Abstract: Whole genome sequencing is helping generate robust phylogenetic hypotheses for a range of taxonomic groups that were previously recalcitrant to classical molecular phylogenetic approaches. As a case study, we performed a shallow shotgun sequencing of eight species in the tropical tree family Chrysobalanaceae to retrieve large fragments of high-copy number DNA regions and test the potential of these regions for phylogeny reconstruction. We were able to assemble the nuclear ribosomal cluster (nrDNA), the complete plastid genome (ptDNA) and a large fraction of the mitochondrial genome (mtDNA) with approximately 1000×, 450× and 120× sequencing depth respectively. The phylogenetic tree obtained with ptDNA resolved five of the seven internal nodes. In contrast, the tree obtained with mtDNA and nrDNA data were largely unresolved. This study demonstrates that genome skimming is a cost-effective approach and shows potential in plant molecular systematics within Chrysobalanaceae and other under-studied groups. © 2014 John Wiley & Sons Ltd.

Abstract: Rationale Compared with other animal venoms, ant venoms remain little explored. Ants have evolved complex venoms to rapidly immobilize arthropod prey and to protect their colonies from predators and pathogens. Many ants have retained peptide-rich venoms that are similar to those of other arthropod groups. Methods With the goal of conducting a broad and comprehensive survey of ant venom peptide diversity, we investigated the peptide composition of venoms from 82 stinging ant species from nine subfamilies using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOFMS). We also conducted an in-depth investigation of eight venoms using reversed-phase high-performance liquid chromatography (RP-HPLC) separation coupled with offline MALDI-TOFMS. Results Our results reveal that the peptide compositions of ant venom peptidomes from both poneroid and formicoid ant clades comprise hundreds of small peptides (<4 kDa), while large peptides (>4 kDa) are also present in the venom of formicoids. Chemical reduction revealed the presence of disulfide-linked peptides in most ant subfamilies, including peptides structured by one, two or three disulfide bonds as well as dimeric peptides reticulated by three disulfide bonds. Conclusions The biochemical complexity of ant venoms, associated with an enormous ecological and taxonomic diversity, suggests that stinging ant venoms constitute a promising source of bioactive molecules that could be exploited in the search for novel drug and biopesticide leads. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

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.

Abstract: Geomorphic landscape features have been suggested as indicators of forest diversity. However, their explanatory power has not yet been explicitly tested at a regional scale in tropical rainforest. We used forest inventories conducted according to a stratified sampling design (3,132 plots in 111 transects at 33 sites) and holistic multi-scale geomorphological mapping derived from a Shuttle Radar Topography Mission digital elevation model to describe and explain spatial patterns in floristic composition across French Guiana (80,000 km2). We measured and identified 123,906 trees with DBH ≥20 cm and used constrained and unconstrained ordinations to analyze variations in the abundance of 221 taxa and 51 families. Variance partitioning and variograms were used to detect spatial patterns in species composition, compare the explanatory power of spatial and environmental factors, and select the variables that best explain forest composition. Strong floristic patterns corresponded to a major latitudinal gradient and significant sub-regional floristic structure. Geomorphological landscapes shaped by historic climate fluctuations and major geological events successfully captured these patterns and explained the variation in abundance of 80 taxa, corresponding to 65 % of the inventoried trees. Our findings suggest that long-term forest dynamics are under substantial “geomorphographic control”. A geomorphological perspective on landscapes that incorporates current and past environmental filters and historical biogeographical processes could thus be used more systematically in tropical regions for regional planning and forest conservation. © 2014, Springer Science+Business Media Dordrecht.

Abstract: Whereas broad-scale Amazonian forest types have been shown to influence the structure of the communities of medium-to large-bodied vertebrates, their natural heterogeneity at smaller scale or within the terra firme forests remains poorly described and understood. Diversity indices of such communities and the relative abundance of the 21 most commonly observed species were compared from standardized line-transect data across 25 study sites distributed in undisturbed forests in French Guiana. We first assessed the relevance of a forest typology based on geomorphological landscapes to explain the observed heterogeneity. As previously found for tree beta-diversity patterns, this new typology proved to be a non-negligible factor underlying the beta diversity of the communities of medium-to large bodied vertebrates in French Guianan terra firme forests. Although the species studied are almost ubiquitous across the region, they exhibited habitat preferences through significant variation in abundance and in their association index with the different landscape types. As terra firme forests represent more than 90% of the Amazon basin, characterizing their heterogeneity-including faunal communities-is a major challenge in neotropical forest ecology. © 2015 Cambridge University Press.