25 Works

Data from: Bee pollinator functional responses and functional effects in restored tropical forests

Paula María Montoya-Pfeiffer, Ricardo Ribeiro Rodrigues & Isabel Alves Dos Santos
Wild pollinators are necessary for ensuring plant reproduction not only among crop fields but also remnant and restored ecosystems. Restoration activities should, therefore, lead to wild pollinator recovery, and thus be monitored to evaluate effects on pollinator diversity and functionality. We assessed bee pollinator functional responses in restoration plantings by creating functional groups (traits: body size, nesting location, sociality and foraging strategy), comparing their abundance and diversity to that of other habitats (i.e. conserved and...

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...

Data from: A macroecological approach to evolutionary rescue and adaptation to climate change

Jose Alexandre Felizola Diniz-Filho, Kelly S. Souza, Luis Mauricio Bini, Rafael Loyola, Ricardo Dobrovolski, Fabrício Rodrigues, Matheus De S. Lima-Ribeiro, Levi C. Terribile, Thiago F. Rangel, Igor Bione, Roniel Freitas, Ibere F. Machado, Tainá Rocha, Maria L. Lorini, Mariana M. Vale, Carlos A. Navas, Natan M. Maciel, Fabricio Villalobos, Miguel A. Olalla-Tárraga & Sidney Gouveia
Despite the widespread use of Ecological Niche Models (ENMs) for predicting the responses of species to climate change, these models do not explicitly incorporate any population-level mechanism. On the other hand, mechanistic models adding population processes (e.g., biotic interactions, dispersal and adaptive potential to abiotic constraints) are much more complex and difficult to parameterize, especially if the goal is to predict range shifts for many species simultaneously. In particular, the adaptive potential (based on genetic...

Data from: Reticulate evolution in nuclear Middle America causes discordance in the phylogeny of palm‐pitvipers (Viperidae: Bothriechis)

Andrew J. Mason, Felipe G. Grazziotin, Hussam Zaher, Alan R. Lemmon, Emily Moriarty Lemmon & Christopher L. Parkinson
Aim: A number of processes can lead to weak or conflicting phylogenetic signals, especially in geographically dynamic regions where unstable landscapes and climates promote complex evolutionary histories. The Middle American pitviper genus Bothriechis has a complex biogeographic distribution and previous phylogenetic analyses have recovered conflicting topologies based on the data type used. Here, we tested whether historic conflicts in the phylogeny were the result of reticulate evolution and whether the inferred biogeographic history of the...

Hidden in the DNA: insights on how multiple historical processes and natural history traits shaped patterns of cryptic diversity in an Amazon leaf-litter lizard Loxopholis osvaldoi (Squamata: Gymnophthalmidae).

Sergio Marques De Souza, Katia Machado Pellegrino, Tuliana Oliveira Brunes, Ana Carnaval, Roberta Pacheco Damasceno, Manoela Lima De Oliveira Borges, Carlos Candia Gallardo & Miguel Rodrigues
Aim: To investigate cryptic diversity and diversification timing in the putatively low-dispersal Amazonian leaf-litter lizard Loxopholis osvaldoi, and to ask how geography (rivers, isolation by distance, IBD), ecological drivers (isolation by environment, IBE) and historical factors (climatic refugia) explain intraspecific genetic variation. Location: Central Amazonia, Brazil. Taxon: Squamata; Gymnophthalmidae; Loxopholis osvaldoi. Methods: We sequenced two mitochondrial and two nuclear markers in 157 individuals. Phylogeographic structure and the occurrence of independent evolving lineages where explored through...

Data from: A link between heritable parasite resistance and mate choice in dung beetles

Bruno A. Buzatto, Janne S. Kotiaho, Larissa A. F. Assis & Leigh W. Simmons
Parasites play a central role in the adaptiveness of sexual reproduction. Sexual selection theory suggests a role for parasite resistance in the context of mate choice, but the evidence is mixed. The parasite-mediated sexual selection (PMSS) hypothesis derives a number of predictions, among which that resistance to parasites is heritable, and that female choice favours parasite resistance genes in males. Here we tested the PMSS hypothesis using the dung beetle Onthophagus taurus, a species that...

Data from: Patterns of nitrogen-fixing tree abundance in forests across Asia and America

Duncan N. L. Menge, Ryan A. Chisholm, Stuart J. Davies, Kamariah Abu Salim, David Allen, Mauricio Alvarez, Norm Bourg, Warren Y. Brockelman, Sarayudh Bunyavejchewin, Nathalie Butt, Min Cao, Wirong Chanthorn, Wei-Chun Chao, Keith Clay, Richard Condit, Susan Cordell, João Batista Da Silva, H. S. Dattaraja, Ana Cristina Segalin De Andrade, Alexandre A. Oliveira, Jan Den Ouden, Michael Drescher, Christine Fletcher, Christian P. Giardina, C. V. Savitri Gunatilleke … & Tak Fung
Symbiotic nitrogen (N)‐fixing trees can provide large quantities of new N to ecosystems, but only if they are sufficiently abundant. The overall abundance and latitudinal abundance distributions of N‐fixing trees are well characterised in the Americas, but less well outside the Americas. Here, we characterised the abundance of N‐fixing trees in a network of forest plots spanning five continents, ~5,000 tree species and ~4 million trees. The majority of the plots (86%) were in America...

Data from: Climate change, extinction, and Sky Island biogeography in a montane lizard

John J. Wiens, Agustin Camacho, Aaron Goldberg, Tereza Jezkova, Matthew E. Kaplan, Shea M. Lambert, Elizabeth C. Miller, Jeffrey W. Streicher & Ramona L. Walls
Around the world, many species are confined to “Sky Islands,” with different populations in isolated patches of montane habitat. How does this pattern arise? One scenario is that montane species were widespread in lowlands when climates were cooler, and were isolated by local extinction caused by warming conditions. This scenario implies that many montane species may be highly susceptible to anthropogenic warming. Here, we test this scenario in a montane lizard (Sceloporus jarrovii) from the...

Data from: The sugarcane mitochondrial genome: assembly, phylogenetics and transcriptomics

Dyfed Lloyd Evans, Thandekile T. Hlongwane, Shailesh V. Joshi & Diego M. Riaño-Pachón
Background: Chloroplast genomes provide insufficient phylogenetic information to distinguish between closely related sugarcane cultivars, due to the recent origin of many cultivars and the conserved sequence of the chloroplast. In comparison, the mitochondrial genome of plants is much larger and more plastic and could contain increased phylogenetic signals. We assembled a consensus reference mitochondrion with Illumina TruSeq synthetic long reads and ONT MinION long reads. Based on this assembly we also analyzed the mitochondrial transcriptomes...

The role of non-glandular emergences in Croton floribundus (Euphorbiaceae) upon elevated ozone exposures

Márcia Gonçalves Dias, Bárbara Baêsso Moura, Giselle Da Silva Pedrosa, Silvia Ribeiro De Souza & Poliana Cardoso-Gustavson
The role of non-glandular emergences in avoiding ozone (O3) damages by preventing its entrance into leaf tissues was previously suggested to the O3-tolerant species Croton floribundus (Euphorbiaceae). However, this function against O3 damage has been underestimated due to the covering wax layer mostly composed of saturated hydrocarbon with low reactivity to this gas. To evaluate the role of these structures in conferring tolerance to O3, we mechanically removed the non-glandular emergences from leaf blades of...

Calcareous defense structures of prey mediate the effects of predation and biotic resistance towards the tropics

Gustavo M Dias, Edson A Vieira, Lueji Pestana, Antonio C Marques, Simon Karythis, Stuart R Jenkins & Katherine Griffith
Aims The importance of biotic interactions in creating and maintaining diversity is expected to increase toward low latitudes. However, the way in which predation affects diversity, can depend on how predators mediate competitive interactions and also on defensive traits of prey. Here we assessed the role of physical defences of prey to escape predation and how the importance of predation on community structure and diversity changes across latitude. Location Six sites, in three regions distributed...

Data from: Isolation by instability: historical climate change shapes population structure and genomic divergence of treefrogs in the Neotropical Cerrado savanna

Mariana M. Vasconcellos, Guarino R. Colli, Jesse N. Weber, Edgardo M. Ortiz, T. Rodrigues Miguel & David C. Cannatella
Although the impact of Pleistocene glacial cycles on the diversification of the tropical biota was once dismissed, increasing evidence suggests that Pleistocene climatic fluctuations greatly affected the distribution and population divergence of tropical organisms. Landscape genomic analyses coupled with paleoclimatic distribution models provide a powerful way to understand the consequences of past climate changes on the present-day tropical biota. Using genome-wide SNP data and mitochondrial DNA, combined with projections of the species distribution across the...

Data from: Earth history and the passerine superradiation

Carl H. Oliveros, Daniel J. Field, Daniel T. Ksepka, F. Keith Barker, Alexandre Aleixo, Michael J. Andersen, Per Alström, Brett W. Benz, Edward L. Braun, Michael J. Braun, Gustavo A. Bravo, Robb T. Brumfield, R. Terry Chesser, Santiago Claramunt, Joel Cracraft, Andrés M. Cuervo, Elizabeth P. Derryberry, Travis C. Glenn, Michael G. Harvey, Peter A. Hosner, Leo Joseph, Rebecca T. Kimball, Andrew L. Mack, Colin M. Miskelly, A. Townsend Peterson … & Brant C. Faircloth
Avian diversification has been influenced by global climate change, plate tectonic movements, and mass extinction events. However, the impact of these factors on the diversification of the hyperdiverse perching birds (passerines) is unclear because family level relationships are unresolved and the timing of splitting events among lineages is uncertain. We analyzed DNA data from 4,060 nuclear loci and 137 passerine families using concatenation and coalescent approaches to infer a comprehensive phylogenetic hypothesis that clarifies relationships...

Data from: Gone with the rain: negative effects of rainfall on male mating success in a nest-building arachnid

Andrés Rojas, Diego Solano-Brenes, Danilo G. Muniz & Glauco Machado
In nest-building species, offspring survival and reproductive success of parental individuals are strongly influenced by nest quality. Thus, quantifying the influence of abiotic conditions on nest integrity is important to predict the effects of weather variability on the fitness of parental individuals. Here we investigated how rainfall affects nest integrity and how nest integrity influences males’ attractiveness and nest tenure. Our study species was the harvestman Quindina limbata, in which males build mud nests on...

Data from: A multiple peak adaptive landscape based on feeding strategies and roosting ecology shaped the evolution of cranial covariance structure and morphological differentiation in phyllostomid bats

Daniela Munhoz Rossoni, Bárbara M.A. Costa, Norberto P. Giannini & Gabriel Marroig
We explored the evolution of morphological integration in the most noteworthy example of adaptive radiation in mammals, the New World leaf-nosed bats, using a massive dataset and by combining phylogenetic comparative methods and quantitative genetic approaches. We demonstrated that the phenotypic covariance structure remained conserved on a broader phylogenetic scale but also showed a substantial divergence between inter-clade comparisons. Most of the phylogenetic structure in the integration space can be explained by splits at the...

FragSAD: A database of diversity and species abundance distributions from habitat fragments

Jonathan M. Chase, Mario Liebergesell, Alban Sagouis, Felix May, Shane A. Blowes, Åke Berg, Enrico Bernard, Berry J. Brosi, Marc W. Cadotte, Luis Cayuela, Adriano G. Chiarello, Jean-François Cosson, Will Cresswell, Filibus Danjuma Dami, Jens Dauber, Christopher R. Dickman, Raphael K. Didham, David P. Edwards, Fabio Z. Farneda, Yoni Gavish, Thiago Gonçalves-Souza, Demetrio Luis Guadagnin, Mickaël Henry, Adrià López-Baucells, Heike Kappes … & Yaron Ziv
Habitat destruction is the single greatest anthropogenic threat to biodiversity. Decades of research on this issue have led to the accumulation of hundreds of data sets comparing species assemblages in larger, intact, habitats to smaller, more fragmented, habitats. Despite this, little synthesis or consensus has been achieved, primarily because of non‐standardized sampling methodology and analyses of notoriously scale‐dependent response variables (i.e., species richness). To be able to compare and contrast the results of habitat fragmentation...

Exploration of the yield potential of mesoamerican wild common beans from contrasting eco-geographic regions by nested recombinant inbred populations

Paul Gepts, Jorge Berny Mier Y Teran, Eneas Konzen, Siu Mui Tsai & Antonia Palkovic
Genetic analyzes and utilization of wild genetic variation in common bean (Phaseolus vulgaris L.) for crop improvement have been hampered by evaluation difficulties, identification of advantageous variation, and linkage drag. The lack of adaptation to field conditions and the existence of highly structured populations make association mapping of diversity panels not optimal. Joint linkage mapping of nested populations avoids the later constraint, while populations crossed with a common domesticated parent allow the evaluation of wild...

Data from: Testing main Amazonian rivers as barriers across time and space within widespread taxa

Renata Pirani, Fernanda Werneck, Andréa Thomaz, Mariah Kenney, Marcelo Sturaro, Teresa Cristina Avila-Pires, Pedro Peloso, Miguel Rodrigues & L. Lacey Knowles
Aim: Present Amazonian diversity patterns can result from many different mechanisms and, consequently, the factors contributing to divergence across regions and/or taxa may differ. Nevertheless, the river-barrier hypothesis (RBH) is still widely invoked as a causal process in divergence of Amazonian species. Here we use model-based phylogeographic analyses to test the extent to which major Amazonian rivers act similarly as barriers across time and space in two broadly distributed Amazonian taxa. Local: Amazon rainforest. Taxon:...

Data from: Foraging mode, relative prey size and diet breadth: a phylogenetically-explicit analysis of snake feeding ecology

Xavier Glaudas, Kelsey L. Glennon, Marcio Martins, Luca Luiselli, Simon Fearn, Dane F. Trembath, Dusan Jelic & Graham J. Alexander
1. Foraging modes (ambush vs. active foraging) are often correlated with a suite of morphological, physiological, behavioral and ecological traits known as the adaptive syndrome or syndrome hypothesis. In snakes, an ecological correlate often reported in the literature is that ambush-hunting snakes have a higher relative meal size compared to actively foraging snakes which feed on smaller prey items. This “large meal vs. small meal” feeding hypothesis between ambush and active foragers has become a...

Data from: Individual factors associated with time to non-adherence to ART pick-up within HIV care and treatment services in three health facilities of Zambézia Province, Mozambique

Dercio B.C. Filimao, Troy D. Moon, Jorge F. Senise, Ricardo S. Diaz, Mohsin Sidat & Adauto Castelo
Introduction: Mozambique has made significant gains in addressing its HIV epidemic, yet adherence to visit schedules remains a challenge. HIV programmatic gains to date could be impaired if adherence and retention to ART remains low. We investigate individual factors associated with non-adherence to ART pick-up in Mozambique. Methods: This was a retrospective cohort of patients initiating ART between January 2013 and June 2014. Non-adherence to ART pick-up was defined as a delay in pick-up ?...

Effect of Drought Stress on the Genetic Architecture of Photosynthate Allocation and Remobilization in Pods of Common Bean (Phaseolus vulgaris L.), a Key Species for Food Security

Paul Gepts, Jorge Carlos Berny Mier Y Teran, Enéas R. Konzen, Antonia Palkovic, Siu M. Tsai, Idupulapati M. Rao & Stephen Beebe
Background: Common bean is the most important staple grain legume for direct human consumption and nutrition. It complements major sources of carbohydrates, including cereals, root crop, or plantain, as a source of dietary proteins. It is also a significant source of vitamins and minerals like iron and zinc. To fully play its nutritional role, however, its robustness against stresses needs to be strengthened. Foremost among these is drought, which commonly affects its productivity and seed...

Data from: Measuring the magnitude of morphological integration: the effect of differences in morphometric representations and the inclusion of size

Fabio A Machado, Alex Hubbe, Diogo Melo, Arthur Porto & Gabriel Marroig
The magnitude of morphological integration is a major aspect of multivariate evolution, providing a simple measure of the intensity of association between morphological traits. Studies concerned with morphological integration usually translate phenotypes into morphometric representations to quantify how different morphological elements covary. Geometric and classic morphometric representations translate biological form in different ways, raising the question if magnitudes of morphological integration estimates obtained from different morphometric representations are compatible. Here we sought to answer this...

Similar but different: Revealing the relative roles of species‐traits versus biome properties structuring genetic variation in South American marsh rats

Joyce Rodrigues Do Prado, Joyce R. Prado, Alexandre R. Percequillo, Andréa T. Thomaz & L. Lacey Knowles
Aim: Wetland habitats, and the ecological restrictions imposed by them, structure patterns of genetic variation in constituent taxa. As such, genetic variation may reflect properties of the specific biomes species inhabit, or shared life history traits among species may result in similar genetic structure. We evaluated these hypotheses jointly by quantifying the similarity of genetic structure in three South American marsh rat species (Holochilus), and test how genetic variation in each species relates to biome‐specific...

Data from: Canopy height explains species richness in the largest clade of Neotropical lianas

Leila Meyer, José Alexandre F. Diniz-Filho, Lúcia G. Lohmann, Joaquín Hortal, Elisa Barreto, Thiago Rangel & W. Daniel Kissling
Aim: Tall and structurally complex forests can provide ample habitat and niche space for climbing plants, supporting high liana species richness. We test to what extent canopy height (as proxy of 3D habitat structure), climate and soil interact to determine species richness in the largest clade of Neotropical lianas. We expect that the effect of canopy height on species richness is higher for lianas from closed tropical rainforests compared to riparian and savanna habitats. Location:...

Development and uncertainty assessment of pedotransfer functions for predicting water contents at specific pressure heads

Ali Mehmandoostkotlar, Quirijn De Jong Van Lier, Bo V Iversen, Alexandre Barros & Harry Vereecken
There has been much effort to improve the performance of pedotransfer functions (PTFs) using intelligent algorithms, but the issue of covariate shift, i.e. different probability distributions in training and testing datasets, and its impact on prediction uncertainty of PTFs has been rarely addressed. The common practice in PTF generation is to randomly separate the dataset in training and testing subsets, and outcomes of this random selection may be different if the process is subject to...

Registration Year

  • 2019

Resource Types

  • Dataset


  • University of Sao Paulo
  • National Institute of Amazonian Research
  • Universidade Federal do ABC
  • Federal University of Sao Paulo
  • Universidade Federal de Goiás
  • University of Michigan–Ann Arbor
  • Museu Paraense Emílio Goeldi
  • University of Minnesota
  • University of Kansas
  • University of Bath