78 Works

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: 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: 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...

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...

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...

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...

Additional file 2 of The protein aggregation inhibitor YAT2150 has potent antimalarial activity in Plasmodium falciparum in vitro cultures

Inés Bouzón-Arnáiz, Yunuen Avalos-Padilla, Arnau Biosca, Omar Caño-Prades, Lucía Román-Álamo, Javier Valle, David Andreu, Diana Moita, Miguel Prudêncio, Elsa M. Arce, Diego Muñoz-Torrero & Xavier Fernàndez-Busquets
Additional file 2. Individual data values.

Additional file 3 of The protein aggregation inhibitor YAT2150 has potent antimalarial activity in Plasmodium falciparum in vitro cultures

Inés Bouzón-Arnáiz, Yunuen Avalos-Padilla, Arnau Biosca, Omar Caño-Prades, Lucía Román-Álamo, Javier Valle, David Andreu, Diana Moita, Miguel Prudêncio, Elsa M. Arce, Diego Muñoz-Torrero & Xavier Fernàndez-Busquets
Additional file 3. Original, uncropped blots from Fig. 9.

Additional file 4 of scTAM-seq enables targeted high-confidence analysis of DNA methylation in single cells

Agostina Bianchi, Michael Scherer, Roser Zaurin, Kimberly Quililan, Lars Velten & Renée Beekman
Additional file 4: Table S3. Complete list of CpG methylation-sensitive endonucleases potentially compatible with scTAM-seq.

Additional file 7 of scTAM-seq enables targeted high-confidence analysis of DNA methylation in single cells

Agostina Bianchi, Michael Scherer, Roser Zaurin, Kimberly Quililan, Lars Velten & Renée Beekman
Additional file 7: Table S6. Doublet detection details per sample and condition.

Additional file 8 of scTAM-seq enables targeted high-confidence analysis of DNA methylation in single cells

Agostina Bianchi, Michael Scherer, Roser Zaurin, Kimberly Quililan, Lars Velten & Renée Beekman
Additional file 8: Table S7 and Table S8. Correlation analysis between target CpGs and gene expression.

Association of corticosteroid use and attention deficit/hyperactivity disorder in asthmatic children varies by age

Luyu Xie, Andrew Gelfand, M. Sunil Mathew, Folefac D. Atem, George L. Delclos & Sarah E. Messiah
We aim to examine the impact of corticosteroids use on ADHD among children with asthma by administration routes. A population-based, cross-sectional analysis included pediatric patients ages 5–20 years old from the 2016 and 2019 Kids Inpatient Database (unweighted N = 111,702). ICD-10-CM codes were used to identify corticosteroids use, asthma, and ADHD cases. Survey logistic regression models with purposeful variable selection algorithms were built to examine the association between corticosteroids use, and ADHD by asthma...

Data from: The ‘duck-billed’ dinosaurs of Careless Creek (Upper Cretaceous of Montana, USA), with comments on hadrosaurid ontogeny

Albert Prieto-Márquez & Susana Gutarra
The Careless Creek Quarry (CCQ) is a multitaxic bonebed in the Campanian Judith River Formation of south-central Montana (USA) that produced a diverse assemblage of vertebrates, including several dinosaurian clades. We describe the morphology of the CCQ hadrosaurid material and reevaluate its taxonomic affinities. Our osteological comparative observations, coupled with maximum parsimony phylogenetic analyses, indicate that the majority of the hadrosaurid material is referable to kritosaurin saurolophines. Only an ischium is unambiguously referable to Lambeosaurinae....

Data from: Protein expression parallels thermal tolerance and ecologic changes in the diversification of a diving beetle species complex

Amparo Hidalgo-Galiana, Marta Monge, David G. Biron, Francesc Canals, Ignacio Ribera & Alexandra Cieslak
Physiological changes associated with evolutionary and ecological processes such as diversification, range expansion or speciation are still incompletely understood, especially for non-model species. Here we study differences in protein expression in response to temperature in a western Mediterranean diving beetle species complex, using two-dimensional differential gel electrophoresis with one Moroccan and one Iberian population each of Agabus ramblae and Agabus brunneus. We identified proteins with significant expression differences after thermal treatments comparing them with a...

Data from: Interpreting the genomic landscape of speciation: a road map for finding barriers to gene flow

Mark Ravinet, Rui Faria, Roger K. Butlin, Juan Galindo, Nicolas Bierne, Marina Rafajlović, Mohamed A. F. Noor, Bernhard Mehlig & Anja M. Westram
Speciation, the evolution of reproductive isolation amongst populations, is continuous, complex, and involves multiple, interacting barriers. Until it is complete, the effects of this process vary along the genome and can lead to a heterogeneous genomic landscape with peaks and troughs of differentiation and divergence. When gene flow occurs during speciation, barriers restricting migration locally in the genome lead to patterns of heterogeneity. However, genomic heterogeneity can also be produced or modified by variation in...

A historical-genetic reconstruction of human extra-pair paternity

Maarten H.D. Larmuseau, Pieter Van Den Berg, Sofie Claerhout, Francesc Calafell, Alessio Boattini, Leen Gruyters, Michiel Vandenbosch, Kelly Nivelle, Ronny Decorte & Tom Wenseleers
Paternity testing using genetic markers has shown that extra-pair paternity (EPP) is common in many pair-bonded species. Evolutionary theory and empirical data show that extra-pair copulations can increase the fitness of males as well as females. This can carry a significant fitness cost for the social father, who then invests in rearing offspring that biologically are not his own. In human populations, the incidence and correlates of extra-pair paternity remain highly contentious. Here, we use...

Data from: Validation of the Regicor short physical activity questionnaire for the adult population

Judith Peñafiel, Roberto Elosua, Mireia Ble, Jaume Marrugat, Miguel Gomez, David Donaire, Helmut Schröder, Luis Molina, Manuel Sarmiento, Sonia Ruiz, Albert Frances & Judith Garcia-Aymerich
Objective: To develop and validate a short questionnaire to estimate physical activity (PA) practice and sedentary behavior for the adult population. Methods: The short questionnaire was developed using data from a cross-sectional population-based survey (n=6352) that included the Minnesota leisure-time PA questionnaire. Activities that explained a significant proportion of the variability of population PA practice were identified. Validation of the short questionnaire included a cross-sectional component to assess validity with respect to the data collected...

Data from: A comprehensive and dated phylogenomic analysis of butterflies

Marianne Espeland, Jesse W. Breinholt, Keith R. Willmott, Andrew D. Warren, Roger Vila, Emmanuel F. A. Toussaint, Sarah C. Maunsell, Kwaku Aduse-Poku, Gerard Talavera, Rodney Eastwood, Marta A. Jarzyna, Robert Guralnick, David J. Lohman, Naomi E. Pierce, Akito Y. Kawahara, Jesse Breinholt & Emmanuel F.A. Toussaint
Butterflies (Papilionoidea), with over 18,000 described species [1], have captivated naturalists and scientists for centuries. They play a central role in the study of speciation, community ecology, biogeography, climate change, and plant-insect interactions and include many model organisms and pest species [2, 3]. However, a robust higher-level phylogenetic framework is lacking. To fill this gap, we inferred a dated phylogeny by analyzing the first phylogenomic dataset, including 352 loci (> 150,000 bp) from 207 species...

Data from: Task-related effective connectivity reveals that the cortical rich club gates cortex-wide communication

Mario Senden, Niels Reuter, Martijn P. Van Den Heuvel, Rainer Goebel, Gustavo Deco & Matthieu Gilson
Higher cognition may require the globally coordinated integration of specialized brain regions into functional networks. A collection of structural cortical hubs—referred to as the rich club—has been hypothesized to support task-specific functional integration. In the present paper, we use a whole-cortex model to estimate directed interactions between 68 cortical regions from functional magnetic resonance imaging activity for four different tasks (reflecting different cognitive domains) and resting state. We analyze the state-dependent input and output effective...

Data from: Hemimetabolous genomes reveal molecular basis of termite eusociality

Mark C Harrison, Evelien Jongepier, Hugh M. Robertson, Nicolas Arning, Tristan Bitard-Feildel, Hsu Chao, Christopher P. Childers, Huyen Dinh, Harshavardhan Doddapaneni, Shannon Dugan, Johannes Gowin, Carolin Greiner, Yi Han, Haofu Hu, Daniel S.T. Hughes, Ann-Kathrin Huylmans, Carsten Kemena, Lukas P.M. Kremer, Sandra L. Lee, Alberto Lopez-Ezquerra, Ludovic Mallet, Jose M. Monroy-Kuhn, Annabell Moser, Shwetha C. Murali, Donna M. Muzny … & Erich Bornberg-Bauer
Around 150 million years ago, eusocial termites evolved from within the cockroaches, 50 million years before eusocial Hymenoptera, such as bees and ants, appeared. Here, we report the 2-Gb genome of the German cockroach, Blattella germanica, and the 1.3-Gb genome of the drywood termite Cryptotermes secundus. We show evolutionary signatures of termite eusociality by comparing the genomes and transcriptomes of three termites and the cockroach against the background of 16 other eusocial and non-eusocial insects....

Data from: Transcriptomics in the wild: hibernation physiology in free‐ranging dwarf lemurs

Sheena L. Faherty, José Luis Villanueva‐Cañas, Marina B. Blanco, M. Mar Albà & Anne D. Yoder
Hibernation is an adaptive strategy some mammals use to survive highly seasonal or unpredictable environments. We present the first investigation on the transcriptomics of hibernation in a natural population of primate hibernators: Crossley's dwarf lemurs (Cheirogaleus crossleyi). Using capture–mark–recapture techniques to track the same animals over a period of 7 months in Madagascar, we used RNA‐seq to compare gene expression profiles in white adipose tissue (WAT) during three distinct physiological states. We focus on pathway...

Inversions and genomic differentiation after secondary contact: when drift contributes to maintenance, not loss, of differentiation

Marina Rafajlovic, Jordi Rambla, Jeffrey L. Feder, Arcadi Navarro & Rui Faria
Due to their effects on reducing recombination, chromosomal inversions may play an important role in speciation by establishing and/or maintaining linked blocks of genes causing reproductive isolation (RI) between populations. This view fits empirical data indicating that inversions typically harbour loci involved in RI. However, previous computer simulations of infinite populations with 2-4 loci involved in RI implied that, even with gene flux as low as 10^(-8) per gamete, per generation between alternative arrangements, inversions...

A genome-wide association study of total child psychiatric problems scores: summary statistics

Alexander Neumann, Ilja M. Nolte, Irene Pappa, Tarunveer S. Ahluwalia, Erik Pettersson, Alina Rodriguez, Andrew J.O. Whitehouse, Catharina van Beijsterveldt, Beben Benyamin, Anke Hammerschlag, Quinta Helmer, Ville Karhunen, Eva Krapohl, Yi Lu, Peter van der Most, Teemu Palviainen, Beate St. Pourcain, Ilkka Seppälä, Anna Suarez, Natalia Vilor-Tejedor, Carla M. T. Tiesler, Carol Wang, Amanda Wills, Ang Zhou, Silvia Alemany … & Henning Tiemeier
Summary statistics for EAGLE GWAS on total child psychiatric problems scores.
Data is provided in R binary format and can be loaded within R with load("total_child_psychiatric_GWAS.Rdata").
snp: SNP RS ID effect_allele: Effect allele other_allele: Other allele beta: Change in total psychiatric problem score in SD per number of effect allele se: Standard Error p: p-value n: Sample Size
For more information, see PLOS ONE publication:
Neumann A, Nolte IM, [...], Hartman...

Additional file 2 of scTAM-seq enables targeted high-confidence analysis of DNA methylation in single cells

Agostina Bianchi, Michael Scherer, Roser Zaurin, Kimberly Quililan, Lars Velten & Renée Beekman
Additional file 2: Table S1. Design overview of the panel of targeted regions.

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  • Pompeu Fabra University
  • Barcelona Institute for Science and Technology
  • Centre for Genomic Regulation
  • August Pi i Sunyer Biomedical Research Institute
  • University of Barcelona
  • University College London
  • Institució Catalana de Recerca i Estudis Avançats
  • Saarland University
  • Max Planck Institute for Informatics
  • Hospital Del Mar