374 Works

Dopamine axon population Ca signals in the striatum during odor cue- and reward-based choice tasks in mice

Mitsuko Watabe-Uchida, Iku Tsutsui-Kimura, Hideyuki Matsumoto & Naoshige Uchida
Dopamine axon activity in the ventral, dorsomedial, and dorsolateral striatum was recorded, while mice performed a perceptual and value-based decision-making task. In one experiment, thirsty mice performed a perceptual decision-making task using mixtures of odor A and B (100/0, 90/10, 65/35, 35/65, 10/90, 0/100), in which identity of a dominant odor determined an available water port, and odor C which signaled no outcome. A fixed amount of water was always delivered with a correct choice....

Data from: Molecular physiology of chemical defenses in a poison frog

Stephanie N Caty, Aurora Alvarez-Buylla, Gary` D Byrd, Charles Vidoudez, Alexandre B Roland, Elicio E Tapia, Bogdan Bodnik, Sunia A Trauger, Luis A Coloma & Lauren A O'Connell
Poison frogs sequester small molecule lipophilic alkaloids from their diet of leaf litter arthropods for use as chemical defenses against predation. Although the dietary acquisition of chemical defenses in poison frogs is well-documented, the physiological mechanisms of alkaloid sequestration has not been investigated. Here, we used RNA sequencing and proteomics to determine how alkaloids impact mRNA or protein abundance in the Little Devil Frog (Oophaga sylvatica) and compared wild caught chemically defended frogs to laboratory...

Data from: Carryover effects and the evolution of polyphenism

David Pfennig, Sofia De La Serna Buzón & Ryan Martin
An individual’s early-life environment and phenotype often influence its traits and performance as an adult. We investigated whether such ‘carryover effects’ are associated with alternative, environmentally induced phenotypes (‘polyphenism’), and, if so, whether they influence polyphenism’s evolution. To do so, we studied spadefoot toads, Spea multiplicata, which have evolved a polyphenism consisting of two, dramatically different forms: a carnivore morph and an omnivore morph. We sampled both morphs from a fast-drying and a slow-drying pond...

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...

Data from: Early maternal loss affects diurnal cortisol slopes in immature but not mature wild chimpanzees

Cedric Girard-Buttoz, Patrick Tkaczynski, Liran Samuni, Pawel Fedurek, Cristina Gomes, Therese Löhrich, Virgile Manin, Anna Preis, Prince Valé, Tobias Deschner, Roman Wittig & Catherine Crockford
Biological embedding of stress experienced early in life is a mechanism proposed to explain the fitness costs of maternal loss in mammals. This embedding is expected to lead to long-term alterations of the hypothalamic pituitary adrenal (HPA) axis activity. This idea has, however, rarely been tested in wild long-lived animals. We assessed whether, as in humans, maternal loss had short and long-term impacts on orphan wild chimpanzee urinary cortisol levels and diurnal urinary cortisol slopes,...

The perfect storm: Gene tree estimation error, incomplete lineage sorting, and ancient gene flow explain the most recalcitrant ancient angiosperm clade, Malpighiales

Liming Cai, Zhenxiang Xi, Emily Lemmon, Alan Lemmon, Austin Mast, Christopher Buddenhagen, Liang Liu & Charles Davis
The genomic revolution offers renewed hope of resolving rapid radiations in the Tree of Life. The development of the multispecies coalescent (MSC) model and improved gene tree estimation methods can better accommodate gene tree heterogeneity caused by incomplete lineage sorting (ILS) and gene tree estimation error stemming from the short internal branches. However, the relative influence of these factors in species tree inference is not well understood. Using anchored hybrid enrichment, we generated a data...

Dual DNA/protein tagging of open chromatin unveils dynamics of epigenomic landscapes in leukemia

Jonathan Lee
The architecture of chromatin specifies eukaryotic cell identity by controlling transcription factor access to sites of gene regulation. Here we describe a dual transposase/peroxidase approach, integrative DNA And Protein Tagging (iDAPT), which detects both DNA (iDAPT-seq) and protein (iDAPT-MS) associated with accessible regions of chromatin. In addition to direct identification of bound transcription factors, iDAPT enables the inference of their gene regulatory networks, protein interactors, and regulation of chromatin accessibility. We applied iDAPT to profile...

Data from: Reporting guidelines for community-based participatory research (CBPR) did not improve the reporting quality of published studies: a systematic review of studies on smoking cessation

Daisuke Kato, Yuki Kataoka, Erfen Suwangto, Makoto Kaneko, Hideki Wakabayashi, Daisuke Son & Ichiro Kawachi
Although a guideline for reporting the results of community-based participatory research (CBPR) was published in 2010, the impact on the quality of reporting a CBPR on smoking cessation is unknown. Here we provide the raw data of a systematic review that assessed the impact of a 2010 community-based participatory research reporting guideline. on the quality of reporting a CBPR on smoking cessation. Specifically, we searched the MEDLINE, Embase, the Cochrane Central Register for Controlled Trials...

Data from: Demography, life history trade-offs, and the gastrointestinal virome of wild chimpanzees

Jacob D. Negrey, Melissa Emery Thompson, Kevin E. Langergraber, Zarin P. Machanda, John C. Mitani, Martin N. Muller, Emily Otali, Leah A. Owens, Richard W. Wrangham & Tony L. Goldberg
In humans, senescence increases susceptibility to viral infection. However, comparative data on viral infection in free-living non-human primates—even in our closest living relatives, chimpanzees and bonobos (Pan troglodytes and P. paniscus)—are relatively scarce, thereby constraining an evolutionary understanding of age-related patterns of viral infection. We investigated a population of wild eastern chimpanzees (P. t. schweinfurthii), using metagenomics to characterize viromes (full viral communities) in the feces of 42 sexually mature chimpanzees (22 males, 20 females)...

Quantifying the effects of species traits on predation risk in nature: a comparative study of butterfly wing damage

Freerk Molleman, Juhan Javoiš, Robert Davis, Melissa Whitaker, Toomas Tammaru, Andreas Prinzing, Erki Õunap, Niklas Wahlberg, Ullasa Kodandaramaiah, Kwaku Aduse-Poku, Ants Kaasik & James Carey
1) Evading predators is a fundamental aspect of the ecology and evolution of all prey animals. In studying the influence of prey traits on predation risk, previous researchers have shown that crypsis reduces attack rates on resting prey, predation risk increases with increased prey activity, and rapid locomotion reduces attack rates and increases chances of surviving predator attacks. However, evidence for these conclusions is nearly always based on observations of selected species under artificial conditions....

Data from: Insect herbivory reshapes a native leaf microbiome

Parris Humphrey & Noah Whiteman
Publication abstract: Insect herbivory is pervasive in plant communities, but its impact on microbial plant colonizers is not well-studied in natural systems. By calibrating sequencing-based bacterial detection to absolute bacterial load, we find that the within-host abundance of most leaf microbiome (phyllosphere) taxa colonizing a native forb is amplified within leaves impacted by insect herbivory. Herbivore-associated bacterial amplification reflects community-wide compositional shifts towards lower ecological diversity, but the extent and direction of such compositional shifts...

Data from: Sibling rivalry: males with more brothers develop larger testes

Kristin Hook, Heidi Fisher, W. David Weber & Hopi Hoekstra
When females mate with multiple partners in a reproductive cycle, the relative number of competing sperm from rival males is often the most critical factor in determining paternity. Gamete production is directly related to testis size in most species, and is associated with both mating behavior and perceived risk of competition. Deer mice, Peromyscus maniculatus, are naturally promiscuous and males invest significantly more in sperm production than males of P. polionotus, their monogamous sister‐species. Here,...

Data from: Dynamic reorganization of neuronal activity patterns in parietal cortex dataset

Laura N. Driscoll, Noah L. Pettit, Matthias Minderer, Selmaan N. Chettih & Christopher D. Harvey
Neuronal representations change as associations are learned between sensory stimuli and behavioral actions. However, it is poorly understood whether representations for learned associations stabilize in cortical association areas or continue to change following learning. We tracked the activity of posterior parietal cortex neurons for a month as mice stably performed a virtual-navigation task. The relationship between cells’ activity and task features was mostly stable on single days but underwent major reorganization over weeks. The neurons...

Information transfer efficiency differs in wild chimpanzees and bonobos, but not social-cognition

Cedric Girard-Buttoz, Martin Surbeck, Liran Samuni, Patrick Tkaczynski, Christophe Boesch, Barbara Fruth, Roman Wittig, Gottfried Hohmann & Catherine Crockford
Several theories have been generated to understand the socio-cognitive mechanisms underlying the unique cooperative abilities of humans. The “interdependence hypothesis” posits that the cognitive dimension of human cooperation evolved in contexts when several individuals needed to collaborate to achieve a common goal and that more interdependent individuals are more likely to cooperate (provide services to conspecifics) in non-collaborative contexts. Alternatively, the “social tolerance hypothesis” proposes that higher social tolerance allows conspecifics to cooperate more efficiently...

Data from: The extension of internal humidity levels beyond the soil surface facilitates mound expansion in Macrotermes

Daniel S. Calovi, Paul Bardunias, Nicole Carey, Rupert Soar, Scott Turner, Radhika Nagpal & Justin Werfel
Termites in the genus Macrotermes construct large-scale soil mounds above their nests. The classic explanation for how termites coordinate their labour to build the mound, based on a putative cement pheromone, has recently been called into question. Here we present evidence for an alternate interpretation based on sensing humidity. The high humidity characteristic of the mound internal environment extends a short distance into the low-humidity external world, in a “bubble” that can be disrupted by...

Data from: Specialized breeding in plants affects diversification trajectories in Neotropical frogs

Joao Filipe Tonini, Rodrigo Ferreira & R. Alexander Pyron
Many animals breed exclusively in plants that accumulate rainwater (phytotelma; e.g., bromeliad, bamboo, fruit husk, and tree hole), to which they are either physiologically or behaviorally specialized for this microhabitat. Of the numerous life-history modes observed in frogs, few are as striking or potentially consequential as the transition from pond- or stream-breeding to the deposition of eggs or larvae in phytotelmata. Such specialization can increase offspring survivorship due to reduced competition and predation, representing potential...

Data from: Neighbouring-group composition and within-group relatedness drive extra-group paternity rate in the European badger (Meles meles)

Geetha Annavi, Chris Newman, Hannah L. Dugdale, Christina C. Buesching, Yung W. Sin, Terry Burke & David W. Macdonald
Extra-group paternity (EGP) occurs commonly among group-living mammals and plays an important role in mating systems and the dynamics of sexual selection; however, socio-ecological and genetic correlates of EGP have been underexplored. We use 23 years of demographic and genetic data from a high-density European badger (Meles meles) population, to investigate the relationship between the rate of EGP in litters and mate availability, mate incompatibility and mate quality (heterozygosity). Relatedness between within-group assigned mothers and...

Data from: Associations between changes in city and address specific temperature and QT interval - the VA Normative Aging Study

Amar J. Mehta, Itai Kloog, Antonella Zanobetti, Brent A. Coull, David Sparrow, Pantel Vokonas & Joel Schwartz
Background: The underlying mechanisms of the association between ambient temperature and cardiovascular morbidity and mortality are not well understood, particularly for daily temperature variability. We evaluated if daily mean temperature and standard deviation of temperature was associated with heart rate-corrected QT interval (QTc) duration, a marker of ventricular repolarization in a prospective cohort of older men. Methods: This longitudinal analysis included 487 older men participating in the VA Normative Aging Study with up to three...

Data from: Ancient horizontal gene transfer and the last common ancestors

Gregory P. Fournier, Cheryl P. Andam & Johann Peter Gogarten
Background: The genomic history of prokaryotic organismal lineages is marked by extensive non-vertical inheritance of genes, with horizontal gene transfer (HGT) between many groups of organisms at all taxonomic levels. These HGT events have played an essential role in the origin and distribution of biological innovations. Analyses of ancient gene families show that HGT existed in the distant past, even at the time of the organismal last universal common ancestor (LUCA). Most gene transfers originated...

Data from: MHC class II assortative mate choice in European badgers (Meles meles)

Yung Wa Sin, Geetha Annavi, Chris Newman, Christina Buesching, Terry Burke, David W. Macdonald & Hannah L. Dugdale
The major histocompatibility complex (MHC) plays a crucial role in the immune system, and in some species, it is a target by which individuals choose mates to optimize the fitness of their offspring, potentially mediated by olfactory cues. Under the genetic compatibility hypothesis, individuals are predicted to choose mates with compatible MHC alleles, to increase the fitness of their offspring. Studies of MHC-based mate choice in wild mammals are under-represented currently, and few investigate more...

Data from: Size-related scaling of tree form and function in a mixed-age forest

Kristina J. Anderson-Teixeira, Jennifer C. McGarvey, Helene C. Muller-Landau, Janice Y. Park, Erika B. Gonzalez-Akre, Valentine Herrmann, Amy C. Bennett, Christopher V. So, Norman A. Bourg, Jonathan R. Thompson, Sean M. McMahon & William J. McShea
Many morphological, physiological and ecological traits of trees scale with diameter, shaping the structure and function of forest ecosystems. Understanding the mechanistic basis for such scaling relationships is key to understanding forests globally and their role in Earth's changing climate system. Here, we evaluate theoretical predictions for the scaling of nine variables in a mixed-age temperate deciduous forest (CTFS-ForestGEO forest dynamics plot at the Smithsonian Conservation Biology Institute, Virginia, USA) and compare observed scaling parameters...

Data from: Low cost, high performance processing of single particle cryo-electron microscopy data in the cloud

Michael A. Cianfrocco & Andres E. Leschziner
The advent of a new generation of electron microscopes and direct electron detectors has realized the potential of single particle cryo-electron microscopy (cryo-EM) as a technique to generate high-resolution structures. Calculating these structures requires high performance computing clusters, a resource that may be limiting to many likely cryo-EM users. To address this limitation and facilitate the spread of cryo-EM, we developed a publicly available 'off-the-shelf' computing environment on Amazon's elastic cloud computing infrastructure. This environment...

Data from: Sign epistasis limits evolutionary trade-offs at the confluence of single- and multi-carbon metabolism in Methylobacterium extorquens AM1

Sean Michael Carroll, Ming-Chun Lee & Christopher James Marx
Adaptation of one set of traits is often accompanied by attenuation of traits important in other selective environments, leading to fitness trade-offs. The mechanisms that either promote or prevent the emergence of trade-offs remain largely unknown, and are difficult to discern in most systems. Here, we investigate the basis of trade-offs that emerged during experimental evolution of Methylobacterium extorquens AM1 to distinct growth substrates. After 1500 generations of adaptation to a multi-carbon substrate, succinate (S),...

Data from: Extracting spatio-temporal patterns in animal trajectories: an ecological application of sequence analysis methods

Johannes De Groeve, Nico Van De Weghe, Nathan Ranc, Tijs Neutens, Lino Ometto, Omar Rota-Stabelli & Francesca Cagnacci
Digital tracking technologies have considerably increased the amount and quality of animal trajectories, enabling the study of habitat use and habitat selection at a fine spatial and temporal scale. However, current approaches do not yet explicitly account for a key aspect of habitat use, namely the sequential variation in the use of different habitat features. To overcome this limitation, we propose a tree-based approach that makes use of sequence analysis methods, derived from molecular biology,...

Data from: The ontogeny of fairness in seven societies

Peter R. Blake, Katherine McAuliffe, John Corbit, Tara C. Callaghan, Oumar Barry, Aleah Bowie, Lauren Kleutsch, Karen L. Kramer, Elizabeth Ross, Hurnan Vongsachang, Richard Wrangham & Felix Warneken
A sense of fairness plays a critical role in supporting human cooperation. Adult norms of fair resource sharing vary widely across societies, suggesting that culture shapes the acquisition of fairness behaviour during childhood. Here we examine how fairness behaviour develops in children from seven diverse societies, testing children from 4 to 15 years of age (n = 866 pairs) in a standardized resource decision task. We measured two key aspects of fairness decisions: disadvantageous inequity...

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