18 Works

Data from: Genomic selection signatures and genetic variability of farmed tambaqui (Colossoma macropomum) in South America

Vito Mastrochirico-Filho, John Agudelo & Diogo Hashimoto
Tambaqui (Colossoma macropomum) represents the most important neotropical freshwater fish used in aquaculture from South America, whose production is concentrated at low latitudes (close to Equator 0º) where the water temperature is warmer. Understanding how selection shapes genetic variation and the level of genetic structure in farmed populations is of paramount meaning in evolutionary biology. High-throughput sequencing to generate genome-wide data for non-model species allows determining the genomic basis of adaptation to local or farmed...

Tayra (eira barbara) landscape use as a function of cover types, forest protection, and the presence of puma and free-ranging dogs

Rita Bianchi, Julianna Jenkins, Damon Lesmeister, Jéssica Gouvea, Clarice Cesário, Larissa Fornitano, Mateus Oliveira, Kimberly Morais, Renan Ribeiro & Matthew Gompper
The tayra (Eira barbara) is a common and broadly distributed Neotropical carnivore, yet is not well-studied. While this species is apparently associated with forested habitats, it also appears tolerant of some anthropogenic disturbance. We deployed 57 unbaited camera traps (n = 4,923 trap-days) in and around a protected area (Furnas do Bom Jesus State Park, São Paulo, Brazil) to survey for tayra and two potentially interactive species: puma (Puma concolor) and free-ranging dogs (Canis familiaris)....

Landscape structure and local variables affect plant community

Juliana Silveira Dos Santos, Carlos M. Silva-Neto, Thiago Castro Silva, Karoline Nascimento Siqueira, Milton Cezar Ribeiro & Rosane Collevatti
The biodiversity in agricultural landscapes depends on land-use types, natural elements, and farming intensity. The Brazilian Cerrado is a biodiversity hotspot, however, the native vegetation loss rates have increased in the last years, leading several plant species to extinction risk. Here, we analyze the effects of local (soil fertility and litter amount) and landscape variables (patch shape, habitat amount, compositional heterogeneity, matrix dominance and connectivity) on alpha species richness and diversity, and basal area of...

Phylogenomic reconstruction reveals new insights into the evolution and biogeography of Atta leaf-cutting ants (Hymenoptera: Formicidae)

Corina Barrera, Jeffrey Sosa-Calvo, Ted Schultz, Christian Rabeling & Maurício Bacci
Atta Fabricius is an ecologically dominant leaf-cutting ant genus, the major herbivore of the Neotropics, and an agricultural pest of great economic importance. Phylogenetic relationships within Atta have until now remained uncertain, and the delimitation and identification of a subset of Atta species are problematic. To address these phylogenetic uncertainties, we reconstruct the most comprehensive phylogenetic estimate to date of Atta by employing ultraconserved elements (UCEs). We recovered 2340 UCE loci from 224 Atta specimens,...

Data from: Frugivore diversity increases evenness in the seed rain on deforested tropical landscapes

Paulo Henrique Santos Camargo, Tomás A. Carlo, Pedro H. S. Brancalion & Marco A. Pizo
The diversity of tropical forests is strongly shaped by mutualistic interactions involving plants and frugivores that disperse their seeds. However, it is little known how decreases in the diversity of frugivores can affect seed dispersal patterns, plant community composition and species' coexistence in tropical forest landscapes. Here, we investigated the effects of bird frugivore diversity on seed dispersal of rare plant species and on the magnitude of equalizing effects on the seed rain in open...

Underlying microevolutionary processes parallel macroevolutionary patterns in ancient Neotropical Mountains - Ecological Niche Modeling and Corridors files

Marcos Vinicius Dantas-Queiroz, Tami Da Costa Cacossi, Bárbara Simões Santos Leal, Cleber Juliano Neves Chaves, Thais Vasconcelos, Leonardo De Melo Versieux & Clarisse Palma-Silva
Aim Ancient climatic fluctuations are invoked as the main driving force that generates the astonishing biodiversity in ancient mountains. As a result, endemism and spatial turnover are usually high and few species are widespread among entire mountain ranges, precluding the understanding of origins of macroevolutionary patterns. Here, we used a species endemic to, but widespread in, one of the most species-rich ancient mountains on the globe to test how environmental changes acted on them and...

Data from: Accelerated diversification explains the exceptional species richness of tropical characoid fishes

Bruno Melo, Brian Sidlauskas, Thomas Near, Fabio Roxo, Ava Ghezelayagh, Luz Ochoa, Melanie Stiassny, Jairo Arroyave, Jonathan Chang, Brant Faircloth, Daniel MacGuigan, Richard Harrington, Ricardo Benine, Michael Burns, Kendra Hoekzema, Natalia Sanches, Javier Maldonado-Ocampo, Ricardo Castro, Fausto Foresti, Michael Alfaro & Claudio Oliveira
The Neotropics harbor the most species-rich freshwater fish fauna on the planet, but the timing of that exceptional diversification remains unclear. Did the Neotropics accumulate species steadily throughout their long history, or attain their remarkable diversity recently? Biologists have long debated the relative support for these museum and cradle hypotheses, but few phylogenies of megadiverse tropical clades have included sufficient taxa to distinguish between them. We used 1288 ultraconserved element loci spanning 293 species, 211...

Data from: Isotopic niches of tropical birds reduced by anthropogenic impacts: A 100-year perspective

Ana B. Navarro, Marcelo Magioli, Juliano A. Bogoni, Luís F. Silveira, Marcelo Z. Moreira, Eduardo R. Alexandrino, Daniela T. A. Luz, Wesley R. Silva, Marco A. Pizo, Vanessa C. Oliveira & Katia M. P. M. B. Ferraz
The intensification of land use changes in tropical forests during the 20th century, mainly caused by deforestation for agricultural uses, had an overwhelming influence on bird assemblages. However, how these historical anthropogenic changes have impacted the habitat use and diet of tropical birds is poorly known. Stable isotope analysis (δ13C and δ15N) can be useful in this regard since it provides information not only on the habitat and food resource use but also insights on...

Many roads to success: Different combinations of life-history traits provide accurate germination timing in seasonally dry environments

Diego Fernando Escobar, Rafael Rubio De Casas & Leonor P. Cerdeira Morellato
Germination timing is determined by several plant life-history traits. Seed dormancy regulates the time and place of early plant development and spreads recruitment risks over time. Dispersal phenology and syndrome can influence germination timing and buffer spatial heterogeneity. The ecological requirements for germination (the germination niche) can also influence when and where germination takes place. To date, the relative importance of each of these four traits to ensure the phenological adaptation of individual species in...

Enduring evolutionary embellishment of cloudinids

Tae-Yoon Park, Jikhan Jung, Mirinae Lee, Sangmin Lee, Yong Yi Zhen, Hong Hua, Lucas V. Warren & Nigel C. Hughes
The Ediacaran–Cambrian transition and the following Cambrian Explosion are among the most fundamental events in the evolutionary history of animals. Understanding these events is enhanced when phylogenetic linkages can be established among animal fossils across this interval and their trait evolution monitored. Doing this is challenging because the fossil record of animal lineages that span this transition is sparse, preserved morphologies generally simple, and lifestyles in the Ediacaran and Cambrian quite different. Here we identify...

Data and scripts from: Total evidence phylogenetic analysis reveals polyphyly of Anostomoides and uncovers an unexpectedly ancient genus of anostomid fishes

Brian Sidlauskas, Fernando Assega, Bruno Melo, Claudio Oliveira & José Birindelli
The nearly 150 species of Anostomidae comprise one of the most diverse and taxonomically dynamic families of Neotropical freshwater fishes. A recent revision of the enigmatic and poorly diagnosed genus Anostomoides demonstrated that it contains two valid species, each with complicated taxonomic histories; however, that study did not address their phylogenetic placement. Herein, we provide the integrated molecular and morphological data and scripts used to demonstrate their distant evolutionary relationship, and thus the polyphyly of...

The individual-based network structure of palm-seed dispersers is explained by a rainforest gradient

Pâmela Friedemann, Marina Côrtes, Everaldo Castro, Mauro Galetti, Pedro Jordano &
How species interactions change in space and time is a major question in ecology. In tropical forests, plant individuals share mutualistic partners (pollinators or seed dispersers), yet we have little understanding of the factors affecting these individual interaction patterns. We used a seed dispersal individual-based network describing interactions between individuals of a palm species with bird species to investigate how intrinsic and extrinsic characteristics of individual plants influence the network structure. In our work we...

Taxonomic revision of Ediacaran tubular fossils: Cloudina, Sinotubulites and Conotubus

Ben Yang, Lucas Warren, Michael Steiner, Emily Smith & Pengju Liu
The Ediacaran tubular fossils, Cloudina, Sinotubulites, and Conotubus, are taxonomically revised with type materials. It is proposed that Aulophycus lucianoi Beurlen and Sommer, 1957 is not a senior synonym of Cloudina hartmannae Germs, 1972. Instead, most of its syntypes may be assigned to Sinotubulites or other taxa. Lectotypes of Sinotubulites baimatuoensis Chen et al., 1981 and Conotubus hemiannulatus Zhang and Lin, 1986 are designated from rediscovered syntypes. Sinotubulites baimatuoensis Chen et al., 1981 is reported...

Three phylogenetically distinct and culturable diazotrophs are perennial symbionts of leaf-cutting ants

Renata De Oliveira Aquino Zani, Milene Ferro & Maurício Bacci
The obligate mutualistic basidiomycete fungus, Leucocoprinus gongylophorus, mediates nutrition of leaf-cutting ants with carbons from vegetal matter. In addition, diazotrophic Enterobacteriales in the fungus garden and intestinal Rhizobiales supposedly mediate assimilation of atmospheric nitrogen; and Entomoplasmatales in the genus Mesoplasma, as well as other yet unidentified strains, supposedly mediate ant assimilation of other compounds from vegetal matter, such as citrate, fructose and aminoacids. Together, these nutritional partners would support the production of high yields of...

Native ants help to spread an invasive African grass in the Cerrado

Isabele F. Rebolo, Heloiza L. Zirondi, Alessandra Fidelis & Alexander V. Christianini
Plant-animal interactions may facilitate biological invasions. The African grass Urochloa decumbens is an aggressive invader in the Cerrado. We demonstrate that native ants are dispersing the seeds to short distances, allowing the gradual spread of the invasive to sites without the need of great anthropogenic soil disturbances.

Power and limitations of environmental DNA metabarcoding for surveying leaf litter eukaryotic communities

Carla Martins Lopes, Délio Baêta, Thais Sasso, Agustín Vanzetti, Kelly Zamudio, Pierre Taberlet & Célio Haddad
Leaf litter habitats shelter a great variety of organisms, which play an important role in ecosystem dynamics. However, monitoring species in leaf litter is challenging, especially in highly diverse environments such as tropical forests, because individuals may easily camouflage themselves or hide in the litter layer. Identifying species based on environmental DNA (eDNA) would allow us to assess biodiversity in this microhabitat, without the need for direct observation of individuals. We applied eDNA metabarcoding to...

Data for: Phylogenomic analyses reveal non-monophyly of the antbird genera Herpsilochmus and Sakesphorus (Thamnophilidae), with description of a new genus for Herpsilochmus sellowi

Gustavo Bravo, Bret Whitney, Ricardo Belmonte-Lopes, Marcos Bornschein, Natalia Aristizabal, Renata Beco, Jaqueline Battilana, Luciano Naka, Alexandre Aleixo, Marcio Pie, Luis Silveira, Elizabeth Derryberry & Robb Brumfield
The family Thamnophilidae is a species-rich Neotropical radiation of passerine birds. Current classification of its 235 species is mostly based on morphological similarities, but recent studies integrating comprehensive phenotypic and phylogenetic data have redefined taxonomic limits of several taxa. Here, we assess generic relationships of Herpsilochmus, Sakesphorus, Thamnophilus, Biatas, and Dysithamnus using DNA sequences from the mitochondrion, nuclear exons, and ultraconserved elements (UCEs), with further attention to interspecific relationships within Herpsilochmus. We show that Herpsilochmus...

Environmental DNA as a non-invasive alternative for surveying aquatic communities in tank bromeliads

Carla M. Lopes, Marcus T. T. Santos, Délio Baêta, Ariadne F. Sabbag & Célio F. B. Haddad
Tank bromeliads provide a freshwater microhabitat for a rich aquatic community, including amphibian species. Some of these amphibians are threatened, among other factors, because their host plants are also threatened. DNA traces left behind by amphibians in the water accumulated in bromeliads provide us a clue to track the presence and geographical distribution of these species in the environment, even when they have a low population abundance. We used an environmental DNA metabarcoding approach to...

Registration Year

  • 2021

Resource Types

  • Dataset


  • Sao Paulo State University
  • University of Sao Paulo
  • Oregon State University
  • State University of Campinas
  • Cornell University
  • Louisiana State University
  • Universidade Federal de Goiás
  • Federal Institute of São Paulo
  • Estación Biológica de Doñana
  • New Mexico State University