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Species may co-occur due to responses to similar environmental conditions, biological associations, or simply because of coincident geographical distributions. Disentangling patterns of co-occurrence and potential biotic and abiotic interactions is crucial to understand ecosystem function. Here, we used DNA metabarcoding data from litter and mineral soils collected from a longitudinal transect in Amazonia to explore patterns of co-occurrence. We compared data from different Amazonian habitat types, each with a characteristic biota and environmental conditions. These included non-flooded rainforests (terra-firme), forests seasonally flooded by fertile white waters (várzeas) or by unfertile black waters (igapós), and open areas associated with white sand soil (campinas). We ran co-occurrence network analyses based on null models and Spearman correlation for all samples and for each habitat separately. We found that one third of all operational taxonomic units (OTUs) were bacteria and two thirds were eukaryotes. The resulting networks were nevertheless mostly composed of bacteria, with fewer fungi, protists, and metazoans. Considering the functional traits of the OTUs, there is a combination of metabolism modes including respiration and fermentation for bacteria, and a high frequency of saprotrophic fungi (those that feed on dead organic matter), indicating a high turnover of organic material. The organic carbon and base saturation indices were important in the co-occurrences in Amazonian networks, whereas several other soil properties were important for the co-exclusion. Different habitats had similar network properties with some variation in terms of modularity, probably associated with flooding pulse. We show that Amazonian microorganism communities form highly interconnected co-occurrence and co-exclusion networks, which highlights the importance of complex biotic and abiotic interactions in explaining the outstanding biodiversity of the region. [ABSTRACT FROM AUTHOR]

Despite the disjunct distribution of the Amazonian and the Atlantic forests, three historical connections between those biomes have been hypothesized: through Northeast Brazil, the Brazilian Cerrado, and the Southeast–Northwest. Temporal variation has been suggested to occur in these connections, with recent connections for the Northeast and older connections for the Southeast–Northwest. We tested for the hypothesis of temporal variation in these connections using Neotropical mammals as a study group. Phylogenetic and spatial data of sister groups from each forest were combined to access the spatiotemporal patterns of these connections. The relationship between distance route and divergence times was tested using linear regression. The results revealed that the previously suggested spatiotemporal pattern was corroborated only for Rodentia but not for Didelphimorphia and Chiroptera, showing both old and recent connections for all routes. In addition, each family revealed specific connections at different times. We refute the previously proposed absence of old connections through the Northeast route. Rather, temporal variation in the Northeast differs among the mammalian groups according to their evolutionary histories. Owing to the biogeographical history of each group, different connections were found at different times. Therefore, connections between these forests cannot be explained by a single spatiotemporal pattern. [ABSTRACT FROM AUTHOR]

Much evidence suggests that Amazonia and the Atlantic Forest were connected through at least three dispersion routes in the past: the Eastern route, the central route, and the Western route. However, few studies have assessed the use of these routes based on multiple species. Here we present a compilation of mammal species that potentially have dispersed between the two forest regions and which may serve to investigate these connections. We evaluate the present-day geographic distributions of mammals occurring in both Amazonia and the Atlantic Forest and the likely connective routes between these forests. We classified the species per habitat occupancy (strict forest specialists, species that prefer forest habitat, or generalists) and compiled the genetic data available for each species. We found 127 mammalian species presently occurring in both Amazonia and the Atlantic Forest for which, substantial genetic data was available. Hence, highlighting their potential for phylogeographic studies investigating the past connections between the two forests. Differently from what was previously proposed, the present-day geographic distribution of mammal species found in both Amazonia and the Atlantic Forest points to more species in the eastern portion of the dry diagonal (and adjoining forested habitats). The Central route was associated with the second most species. Although it remains to be seen how this present-day geography reflects the paleo dispersal routes, our results show the potential of using mammal species to investigate and bring new insights about the past connections between Amazonia and the Atlantic Forest. [ABSTRACT FROM AUTHOR]

Thirteen novel polymorphic microsatellite loci were isolated and characterized from the Amazonian Black Manakin, Xenopipo atronitens. The loci were screened using 30 samples from Brazil. A total of 13 loci were variable with number of alleles per locus ranging from 2 to 17, whilst the observed and expected heterozygosities varied from 0.067-0.900 and 0.310-0.910, respectively. Five loci deviated significantly from the Hardy-Weinberg equilibrium, whereas one pair of loci deviated significantly from linkage disequilibrium. The set of markers will be a useful tool for future population genetic and kinship studies of X. atronitens, an Amazonian white-sand vegetation specialist. [ABSTRACT FROM AUTHOR]

Wholesale conversion of natural Amazonian ecosystems has been encouraged by Brazil's extreme antienvironmental government, and historical forest loss explains municipal-scale voting prevalence. Embracing a new administration would strengthen local-to-regional governance, suppress illegal land grabbing, deforestation, logging, and gold mining, thereby protecting the world's most species-rich forest domain and ensuring global sustainability. [ABSTRACT FROM AUTHOR]

Due to increasing human transformation of virtually all habitats on Earth, setting global priorities for conservation is essential. The emerging disciplines of macroecology and macroevolution (MEE) can provide a global perspective and information for such prioritization but remain relatively separated from conservation prioritization, partly because MEE researchers are unaware of the requirements for effective conservation prioritization and existing approaches implementing these. Indeed, existing approaches for conservation prioritization at large scale are scattered across literature. Here, we systematically review this literature and provide a guideline for researchers in MEE as to which of approaches might be suitable for their needs. From >11 000 scientific publications, we identified 134 methods suitable for commonly used MEE data and geographic scale. Furthermore, we use a 'trait matrix' to identify families of similar approaches and to design a guideline to select the most suitable method, given a user‐defined set of data and analysis scope. The guidelines are freely available via the conserveR R‐package (). Finally, we used our review to identify increasing scalability, continuous monitoring and the integration of molecular, remote sensing and animal movement data as key areas for future impacts of MEE in conservation prioritization. We anticipate that our review can serve as a guide to MEE researchers interested in linking their data to conservation as well as for conservation scientists interested in using MEE approaches. [ABSTRACT FROM AUTHOR]

Environmental sequencing regularly recovers fungi that cannot be classified to any meaningful taxonomic level beyond "Fungi". There are several examples where evidence of such lineages has been sitting in public sequence databases for up to ten years before receiving scientific attention and formal recognition. In order to highlight these unidentified lineages for taxonomic scrutiny, a search function is presented that produces updated lists of approximately genus-level clusters of fungal ITS sequences that remain unidentified at the phylum, class, and order levels, respectively. The search function (https://unite.ut.ee/top50.php) is implemented in the UNITE database for molecular identification of fungi, such that the underlying sequences and fungal lineages are open to third-party annotation. We invite researchers to examine these enigmatic fungal lineages in the hope that their taxonomic resolution will not have to wait another ten years or more. [ABSTRACT FROM AUTHOR]