224 Works

Data from: Key ornamental innovations facilitate diversification in an avian radiation

Rafael Maia, Dustin R. Rubenstein & Matthew D. Shawkey
Patterns of biodiversity are often explained by ecological processes, where traits that promote novel ways of interacting with the environment (key innovations) play a fundamental role in promoting diversification. However, sexual selection and social competition can also promote diversification through rapid evolution of ornamental traits. Because selection can operate only on existing variation, the tendency of ornamental traits to constrain or enable the production of novel phenotypes is a crucial but often overlooked aspect of...

Data from: Repeated losses of PRDM9-directed recombination despite the conservation of PRDM9 across vertebrates

Zachary Baker, Molly Schumer, Yuki Haba, Lisa Bashkirova, Chris Holland, Gil G Rosenthal & Molly Przeworski
Studies of highly diverged species have revealed two mechanisms by which meiotic recombination is directed to the genome—through PRDM9 binding or by targeting promoter-like features—that lead to dramatically different evolutionary dynamics of hotspots. Here, we identify PRDM9 orthologs from genome and transcriptome data in 225 species. We find the complete PRDM9 ortholog across distantly related vertebrates but, despite this broad conservation, infer a minimum of six partial and three complete losses. Strikingly, taxa carrying the...

Data from: Distinct neural and neuromuscular strategies underlie independent evolution of simplified advertisement calls

Elizabeth C. Leininger & Darcy B. Kelley
Independent or convergent evolution can underlie phenotypic similarity of derived behavioural characters. Determining the underlying neural and neuromuscular mechanisms sheds light on how these characters arose. One example of evolutionarily derived characters is a temporally simple advertisement call of male African clawed frogs (Xenopus) that arose at least twice independently from a more complex ancestral pattern. How did simplification occur in the vocal circuit? To distinguish shared from divergent mechanisms, we examined activity from the...

Data from: Catechol-O-Methyltransferase moderates effect of stress mindset on affect and cognition

Alia J. Crum, Modupe Akinola, Bradley P. Turnwald, Ted J. Kaptchuk & Kathryn T. Hall
There is evidence that altering stress mindset— the belief that stress is enhancing vs. debilitating —can change cognitive, affective and physiological responses to stress. However individual differences in responsiveness to stress mindset manipulations have not been explored. Given the previously established role of catecholamines in both placebo effects and stress, we hypothesized that genetic variation in catechol-O-methyltransferase (COMT), an enzyme that metabolizes catecholamines, would moderate responses to an intervention intended to alter participants’ mindsets about...

Data from: Quantifying the human impacts on Papua New Guinea reef fish communities across space and time

Joshua A. Drew, Ruth A. Hufbauer & Kathryn L. Amatangelo
Describing the drivers of species loss and of community change are important goals in both conservation and ecology. However, it is difficult to determine whether exploited species decline due to direct effects of harvesting or due to other environmental perturbations brought about by proximity to human populations. Here we quantify differences in species richness of coral reef fish communities along a human population gradient in Papua New Guinea to understand the relative impacts of fishing...

Data from: Multiple benefits of alloparental care in a fluctuating environment

Sarah Guindre-Parker & Dustin R. Rubenstein
Although cooperatively breeding vertebrates occur disproportionately in unpredictable environments, the underlying mechanism shaping this biogeographic pattern remains unclear. Cooperative breeding may buffer against harsh conditions (hard life hypothesis), or additionally allow for sustained breeding under benign conditions (temporal variability hypothesis). To distinguish between the hard life and temporal variability hypotheses, we investigated whether the number of alloparents at a nest increased reproductive success or load-lightening in superb starlings (Lamprotornis superbus), and whether these two types...

Data from: Effects of fertilizer on inorganic soil N in East Africa maize systems: vertical distributions and temporal dynamics

Katherine L. Tully, Jonathan Hickman, Madeline McKenna, Christopher Neill & Cheryl A. Palm
Fertilizer applications are poised to increase across sub-Saharan Africa (SSA), but the fate of added nitrogen (N) is largely unknown. We measured vertical distributions and temporal variations of soil inorganic N following fertilizer application in two maize (Zea mays L.)-growing regions of contrasting soil type. Fertilizer trials were established on a clayey soil in Yala, Kenya, and on a sandy soil in Tumbi, Tanzania, with application rates of 0–200 kg N/ha/yr. Soil profiles were collected...

Data from: Publication and reporting of clinical trial results: cross sectional analysis across academic medical centers

Ruijun Chen, Nihar R. Desai, Joseph S. Ross, Weiwei Zhang, Katherine H. Chau, Brian Wayda, Karthik Murugiah, Daniel Y. Lu, Amit Mittal & Harlan M. Krumholz
Objective: To determine rates of publication and reporting of results within two years for all completed clinical trials registered in ClinicalTrials.gov across leading academic medical centers in the United States. Design: Cross sectional analysis. Setting: Academic medical centers in the United States. Participants: Academic medical centers with 40 or more completed interventional trials registered on ClinicalTrials.gov. Methods: Using the Aggregate Analysis of ClinicalTrials.gov database and manual review, we identified all interventional clinical trials registered on...

Data from: Abundance-dependent effects of neighborhood dissimilarity and growth rank reversal in a Neotropical forest

Yuxin Chen, María Natalia Umaña, María Uriarte & Shixiao Yu
Why tropical forests harbor an exceptional number of species with striking differences in abundances remains an open question. We propose a theoretical framework to address this question in which rare species may have different extirpation risks depending on species ranks in tree growth and sensitivities to neighborhood interactions. To evaluate the framework, we studied tree growth and its responses to neighborhood dissimilarity (ND) in traits and phylogeny for 146 species in a Neotropical forest. We...

Data from: Etiology of respiratory tract infections in the community and clinic in Ilorin, Nigeria

Olatunji Kolawole, Michael Oguntoye, Tina Dam & Rumi Chunara
Objective: Recognizing increasing interest in community disease surveillance globally, the goal of this study was to investigate whether respiratory viruses circulating in the community may be represented through clinical (hospital) surveillance in Nigeria. Results: Children were selected via convenience sampling from communities and a tertiary care center (n = 91) during spring 2017 in Ilorin, Nigeria. Nasal swabs were collected and tested using polymerase chain reaction. The majority (79.1%) of subjects were under 6 years...

Data from: Elevated substitution rates estimated from ancient DNA sequences

Simon Y. W. Ho, Sergios-Orestis Kolokotronis, Robin G. Allaby & Simon Y.W Ho
Ancient DNA sequences are able to offer valuable insights into molecular evolutionary processes, which are not directly accessible via modern DNA. They are particularly suitable for the estimation of substitution rates because their ages provide calibrating information in phylogenetic analyses, circumventing the difficult task of choosing independent calibration points. The substitution rates obtained from such datasets have typically been high, falling between the rates estimated from pedigrees and species phylogenies. Many of these estimates have...

Variable prediction accuracy of polygenic scores within an ancestry group

Hakhamanesh Mostafavi, Arbel Harpak, Ipsita Agarwal, Dalton Conley, Jonathan Pritchard & Molly Przeworski
Fields as diverse as human genetics and sociology are increasingly using polygenic scores based on genome-wide association studies (GWAS) for phenotypic prediction. However, recent work has shown that polygenic scores have limited portability across groups of different genetic ancestries, restricting the contexts in which they can be used reliably and potentially creating serious inequities in future clinical applications. Using the UK Biobank data, we demonstrate that even within a single ancestry group (i.e., when there...

Data from: Effects of female group size on the number of males in blue monkey (Cercopithecus mitis) groups

Marina Cords & Lu Gao
The number of males per group varies substantially in group-living primates, both between and within species. In blue monkeys (Cercopithecus mitis), males may temporarily join groups during annual mating seasons when sexually receptive females are present. A likely determinant of the number of males per group is female group size (the number of adult females in a group). To clarify the role of female group size in driving variation in the number of males per...

Data from: Daily protein prioritization and longterm nutrient balancing in a dietary generalist, the blue monkey

Maressa Takahashi & Marina Cords
Animals must make dietary choices to achieve adequate nutrient intake, however it is challenging to study in the field such nutritional strategies in wild populations. We explored the nutritional strategy of a generalist social primate, the blue monkey (Cercopithecus mitis). We hypothesized that females balance the intake of nutrients, specifically non-protein energy and available protein (hereafter, protein), both on a daily and long-term basis. When balancing was not possible, we expected subjects to prioritize constant...

Data from: Vitamin D status and COVID-19 clinical outcomes in hospitalized patients

Betsy Szeto, Jason E. Zucker, Elijah D. LaSota, Mishaela R. Rubin, Marcella D. Walker, Michael T. Yin & Adi Cohen
Context: Populations severely affected by COVID-19 are also at risk for vitamin D deficiency. Common risk factors include older age, chronic illness, obesity, and non-Caucasian race. Vitamin D deficiency has been associated with risk for respiratory infections and failure, susceptibility and response to therapy for enveloped virus infection, and immune-mediated inflammatory reaction. Objective: To test the hypothesis that 25-hydroxyvitamin D[25(OH)D] deficiency is a risk factor for severity of COVID-19 respiratory and inflammatory complications. Design: We...

Data from: The COVID-19 trial finder

Yingcheng Sun, Alex Butler, Fengyang Lin, Hao Liu, Latoya Stewart, Jae Hyun Kim, Betina Ross Idnay, Qingyin Ge, Xinyi Wei, Cong Liu, Chi Yuan & Chunhua Weng
Clinical trials are the gold standard for generating reliable medical evidence, but patient search of relevant trials often suffers from information overload. With nearly 700 COVID-19 trials conducted in the United States as of August 2020, it is imperative that trial seekers can search for COVID-related clinical trials efficiently to enable rapid recruitment to these studies. We developed a web application called COVID-19 Trial Finder, which facilitates COVID-19 trial search in the United States, first...

Socioeconomic disparities in subway use and COVID-19 outcomes in New York City

Karla Therese L. Sy, Micaela E. Martinez, Benjamin Rader & Laura F. White
Using data from New York City, we found that there was an estimated 28-day lag between the onset of reduced subway use and the end of the exponential growth period of SARS-CoV-2 within New York City boroughs. We also conducted a cross-sectional analysis of the associations between human mobility (i.e., subway ridership), sociodemographic factors, and COVID-19 incidence as of April 26, 2020. Areas with lower median income, a greater percentage of individuals who identify as...

Long-term stability of cortical ensembles

Jesús Pérez-Ortega, Tzitzitlini Alejandre-García & Rafael Yuste
Neuronal ensembles, coactive groups of neurons found in spontaneous and evoked cortical activity, are causally related to memories and perception, but it still unknown how stable or flexible they are over time. We used two-photon multiplane calcium imaging to track over weeks the activity of the same pyramidal neurons in layer 2/3 of the visual cortex from awake mice and recorded their spontaneous and visually evoked responses. Less than half of the neurons were commonly...

Prenatal environmental conditions underlie alternative reproductive tactics that drive the formation of a mixed-kin cooperative society

Shailee Shah & Dustin Rubenstein
Although animal societies often evolve due to limited natal dispersal that results in kin clustering and facilitates cooperation among relatives, many species form cooperative groups with low kin structure. Such groups often comprise residents and immigrants of the same sex that compete for breeding opportunities. To understand how such mixed-kin societies form, we investigated the causes and fitness consequences of dispersal decisions in male cooperatively breeding superb starlings (Lamprotornis superbus) inhabiting a climatically unpredictable environment....

Statistical data from: Cholinergic modulation of hippocampally mediated attention and perception

Nicholas Ruiz, Monica Thieu & Mariam Aly
Attention to the relations between visual features modulates hippocampal representations. Moreover, hippocampal damage impairs discrimination of spatial relations. We explore a mechanism by which this might occur: modulation by the acetylcholine system. Acetylcholine enhances afferent input to the hippocampus and suppresses recurrent connections within it. This biases hippocampal processing toward environmental input, and should improve externally-oriented, hippocampally mediated attention and perception. We examined cholinergic modulation on an attention task that recruits the hippocampus. On each...

Social rank modulates how environmental quality influences cooperation and conflict within animal societies

Mark Liu, Bo-Fei Chen, Dustin Rubenstein & Sheng-Feng Shen
Although dominance hierarchies occur in most societies, our understanding of how these power structures influence individual investment in cooperative and competitive behaviors remains elusive. Both conflict and cooperation in animal societies are often environmentally-regulated, yet how individuals alter their cooperative and competitive investments as environmental quality changes remains unclear. Using game theoretic modeling, we predict that individuals of all ranks will invest more in cooperation and less in social conflict in harsh environments than individuals...

Lack of vulnerability segmentation among woody species in a diverse dry sclerophyll woodland community

Chris Smith-Martin, Robert Paul Skelton, Kate Johnson, Christopher Lucani & Tim Brodribb
1. Recent findings suggest that tree mortality and post-drought recovery of gas exchange can be predicted from loss of function within the water transport system. Understanding the susceptibility of plants to hydraulic damage requires knowledge about the vulnerability of different plant organs to stress-induced hydraulic dysfunction. This is particularly important in the context of vulnerability segmentation between plant tissues which is believed to protect more energetically “costly” tissues, such as woody stems, by sacrificing “cheaper”...

Data from: Stressed connections: cortisol levels following acute psychosocial stress disrupt affiliative mimicry in humans

Jonas P. Nitschke, Cecile S. Sunahara, Evan W. Carr, Piotr Winkielman, Jens C. Pruessner & Jennifer A. Bartz
Mimicry, and especially spontaneous facial mimicry, is a rudimentary element of social–emotional experience that is well-conserved across numerous species. Although such mimicry is thought to be a relatively automatic process, research indicates that contextual factors can influence mimicry, especially in humans. Here, we extend this work by investigating the effect of acute psychosocial stress on spontaneous facial mimicry. Participants performed a spontaneous facial mimicry task with facial electromyography (fEMG) at baseline and approximately one month...

Genetic Adaptation in New York City Rats

Arbel Harpak, Nandita Garud, Noah Rosenberg, Dmitri Petrov, Pleuni Pennings & Jason Munshi-South
Brown rats (Rattus norvegicus) thrive in urban environments by navigating the anthropocentric environment and taking advantage of human resources and by-products. From the human perspective, rats are a chronic problem that causes billions of dollars in damage to agriculture, health and infrastructure. Did genetic adaptation play a role in the spread of rats in cities? To approach this question, we collected whole-genome sequences from 29 brown rats from New York City (NYC) and scanned for...

Data from: Entropic bonding of the type 1 pilus from experiment and simulation

Fabiano Corsetti, Alvaro Alonso-Caballero, Simon Poly, Raul Perez-Jimenez & Emilio Artacho
The type 1 pilus is a bacterial filament consisting of a long coiled proteic chain of subunits joined together by non-covalent bonding between complementing β-strands. Its strength and structural stability are critical for its anchoring function in uropathogenic Escherichia coli bacteria. The pulling and unravelling of the FimG subunit of the pilus was recently studied by atomic force microscopy (AFM) experiments and steered molecular dynamics (SMD) simulations [A. Alonso-Caballero et al., Nature Commun. 9, 2758...

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