26 Works

Shallow population structure and shared phylogeographic and demographic patterns in seven Amazonian White-Sand ecosystems birds

João Marcos Guimarães Capurucho, Mary Ashley, Cintia Cornelius, Sérgio Borges, Camila Ribas & John Bates
White-sand ecosystems (WSE) have a patchy distribution throughout Amazonia and harbor a specialized community of birds. The patchiness of WSE lead to the expectation of highly fragmented and isolated populations across Amazonia. Additionally, the sandy substrate could render these ecosystems vulnerable climatic changes. We performed a comparative phylogeographic study of seven WSE birds using Ultra-conserved elements to evaluate their relation to Amazonian environmental and landscape history and the occurrence of shared patterns. Genetic structure varied...

Litterfall ant genus and abundance in a fertiliser experiment area in Central Amazon, 2018-2019

C.R. Santos Neto, F.B. Baccaro & C.A. Quesada
Data are presented showing litterfall ant species and abundance from a plot based fertilisation experiment. The experiment was carried out at the Biological Dynamics of Forest Fragments Project (BDFFP) approximately 100 km north of Manaus. Data were collected in October 2018 and September 2019 by Santos-Neto. Sampling was carried out using a Wrinkler extractor. The data were collected to investigate the possible effects of different fertiliser applications on litterfall ant species and abundance. The work...

Data from: The evolution of polymorphism in the warning coloration of the Amazonian poison frog Adelphobates galactonotus

Diana Rojas, Paolo Momigliano, Albertina Pimentel Lima, Pedro Ivo Simões, Rachel Y. Dudaniec, Teresa C. S. Avila-Pires, Marinus S. Hoogmoed, Youszef O. C. Bitar, Igor Luis Kaefer, Adolfo Amézquita & Adam Stow
While intraspecific variation in aposematic signals can be selected for by different predatory responses, their evolution is also contingent on other processes shaping genetic variation. We evaluate the relative contributions of selection, geographic isolation and random genetic drift to the evolution of aposematic color polymorphism in the poison frog Adelphobates galactonotus, distributed throughout eastern Brazilian Amazonia. Dorsal coloration was measured for 111 individuals and genetic data were obtained from 220 individuals at two mitochondrial genes...

Islands in a green ocean: spatially structured endemism in Amazonian white-sand vegetation

Flavio Costa, Mario Terra-Araújo, Charles Zartman, Cintia Cornelius, Fernanda Carvalho, Michael Hopkins, Pedro Viana, Eduardo Prata & Alberto Vicentini
Here, we examine the influence of the spatial distribution of open White-Sand Campina (WSC) in the Amazon on the species richness and beta-diversity of their vascular plants. It is well known that beta-diversity tends to increase with geographical distance, but the influence of habitat insularity on floristic composition and endemism is still unclear. We surveyed WSC in Central and Southwestern Amazon, generating lists of species occurrences by rapid-inventory techniques to evaluate the influence of island...

Genetic structure in populations of Euterpe precatoria Mart. in the Brazilian Amazon

Santiago Ramos & Maria Lopes
Euterpe precatoria is a palm tree belonging to the Arecaceae family, occurring in Western and Central Brazilian Amazonia Its fruit, which is very appreciated in the Amazon region, produces pulp that is consumed in fresh form. Its production is carried out almost exclusively by extractive farmers. In order to establish adequate strategies to sustain this genetic resource. We need knowledge about its diversity and genetic structure in natural populations. This study aimed to evaluate the...

Data from: Human management and hybridization shape treegourd fruits in the Brazilian Amazon Basin

Priscila Ambrosio Moreira, Cédric Mariac, Leila Zekraoui, Marie Couderc, Doriane Picanco Rodrigues, Charles R. Clement & Yves Vigouroux
Local people's perceptions of cultivated and wild agrobiodiversity, as well as their management of hybridization are still understudied in Amazonia. Here we analyze domesticated treegourd (Crescentia cujete), whose versatile fruits have technological, symbolic and medicinal uses. A wild relative (C. amazonica) of the cultivated species grows spontaneously in Amazonian flooded forests. We demonstrated, using whole chloroplast sequences and nuclear microsatellites, that the two species are strongly differentiated. Nonetheless, they hybridize readily throughout Amazonia and the...

Variation in the production of plant tissues bearing extrafloral nectaries explains temporal patterns of ant attendance in Amazonian understory plants

Anselmo Nogueira, Fabricio Baccaro, Laura Leal, Pedro Rey, Lúcia Lohmann & Judith Bronstein
1. Information on direct and indirect drivers of temporal variation in ant-plant interactions is scarce, compromising our ability to predict the functioning of these ecologically important interactions. 2. We investigated the roles of precipitation, ant activity, abundance of young plant tissues bearing extrafloral nectaries (EFNs), and EFN phenotypes in the establishment of EFN-mediated ant-plant interactions throughout the year in Amazonia, Brazil. We hypothesized that the frequency of ant-plant interactions follows a predictable seasonal pattern, being...

Diversification history of clown tree frogs in Neotropical rainforests (Anura, Hylidae, Dendropsophus leucophyllatus group)

Renata Pirani, Pedro Peloso, Joyce Prado, Érico Polo, Lacey Knowles, Santiago Ron, Miguel Rodrigues, Marcelo Sturaro & Fernanda Werneck
General consensus emphasizes that no single biological process can explain the patterns of species’ distributions and diversification in the Neotropics. Instead, the interplay of several processes across space and time must be taken into account. Here we investigated the phylogenetic relationships and biogeographic history of tree frogs in the Dendropsophus leucophyllatus species group (Amphibia: Hylidae), which is distributed across Amazonia and the Atlantic rainforests. Using Next Generation Sequencing (NGS) and double digest restriction-site associated DNA...

Data from: Paleoclimatic evolution as the main driver of current genomic diversity in the widespread and polymorphic Neotropical songbird Arremon taciturnus

Nelson Buainain, Roberta Canton, Gabriela Zuquim, Hanna Tuomisto, Tomas Hrbek, Hiromitsu Sato & Camila Ribas
Several factors have been proposed as drivers of species diversification in the Neotropics, including environmental heterogeneity, the development of drainage systems and historical changes in forest distribution due to climatic oscillations. Here, we investigate which drivers contributed to the evolutionary history and current patterns of diversity of a polymorphic songbird (Arremon taciturnus) that is widely distributed in Amazonian and Atlantic forests as well as in Cerrado gallery and seasonally-dry forests. We use genomic, phenotypic and...

Eighty-four per cent of all Amazonian arboreal plant individuals are useful to humans

Sara D. Coelho, Carolina Levis, Fabrício B. Baccaro, Fernando O. G. Figueiredo, André Pinassi Antunes, Hans Ter Steege, Marielos Peña-Claros, Juliana Schietti & Charles R. Clement
Plants have been used in Amazonian forests for millennia and some of these plants are disproportionally abundant (hyperdominant). At local scales, people generally use the most abundant plants, which may be abundant as the result of management of indigenous peoples and local communities. However, it is unknown whether plant use is also associated with abundance at larger scales. We used the population sizes of 4,454 arboreal species (trees and palms) estimated from 1946 forest plots...

Data from: Natural selection in the water: freshwater invasion and adaptation by water color in the Amazonian pufferfish

Georgina M. Cooke, Ning L. Chao & Luciano B. Beheregaray
Natural selection and ecological adaptation are ultimately responsible for much of the origin of biodiversity. Yet the identification of divergent natural selection has been hindered by the spatial complexity of natural systems, the difficulty in identifying genes under selection and their relationship to environment, and the confounding genomic effects of time. Here we employed genome scans, population genetics and sequence-based phylogeographic methods to identify divergent natural selection on population boundaries in a freshwater invader, the...

Data from: An in silico comparison of protocols for dated phylogenomics

Rupert A. Collins & Tomas Hrbek
In the age of genome-scale DNA sequencing, choice of molecular marker arguably remains an important decision in planning a phylogenetic study. Using published genomes from 23 primate species, we make a standardized comparison of four of the most frequently used protocols in phylogenomics, viz., targeted sequence-enrichment using ultraconserved element and exon-capture probes, and restriction-site-associated DNA sequencing (RADseq and ddRADseq). Here we present a procedure to perform in silico extractions from genomes and create directly comparable...

Data from: Subtle changes in elevation shift bat-assemblage structure in Central Amazonia

, Lucas Gabriel Do Amaral Pereirab, Valéria Da Cunha Tavaresc, William E. Magnussond, Fabricio Beggiato Baccaroe & Paulo Estefano D. Bobrowiec
The distribution patterns of animal species at local scales have been explained by direct influences of vegetation structure, topography, food distribution and availability. However, these variables can also interact and operate indirectly on the distribution of species. Here, we examined the direct and indirect effects of food availability (fruits and insects), vegetation clutter and elevation in structuring phyllostomid-bat assemblages in a continuous terra firme forest in Central Amazonia. Bats were captured in 49 plots over...

Surveys of crocodilians in the hydroelectric dam, Brazilian Amazonia

Zilca Campos, Fábio Muniz, Guilherme Mourão & William Magnusson
We counts caimans in the Madeira River, before (2010-2011) and after (2012-2014, 2016-2019) hydroelectric dam.

Data from: Climate mediates the effects of disturbance on ant assemblage structure

Heloise Gibb, Nathan J. Sanders, Robert R. Dunn, Simon Watson, Manoli Photakis, Silvia Abril, Alan N. Andersen, Elena Angulo, Inge Armbrecht, Xavier Arnan, Fabricio B. Baccaro, Tom R. Bishop, Raphael Boulay, Cristina Castracani, Israel Del Toro, Thibaut Delsinne, Mireia Diaz, David A. Donoso, Martha L. Enríquez, Tom M. Fayle, Donald H. Feener, Matthew C. Fitzpatrick, Crisanto Gómez, Donato A. Grasso, Sarah Groc … & C. Gomez
Many studies have focused on the impacts of climate change on biological assemblages, yet little is known about how climate interacts with other major anthropogenic influences on biodiversity, such as habitat disturbance. Using a unique global database of 1128 local ant assemblages, we examined whether climate mediates the effects of habitat disturbance on assemblage structure at a global scale. Species richness and evenness were associated positively with temperature, and negatively with disturbance. However, the interaction...

Data from: Known knowns, known unknowns, unknown unknowns and unknown knowns in DNA barcoding: a comment on Dowton et al.

Rupert A. Collins & Robert H. Cruickshank
In a recent commentary, Dowton et al. (2014) propose a framework for "next-generation" DNA barcoding, whereby multi-locus datasets are coupled with coalescent-based species delimitation methods to make specimen identifications. They claim single-locus DNA barcoding is outdated, and a multilocus approach superior, with their assertions supported by an analysis of 33 species of Sarcophaga flesh flies. Here, we reanalyse their data and show that a standard DNA barcode analysis is in fact capable of identifying 99.8%...

Data from: Genetic evidence for polygamy as a mating strategy in Caiman crocodilus

Deyla Oliveira, Boris Marioni, Izeni Farias & Tomas Hrbek
The mating system of the spectacled caiman (Caiman crocodilus) was investigated in the Piagaçu-Purus Sustainable Development Reserve, Amazonas, Brazil. We used six polymorphic microsatellite loci to genotype 15 females and 174 hatchlings representing 20 nests sampled over four consecutive reproductive seasons (2007 to 2010). Paternity was determined by two methods: simple counts, and statistical analysis using Gerud 2.0. Results were congruent between the two approaches, and the null hypothesis of single paternity was rejected in...

Data from: Intraspecific and interspecific trait variability in tadpole metacommunities from the Brazilian Atlantic rainforest

Mainara Xavier Jordani, Nicolas Mouquet, Lilian Casatii, Marcelo Menin, Denise De Cerqueira Rossa-Feres & Cécile H. Albert
1. A better understanding of species coexistence and community dynamics may benefit from more insights on trait variability at the individual and species levels. 2. Tadpole assemblages offer an excellent system to understand the relative influence of intra- and interspecific variability on community assembly, due to their high phenotypic plasticity, and the strong influence that environmental variables have on their spatial distribution and individual performance. 3. Here we quantified the intra- and interspecific components of...

Data from: Divergent natural selection with gene flow along major environmental gradients in Amazonia: insights from genome scans, population genetics and phylogeography of the characin fish Triportheus albus

Georgina M. Cooke, Ning L. Chao & Luciano B. Beheregaray
The unparalleled diversity of tropical ecosystems like the Amazon Basin has been traditionally explained using spatial models within the context of climatic and geological history. Yet, it is adaptive genetic diversity that defines how species evolve and interact within an ecosystem. Here we combine genome scans, population genetics and sequenced-based phylogeographic analyses to examine spatial and ecological arrangements of selected and neutrally evolving regions of the genome of an Amazonian fish, Triportheus albus. Using a...

Pied tamarins go multimodal in response to anthropogenic noise

Tainara Sobroza, Jacob Dunn, Marcelo Gordo & Adrian Barnett
Sounds produced by human activities are often loud and may mask acoustic signals used by other species for communication. To circumvent this, animals may use various strategies, including shifting modality completely or complementing acoustic information by also using another modality of communication. Here we tested the overlooked multimodal shift hypothesis using pied tamarins (Saguinus bicolor) as models. We predicted that in noisier areas the species would exhibit more scent marking behaviour (i.e., olfactory communication), while...

Juggling options: manipulation ease determines primate optimal fruit size choice

Renann H. P. Dias-Silva, Matheus J. Castro Sa, Fabricio B. Baccaro, Pavel Tománek & Adrian A. Barnett
Optimal foraging theory predicts that animals will seek simultaneously to minimize food processing time and maximize energetic gain. To test this hypothesis, we evaluated whether a specialist seed-predator primate forages optimally when choosing among variable-sized thick-husked fruits. Our objects of study were the golden-backed-uacari (Cacajao ouakary, Pitheciidae) and single seeded pods of the macucu tree (Aldina latifolia, Fabaceae). We predicted that golden-backed-uacari will consume fruits of the size class that requires the least time to...

A “Dirty” Footprint: Soil macrofauna biodiversity and fertility in Amazonian Dark Earths and adjacent soils

Wilian C. Demetrio, Ana C. Conrado, Agno N. S. Acioli, Alexandre C. Ferreira, Marie L. C. Bartz, Samuel W. James, Elodie Silva, Lilianne S. Maia, Gilvan C. Martins, Rodrigo S. Macedo, David W. G. Stanton, Patrick Lavelle, Elena Velasquez, Anne Zangerlé, Rafaella Barbosa, Sandra C. Tapia‐Coral, Aleksander W. Muniz, Alessandra Santos, Talita Ferreira, Rodrigo F. Segalla, Thibaud Decaëns, Herlon S. Nadolny, Clara P. Peña‐Venegas, Cláudia M. B. F. Maia, Amarildo Pasini … & George G. Brown
Amazonian rainforests once thought to hold an innate pristine wilderness, are increasingly known to have been densely inhabited by populations showing a diverse and complex cultural background prior to European arrival. To what extent these societies impacted their landscape is unclear. Amazonian Dark Earths (ADEs) are fertile soils found throughout the Amazon Basin, created by pre-Columbian societies as a result of more sedentary habits. Much is known of the chemistry of these soils, yet their...

Data from: Is environmental legislation conserving tropical stream faunas? a large-scale assessment of local, riparian and catchment-scale influences on Amazonian stream fish

Cecília G. Leal, Jos Barlow, Toby Gardner, Robert M. Hughes, Rafael P. Leitão, Ralph Mac Nally, Philip R. Kaufmann, Silvio F. B. Ferraz, Jansen Zuanon, Felipe R. De Paula, Joice Ferreira, James R. Thomson, Gareth D. Lennox, Eurizângela P. Dary, Cristhiana P. Röpke, Paulo S. Pompeu & Toby A. Gardner
1.Agricultural expansion and intensification are major threats to tropical biodiversity. In addition to the direct removal of native vegetation, agricultural expansion often elicits other human-induced disturbances, many of which are poorly addressed by existing environmental legislation and conservation programmes. This is particularly true for tropical freshwater systems, where there is considerable uncertainty about whether a legislative focus on protecting riparian vegetation is sufficient to conserve stream fauna. 2.To assess the extent to which stream fish...

Data from: Relationships between forest cover and fish diversity in the Amazon River floodplain

Caroline C. Arantes, Kirk O. Winemiller, Miguel Petrere, Leandro Castello, Laura L. Hess, Carlos E.C. Freitas & Carlos E. C. Freitas
1.Habitat degradation leads to biodiversity loss and concomitant changes in ecosystem processes. Tropical river floodplains are highly threatened by land cover changes and support high biodiversity and important ecosystems services, but the extent to which changes in floodplain land cover affect fish biodiversity remains unknown. 2.We combined fish and environmental data collected in situ and satellite-mapped landscape features to evaluate how fish species with different ecological strategies and assemblage structures respond to deforestation in floodplains...

Data from: Diversification by host switching and dispersal shaped the diversity and distribution of avian malaria parasites in Amazonia

Alan Fecchio, Jeffrey Andrew Bell, Michael David Collins, Izeni Pires Farias, Christopher Harry Trisos, Joseph Andrew Tobias, Vasyl Volodymyr Tkach, Jason David Weckstein, Robert Eric Ricklefs & Henrique Batalha-Filho
Understanding how pathogens and parasites diversify through time and space is fundamental to predicting emerging infectious diseases. Here, we use biogeographic, coevolutionary and phylogenetic analyses to describe the origin, diversity, and distribution of avian malaria parasites in the most diverse avifauna on Earth. We first performed phylogenetic analyses using the mitochondrial cytochrome b (cyt b) gene to determine relationships among parasite lineages. Then, we estimated divergence times and reconstructed ancestral areas to uncover how landscape...

Registration Year

  • 2021
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  • 2012

Resource Types

  • Dataset


  • Federal University of Amazonas
  • National Institute of Amazonian Research
  • Museu Paraense Emílio Goeldi
  • University of Sao Paulo
  • Macquarie University
  • Field Museum of Natural History
  • Universidade Federal de Minas Gerais
  • La Trobe University
  • Federal University of Sao Paulo
  • Federal University of Paraná