The Origins and Historical Assembly of the Brazilian Caatinga Seasonally Dry Tropical Forests

This is the final version. Available on open access from Frontiers Media via the DOI in this recordData Availability Statement: The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material.The Brazilian Caatinga is considered the richest nucleus of the Seasonally Dry Tropical Forests (SDTF) in the Neotropics, also exhibiting high levels of endemism, but the timing of origin and the evolutionary causes of its plant diversification are still poorly understood. In this study, we integrate comprehensive sampled dated molecular phylogenies of multiple flowering plant groups and estimations of ancestral areas to elucidate the forces driving diversification and historical assembly in the Caatinga flowering plants. Our results show a pervasive floristic exchange between Caatinga and other neotropical regions, particularly those adjacent. While some Caatinga lineages arose in the Eocene/Oligocene, most dry-adapted endemic plant lineages found in region emerged from the middle to late Miocene until the Pleistocene, indicating that only during this period the Caatinga started to coalesce into a SDTF like we see today. Our findings are temporally congruent with global and regional aridification events and extensive denudation of thick layers of sediments in Northeast (NE) Brazil. We hypothesize that global aridification processes have played important role in the ancient plant assembly and long-term Caatinga SDTF biome stability, whereas climate-induced vegetation shifts, as well as the newly opened habitats have largely contributed as drivers of in situ diversification in the region. Patterns of phylogenetic relatedness of Caatinga endemic clades revealed that much modern species diversity has originated in situ and likely evolved via recent (Pliocene/Pleistocene) ecological specialization triggered by increased environmental heterogeneity and the exhumation of edaphically disparate substrates. The continuous assembly of dry-adapted flora of the Caatinga has been complex, adding to growing evidence that the origins and historical assembly of the distinct SDTF patches are idiosyncratic across the Neotropics, driven not just by continental-scale processes but also by unique features of regional-scale geological history

Mapping the root systems of individual trees in a natural community using genotyping-by-sequencing

•The architecture of root systems is an important driver of plant fitness, competition and ecosystem processes. However, the methodological difficulty of mapping roots hampers the study of these processes. Existing approaches to match individual plants to belowground samples are low throughput and species specific. Here, we developed a scalable sequencing-based method to map the root systems of individual trees across multiple species. We successfully applied it to a tropical dry forest community in the Brazilian Caatinga containing 14 species. • We sequenced all 42 individual shrubs and trees in a 14 × 14 m plot using double-digest restriction site-associated sequencing (ddRADseq). We identified species-specific markers and individual-specific haplotypes from the data. We matched these markers to the ddRADseq data from 100 mixed root samples from across the centre (10 × 10 m) of the plot at four different depths using a newly developed R package. • We identified individual root samples for all species and all but one individual. There was a strong significant correlation between belowground and aboveground size measurements, and we also detected significant species-level root-depth preference for two species. • The method is more scalable and less labour intensive than the current techniques and is broadly applicable to ecology, forestry and agricultural biology

Mapping the root systems of individual trees in a natural community using genotyping-by-sequencing.

This is the final version. Available from Wiley via the DOI in this record.The architecture of root systems is an important driver of plant fitness, competition and ecosystem processes. However, the methodological difficulty of mapping roots hampers the study of these processes. Existing approaches to match individual plants to belowground samples are low throughput and species specific. Here, we developed a scalable sequencing-based method to map the root systems of individual trees across multiple species. We successfully applied it to a tropical dry forest community in the Brazilian Caatinga containing 14 species. We sequenced all 42 individual shrubs and trees in a 14 × 14 m plot using double-digest restriction site-associated sequencing (ddRADseq). We identified species-specific markers and individual-specific haplotypes from the data. We matched these markers to the ddRADseq data from 100 mixed root samples from across the centre (10 × 10 m) of the plot at four different depths using a newly developed R package. We identified individual root samples for all species and all but one individual. There was a strong significant correlation between belowground and aboveground size measurements, and we also detected significant species-level root-depth preference for two species. The method is more scalable and less labour intensive than the current techniques and is broadly applicable to ecology, forestry and agricultural biology.Natural Environment Research Council (NERC)Natural Environment Research Council (NERC)Fundação de Amparo à Pesquisa do Estado de São Paul

Precipitation is the main axis of tropical plant phylogenetic turnover across space and time.

This is the final version. Available from the American Association for the Advancement of Science via the DOI in this record. Data and materials availability: All data needed to evaluate the conclusions in the paper are present in the paper and/or the Supplementary Materials. All phylogenies, both occurrence datasets, and the taxonomic checklist are available as data S1 on Zenodo (https://doi.org/10.5281/zenodo.7568716). GenBank or European Nucleotide Archive accession codes for new genetic sequences generated here are listed in tables S1 and S4 to S10.Early natural historians-Comte de Buffon, von Humboldt, and De Candolle-established environment and geography as two principal axes determining the distribution of groups of organisms, laying the foundations for biogeography over the subsequent 200 years, yet the relative importance of these two axes remains unresolved. Leveraging phylogenomic and global species distribution data for Mimosoid legumes, a pantropical plant clade of c. 3500 species, we show that the water availability gradient from deserts to rain forests dictates turnover of lineages within continents across the tropics. We demonstrate that 95% of speciation occurs within a precipitation niche, showing profound phylogenetic niche conservatism, and that lineage turnover boundaries coincide with isohyets of precipitation. We reveal similar patterns on different continents, implying that evolution and dispersal follow universal processes.Natural Environment Research Council (NERC)Swiss National Science Foundation (SNSF)Swiss National Science Foundation (SNSF)Swiss National Science Foundation (SNSF)Claraz Schenkung Foundation, SwitzerlandU.S. National Science FoundationU.S. National Science FoundationNatural Sciences and Engineering Research Council of Canada (NSERC)Biotechnology and Biological Sciences Research CouncilFAPESB, BrazilFAPESB, BrazilFAPESB, BrazilCNPq, BrazilCNPq, BrazilCNPq, BrazilCNPq, BrazilConsejo Nacional de Investigaciones Científicas y Técnicas (CONICET), ArgentinaAgencia Nacional de Promoción Científica y Tecnológica (ANPCyT), ArgentinaInstituto Nacional de Tecnología Agropecuaria (INTA), ArgentinaInstituto Nacional de Tecnología Agropecuaria (INTA), ArgentinaUniversidad de Morón, ArgentinaCoordination for the Improvement of Higher Education Personnel (CAPES), BrazilEmbrapa Recursos Genéticos e Biotecnologia (CENARGEN), Brazi

DNA Barcode Detects High Genetic Structure within Neotropical Bird Species

BACKGROUND: Towards lower latitudes the number of recognized species is not only higher, but also phylogeographic subdivision within species is more pronounced. Moreover, new genetically isolated populations are often described in recent phylogenies of Neotropical birds suggesting that the number of species in the region is underestimated. Previous COI barcoding of Argentinean bird species showed more complex patterns of regional divergence in the Neotropical than in the North American avifauna. METHODS AND FINDINGS: Here we analyzed 1,431 samples from 561 different species to extend the Neotropical bird barcode survey to lower latitudes, and detected even higher geographic structure within species than reported previously. About 93% (520) of the species were identified correctly from their DNA barcodes. The remaining 41 species were not monophyletic in their COI sequences because they shared barcode sequences with closely related species (N = 21) or contained very divergent clusters suggestive of putative new species embedded within the gene tree (N = 20). Deep intraspecific divergences overlapping with among-species differences were detected in 48 species, often with samples from large geographic areas and several including multiple subspecies. This strong population genetic structure often coincided with breaks between different ecoregions or areas of endemism. CONCLUSIONS: The taxonomic uncertainty associated with the high incidence of non-monophyletic species and discovery of putative species obscures studies of historical patterns of species diversification in the Neotropical region. We showed that COI barcodes are a valuable tool to indicate which taxa would benefit from more extensive taxonomic revisions with multilocus approaches. Moreover, our results support hypotheses that the megadiversity of birds in the region is associated with multiple geographic processes starting well before the Quaternary and extending to more recent geological periods

Evolutionary diversity in tropical tree communities peaks at intermediate precipitation

This is the final version. Available from Nature Research via the DOI in this record. Time-calibrated molecular phylogenies are deposited at the Dryad Digital Repository (https://doi.org/10.5061/dryad.gf1vhhmk0). A full description with details of data accessibility for Neo-TropTree can be found at http://www.neotroptree.info/.Global patterns of species and evolutionary diversity in plants are primarily determined by a temperature gradient, but precipitation gradients may be more important within the tropics, where plant species richness is positively associated with the amount of rainfall. The impact of precipitation on the distribution of evolutionary diversity, however, is largely unexplored. Here we detail how evolutionary diversity varies along precipitation gradients by bringing together a comprehensive database on the composition of angiosperm tree communities across lowland tropical South America (2,025 inventories from wet to arid biomes), and a new, large-scale phylogenetic hypothesis for the genera that occur in these ecosystems. We find a marked reduction in the evolutionary diversity of communities at low precipitation. However, unlike species richness, evolutionary diversity does not continually increase with rainfall. Rather, our results show that the greatest evolutionary diversity is found in intermediate precipitation regimes, and that there is a decline in evolutionary diversity above 1,490 mm of mean annual rainfall. If conservation is to prioritise evolutionary diversity, areas of intermediate precipitation that are found in the South American ‘arc of deforestation’, but which have been neglected in the design of protected area networks in the tropics, merit increased conservation attention.Natural Environment Research Council (NERC)Conselho Nacional de Desenvolvimento Científico e TecnológicoConselho Nacional de Desenvolvimento Científico e TecnológicoConselho Nacional de Desenvolvimento Científico e TecnológicoNational Science Foundation (NSF)Mohamed bin Zayed Species Conservation FundLeverhulme TrustCoordenação de Aperfeiçoamento de Pessoal de Nível Superio

Neutrophil Paralysis in Plasmodium vivax Malaria

Plasmodium vivax is responsible for approximately 60–80% of the malaria cases in the world, and contributes to significant social and economic instability in the developing countries of Latin America and Asia. The pathogenesis of P. vivax malaria is a consequence of host derived inflammatory mediators. Hence, a better understanding of the mechanisms involved in induction of systemic inflammation during P. vivax malaria is critical for the clinical management and prevention of severe disease. The innate immune receptors recognize Plasmodium sp. and initiate a broad spectrum of host defense mechanisms that mediate resistance to infection. However, the innate immune response is the classic “two-edged sword”, and clinical malaria is associated with high levels of circulating pro-inflammatory cytokines. Our findings show that both monocytes and neutrophils are highly activated during malaria. Monocytes produced high levels of IL-1β, IL-6 and TNF-α during acute malaria. On the other hand, neutrophils were a poor source of cytokines, but displayed an enhanced phagocytic activity and superoxide production. Unexpectedly, we noticed an impaired chemotaxis of neutrophils towards an IL-8 (CXCL8) gradient. We proposed that neutrophil paralysis is in part responsible for the enhanced susceptibility to bacterial infection observed in malaria patients