should be accounted for in spatial models of tropical soil food webs.

Abstract: Beta diversity is among the most employed theoretical concepts in ecology and biodiversity conservation. Up to date, a self-contained definition of it, with no reference to alpha and gamma diversity, has never been proposed. Using Kullback-Leibler divergence, we present the explicit formula of Shannon's β entropy, a bias correction for its estimator and a confidence interval. We also provide the mathematical framework to decompose Shannon diversity into several hierarchical nested levels. From botanical inventories of tropical forest plots in French Guiana, we estimate Shannon diversity at the plot, forest and regional level. We believe this is a complete and usefulness toolbox for ecologists interested in partitioning biodiversity. © 2011 The Authors. Oikos © 2012 Nordic Society Oikos.

Abstract: Key message: Forest disturbance affects the within-population distribution of genetic diversity, but not its overall levels, in a tropical pioneer tree species. In particular, clumps of related saplings with impoverished diversity are found in canopy gaps but not under forest cover. Context: Forest disturbances can have long-term consequences on the genetic structure of tree populations, because they can alter the demographic properties of the regeneration process and favour some subpopulations/genotypes, both by stochastic processes and by selection. Intermediate disturbances tend to favour species diversity, at least in highly diverse communities, but their effect on intra-specific diversity is unknown. Aims: In this study, we have looked at the genetic consequences of forest disturbance in a stand of the long-lived Neotropical pioneer species, Jacaranda copaia. Methods: The study site was experimentally logged in 1984, and the canopy gaps generated by the logging were mapped. Seedlings of J. copaia colonised the gaps, as expected, at a higher density than in the surrounding forest. In 2006, we exhaustively sampled all saplings and adult trees available in a 25-ha area. The samples were genotyped at nine microsatellite loci, and the distribution of genetic diversity was inspected by analyses of spatial autocorrelation, automated Bayesian assignment and comparisons of diversity between cohorts by bootstrap (RaBoT). Results: Spatial autocorrelation was found to extend farther in post-disturbance saplings than in the undisturbed population (100 m and beyond versus less than 50 m), and divergent clumps (F<inf>ST</inf> = 0.05) of related genotypes were found; genetic diversity was found to be impoverished in each clump relative to the global population at about half of the loci. Conclusion: Overall, our results suggest that forest disturbance has changed the patterns of distribution of genetic diversity, with potential consequences on long-term population viability. © 2015, INRA and Springer-Verlag France.