45 Works

Data from: Theta-modulation drives the emergence of connectivity patterns underlying replay in a network model of place cells

Panagiota Theodoni, Bernat Rovira, Yingxue Wang & Alex Roxin
Place cells of the rodent hippocampus fire action potentials when the animal traverses a particular spatial location in any environment. Therefore for any given trajectory one observes a repeatable sequence of place cell activations. When the animal is quiescent or sleeping, one can observe similar sequences of activation known as replay, which underlie the process of memory consolidation. However, it remains unclear how replay is generated. Here we show how a temporally asymmetric plasticity rule...

Data from: Climatic niche evolution is faster in sympatric than allopatric lineages of the butterfly genus Pyrgus

Camille Pitteloud, Nils Arrigo, Tomasz Suchan, Alicia Mastretta-Yanes, Roger Vila, Vlad Dinca, Juan Hernández-Roldán, Ernst Brockmann, Yannick Chittaro, Irena Kleckova, Luca Fumagalli, Sven Buerki, Loïc Pellissier & Nadir Alvarez
Understanding how speciation relates to ecological divergence has long fascinated biologists. It is assumed that ecological divergence is essential to sympatric speciation, as a mechanism to avoid competition and eventually lead to reproductive isolation, while divergence in allopatry is not necessarily associated with niche differentiation. The impact of the spatial context of divergence on the evolutionary rates of abiotic dimensions of the ecological niche has rarely been explored for an entire clade. Here, we compare...

Data from: Bottlenecks and selective sweeps during domestication have increased deleterious genetic variation in dogs

Clare D. Marsden, Diego Ortega-Del Vecchyo, Dennis P. O'Brien, Jeremy F. Taylor, Oscar Ramirez, Carles Vila, Tomas Marques-Bonet, Robert D. Schnabel, Robert K. Wayne & Kirk E. Lohmueller
Population bottlenecks, inbreeding, and artificial selection can all, in principle, influence levels of deleterious genetic variation. However, the relative importance of each of these effects on genome-wide patterns of deleterious variation remains controversial. Domestic and wild canids offer a powerful system to address the role of these factors in influencing deleterious variation because their history is dominated by known bottlenecks and intense artificial selection. Here, we assess genome-wide patterns of deleterious variation in 90 whole-genome...

Data from: Automated DNA-based plant identification for large-scale biodiversity assessment

Anna Papadopoulou, Douglas Chesters, Indiana Coronado, Gissela De La Cadena, Anabela Cardoso, Jazmina C. Reyes, Jean-Michel Maes, Ricardo M. Rueda & Jesús Gómez-Zurita
Rapid degradation of tropical forests urges to improve our efficiency in large-scale biodiversity assessment. DNA-barcoding can assist greatly in this task, but commonly used phenetic approaches for DNA-based identifications rely on the existence of comprehensive reference databases, which are infeasible for hyperdiverse tropical ecosystems. Alternatively, phylogenetic methods are more robust to sparse taxon sampling but time-consuming, while multiple alignment of species-diagnostic, typically length-variable markers can be problematic across divergent taxa. We advocate the combination of...

Supporting data: Can molecular dynamics simulations improve the structural accuracy and virtual screening performance of GPCR models?

Jon Kapla, Ismael Rodriguez Espigares, Flavio Ballante, Jana Selent & Jens Carlsson
The determination of G protein-coupled receptor (GPCR) structures at atomic resolution has improved understanding of cellular signaling and will accelerate the development of new drug candidates. However, experimental structures still remain unavailable for a majority of the GPCR family. GPCR structures and their interactions with ligands can also be modelled computationally, but such predictions have limited accuracy. In this work, we explored if molecular dynamics (MD) simulations could be used to refine the accuracy of...

Synthetic soil crusts against green-desert transitions: a spatial model

Josep Sardanyés, Blai Vidiella & Ricard Solé
Semiarid ecosystems are threatened by global warming due to longer dehydration times and increasing soil degradation. Mounting evidences indicate that, given the current trends, drylands are likely to expand and possibly experience catastrophic shifts from vegetated to desert states. Here we explore a recent suggestion based on the concept of ecosystem terraformation, where a synthetic organism is used to counterbalance some of the nonlinear effects causing the presence of such tipping points. Using an explicit...

Horse or pony? Visual Typicality and Lexical Frequency Affect Variability in Object Naming

Eleonora Gualdoni, Thomas Brochhagen, Andreas Mädebach & Gemma Boleda

NOX5-induced uncoupling of endothelial NO synthase is a causal mechanism and theragnostic target of an age-related hypertension endotype

Harald H. H. W. Schmidt, Mahmoud H. Elbatreek, Sepideh Sadegh, Elisa Anastasi, Emre Guney, Cristian Nogales, Tim Kacprowski, Ahmed A. Hassan, Andreas Teubner, Po-Hsun Huang, Chien-Yi Hsu, Paul M. H. Schiffers, Ger M. Janssen, Pamela W. M. Kleikers, Anil Wipat, Jan Baumbach & Jo G. R. De Mey
Hypertension is the most important cause of death and disability in the elderly. In 9 out of 10 cases, the molecular cause, however, is unknown. One mechanistic hypothesis involves impaired endothelium-dependent vasodilation through reactive oxygen species (ROS) formation. Indeed, ROS forming NADPH oxidase (Nox) genes associate with hypertension, yet target validation has been negative. We re-investigate this association by molecular network analysis and identify NOX5, not present in rodents, as a sole neighbor to human...

Data from: Evolution of multiple sex-chromosomes associated with dynamic genome reshuffling in Leptidea wood-white butterflies

Atsuo Yoshido, Jindra Šíchová, Kristýna Pospíšilová, Petr Nguyen, Anna Voleníková, Jan Šafář, Jan Provazník, Roger Vila & František Marec
Sex chromosome systems tend to be highly conserved and knowledge about their evolution typically comes from macroevolutionary inferences. Rapidly evolving complex sex chromosome systems represent a rare opportunity to study the mechanisms of sex chromosome evolution at unprecedented resolution. Three cryptic species of wood white butterflies – Leptidea juvernica, L. sinapis, and L. reali – have each a unique set of multiple sex chromosomes with 3–4 W and 3–4 Z chromosomes. Using a transcriptome-based microarray...

Reconstructing squamate biogeography in Afro-Arabia reveals the influence of a complex and dynamic geologic past

Héctor Tejero-Cicuéndez, Austin H. Patton, Daniel S. Caetano, Jiří Šmíd, Luke J. Harmon & Salvador Carranza
The geographic distribution of biodiversity is central to understanding evolutionary biology. Paleogeographic and paleoclimatic histories often help to explain how biogeographic patterns unfold through time. However, such patterns are also influenced by a variety of other factors, such as lineage diversification, that may affect the probability of certain types of biogeographic events. The complex and well-known geologic and climatic history of Afro-Arabia, together with the extensive research on reptile systematics in the region, makes Afro-Arabian...

Data from: High evolutionary turnover of satellite families in Caenorhabditis

Juan A. Subirana, M. Mar Alba & Xavier Messeguer
Background: The high density of tandem repeat sequences (satellites) in nematode genomes and the availability of genome sequences from several species in the group offer a unique opportunity to better understand the evolutionary dynamics and the functional role of these sequences. We take advantage of the previously developed SATFIND program to study the satellites in four Caenorhabditis species and investigate these questions. Methods: The identification and comparison of satellites is carried out in three steps....

Data from: Key innovations and island colonization as engines of evolutionary diversification: a comparative test with the Australasian diplodactyloid geckos

Joan Garcia-Porta & Terry J. Ord
The acquisition of key innovations and the invasion of new areas constitute two major processes that facilitate ecological opportunity and subsequent evolutionary diversification. Using a major lizard radiation as a model, the Australasian diplodactyloid geckos, we explored the effects of two key innovations (adhesive toepads and a snake-like phenotype) and the invasion of new environments (island colonization) in promoting the evolution of phenotypic and species diversity. We found no evidence that toepads had significantly increased...

Data from: Using relatedness networks to infer contemporary dispersal: application to the endangered mammal Galemys pyrenaicus

Lídia Escoda, Jorge González-Esteban, Asunción Gómez & Jose Castresana
Information about the degree of contemporary dispersal is important when trying to understand how populations interchange individuals and identify the specific barriers that prevent these movements. In the case of endangered species, this can represent crucial information when designing appropriate strategies that favor natural genetic exchange between populations. Here we analyze the parentage relationships between individuals from different localities and use these data to infer dispersal occurred in recent generations. We applied this approach to...

Data from: Speciation below ground: tempo and mode of diversification in a radiation of endogean ground beetles

Carmelo Andújar, Sergio Pérez-González, Paula Arribas, Juan P. Zaballos, Alfried P. Vogler & Ignacio Ribera
Dispersal is a critical factor determining the spatial scale of speciation, which is constrained by the ecological characteristics and distribution of a species' habitat and the intrinsic traits of species. Endogean taxa are strongly affected by the unique qualities of the below-ground environment and its effect on dispersal, and contrasting reports indicate either high dispersal capabilities favoured by small body size and mediated by passive mechanisms, or low dispersal due to restricted movement and confinement...

Data from: Quantification of gene expression patterns to reveal the origins of abnormal morphogenesis

Neus Martinez-Abadias, Roger Mateu Estivill, Jaume Sastre Tomas, Susan Motch Perrine, Melissa Yoon, Alex Robert-Moreno, Jim Swoger, Lucia Russo, Kazuhiko Kawasaki, Joan Richtsmeier, James Sharpe & Alexandre Robert-Moreno
The earliest developmental origins of dysmorphologies are poorly understood in many congenital diseases. They often remain elusive because the first signs of genetic misregulation may initiate as subtle changes in gene expression, which are hard to detect and can be obscured later in development by secondary effects. Here, we develop a method to trace the origins of phenotypic abnormalities by accurately quantifying the 3D spatial distribution of gene expression domains in developing organs. By applying...

Data from: Drosophila wing modularity revisited through a quantitative genetic approach

Francesc Muñoz-Muñoz, Valeria Paula Carreira, Neus Martínez-Abadías, Victoria Estefanía Ortiz, Rolando González-José, Ignacio M. Soto & Victoria Ortiz
To predict the response of complex morphological structures to selection it is necessary to know how the covariation among its different parts is organized. Two key features of covariation are modularity and integration. The Drosophila wing is currently considered a fully integrated structure. Here, we study the patterns of integration of the Drosophila wing and test the hypothesis of the wing being divided into two modules along the proximo-distal axis, as suggested by developmental, biomechanical,...

Data from: The causes of epistasis in genetic networks

Javier Macía, Ricard V. Solé & Santiago F. Elena
Epistasis refers to the non-additive interactions between genes in determining phenotypes. Considerable efforts have shown that, even for a given organism, epistasis may vary both in intensity and sign. Recent comparative studies supported that the overall sign of epistasis switches from positive to negative as the complexity of an organism increases, and it has been hypothesized that this change shall be a consequence of the underlying gene network properties. Why should this be the case?...

Data from: Repeated evolution of exaggerated dewlaps and other throat morphology in lizards

Terry J. Ord, Danielle A. Klomp, Joan Garcia-Porta & Mattias Hagman
The existence of elaborate ornamental structures in males is often assumed to reflect the outcome of female mate choice for showy males. However, female mate choice appears weak in many iguanian lizards, but males still exhibit an array of ornament-like structures around the throat. We performed a phylogenetic comparative study to assess whether these structures have originated in response to male-male competition or the need for improved signal efficiency in visually difficult environments. We found...

Data from: Implementation of complex biological logic circuits using spatially distributed multicellular consortia

Javier Macia, Romilde Manzoni, Nuria Conde, Arturo Urrios, Eulàlia De Nadal, Ricard Solé & Francesc Posas
Engineered synthetic biological devices have been designed to perform a variety of functions from sensing molecules and bioremediation to energy production and biomedicine. Notwithstanding, a major limitation of in vivo circuit implementation is the constraint associated to the use of standard methodologies for circuit design. Thus, future success of these devices depends on obtaining circuits with scalable complexity and reusable parts. Here we show how to build complex computational devices using multicellular consortia and space...

The impact of genetic adaptation on chimpanzee subspecies differentiation

Joshua Schmidt, Sergi Castellano, Marc De Manuel, Aida Andrés & Tomas Marques-Bonet
Chimpanzees, humans’ closest relatives, are in danger of extinction. Aside from direct human impacts such as hunting and habitat destruction, a key threat is transmissible disease. As humans continue to encroach upon their habitats, which shrink in size and grow in density, the risk of inter-population and cross-species viral transmission increases, a point dramatically made in the reverse with the global HIV/AIDS pandemic. Inhabiting central Africa, the four subspecies of chimpanzees differ in demographic history...

Memory reactivation in rat medial prefrontal cortex occurs in a subtype of cortical UP state during slow-wave sleep

Soroush Malek, Masami Tatsuno, LeAnna Kalvi, Adrian Ponce-Alvarez, Karim Ali, David R. Euston, Sonja Gruen & Bruce L. McNaughton
Interaction between hippocampal sharp-wave ripples (SWRs) and UP states, possibly by coordinated reactivation of memory traces, is conjectured to play an important role in memory consolidation. Recently, it was reported that SWRs were differentiated into multiple subtypes. However, whether cortical UP states can also be classified into subtypes is not known. Here, we analysed neural ensemble activity from the medial prefrontal cortex from rats trained to run a spatial sequence-memory task. Application of the hidden...

Data from: The perceptual shaping of anticipatory actions

Giovanni Maffei, Ivan Herreros, Marti Sanchez-Fibla, Karl J. Friston & Paul F.M.J. Verschure
Humans display anticipatory motor responses to minimize the adverse effects of predictable perturbations. A widely accepted explanation for this behavior relies on the notion of an inverse model that, learning from motor errors, anticipates corrective responses. Here, we propose and validate the alternative hypothesis that anticipatory control can be realized through a cascade of purely sensory predictions that drive the motor system, reflecting the causal sequence of the perceptual events preceding the error. We compare...

Genetic data from the extinct giant rat from Tenerife (Canary Islands)

Toni De-Dios
Evolution of vertebrate endemics in oceanic islands follows a predictable pattern, known as the island rule, according to which gigantism arises in originally small-sized species and dwarfism in large ones. Species of extinct insular giant rodents are known from all over the world. In the Canary Islands, two examples of giant rats, Canariomys bravoi and Canariomys tamarani, endemic to Tenerife and Gran Canaria islands, respectively, disappeared soon after human settlement. The highly derived morphological features...

The interaction between cognitive ease and informativeness shapes the lexicons of natural languages

Thomas Brochhagen & Gemma Boleda

Data from: The chicken or the egg? Adaptation to desiccation and salinity tolerance in a lineage of water beetles

Susana Pallarés, Paula Arribas, David T. Bilton, Andrés Millán, Josefa Velasco & Ignacio Ribera
Transitions from fresh to saline habitats are restricted to a handful of insect lineages, as the colonization of saline waters requires specialized mechanisms to deal with osmotic stress. Previous studies have suggested that tolerance to salinity and desiccation could be mechanistically and evolutionarily linked, but the temporal sequence of these adaptations is not well established for individual lineages. We combined molecular, physiological and ecological data to explore the evolution of desiccation resistance, hyporegulation ability (i.e.,...

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