Browse
Submit Data
Databases
API
Help

Dataset Information

22 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A Biogeographic Barrier Test Reveals a Strong Genetic Structure for a Canopy-Emergent Amazon Tree Species.

ABSTRACT: Wallace's (1854) Riverine Barrier hypothesis is one of the earliest explanations for Amazon biotic diversification. Despite the importance of this hypothesis for explaining speciation in some animal groups, it has not been studied extensively for plant species. In this study we use a prominent Amazon tree, Buchenavia oxycarpa (Mart.) Eichler (Combretaceae), to evaluate Wallace's hypothesis along the Rio Negro, a major Amazon tributary that has driven allopatric speciation for several animal taxa. We sampled six individuals from sixteen localities along both river banks, and used a modified ddRADseq protocol to identify SNP markers. Our population genomic data revealed strong genetic structure for B. oxycarpa sampled across banks of the Rio Negro (?_CT?=?0.576, P?

SUBMITTER: Nazareno AG

PROVIDER: S-EPMC6901565 | biostudies-literature | 2019 Dec

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

A Biogeographic Barrier Test Reveals a Strong Genetic Structure for a Canopy-Emergent Amazon Tree Species.

Nazareno Alison G AG Dick Christopher W CW Lohmann Lúcia G LG

Scientific reports 20191209 1

Wallace's (1854) Riverine Barrier hypothesis is one of the earliest explanations for Amazon biotic diversification. Despite the importance of this hypothesis for explaining speciation in some animal groups, it has not been studied extensively for plant species. In this study we use a prominent Amazon tree, Buchenavia oxycarpa (Mart.) Eichler (Combretaceae), to evaluate Wallace's hypothesis along the Rio Negro, a major Amazon tributary that has driven allopatric speciation for several animal taxa ...[more]

PMID: 31819128

Similar Datasets

Are temperate canopy spiders tree-species specific?

Project description:Arboreal spiders in deciduous and coniferous trees were investigated on their distribution and diversity. Insecticidal knock-down was used to comprehensively sample spiders from 175 trees from 2001 to 2003 in the Białowieża forest and three remote forests in Poland. We identified 140 species from 9273 adult spiders. Spider communities were distinguished between deciduous and coniferous trees. The richest fauna was collected from Quercus where beta diversity was also highest. A tree-species-specific pattern was clearly observed for Alnus, Carpinus, Picea and Pinus trees and also for those tree species that were fogged in only four or three replicates, namely Betula and Populus. This hitherto unrecognised association was mainly due to the community composition of common species identified in a Dufrene-Legendre indicator species analysis. It was not caused by spatial or temporal autocorrelation. Explaining tree-species specificity for generalist predators like spiders is difficult and has to involve physical and ecological tree parameters like linkage with the abundance of prey species. However, neither did we find a consistent correlation of prey group abundances with spiders nor could differences in spider guild composition explain the observed pattern. Our results hint towards the importance of deterministic mechanisms structuring communities of generalist canopy spiders although the casual relationship is not yet understood.

| S-EPMC3930551 | biostudies-literature

tree canopy fungi

Project description:Tree Canopy of Parque Nacional Tapanti Targeted loci environmental

| PRJNA762332 | ENA

Neogene origins and implied warmth tolerance of Amazon tree species.

Project description:Tropical rain forest has been a persistent feature in South America for at least 55 million years. The future of the contemporary Amazon forest is uncertain, however, as the region is entering conditions with no past analogue, combining rapidly increasing air temperatures, high atmospheric carbon dioxide concentrations, possible extreme droughts, and extensive removal and modification by humans. Given the long-term Cenozoic cooling trend, it is unknown whether Amazon forests can tolerate air temperature increases, with suggestions that lowland forests lack warm-adapted taxa, leading to inevitable species losses. In response to this uncertainty, we posit a simple hypothesis: the older the age of a species prior to the Pleistocene, the warmer the climate it has previously survived, with Pliocene (2.6-5 Ma) and late-Miocene (8-10 Ma) air temperature across Amazonia being similar to 2100 temperature projections under low and high carbon emission scenarios, respectively. Using comparative phylogeographic analyses, we show that 9 of 12 widespread Amazon tree species have Pliocene or earlier lineages (>2.6 Ma), with seven dating from the Miocene (>5.6 Ma) and three >8 Ma. The remarkably old age of these species suggest that Amazon forests passed through warmth similar to 2100 levels and that, in the absence of other major environmental changes, near-term high temperature-induced mass species extinction is unlikely.

| S-EPMC3568851 | biostudies-other

Tree species identity, canopy structure and prey availability differentially affect canopy spider diversity and trophic composition.

Project description:Forest canopies maintain a high proportion of arthropod diversity. The drivers that structure these communities, however, are poorly understood. Therefore, integrative research connecting tree species identity and environmental stand properties with taxonomic and functional community composition of canopy arthropods is required. In this study, we investigated how the taxonomic, functional and trophic composition of arboreal spider communities is affected by tree species composition and associated differences in canopy structure and prey availability in temperate forests. We sampled canopy spiders as well as their potential prey using insecticidal fogging in monospecific and mixed stands of native European beech, native Norway spruce and non-native Douglas fir. Trophic metrics were obtained from stable isotope analysis and structural canopy properties were assessed with mobile laser scanning. Monospecific native spruce stands promoted local canopy spider abundance and diversity, but native beech and beech-conifer mixtures had the highest diversity at landscape scale. Spider community composition differed between monospecific stands, with broadleaf-conifer mixtures mitigating these differences. Irrespective of tree species identity, spider abundance, taxonomic diversity, functional richness and isotopic richness increased in structurally heterogeneous canopies with high prey abundances, but functional evenness and trophic divergence decreased. Our study shows that canopy spiders are differentially affected by tree species identity, canopy structure and prey availability. Broadleaf-conifer mixtures mitigated negative effects of (non-native) conifers, but positive mixture effects were only evident at the landscape scale. Structurally heterogeneous canopies promoted the dominance of only specific trait clusters. This indicates that intermediate heterogeneity might result in high stability of ecological communities.

| S-EPMC10615988 | biostudies-literature

Admixture may be extensive among hyperdominant Amazon rainforest tree species.

Project description:Admixture is a mechanism by which species of long-lived plants may acquire novel alleles. However, the potential role of admixture in the origin and maintenance of tropical plant diversity is unclear. We ask whether admixture occurs in an ecologically important clade of Eschweilera (Parvifolia clade, Lecythidaceae), which includes some of the most widespread and abundant tree species in Amazonian forests. Using target capture sequencing, we conducted a detailed phylogenomic investigation of 33 species in the Parvifolia clade and investigated specific hypotheses of admixture within a robust phylogenetic framework. We found strong evidence of admixture among three ecologically dominant species, E. coriacea, E. wachenheimii and E. parviflora, but a lack of evidence for admixture among other lineages. Accepted species were largely distinguishable from one another, as was geographic structure within species. We show that hybridization may play a role in the evolution of the most widespread and ecologically variable Amazonian tree species. While admixture occurs among some species of Eschweilera, it has not led to widespread erosion of most species' genetic or morphological identities. Therefore, current morphological based species circumscriptions appear to provide a useful characterization of the clade's lineage diversity.

| S-EPMC9292926 | biostudies-literature

Classification of Tree Species in Overstorey Canopy of Subtropical Forest Using QuickBird Images.

Project description:This paper proposes a supervised classification scheme to identify 40 tree species (2 coniferous, 38 broadleaf) belonging to 22 families and 36 genera in high spatial resolution QuickBird multispectral images (HMS). Overall kappa coefficient (OKC) and species conditional kappa coefficients (SCKC) were used to evaluate classification performance in training samples and estimate accuracy and uncertainty in test samples. Baseline classification performance using HMS images and vegetation index (VI) images were evaluated with an OKC value of 0.58 and 0.48 respectively, but performance improved significantly (up to 0.99) when used in combination with an HMS spectral-spatial texture image (SpecTex). One of the 40 species had very high conditional kappa coefficient performance (SCKC ≥ 0.95) using 4-band HMS and 5-band VIs images, but, only five species had lower performance (0.68 ≤ SCKC ≤ 0.94) using the SpecTex images. When SpecTex images were combined with a Visible Atmospherically Resistant Index (VARI), there was a significant improvement in performance in the training samples. The same level of improvement could not be replicated in the test samples indicating that a high degree of uncertainty exists in species classification accuracy which may be due to individual tree crown density, leaf greenness (inter-canopy gaps), and noise in the background environment (intra-canopy gaps). These factors increase uncertainty in the spectral texture features and therefore represent potential problems when using pixel-based classification techniques for multi-species classification.

| S-EPMC4433356 | biostudies-literature

Canine filariasis in the Amazon: Species diversity and epidemiology of these emergent and neglected zoonoses.

Project description:Dirofilaria immitis and Acanthocheilonema reconditum are common parasites in dogs but have also been reported parasitizing humans. The differential diagnosis and epidemiological evaluation of these zoonoses are important to the development of efficient public health policies and control strategies. The purpose of this study was to carry out an epidemiological survey by using molecular methods for the specific identification of filarid parasites of domestic dogs in the Marajó mesoregion, State of Pará (PA), Brazil. A total of 418 canine blood samples from Marajó mesoregion (Northern Brazil) were collected, submitted to DNA extraction, polymerase chain reaction (PCR) with "pan filarial" primer, subsequent sequencing and sequence analysis using BLASTn software comparison with previously deposited sequences in GenBank. After that, a phylogenetic analysis by Maximum Parsimony was performed to aid the specific diagnosis. The obtained sequences showed the occurrence of 9 (2.15%) dogs infected with D. immitis and 30 (7.18%) by A. reconditum, with a confidence interval of 95%, there were no cases of co-infection. We observed that male dogs were more likely to D. immits and A. reconditum infection. However, age was not significant to both infections. This study reports for the first time the occurrence of A. reconditum in the northern region of Brazil and confirmed the presence of D. immitis in the Marajó mesoregion.

| S-EPMC6040735 | biostudies-literature

Large-scale variations in the dynamics of Amazon forest canopy gaps from airborne lidar data and opportunities for tree mortality estimates.

Project description:We report large-scale estimates of Amazonian gap dynamics using a novel approach with large datasets of airborne light detection and ranging (lidar), including five multi-temporal and 610 single-date lidar datasets. Specifically, we (1) compared the fixed height and relative height methods for gap delineation and established a relationship between static and dynamic gaps (newly created gaps); (2) explored potential environmental/climate drivers explaining gap occurrence using generalized linear models; and (3) cross-related our findings to mortality estimates from 181 field plots. Our findings suggest that static gaps are significantly correlated to dynamic gaps and can inform about structural changes in the forest canopy. Moreover, the relative height outperformed the fixed height method for gap delineation. Well-defined and consistent spatial patterns of dynamic gaps were found over the Amazon, while also revealing the dynamics of areas never sampled in the field. The predominant pattern indicates 20-35% higher gap dynamics at the west and southeast than at the central-east and north. These estimates were notably consistent with field mortality patterns, but they showed 60% lower magnitude likely due to the predominant detection of the broken/uprooted mode of death. While topographic predictors did not explain gap occurrence, the water deficit, soil fertility, forest flooding and degradation were key drivers of gap variability at the regional scale. These findings highlight the importance of lidar in providing opportunities for large-scale gap dynamics and tree mortality monitoring over the Amazon.

| S-EPMC7809196 | biostudies-literature

Forest canopy gap distributions in the southern Peruvian Amazon.

Project description:Canopy gaps express the time-integrated effects of tree failure and mortality as well as regrowth and succession in tropical forests. Quantifying the size and spatial distribution of canopy gaps is requisite to modeling forest functional processes ranging from carbon fluxes to species interactions and biological diversity. Using high-resolution airborne Light Detection and Ranging (LiDAR), we mapped and analyzed 5,877,937 static canopy gaps throughout 125,581 ha of lowland Amazonian forest in Peru. Our LiDAR sampling covered a wide range of forest physiognomies across contrasting geologic and topographic conditions, and on depositional floodplain and erosional terra firme substrates. We used the scaling exponent of the Zeta distribution (?) as a metric to quantify and compare the negative relationship between canopy gap frequency and size across sites. Despite variable canopy height and forest type, values of ? were highly conservative (? mean ?=?1.83, s ?=?0.09), and little variation was observed regionally among geologic substrates and forest types, or at the landscape level comparing depositional-floodplain and erosional terra firme landscapes. ?-values less than 2.0 indicate that these forests are subjected to large gaps that reset carbon stocks when they occur. Consistency of ?-values strongly suggests similarity in the mechanisms of canopy failure across a diverse array of lowland forests in southwestern Amazonia.

| S-EPMC3626694 | biostudies-literature

Biogeographic evidence supports the Old Amazon hypothesis for the formation of the Amazon fluvial system.

Project description:The Amazon has high biodiversity, which has been attributed to different geological events such as the formation of rivers. The Old and Young Amazon hypotheses have been proposed regarding the date of the formation of the Amazon basin. Different studies of historical biogeography support the Young Amazon model, however, most studies use secondary calibrations or are performed at the population level, preventing evaluation of a possible older formation of the Amazon basin. Here, we evaluated the fit of molecular phylogenetic and biogeographic data to previous models regarding the age of formation of the Amazon fluvial system. We reconstructed time-calibrated molecular phylogenies through Bayesian inference for six taxa belonging to Amphibia, Aves, Insecta and Mammalia, using both, nuclear and mitochondrial DNA sequence data and fossils as calibration points, and explored priors for both data sources. We detected the most plausible vicariant barriers for each phylogeny and performed an ancestral reconstruction analysis using areas bounded by major Amazonian rivers, and therefore, evaluated the effect of different dispersal rates over time based on geological and biogeographical information. The majority of the genes analyzed fit a relaxed clock model. The log normal distribution fits better and leads to more precise age estimations than the exponential distribution. The data suggested that the first dispersals to the Amazon basin occurred to Western Amazonia from 16.2-10.4 Ma, and the taxa covered most of the areas of the Amazon basin between 12.2-6.2 Ma. Additionally, regardless of the method, we obtained evidence for two rivers: Tocantins and Madeira, acting as vicariant barriers. Given the molecular and biogeographical analyses, we found that some taxa were fitted to the "Old Amazon" model.

| S-EPMC8627654 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data