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445 results for “Neotropical diversity”
Linked collectors and determiners for: Combining target enrichment and Sanger sequencing data to clarify the systematics of the diverse Neotropical butterfly subtribe Euptychiina (Nymphalidae, Satyrinae).
Natural history specimen data linked to collectors and determiners held within, "Combining target enrichment and Sanger sequencing data to clarify the systematics of the diverse Neotropical butterfly subtribe Euptychiina (Nymphalidae, Satyrinae)". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/bfb878f3-8a74-46d3-a104-36485c32aaba">https://bionomia.net/dataset/bfb878f3-8a74-46d3-a104-36485c32aaba</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/bfb878f3-8a74-46d3-a104-36485c32aaba">https://gbif.org/dataset/bfb878f3-8a74-46d3-a104-36485c32aaba</a>. Formatted as a Frictionless Data package.
FIG. 1 in A revision of species diversity in the Neotropical genus Oreobates (Anura: Strabomantidae), with the description of three new species from the Amazonian slopes of the Andes
FIG. 1. Main tree (left and right pages): one of 16 equally optimal maximum parsimony trees with branch length depicting phylogenetic relationships of species of Oreobates (3936 steps; differences with the strict consensus only affect unresolved intraspecific relationships). Schematic tree (far left): maximum likelihood best tree topology for 145 terminals of Strabomantid frogs inferred from the 16S rRNA barcode fragment of amphibians (see methods). Numbers above nodes for both trees are maximum parsimony bootstrap values followed by maximum likelihood bootstrap values.
Fig. 4 in Surprising genomic diversity in the Neotropical fish Synbranchus marmoratus (Teleostei: Synbranchidae): how many species?
Fig. 4. Cluster analysis based on karyotypes and genome sizes. The vertical bars on the right-hand side of the figure illustrate the closeness of samples found in different rivers and appearing in the same branch of the cluster (cf. Fig. 3). Letters A-E indicate cytotypes described in Fig. 2.
Fig. 3 in Surprising genomic diversity in the Neotropical fish Synbranchus marmoratus (Teleostei: Synbranchidae): how many species?
Fig. 3. Nuclear DNA content per individual (pg, + 95% confidence interval) among the sampled fishes. Rectangles include individuals with the same karyotype and dotted lines within rectangles subdivide samples into groupings of individuals with similar nuclear DNA contents.
Fig. 2 in Surprising genomic diversity in the Neotropical fish Synbranchus marmoratus (Teleostei: Synbranchidae): how many species?
Fig. 2. Five different cytotypes found among the samples of Synbranchus marmoratus analyzed. A – from the samples coded as PR, PR, and MS; B – from the samples coded as 2 3 2 SP and SP; C – from the sample coded as PR; D – karyotype 2 3 1
Fig. 1 in Surprising genomic diversity in the Neotropical fish Synbranchus marmoratus (Teleostei: Synbranchidae): how many species?
Fig. 1. South America map showing the major river drainages. The detail show the collecting locations. The bold dashed line in the detail indicates the limit of the last great marine incursion into South America (from the south) at approximately five million years ago (modified from Frailey, 2002). The lighter dashed lines indicate the state-specific boundaries hosting the collecting locations. MS 1,2 = rio Miranda (state of Mato Grosso do Sul; 2n=46 and 2n=42); SP 1 = rio Mogi-Guaçu (state of São Paulo; 2n=44); SP 2 = rio Tietê (state of São Paulo; 2n=42); SP 3 = rio Paraná (state of São Paulo; 2n=42); PR 1 = ribeirão Água do Caixão (state of Paraná; 2n=46); PR = rio Tibagi (state of Paraná; 2n=42); PR = rio Paraná (state of Paraná; 2n=42).
Raw data for: Habitat edges affect tree diversity more than biomass regeneration in a reforested wet neotropical timber plantation
<p>Raw data for: Habitat edges affect tree diversity more than biomass regeneration in a reforested wet neotropical timber plantation. Code hosted on GitHub/Zenodo.</p>
Genotype and genetic diversity data for: Contrasts in riverscape patterns of intraspecific genetic variation in a diverse Neotropical fish community of high conservation value
<p><span>Spatial patterns in genetic variation compared across species provide information about the predictability of genetic diversity of natural populations and areas requiring conservation measures. Due to their remarkable fish diversity, rivers in Neotropical regions are ideal systems to confront theory with observations and would benefit greatly from such approaches given their increasing vulnerability to anthropogenic pressures. We used SNP data from 18 fish species with contrasting life-history traits, co-sampled across 12 sites in the Maroni – a major river system from the Guiana Shield – to compare patterns of intraspecific genetic variation and identify their underlying drivers. Analyses of covariance revealed a decrease in genetic diversity as distance from the river outlet increased for 5 of the 18 species, illustrating a pattern commonly observed in riverscapes for species with low-to-medium dispersal abilities. However, mean within-site genetic diversity was lowest in the two easternmost tributaries of the Upper Maroni and around an urbanized location downstream, indicating the need to address the potential influence of local pressures in these areas, such as goldmining or fishing. Finally, the relative influence of isolation by stream distance, isolation by discontinuous river flow and isolation by spatial heterogeneity in effective size on pairwise genetic differentiation varied across species. Species with similar dispersal and reproductive guilds did not necessarily display shared patterns of population structure. Increasing the knowledge of specific life history traits and ecological requirements of fish species in these remote areas should help further understand factors that influence their current patterns of genetic variation.</span></p>
R codes from: Breakdown of the growth–mortality trade-off along a soil phosphorus gradient in diverse neotropical forest
<p><span>An ecological paradigm predicts that plant species adapted to low resource availability grow slower and live longer than those adapted to high resource availability when growing together. We tested this by using hierarchical Bayesian analysis to quantify variations in growth and mortality of ~ 40,000 individual trees from > 400 species in response to limiting resources in the tropical forests of Panama. In contrast to theoretical expectations of the growth–mortality paradigm, we find that tropical tree species restricted to low-phosphorus soils simultaneously achieve faster growth rates and lower mortality rates than species restricted to high-phosphorus soils. This result demonstrates that adaptation to phosphorus limitation in diverse plant communities modifies the growth–mortality trade-off, with important implications for understanding long-term ecosystem dynamics.</span></p>
Museum records for "Determinants of genetic diversity in Neotropical salamanders (Plethodontidae: Bolitoglossini)"
<p>This dataset contains museum records for 59 species of Neotropical salamanders (tribe Bolitoglossini) from GBIF. These records were used to estimate the area of species' distributions as well as to extract climatic variability data for each species from Worldclim layers. After downloading the data from GBIF, we checked all records for each species against the species' known range and eliminated records outside the range or that were taxonomically misidentified.</p>
Phylogenomics and macroevolution of a florally diverse Neotropical plant clade
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Phylogenomics indicates Amazonia as the major source of Neotropical swarm-founding social wasp diversity
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Data from: Transposable element diversity and activity patterns in neotropical salamanders
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Genotype and genetic diversity data for: Contrasts in riverscape patterns of intraspecific genetic variation in a diverse Neotropical fish community of high conservation value
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R codes from: Breakdown of the growth–mortality trade-off along a soil phosphorus gradient in diverse neotropical forest
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Phylogenetic and ecological correlates of pollen morphological diversity in a neotropical rainforest
Morphology varies enormously across clades, and the morphology of a trait may reflect ecological function or the retention of ancestral features. We examine the tension between ecological and phylogenetic correlates of morphological diversity through a case study of pollen grains produced by angiosperms in Barro Colorado Island, Panama (BCI). Using a molecular phylogeny of 730 taxa we demonstrate a statistically significant association between morphological and genetic distance for these plants. However, the relationship is non-linear, and while close relatives share more morphological features than distant relatives, above a genetic distance of ~0.7 increasingly distant relatives are not more divergent in phenotype. The pollen grains of biotically pollinated and abiotically pollinated plants overlap in morphological space, but certain pollen morphotypes and individual morphological traits are unique to these pollination ecologies. Our data show that the pollen grains of biotically pollinated plants are significantly more morphologically diverse than those of abiotically pollinated plants.
Evolutionary history of Neotropical savannas geographically concentrates species, phylogenetic and functional diversity of lizards
<p>Supporting information (scripts) to compute diversity and endemism indices copied and available by Dan Rosauer (https ://github.com/DanRosauer/phylospatial).</p> <p>Aim: Understanding where and why species diversity is geographically concentrated remains a challenge in biogeography and macroevolution. This is true for the Cerrado, the most biodiverse tropical savanna in the world, which has experienced profound biodiversity loss. Previous studies have focused on a single metric (species composition), neglecting the fact that 'species' within the biome are often composed of cryptic species. In order to identify biodiversity hotspots more robustly and across multiple dimensions we integrate functional, spatial and new phylogeographic data for the Cerrado lizard fauna by (a) mapping the spatial patterns of species and phylogenetic diversity; and (b) using endemism measures to identify areas of unique diversity. We then quantify the extent to which existing protected areas represent the diversity.</p> <p>Location: Brazilian savanna (Cerrado).</p> <p>Methods: We generated species distribution models using distribution records for all Cerrado lizard species. These, combined with mitochondrial DNA phylogenies and natural history data, allowed us to map species richness, phylogenetic and functional diversity and phylogenetic and weighted endemism. Phylogenetic endemism maps were then cross-referenced against protected areas to calculate the amount of evolutionary history preserved within these areas.</p> <p>Results: The central region of the Cerrado, a vast and climatically stable plateau, stands out as important under all biodiversity metrics. Including evolutionary relationships in biodiversity assessment, we detected four regional hotspots with high concentration of spatially restricted evolutionary diversity. Protected areas cover only 10% of the Cerrado area and hold 11.64% of the summed phylogenetic endemism of all lizards in the biome.</p> <p>Main Conclusions: We highlighted both stable (Chapada dos Veadeiros and Serra do Espinhaço plateaus) and environmentally heterogenous regions (Araguaia and Tocantins valleys) as hotspots of evolutionary diversity. The creation and/or manipulation of areas for conservation are essential for the conservation and survival of the rich and endemic lizard fauna of the Cerrado.</p>
Data from: Genomic diversity and structure of a Neotropical microendemic fig tree
<p>Genetic diversity is a key component of evolution and unraveling factors that promote genetic differentiation in space and time is a central question in evolutionary biology. One of the most diverse and ecologically important tree genera in tropical forests worldwide is <em>Ficus (Moraceae)</em>. It has been suggested that, given the great dispersal capacity of pollinating fig wasps (Chalcidoidea; Agaonidae), the spatial genetic structure, particularly in monoecious fig species, should be weak. However, no studies have addressed the factors that determine the genetic structure of <em>Ficus</em> species in regions of high geological, geographic, and climatic complexity, such as the Mexican Transition Zone. Using nuclear single nucleotide polymorphisms (5,311 SNPs) derived from low-coverage whole genomes and 17 populations, we analyzed the population genomics of <em>Ficus</em> <em>pringlei</em> to characterize neutral and adaptive genetic variation and structure and its association with geographic barriers such as the Trans-Mexican Volcanic Belt, environmental heterogeneity, and wind connectivity. From genomic data of 71 individuals, high genetic diversity, and the identification of three genomic lineages were recorded (North, South, and Churumuco). The results suggest that genetic variation is primarily determined by climatic heterogeneity. <em>Ficus</em> <em>pringlei</em> populations from the north and south of the Trans-Mexican Volcanic Belt also exhibited minimal genetic differentiation (F<sub>ST</sub>= 0.021), indicating that this mountain range may not act as an insurmountable barrier to gene flow. Wind connectivity is also highlighted in structuring putative adaptive genetic variation, underscoring the intricate complexity of the various factors influencing genetic variation in the species. This study provides information on the possible mechanisms underlying the genetic variation of endemic species of the tropical dry forest of Western Mexico, such as <em>F</em>. <em>pringlei</em>.</p>
Landscape heterogeneity increases bird functional diversity within Neotropical vineyards
<p>Conversion of lands to agroecosystems has resulted in a decline in bird biodiversity. Analyzing functional diversity is a central tool for detecting changes in the ecological functions performed by birds in these landscapes. This paper aims to investigate the responses of bird taxonomic and functional diversity to landscape heterogeneity and native forest cover in Neotropical vineyards. We sampled 19 vineyard landscapes in southeastern Brazil. These landscapes covered a gradient of forest cover and heterogeneity resulting from various land uses. To assess bird diversity, we considered both taxonomic diversity and functional diversity (i.e., functional richness, evenness, and divergence). To examine the potential interactions between landscapes and bird assemblages, we employed generalized linear models (GLM). Taxonomic diversity showed no correlation with any landscape metrics. On the other hand, variation in the three metrics of functional diversity was related to landscape heterogeneity. However, in heterogeneous landscapes, these communities can be structured by limiting similarity processes. We highlight the impact of landscape homogenization on the ecological functions performed by birds in vineyards while finding no significant effect on species diversity. These findings can provide valuable support for the formulation of public policies aimed at striking a balance between agricultural production and biodiversity conservation.</p>
Data from: Historical field records reveal habitat as an ecological correlate of locomotor phenotypic diversity in the radiation of Neotropical Geophagini fishes
<p>Phenotypic macroevolutionary studies provide insight into how ecological processes shape biodiversity. However, the complexity of phenotype-ecology relationships underscores the importance of also validating phenotype-based ecological inference with direct evidence of resource use. Unfortunately, macroevolutionary scale ecological studies are often hindered by the challenges of acquiring taxonomically and spatially representative ecological data for large and widely distributed clades. The South American cichlid fish tribe Geophagini represents a continentally distributed radiation whose early locomotor morphological divergence suggests habitat as one ecological correlate of diversification, but an association between locomotor traits and habitat preference has not been corroborated. Field notes accumulated over decades of collecting across South America provide first-hand environmental records that can be mined for habitat data in support of macroevolutionary ecological research. In this study, we applied a newly developed method to transform descriptive field note information into quantitative habitat data, and used it to assess habitat preference and its relationship to locomotor morphology in Geophagini. Field note-derived data shed light on geophagine habitat use patterns and reinforced habitat as an ecological correlate of locomotor morphological diversity. Our work emphasizes the rich data potential of museum collections, including often overlooked material such as field notes, for evolutionary and ecological research.</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.