53 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: 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)...

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...

Respiratory virus shedding in exhaled breath and efficacy of face masks

Nancy H. L. Leung, Daniel K. W. Chu, Eunice Y. C. Shiu, Kwok-Hung Chan, James J. McDevitt, Benien J. P. Hau, Hui-Ling Yen, Yuguo Li, Dennis K. M. Ip, J. S. Malik Peiris, Wing-Hong Seto, Gabriel M. Leung, Donald K. Milton & Benjamin J. Cowling
We identified seasonal human coronaviruses, influenza viruses and rhinoviruses in the exhaled breath and coughs of children and adults with acute respiratory illness. Surgical face masks significantly reduced detection of influenza virus RNA in respiratory droplets and coronavirus RNA in aerosols, with a marginally significant reduction in coronavirus RNA in respiratory droplets. Our results indicate that surgical facemasks could prevent transmission of human coronaviruses and influenza viruses from symptomatic individuals.

Data from: Combining experimental evolution and genomics to understand how seed beetles adapt to a marginal host plant

Zachariah Gompert, Alexandre Rego, Samridhi Chaturvedi, Alexandra Lish, Caroline Barton, Karen Kapheim & Frank Messina
Genes that affect adaptive traits have been identified, but our knowledge of the genetic basis of adaptation in a more general sense (across multiple traits) remains limited. We combined population-genomic analyses of evolve and resequence experiments, genome-wide association mapping of performance traits, and analyses of gene expression to fill this knowledge gap, and shed light on the genomics of adaptation to a marginal host (lentil) by the seed beetle Callosobruchus maculatus. Using population-genomic approaches, we...

Association of caffeine and related analytes with resistance to Parkinson’s disease among LRRK2 mutation carriers: a metabolomic study

Grace F Crotty, Romeo Maciuca, Eric A Macklin, Junhua Wang, Manuel Montalban, Sonnet S. Davis, Jamal I Alkabsh, Rachit Bakshi, Xiqun Chen, Alberto Ascherio, Giuseppe Astarita, Sarah Huntwork-Rodriguez & Michael A Schwarzschild
Objective: To identify markers of resistance to developing Parkinson’s disease (PD) among LRRK2 mutation (LRRK2+) carriers, we carried out metabolomic profiling in individuals with PD and unaffected controls (UC), with and without the LRRK2 mutation. Methods: Plasma from 368 PD and UC subjects in the LRRK2 Cohort Consortium (LCC), comprising 118 LRRK2+/PD+, 115 LRRK2+/UC, 70 LRRK2-/PD+ and 65 LRRK2-/UC, and CSF available from 68 of them were analyzed by liquid chromatography with mass spectrometry. For...

Risk of hemorrhagic and ischemic stroke in patients with Alzheimer disease: A synthesis of the literature

Reem Waziry, Lori B Chibnik, Daniel Bos, M Kamran Ikram & Hofman Albert
Objective To assess the risk of hemorrhagic and ischemic stroke in patients with Alzheimer disease (AD) compared to non-AD subjects with similar risk profiles. Methods A search was conducted on Embase and Medline for reports published up to September 26, 2018. Studies were included if they: 1) assessed incidence of stroke in patients diagnosed with AD; 2) included patients with no history of stroke; and 3) reported outcomes by stroke subtype. The main outcome was...

Data from: Evolutionary trade-offs in the chemical defense of floral and fruit tissues across genus Cornus

Chase M. Mason, Danielle R. De La Pascua, Corrinne Smith-Winterscheidt, Jordan A. Dowell & Eric W. Goolsby
Premise of the study Defense investment in plant reproductive structures is relatively understudied compared to the defense of vegetative organs. Here the evolution of chemical defenses in reproductive structures is examined in light of the optimal defense, apparency, and resource availability hypotheses within the genus Cornus using a phylogenetic comparative approach in relation to phenology and native habitat environmental data. Methods Individuals representing 25 Cornus species were tracked for reproductive phenology over a full growing...

Variation in mouse pelvic morphology maps to locations enriched in Sox9 Class II and Pitx1 regulatory features

Charles Roseman, Terrence Capellini, Evelyn Jagoda, Scott Williams, Mark Grabowski, Christine O'Connor, John Polk & James Cheverud
Variation in pelvic morphology has a complex genetic basis and its patterning and specification is governed by conserved developmental pathways. Whether the mechanisms underlying the differentiation and specification of the pelvis also produce the morphological covariation on which natural selection may act is still an open question in evolutionary developmental biology. We use high-resolution Quantitative Trait Locus (QTL) mapping in the F34 generation of an advanced intercross experiment (LG,SM-G34) to characterize the genetic architecture of...

Phylogeographic and phenotypic outcomes of brown anole colonization across the Caribbean provide insight into the beginning stages of an adaptive radiation

Jason J. Kolbe, Richard E. Glor, Marta López‐Darias, C. Verónica Gómez Pourroy, Alexis S. Harrison, Kevin De Queiroz, Liam J. Revell, Jonathan B. Losos & Robert Graham Reynolds
Some of the most important insights into the ecological and evolutionary processes of diversification and speciation have come from studies of island adaptive radiations, yet relatively little research has examined how these radiations initiate. We suggest that Anolis sagrei is a candidate for understanding the origins of the Caribbean Anolis adaptive radiation and how a colonizing anole species begins to undergo allopatric diversification, phenotypic divergence and, potentially, speciation. We undertook a genomic and morphological analysis...

No state change in pelagic fish production and biodiversity during the Eocene-Oligocene Transition

Elizabeth Sibert, Michelle Zill, Ella Frigyik & Richard Norris
The Eocene-Oligocene (E/O) boundary ~33.9 million years ago, has been described as a state change in the Earth system marked by the permanent glaciation of Antarctica and a proposed increase in oceanic productivity. Here we quantified the response of fish production and biodiversity to this event using microfossil fish teeth (ichthyoliths) in seven deep-sea sediment cores from around the world. Ichthyolith accumulation rate (a proxy for fish biomass production) shows no synchronous trends across the...

Allometric escape from acoustic constraints in frog calls is rare

Joao Filipe Tonini, Diogo Provete, Natan Maciel, Alessandro Morais, Sandra Goutte, Felipe Toledo & R. Alexander Pyron
Allometric constraint is a product of natural selection, particularly with respect to body size and traits constrained by physical properties thereof, such as metabolism, longevity, and vocal frequency. Parameters describing allometric relationships are conserved across most lineages, indicating that physical constraints dictate scaling patterns in deep time, despite substantial genetic and ecological divergence among organisms. Acoustic allometry (sound frequency ~ body size) is conserved across frogs, in defiance of massive variation in both body size...

Data from: The multispecies coalescent model outperforms concatenation across diverse phylogenomic

Xiaodong Jiang, Scott Edwards & Liang Liu
A statistical framework of model comparison and model validation is essential to resolving the debates over concatenation and coalescent models in phylogenomic data analysis. A set of statistical tests are here applied and developed to evaluate and compare the adequacy of substitution, concatenation, and multispecies coalescent (MSC) models across 47 phylogenomic data sets collected across tree of life. Tests for substitution models and the concatenation assumption of topologically concordant gene trees suggest that a poor...

Data from: Longer development provides first‐feeding fish time to escape hydrodynamic constraints

Terry R. Dial & George V. Lauder
What is the functional effect of prolonged development? By controlling for size, we quantify first‐feeding performance and hydrodynamics of zebrafish and guppy offspring (5 ± 0.5 mm in length), which differ fivefold in developmental time and twofold in ontogenetic state. By manipulating water viscosity, we control the hydrodynamic regime, measured as Reynolds number. We predicted that if feeding performance were strictly the result of hydrodynamics, and not development, feeding performance would scale with Reynolds number....

Pleistocene persistence and expansion in tarantulas on the Colorado Plateau and the effects of missing data on phylogeographical inferences from RADseq

Matthew Graham, Carlos Santibanez-Lopez, Shahan Derkarabetian, Brent Hendrixson & Carlos Santibáñez-López
Few phylogeographical studies exist for taxa inhabiting the Colorado Plateau province. We combined mitochondrial and genomic data with species distribution modeling to test Pleistocene hypotheses for Aphonopelma marxi, a large tarantula endemic to the plateau region. Mitochondrial and genomic analyses revealed that the species comprises at least three main clades that diverged in the Pleistocene. A clade distributed along the Mogollon Rim appears to have persisted in place during the last glacial maximum, whereas the...

Mechanics of walking and running up and downhill: A joint-level perspective to guide design of lower-limb exoskeletons

Richard Nuckols, Kota Takahashi, Dominic Farris, Sarai Mizrachi, Raziel Riemer & Gregory Sawicki
Lower-limb wearable robotic devices can improve clinical gait and reduce energetic demand in healthy populations. To help enable real-world use, we sought to examine how assistance should be applied in variable gait conditions and suggest an approach derived from knowledge of human locomotion mechanics to establish a ‘roadmap’ for wearable robot design. We characterized the changes in joint mechanics during walking and running across a range of incline/decline grades and then provide an analysis that...

Registration Year

  • 2020

Resource Types

  • Dataset


  • Harvard University
  • Stanford University
  • University of Minnesota
  • University of British Columbia
  • University of New Mexico
  • Tufts University
  • University of Kansas
  • Massachusetts General Hospital
  • Utah State University
  • Duke University