Abstract: A major challenge remains to understand the relative contributions of history, dispersal, and environmental filtering to the assembly of hyperdiverse communities across spatial scales. Here, we examine the extent to which biogeographical history and habitat specialization have generated turnover among and within lineages of Amazonian trees across broad geographic and environmental gradients. We replicated standardized tree inventories in 102 0.1-ha plots located in two distant regions—the western Amazon and the eastern Guiana shield. Within each region, we used a nested design to replicate plots on contrasted habitats: white-sand, terra firme, and seasonally flooded forests. Our plot network encompassed 26,386 trees that together represented 2,745 distinct taxa, which we standardized across all plots and regions. We combined taxonomic and phylogenetic data with detailed soil measurements and climatic data to: (1) test whether patterns of taxonomic and phylogenetic composition are consistent with recent or historical processes, (2) disentangle the relative effects of habitat, environment, and geographic distance on taxonomic and phylogenetic turnover among plots, and (3) contrast the proportion of habitat specialists among species from each region. We found substantial species turnover between Peru and French Guiana, with only 8.8% of species shared across regions; genus composition remained differentiated across habitats and regions, whereas turnover at higher taxonomic levels (family, order) was much lower. Species turnover across plots was explained primarily by regions, but also substantially by habitat differences and to a lesser extent by spatial distance within regions. Conversely, the composition of higher taxonomic levels was better explained by habitats (especially comparing white-sand forests to other habitats) than spatial distance. White-sand forests harbored most of the habitat specialists in both regions, with stronger habitat specialization in Peru than in French Guiana. Our results suggest that recent diversification events have resulted in extremely high turnover in species and genus composition with relatively little change in the composition of higher lineages. Our results also emphasize the contributions of rare habitats, such as white-sand forests, to the extraordinary diversity of the Amazon and underline their importance as conservation priorities.

Abstract: The major rDNA genes are composed of tandem repeats and are part of the nucleolus organizing regions (NORs). They are highly conserved and therefore useful in understanding the evolutionary patterns of chromosomal locations. The evolutionary dynamics of the karyotype may affect the organization of rDNA genes within chromosomes. In this study, we physically mapped 18S rDNA genes in 13 Neotropical ant species from four subfamilies using fluorescence in situ hybridization. Furthermore, a survey of published rDNA cytogenetic data for 50 additional species was performed, which allowed us to detect the evolutionary patterns of these genes in ant chromosomes. Species from the Neotropical, Palearctic, and Australian regions, comprising a total of 63 species from 19 genera within six subfamilies, were analysed. Most of the species (48 out of 63) had rDNA genes restricted to a single chromosome pair in their intrachromosomal regions. The position of rDNA genes within the chromosomes appears to hinder their dispersal throughout the genome, as translocations and ectopic recombination are uncommon in intrachromosomal regions because they can generate meiotic abnormalities. Therefore, rDNA genes restricted to a single chromosome pair seem to be a plesiomorphic feature in ants, while multiple rDNA sites, observed in distinct subfamilies, may have independent origins in different genera.

Abstract: French Guiana is a European ultraperipheric region located on the northern Atlantic coast of South America. It constitutes an important forested region for biological conservation in the Neotropics. Although very sparsely populated, with its inhabitants mainly concentrated on the Atlantic coastal strip and along the two main rivers, it is marked by the presence and development of old and new epidemic disease outbreaks, both research and health priorities. In this review paper, we synthetize 15 years of multidisciplinary and integrative research at the interface between wildlife, ecosystem modification, human activities and sociodemographic development, and human health. This study reveals a complex epidemiological landscape marked by important transitional changes, facilitated by increased interconnections between wildlife, land-use change and human occupation and activity, human and trade transportation, demography with substantial immigration, and identified vector and parasite pharmacological resistance. Among other French Guianese characteristics, we demonstrate herein the existence of more complex multi-host disease life cycles than previously described for several disease systems in Central and South America, which clearly indicates that today the greater promiscuity between wildlife and humans due to demographic and economic pressures may offer novel settings for microbes and their hosts to circulate and spread. French Guiana is a microcosm that crystallizes all the current global environmental, demographic and socioeconomic change conditions, which may favor the development of ancient and future infectious diseases.

Abstract: Large carnivores play a pivotal regulating role in maintaining healthy and balanced ecosystems; however, most of them are rare and elusive, and knowledge about their resource consumption is scarce. Traditional methods based on morphological identification of undigested remains are labor intensive and often not sufficiently accurate, leading to errors and biased ecological inferences. Here, we developed a multi-marker DNA metabarcoding approach to analyze the dietary diversity of giant otters (Pteronura brasiliensis) from fecal DNA while controlling predator species identity. We combined two mitochondrial markers, 12S rRNA and cytochrome c oxidase 1 (COI) gene, that target the full range of potential vertebrate and invertebrate prey. We compiled a local reference database of DNA barcodes for most potentially ingested fish, which were used to evaluate the specificity of the metabarcoding primers in silico. Most prey are identified at the species level (>90%) and the dietary profiles provided independently by the two markers are highly similar, whether in terms of list of prey or frequency of occurrences, hence validating the approach. We detected a higher number of rare fish prey with the 12S primers that amplified solely Teleost species while the degenerate COI primers revealed non-fish prey (e.g., amphibians, snakes, birds, and earthworms) and confirmed predator species identity. This study demonstrated that scat DNA metabarcoding is particularly useful to provide in-depth information on elusive carnivorous dietary profile. Our methodology opens up new opportunities to understand how top carnivores diet cope with the effects of anthropogenic alteration of ecosystems and identify conflicts with humans and livestock.

Abstract: Drought is predicted to increase in the future due to climate change, bringing with it myriad impacts on ecosystems. Plants respond to drier soils by reducing stomatal conductance in order to conserve water and avoid hydraulic damage. Despite the importance of plant drought responses for the global carbon cycle and local and regional climate feedbacks, land surface models are unable to capture observed plant responses to soil moisture stress. We assessed the impact of soil moisture stress on simulated gross primary productivity (GPP) and latent energy flux (LE) in the Joint UK Land Environment Simulator (JULES) vn4.9 on seasonal and annual timescales and evaluated 10 different representations of soil moisture stress in the model. For the default configuration, GPP was more realistic in temperate biome sites than in the tropics or high-latitude (cold-region) sites, while LE was best simulated in temperate and high-latitude (cold) sites. Errors that were not due to soil moisture stress, possibly linked to phenology, contributed to model biases for GPP in tropical savanna and deciduous forest sites. We found that three alternative approaches to calculating soil moisture stress produced more realistic results than the default parameterization for most biomes and climates. All of these involved increasing the number of soil layers from 4 to 14 and the soil depth from 3.0 to 10.8 m. In addition, we found improvements when soil matric potential replaced volumetric water content in the stress equation (the “soil14psi” experiments), when the critical threshold value for inducing soil moisture stress was reduced (“soil14p0”), and when plants were able to access soil moisture in deeper soil layers (“soil14_dr*2”). For LE, the biases were highest in the default configuration in temperate mixed forests, with overestimation occurring during most of the year. At these sites, reducing soil moisture stress (with the new parameterizations mentioned above) increased LE and increased model biases but improved the simulated seasonal cycle and brought the monthly variance closer to the measured variance of LE. Further evaluation of the reason for the high bias in LE at many of the sites would enable improvements in both carbon and energy fluxes with new parameterizations for soil moisture stress. Increasing the soil depth and plant access to deep soil moisture improved many aspects of the simulations, and we recommend these settings in future work using JULES or as a general way to improve land surface carbon and water fluxes in other models. In addition, using soil matric potential presents the opportunity to include plant functional type-specific parameters to further improve modeled fluxes.