59 Works

Total Ortholog Median Matrix (TOMM): an alternative unsupervised approach for phylogenomics based on evolutionary distance between protein coding genes

Sandra R. Maruyama, Luana A. Rogerio, Patrícia Domingues Freitas, Marta Maria Teixeira & José Marcos Ribeiro
The increasing number of available genomic data allowed the development of phylogenomic analytical tools. Current methods compile information from single gene phylogenies, whether based on topologies or multiple sequence alignments. Generally, phylogenomic analyses elect gene families or genomic regions to construct phylogenomic trees. Here, we presented an alternative approach for Phylogenomics, named TOMM (Total Ortholog Median Matrix), to construct a representative phylogram composed by amino acid distance measures of all pairwise ortholog protein sequence pairs...

To hop or not to hop? the answer is in the bird trees

Pauline Provini & Elizabeth Höfling
Birds can use different types of gaits to move on the ground: they either walk, hop, or run. Although velocity can easily explain a preference for running, it remains unclear what drives a bird species to favour hopping over walking. As many hopping birds are relatively small and arboreal, we wanted to test the link between size, arboreality and hopping ability. First, we carried out ancestral character state reconstructions of size range, hopping ability and...

Using a coalescent approach to assess gene flow and effective population size of Acrocomia aculeata (Jacq.) Lodd. Ex Mart. in the Brazilian Atlantic Forest

Renan Marcelo Portela, Evandro Vagner Tambarussi, João Ricardo Bachega Feijó Rosa, Ananda Virginia De Aguiar, Fabiana Schmidt Bandeira Peres & Flávio Bertin Gandara
Acrocomia aculeata is a tropical palm tree native to Central and South America that has significant economic, social, and environmental potential. However, land encroachment due to the expansion of agribusiness, and other factors such as urban sprawl, have resulted in the fragmentation and destruction of its habitat, leading to the loss of genes and genotypes in A. aculeata populations. In this context, the objective of this study was to characterize the genetic variability of A....

Data from: Cytogenetics, geographic distribution, conservation and new species of Macrotorus (Mollinedioideae, Monimiaceae) from the Brazilian Atlantic rainforest

Elton John De Lirio, Paulo Ricardo De Oliveira Costa, Ariane Luna Peixoto, Paulo Takeo Sano & Ana Paula Moraes
A new species of Macrotorus (Monimiaceae) from the Brazilian Atlantic rainforest is here described and illustrated: M. genuflexus. This species, restricted to the Poço das Antas Biological Reserve (situated in the central region of Rio de Janeiro state, Brazil), is the second in the genus Macrotorus. The new species description is based on morphological and cytogenetic (karyotype and genome size - GS) comparative analyses. We also report a new record of Macrotorus utriculatus for the...

Data from: Copulatory function and development shape modular architecture of genitalia differently in males and females

Bruno C. Genevcius, Monique N. Simon, Tamara Moraes & Cristiano F. Schwertner
Genitalia are multitasking structures whose development is mediated by numerous regulatory pathways. This multi-factorial nature provides an avenue for multiple sources of selection. As a result, genitalia tend to evolve as modular systems comprising semi-independent subsets of structures, yet the processes that give rise to those patterns are still poorly understood. Here, we ask what are the relative roles of development and function in shaping modular patterns of genitalia within populations and across species of...

Coronavirus prevalence in Brazilian Amazon and Sao Paulo city

Tassila Salomon, Oliver Pybus, Rafael França, Marcia Castro, Ester Cerdeira Sabino, Christopher Dye, Michael Busch, Moritz U. G. Kraemer, Charles Whittaker, Andreza Santos, Nuno Faria, Rafael Pereira, Lewis Buss, , Claudia Abrahim, Maria Carvalho, Allyson Costa, Manoel Barral-Netto, Crispim Myuki, Brian Custer, Cesar De Almeida-Neto, Suzete Ferreira, Nelson Fraiji, Susie Gurzenda, Leonardo Kamaura … & Maria Belotti
SARS-CoV-2 spread rapidly in the Brazilian Amazon. Mortality was elevated, despite the young population, with the health services and cemeteries overwhelmed. The attack rate in this region is an estimate of the final epidemic size in an unmitigated epidemic. Here we show that by June, one month after the epidemic peak in Manaus, capital of the Amazonas state, 44% of the population had detectable IgG antibodies. This equates to a cumulative incidence of 52% after...

Investigating morphological complexes using informational dissonance and bayes factors: A case study in corbiculate bees

Diego Porto, Eduardo Almeida & Matthew Pennell
It is widely recognized that different regions of a genome often have different evolutionary histories and that ignoring this variation when estimating phylogenies can be misleading. However, the extent to which this is also true for morphological data is still largely unknown. Discordance among morphological traits might plausibly arise due to either variable convergent selection pressures or else phenomena such as hemiplasy. Here we investigate patterns of discordance among 282 morphological characters, which we scored...

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 package of Nordeste Plot Metadata and Species list from Brazilian Caatinga Long-term Inventory plots

Peter Moonlight, Jon Lloyd, Colin Prentice, Oliver Phillips, Tomas Domingues, Aurora Levesley, Jarcilene Almeida Cortez, Keith Bloomfield, Domingos Cardoso, Italo Coutinho, John Cunha, Mário Marcos do Espirito Santo, Alberto Jorge Ferias Castro, Francoise Yoko Ishida, Rubens Manuel dos Santos, Salomão Medeiros, Jhonathan Oliveira Silva, Luciano Paganucci de Queiroz, R. Toby Pennington, Priscyla Rodriguez, Tiina Särkinen, Rodolfo Souza, Magna Soelma Beserra de Moura, Romualdo de Sousa Lima & Tony de Sousa Oliveira

11 Sandstones: raw, filtered and segmented data

Rodrigo Neumann, Mariane Andreeta & Everton Lucas-Oliveira
A set of 11 sandstone plugs from Kocurek Industries: Bandera Gray, Parker, Kirby, Bandera Brown, Berea Sister Gray, Berea Upper Gray, Berea, Castlegate, Buff Berea, Leopard and Bentheimer. Source: https://kocurekindustries.com/sandstone-cores. All samples were subject to a combined experimental and computational analysis in order to estimate Porosity and Permeability. For more details, please refer to: https://arxiv.org/abs/2010.10679.

Data from: A 45-year-old man with progressive insomnia, psychiatric and motor symptoms

Jose Eduardo E. Lima, Teddy S. Youn, Christopher P. Robinson, Emily J. Gilmore, Matthew Schrag, Sirisha Sanamandra & Carolina Maciel
A 45-year-old right-handed hypertensive man presented with a 6-month history of worsening neuropsychiatric symptoms, abnormal movements, and weight loss. He was hallucinating, apathetic, and having severe insomnia (total sleep duration of 1–2 hours/night). During sleep, his wife noted labored and sonorous breathing. Six months before admission, he led a healthy and active lifestyle.

Data from: A small podocnemidoid (Pleurodira, Pelomedusoides) from the Late Cretaceous of Brazil, and the innervation and carotid circulation of side-necked turtles

Guilheme Hermanson, Fabiano V. Iori, Serjoscha W. Evers, Max C. Langer & Gabriel S. Ferreira
Pleurodires are less specious than cryptodires, together forming the two major lineages of crown-turtles. Their fossil record, however, is rich. A particularly large number of fossil pleurodires, many belonging to Podocnemidoidae, has been recovered from the Late Cretaceous Bauru Group outcrops in south-central Brazil. Here we describe an additional pleurodire from this region, Amabilis uchoensis gen. et sp. nov., based on a partially preserved skull. A. uchoensis is recognized as a Podocnemidoidae by its small...

Data from: Redescription and phylogenetic affinities of the caimanine Eocaiman cavernensis (Crocodylia, Alligatoroidea) from the Eocene of Argentina

Pedro L. Godoy, Giovanne Cidade, Felipe Montefeltro, Max Langer & Mark Norell
Caimaninae is one of the few crocodylian lineages that still has living representatives. Today, most of its six extant species are restricted to South and Central America. However, recent discoveries revealed a more complex evolutionary history, with a fossil record richer than previously thought and a possible North American origin. Among the oldest caimanines is Eocaiman cavernensis, from the Eocene of Patagonia, Argentina. It was described by George G. Simpson in the 1930s, representing the...

Hard to get, easy to lose: Evolution of mantle photoreceptor organs in bivalves (Bivalvia, Pteriomorphia)

Jorge Audino, Jeanne Marie Serb & José Eduardo Amoroso Rodriguez Marian
Morphologically diverse eyes have evolved numerous times, yet little is known about how eye gain and loss is related to photic environment. The pteriomorphian bivalves (e.g., oysters, scallops, and ark clams), with a remarkable range of photoreceptor organs and ecologies, are a suitable system to investigate the association between eye evolution and ecological shifts. The present phylogenetic framework was based on amino acid sequences from transcriptome datasets and nucleotide sequences of five additional genes. In...

The interplay between local and landscape scales on the density of pond-dwelling anurans in subtropical grasslands

Samanta Iop
We investigated the role of local and landscape environmental variables on anurans density classified as habitat specialists and generalists in grassland landscapes, known as South Brazilian grasslands (SBG). In this region, we surveyed 187 ponds distributed over 40 landscape sampling units. For each pond, 31 local environmental variables were measured. Each landscape sampling unit was embedded within a larger regional sampling unit with different landscape properties. For each landscape and regional sampling units, 16 landscape...

Associated evolution of fruit size, fruit color and spines in Neotropical palms

Lucas Ferreira Do Nascimento, , Renske E. Onstein, W. Daniel Kissling & Mathias M. Pires
Understanding how ecological interactions have shaped the evolutionary dynamics of species traits remains a challenge in evolutionary ecology. Combining trait evolution models and phylogenies, we analyzed the evolution of characters associated with seed dispersal (fruit size and color) and herbivory (spines) in Neotropical palms to infer the role of these opposing animal-plant interactions in driving evolutionary patterns. We found that the evolution of fruit color and fruit size were associated in Neotropical palms, supporting the...

Heterogeneous agroecosystems support high diversity and abundance of trap nesting bees and wasps amongst tropical crops

Jeferson Coutinho, Catalina Coca, Danilo Boscolo & Blandina Viana
Land-use intensification for agricultural purposes modifies the structure of natural environments in various ways and at different spatial scales. These modifications can affect ecological processes and the community structure of multi-environment users such as solitary bees and wasps. Understanding the role of distinct habitat descriptors in promoting such changes is one of the major challenges of empirical studies. In this study, we use a multi-scale approach to evaluate how landscape compositional and configurational heterogeneity, vegetation...

New species boundaries and the diversification history of marsh rat taxa clarify historical connections among ecologically and geographically distinct wetlands of South America

Joyce Prado, Lacey Knowles & Alexandre Percequillo
Taxa with broad geographic ranges that occur in different biomes and exhibit plastic morphological traits and/or adaptations to particular habitats make inferences about species boundaries especially challenging. However, technological and conceptual advances in the generation and analysis of genomic data have advanced the description of biodiversity. Here we address the outstanding questions about the delimitation of species in the genus Holochilus, a rodent with morphological specializations to wetland habitats, distributed through almost all the South...

Fitness implications of nonlethal injuries in scorpions: females, but not males pay reproductive costs

Solimary Garcia-Hernandez & Glauco Machado
The ability to detach a body part in response to a predation attempt is known as autotomy, and it is perhaps the most intensively studied form of nonlethal injury in animals. Although autotomy enhances survival, it may impose reproductive costs to both males and females. We experimentally investigated how autotomy affects the reproductive success of males and females of a scorpion species. Individuals of Ananteris balzani autotomize the last abdominal segments (“tail”), losing the anus...

Phylogenomics of scorpions reveal a co-diversification of scorpion mammalian predators and mammal-specific sodium channel toxins

Carlos Santibanez, Shlomi Aharon, Jesús Ballesteros, Guilherme Gainett, Caitlin Baker, Edmundo González-Santillán, Mark Harvey, Mohamed Hassans, Ali Abu-Almaaty, Shorouk Aldeyarbi, Lionel Monod, Andrés Ojanguren-Affilastro, Robert Raven, Ricardo Pinto Da Rocha, Yoram Zvik, Efrat Gavish-Regev & Prashant Sharma
Scorpions constitute a charismatic lineage of arthropods and comprise more than 2,500 described species. Found throughout various tropical and temperate habitats, these predatory arachnids have a long evolutionary history, with a fossil record that began in the Silurian. While all scorpions are venomous, the asymmetrically diverse family Buthidae harbors nearly half the diversity of extant scorpions, and all but one of the 58 species that are medically significant to humans. Many aspects of scorpion evolutionary...

Global gradients in intraspecific variation in vegetative and floral traits are partially associated with climate and species richness

Jonas Kuppler, Cécile H. Albert, Gregory M. Ames, W. Scott Armbruster, Gerhard Boenisch, Florian C. Boucher, Diane R. Campbell, Liedson T. Carneiro, Eduardo Chacón-Madrigal, Brian J. Enquist, Carlos R. Fonseca, José M. Gómez, Antoine Guisan, Pedro Higuchi, Dirk N. Karger, Jens Kattge, Michael Kleyer, Nathan J. B. Kraft, Anne-Amélie C. Larue-Kontić, Amparo Lázaro, Martin Lechleitner, Deirdre Loughnan, Vanessa Minden, Ülo Niinemets, Gerhard E. Overbeck … & Robert R. Junker
Aim Intraspecific trait variation (ITV) within natural plant communities can be large, influencing local ecological processes and dynamics. Here, we shed light on how ITV in vegetative and floral traits responds to large-scale abiotic and biotic gradients (i.e. climate and species richness). Specifically, we tested if associations of ITV with temperature, precipitation and species richness were consistent with any of from four hypotheses relating to stress-tolerance and competition. Furthermore, we estimated the degree of correlation...

Fast diversification through a mosaic of evolutionary histories characterizes the endemic flora of ancient Neotropical mountains

Thais Vasconcelos, Suzana Alcantara, Caroline Andrino, Félix Forest, Marcelo Reginato, Marcelo Simon & José Pirani
Mountains are among the most biodiverse areas on the globe. In young mountain ranges, exceptional plant species-richness is often associated to recent and rapid radiations linked to the mountain uplift itself. In ancient mountains, however, orogeny vastly precedes the evolution of vascular plants, so species-richness has been explained by species accumulation during long periods of low extinction rates. Here we evaluate these assumptions by analyzing plant diversification dynamicsin thecampo rupestre, an ecosystem associated to pre-Cambrian...

Female-driven intersexual coevolution in beetle genitalia

Bruno Genevcius, Joanna Baker, Filipe Bianchi & Adriana Marvaldi
Genital coevolution is a pervasive phenomenon as changes in one sex tend to impose fitness consequences on the other generating sexual conflict. Sexual conflict is often thought to cause stronger selection on males due to the Darwin-Bateman’s anisogamy paradigm. However, recent studies have demonstrated that female genitalia may be equally elaborated and perform diverse extra-copulatory functions. These characteristics suggest that female genitals can also be primary targets of selection, especially where natural selection acts on...

Root and shoot variation in relation to potential intermittent drought adaptation of Mesoamerican wild common bean (Phaseolus vulgaris L.)

Paul Gepts, Jorge Carlos Berny Mier Y Teran, Enéas R Konzen, Viviana Medina, Antonia Palkovic, Andrea Ariani, Siu M. Tsai & Matthew E. Gilbert
• Background Wild crop relatives have been potentially subjected to stresses on an evolutionary time scale prior to domestication. Among these stresses, drought is one of the main factors limiting crop productivity and its impact is likely to increase under current scenarios of global climate change. We sought to determine to what extent wild common bean (Phaseolus vulgaris) exhibited adaptation to drought stress, whether this potential adaptation is dependent on the climatic conditions of the...

Data from: Analysis of statistical correlations between properties of adaptive walks in fitness landscapes

Sandro M. Reia & Paulo R. A. Campos
The fitness landscape metaphor has been central in our way of thinking about adaptation. In this scenario, adaptive walks are an idealized dynamics that mimics the uphill movement of an evolving population towards a fitness peak of the landscape. Recent works in experimental evolution have demonstrated that the constraints imposed by epistasis are responsible for reducing the number of accessible mutational pathways towards fitness peaks. Here we exhaustively analyze the statistical properties of adaptive walks...

Registration Year

  • 2020

Resource Types

  • Dataset


  • University of Sao Paulo
  • Museu Paraense Emílio Goeldi
  • Federal University of Sao Paulo
  • Federal University of Technology – Paraná
  • Sao Paulo State University
  • University of Michigan–Ann Arbor
  • Federal University of São Carlos
  • Australian National University
  • Universidade Federal do ABC
  • Federal University of Rio Grande do Sul