44 Works

Timing the SARS-CoV-2 index case in Hubei Province

Jonathan Pekar & Joel Wertheim
Understanding when SARS-CoV-2 emerged is critical to evaluating our current approach to monitoring novel zoonotic pathogens and understanding the failure of early containment and mitigation efforts for COVID-19. We employed a coalescent framework to combine retrospective molecular clock inference with forward epidemiological simulations to determine how long SARS-CoV-2 could have circulated prior to the time of the most recent common ancestor. Our results define the period between mid-October and mid-November 2019 as the plausible interval...

Response diversity in corals: hidden differences in bleaching mortality among cryptic Pocillopora species

Scott Burgess, Erika Johnston, Alex Wyatt, James Leichter & Peter Edmunds
Variation among functionally similar species in their response to environmental stress buffers ecosystems from changing states. Functionally similar species may often be cryptic species representing evolutionarily distinct genetic lineages that are morphologically indistinguishable. However, the extent to which cryptic species differ in their response to stress, and could therefore provide a source of response diversity, remains unclear because they are often not identified or are assumed to be ecologically equivalent. Here, we uncover differences in...

Data accompanying manuscript: Allometric analysis of brain cell number in Hymenoptera suggests ant brains diverge from general trends

R Keating Godfrey, Mira Swartzlander & Gronenberg Wulfila
Many comparative neurobiological studies seek to connect sensory or behavioral attributes across taxa with differences in their brain composition. Such studies can only be interpreted in a meaningful way if the general brain-body relationships are known on a larger taxonomic scale. Recent studies in vertebrates suggest cell number and density may be better correlated with behavioral ability than brain mass or volume, but few estimates of such figures exist for insects. Here we use the...

Introgressive hybridization erodes morphological divergence between lentic and lotic habitats in an endangered minnow

Henry Baker, Danielle C. Hankins & Jonathan Shurin
Introgressive hybridization may erode phenotypic divergence along environmental gradients, collapsing locally adapted populations into a hybrid swarm. Alternatively, introgression may promote phenotypic divergence by providing variation on which natural selection can act. In freshwater fishes, water flow often selects for divergent morphological traits in lake versus stream habitats. We tested the effects of introgression on lake-stream morphological divergence in the minnow Owens Tui Chub (Siphateles bicolor snyderi), which has been rendered endangered by introgression from...

Pico-phytoplankton abundance, growth and grazing rates along 110°E in the eastern Indian Ocean

Michael Landry & Selph Karen
Dilution experiments were conducted on R/V Investigator cruise IN2019v03 (17 May to 5 June 2019) on a south-to-north transect along longitude 110°E, west of Australia. Population abundances were measured by flow cytometry. Instantaneous rates of growth and grazing mortality were calculated from 2-treatment dilution incubations at six light levels.

Analysis of ancestry heterozygosity suggests that hybrid incompatibilities in threespine stickleback are environment-dependent

Ken Thompson, Catherine Peichel, Diana Rennison, Matthew McGee, Arianne Albert, Timothy Vines, Anna Greenwood, Abigail Wark, Yaniv Brandvain, Molly Schumer & Dolph Schluter
Hybrid incompatibilities occur when interactions between opposite-ancestry alleles at different loci reduce the fitness of hybrids. Most work on incompatibilities has focused on those that are 'intrinsic', meaning they affect viability and sterility in the laboratory. Theory predicts that ecological selection can also underlie hybrid incompatibilities, but tests of this hypothesis using sequence data are scarce. In this article, we compiled genetic data for F2 hybrid crosses between divergent populations of threespine stickleback fish (Gasterosteus...

Efficient light‐harvesting of mesophotic corals is facilitated by coral optical traits

Netanel Kramer, Raz Tamir, Or Ben Zvi, Steven Jacques, Yossi Loya & Daniel Wangpraseurt
Sustained light-dependent coral reef communities can be found at a wide range of light environments, extending from the sea level to as deep as 150 m (i.e., mesophotic). How mesophotic corals thrive despite extremely limited light conditions still requires further investigation. Here, we undertook a comprehensive ecophysiological and bio-optical study on four depth-generalist coral species aiming to delineate the functional role that optical trait-properties have in light-harvesting, at contrasting light regimes. We show that the...

Drivers and projections of global surface temperature anomalies at the local scale

Susanne Benz, Steven Davis & Jennifer Burney
More than half of the world’s population now lives in urban areas, and trends in rural-to-urban migration are expected to continue through the end of the century. Although cities create efficiencies that drive innovation and economic growth, they also alter the local surface energy balance, resulting in urban temperatures that can differ dramatically from surrounding areas. Here we introduce a global 1-km resolution data set of seasonal and diurnal anomalies in urban surface temperatures relative...

Mapfile and ASV table of whole-body and shell-surface samples from geminate species of gastropods separated by the Isthmus of Panama

Alexander Neu
The rise of the Isthmus of Panama ~3.5 mya separated populations of many marine organisms, which then diverged into new geminate sister species currently living in the Eastern Pacific Ocean and Caribbean Sea. However, we know very little about how such evolutionary divergences of host species have shaped their microbiomes. Here, we compared the microbiomes of whole-body and shell-surface samples of geminate species of marine gastropods in the genera Cerithiumand Cerithideopsis to those of congeneric...

Supplementary data for: Reproductive deficits induced by prenatal anti-Mullerian hormone exposure require androgen receptor in kisspeptin cells

Karen Tonsfeldt, Emily Ho, Chengxian Shi, Michelle He, Ryan Nguyen, Genevieve Ryan & Pamela Mellon
Polycystic ovary syndrome (PCOS) is a common reproductive disorder characterized by elevated androgens and anti-Mullerian hormone (AMH). These hormones remain elevated throughout pregnancy, and potential effects of hormone exposure on offspring from women with PCOS remain largely unexplored. Expanding on recent reports of prenatal AMH exposure in mice, we have fully characterized the reproductive consequences of prenatal AMH (pAMH) exposure throughout the lifespan of first- and second-generation offspring of both sexes. We also sought to...

Genesis locations of the costliest atmospheric rivers impacting the Western United States (insurance claim data)

Hamish Prince
Atmospheric rivers (ARs) are responsible for the vast majority (approximately 88%) of flood damage in the Western U.S, an annual average of USD$1.1 billion. Here, using historical flood insurance data, we investigate the genesis characteristics of damaging ARs in the Western U.S. ARs exceeding USD$20 million in damage (90th percentile), are shown to travel further across the Pacific Ocean, with median genesis locations 8° to 27° further westward compared to typical ARs. Identifying regions of...

Data from: Chimpanzees behave prosocially in a group-specific manner

Edwin J. C. Van Leeuwen, Sarah E. DeTroy, Stephan P. Kaufhold, Clara Dubois, Sebastian Schütte, Josep Call & Daniel B. M. Haun
Chimpanzees act cooperatively in the wild, but whether they afford benefits to others, and whether their tendency to act prosocially varies across communities is unclear. Here, we show that chimpanzees from neighboring communities provide valuable resources to group members at personal cost, and that the magnitude of their prosocial behavior is group specific. Provided with a resource-donation experiment allowing for free (partner) choice, we observed an increase in prosocial acts across the study period in...

Amplicon sequence variant tables of Donax gouldii microbiomes from Scripps Pier, La Jolla, CA, USA

Alexander Neu
Predicting how populations and communities of organisms will respond to anthropogenic change is of paramount concern in ecology today. For communities of microorganisms, however, these predictions remain challenging, primarily due to data limitations. Information about long-term dynamics of host-associated microbial communities, in particular, are lacking. In this study, we use well-preserved and freshly collected samples of soft tissue from a marine bivalve host, Donax gouldii, at a single site to quantify the diversity and composition...

Antimicrobials from a feline skin commensal bacterium inhibit skin colonization and infection by drug-resistant S. pseudintermedius

Alan O'Neill
Methicillin-resistant Staphylococcus pseudintermedius (MRSP) is an important emerging zoonotic pathogen that causes severe skin infections. To combat infections from drug-resistant bacteria, the transplantation of commensal antimicrobial bacteria as a therapeutic has shown clinical promise. We screened a collection of diverse staphylococcus species from domestic dogs and cats for antimicrobial activity against MRSP. A unique strain (S. felis C4) was isolated from feline skin that inhibited MRSP and multiple gram-positive pathogens. Competition experiments in mice showed...

Data from: Precisely timed theta oscillations are selectively required during the encoding phase of memory

Stefan Leutgeb, Jill K Leutgeb, Clare R Quirk, Ipshita Zutshi, Sunandha Srikanth, Maylin L Fu, Naomie Devico Marciano, Morgan K Wright, Darian F Parsey, Stanley Liu, Rachel E Siretskiy & Tiffany L Huynh
Brain oscillations have been hypothesized to support cognitive function by coordinating spike timing within and across brain regions, yet it is often not known when timing is either critical for neural computations or an epiphenomenon. The entorhinal cortex and hippocampus are necessary for learning and memory and exhibit prominent theta oscillations (6–9 Hz), which are controlled by pacemaker cells in the medial septal area. Here we show that entorhinal and hippocampal neuronal activity patterns were...

Lipid mediators detected in COVID-19 patients and healthy controls

Cindy McReynolds, Irene Cortes_Puch, Resmi Ravindran, Imran Khan, Pei-An Betty Shih, Bruce D. Hammock, Jun Yang & Bruce G. Hammock
Polyunsaturated fatty acids are metabolized into regulatory lipids important for initiating inflammatory responses in the event of disease or injury and for signaling the resolution of inflammation and return to homeostasis. The epoxides of linoleic acid (leukotoxins) regulate skin barrier function, perivascular and alveolar permeability and have been associated with poor outcomes in burn patients and in sepsis. It was later reported that blocking metabolism of leukotoxins into the vicinal diols ameliorated the deleterious effects...

Iron sulfides and anomalous electrical resistivity in cratonic environments: electrical resistivity data set

Anne Pommier
The interpretation of low-resistivity anomalies in the lithospheric mantle of several cratonic regions has invoked hydrogen, or connected networks of graphite with iron-rich silicates, and/or metal sulfides. Electrical laboratory measurements are a powerful approach for exploring these alternatives. We report electrical measurements of two xenoliths (pyroxenite and dunite) from Tanzania; two metal sulfides (FeS and Fe-S-Ni); and several mixtures of metal sulfides (3.4–18.2 vol.%) with xenolith. A multi- anvil press was employed to maintain a...

Data from: Coupling between motor cortex and striatum increases during sleep over long-term skill learning

Stefan Lemke, Dhakshin Ramanathan, David Darevsky, Dan Egert, Josh Berke & Karunesh Ganguly
The strength of cortical connectivity to the striatum influences the balance between behavioral variability and stability. Learning to consistently produce a skilled action requires plasticity in corticostriatal connectivity associated with repeated training of the action. However, it remains unknown whether such corticostriatal plasticity occurs during training itself or “offline” during time away from training, such as sleep. Here, we monitor the corticostriatal network throughout long-term skill learning in rats and find that non-REM (NREM) sleep...

Data from: Ultra-slow oscillations in fMRI and resting-state connectivity: Neuronal and vascular contributions and technical confounds

Kevin Turner, Patrick Drew, Céline Matéo, David Kleinfeld & Yu Xin
Ultra-slow, ~0.1-Hz variations in the oxygenation level of brain blood are widely used as an fMRI-based surrogate of ‘‘resting-state’’ neuronal activity. The temporal correlations among these fluctuations across the brain are interpreted as ‘‘functional connections’’ for maps and neurological diagnostics. Ultra-slow variations in oxygenation follow a cascade. First, they closely track changes in arteriole diameter. Second, interpretable functional connections arise when the ultra-slow changes in amplitude of g-band neuronal oscillations, which are shared across even...

Growth hormone pulses are differentially regulated by the circadian clock gene Bmal1

Erica Schoeller, Karen Tonsfeldt, McKenna Sinkovich, Ruijing Shi & Pamela Mellon
In this study, we found that loss of the circadian clock gene Bmal1 causes disruptions throughout the growth hormone (GH) axis, from hepatic gene expression to production of urinary pheromones and pheromone-dependent behavior. First, we show that Bmal1 knockout (KO) males elicit reduced aggressive responses from WT males and secrete lower levels of major urinary proteins (MUPs); however, we also found that a liver-specific KO of Bmal1 (Liver-Bmal1-KO) produces a similar reduction in MUP secretion...

Data-driven versus consensus diagnosis of MCI: enhanced sensitivity for detection of dementia progression, biomarker status, and neuropathological outcomes

Emily Edmonds, Denis Smirnov, Kelsey Thomas, Lisa Graves, Katherine Bangen, Lisa Delano-Wood, Douglas Galasko, David Salmon & Mark Bondi
Objective: Given prior work demonstrating that mild cognitive impairment (MCI) can be empirically differentiated into meaningful cognitive subtypes, we applied actuarial methods to comprehensive neuropsychological data from the University of California San Diego (UCSD) Alzheimer’s Disease Research Center (ADRC) in order to identify cognitive subgroups within nondemented ADRC participants, and to examine cognitive, biomarker, and neuropathological trajectories. Methods: Cluster analysis was performed on baseline neuropsychological data (n=738; mean age=71.8). Survival analysis examined progression to dementia...

Heterogeneity in the Dynamic Effects of Uncertainty on Investment

Sungje Byun & Soojin Jo
How does aggregate profit uncertainty influence investment activity at the firm level? We propose a parsimonious adaptation of a factor-autoregressive conditional heteroscedasticity model to exploit information in a subindustry sales panel for an efficient and tractable estimation of aggregate volatility. The resulting uncertainty measure is then included in an investment forecasting model interacted with firm-specific coefficients. We find that higher profit uncertainty induces firms to lower capital expenditure on average, yet to a considerably different...

Reinforcement learning links spontaneous dopamine transients to reward

Conrad Foo
In their pioneering study on dopamine release, Romo and Schultz speculated "... that the amount of dopamine released by unmodulated spontaneous impulse activity exerts a tonic, permissive influence on neuronal processes more actively engaged in preparation of self-initiated movements, ...". Motivated by the suggestion of "spontaneous impulses", we asked two questions. First, are there spontaneous impulses of dopamine that are released in cortex? This possibility is further motivated by the "ramp up" of dopaminergic neuronal...

Data from : Soil pH determines bacterial distribution and assembly processes in natural mountain forests of eastern China

Yingying Ni, Teng Yang, Yuying Ma, Kaoping Zhang, Pamela Soltis, Douglas Soltis, Jack Gilbert, Yunpeng Zhao, Chengxin Fu & Haiyan Chu
Aim: There have been numerous studies of forest-soil microbial biogeography, but an integrated view of edaphic factors, plant, climatic factors, and geographic distance in determining the variation of bacterial community and assembly processes remains unclear at large spatial scales. Here, we analyzed the factors affecting the biogeographic pattern and assembly processes of soil bacterial communities under 58 tree species in five natural mountain forests. Location: Eastern China. Major taxa studied: Bacterial communities. Methods: Hierarchical partitioning...

Mutualism-enhancing mutations dominate early adaptation in a two-species microbial community

Sandeep Venkataram, Huanyu Kuo, Erik Hom & Sergey Kryazhimskiy
Species interactions drive evolution while evolution shapes these interactions. The resulting eco-evolutionary dynamics, their outcomes and their repeatability depend on how adaptive mutations available to community members affect fitness and ecologically relevant traits. However, the diversity of adaptive mutations is not well characterized, and we do not know how this diversity is affected by the ecological milieu. Here we use barcode lineage tracking to address this gap in a net commensal relationship that contains both...

Registration Year

  • 2021

Resource Types

  • Dataset
  • Output Management Plan
  • Text


  • University of California, San Diego
  • University of Washington
  • Stanford University
  • University of Cambridge
  • Texas A&M University
  • Harvard University
  • Harvard Medical School
  • Brigham and Women's Hospital
  • Emory University School of Medicine
  • Massachusetts General Hospital