73 Works

Respiratory medium and circulatory anatomy constrain size evolution in marine macrofauna

Noel Heim, Saket Bakshi, Loc Buu, Stephanie Chen, Shannon Heh, Ashli Jain, Christopher Noll, Ameya Patkar, Noah Rizk, Sriram Sundararajan, Isabella Villante, Matthew Knope & Jonathan Payne
The typical marine animal has increased in biovolume by more than two orders of magnitude since the beginning of the Cambrian, but the causes of this trend remain unknown. We test the hypothesis that the efficiency of intra-organism oxygen delivery is a major constraint on body size evolution in marine animals. To test this hypothesis, we compiled a dataset comprising 13,723 marine animal genera spanning the Phanerozoic. We coded each genus according to its respiratory...

Lymph node metastases develop through a wider evolutionary bottleneck than distant metastases

Johannes Reiter, Wei-Ting Hung, I-Hsiu Lee, Shriya Nagpal, Peter Giunta, Sebastian Degner, Gang Liu, Emma Wassenaar, William Jeck, Martin Taylor, Alexander Farahani, Hetal Marble, Simon Knott, Onno Kranenburg, Jochen Lennerz & Kamila Naxerova
Genetic diversity among metastases is poorly understood but contains important information about disease evolution at secondary sites. Here we investigate inter- and intra-lesion heterogeneity for two types of metastases that associate with different clinical outcomes: lymph node and distant organ metastases in human colorectal cancer. We develop a rigorous mathematical framework for quantifying metastatic phylogenetic diversity. Distant metastases are typically monophyletic and genetically similar to each other. Lymph node metastases, in contrast, display high levels...

Rethinking megafauna

Marcos Moleón, José Sánchez-Zapata, José Donázar, Eloy Revilla, Berta Martín-López, Cayetano Gutiérrez-Cánovas, Wayne Getz, Zebensui Morales-Reyes, Ahimsa Campos-Arceiz, Larry Crowder, Mauro Galetti, Manuela González-Suárez, Fengzhi He, Pedro Jordano, Rebecca Lewison, Robin Naidoo, Norman Owen-Smith, Nuria Selva, Jens-Christian Svenning, José Tella, Christiane Zarfl, Sonja Jähnig, Matt Hayward, Søren Faurby, Nuria García … & Klement Tochner
Concern for megafauna is increasing among scientists and non-scientists. Many studies have emphasized that megafauna play prominent ecological roles and provide important ecosystem services to humanity. But, what precisely are “megafauna”? Here we critically assess the concept of megafauna and propose a goal-oriented framework for megafaunal research. First, we review definitions of megafauna and analyze associated terminology in the scientific literature. Second, we conduct a survey among ecologists and paleontologists to assess the species traits...

A human IgSF cell-surface interactome reveals a complex network of protein-protein interactions

Woj Wojtowicz, Jost Vielmetter, Ricardo Fernandes, Dirk Siepe, Catharine Eastman, Gregory Chisholm, Sarah Cox, Heath Klock, Paul Anderson, Sarah Rue, Jessica Miller, Scott Glaser, Melisa Bragstad, Julie Vance, Annie Lam, Scott Lesley, Kai Zinn & Christopher Garcia
Cell-surface protein-protein interactions (PPIs) mediate cell-cell communication, recognition and responses. We executed an interactome screen of 564 human cell-surface and secreted proteins, most of which are immunoglobulin superfamily (IgSF) proteins, using a high-throughput, automated ELISA-based screening platform employing a pooled-protein strategy to test all 318,096 PPI combinations. Screen results, augmented by phylogenetic homology analysis, revealed ~380 previously unreported PPIs. We validated a subset using surface plasmon resonance and cell binding assays. Observed PPIs reveal a...

Data from: Solute Production and Transport Processes in Chinese Monsoonal Rivers: Implications for Global Climate Change

Jun Zhong, Si-Liang Li, Daniel E. Ibarra, Hu Ding & Cong-Qiang Liu
Concentration-discharge (C-Q) relationships provide new insights into solute production processes. Temporal sampling and analyses are needed to investigate the chemical weathering behaviors and reduce the estimation errors of fluxes. But few studies have been done in Asian monsoonal rivers, which play an important role in global carbon cycle. We analyzed the dissolved solutes of Three largest rivers in China. Datong and Qingxi in Changjiang River were selected to represent the midterm and outlet of the...

Land use impacts poison frog chemical defenses through changes in leaf litter ant communities

Nora Moskowitz, Lauren O'Connell, David Donoso, Luis Coloma, Sunia Trauger, Eva Fischer, , , Charles Vidoudez, Olivia Nieves, Tammy Fay & Barbara Dorritie
Much of the world’s biodiversity is held within tropical rainforests, which are increasingly fragmented by agricultural practices. In these threatened landscapes, there are many organisms that acquire chemical defenses from their diet and are therefore intimately connected with their local food webs. Poison frogs (Family Dendrobatidae) are one such example, as they acquire alkaloid-based chemical defenses from their diet of leaf litter ants and mites. It is currently unknown how habitat fragmentation impacts chemical defense...

Data for: Landscape scale variation in the hydrologic niche of California coast redwood

Emily J. Francis, Gregory P. Asner, Katharine J. Mach & Christopher B. Field
Topoclimatic diversity within forest landscapes can underlie variation in water availability, which may correspond to patterns in habitat suitability of tree species with differing hydrologic niches. However, the trade-off between the collection of data at a fine grain size over large spatial extents has limited comprehensive analyses of landscape scale variation in habitat suitability. We present a fine scale analysis of the roles of topographic gradients in moisture availability, soil water storage, and fog frequency...

Distinct DNA methylation signatures in neuroendocrine tumors specific for primary site and inherited predisposition

Amit Tirosh, Jonathan Keith Killian, David Petersen, Yuelin Jack Zhu, Robert L Walker, Jenny E Blau, Naris Nilubol, Dhaval Patel, Sunita K Agarwal, Lee Scott Weinstein, Paul Meltzer & Electron Kebebew
Purpose: To compare the deoxyribonucleic acid (DNA) methylation signature of neuroendocrine tumors (NETs) by primary tumor site and inherited predisposition syndromes von Hippel–Lindau disease (VHL) and multiple endocrine neoplasia type 1 (MEN1). Methods Genome-wide DNA methylation (835 424 CpGs) of 96 NET samples. Principal components analysis (PCA) and unsupervised hierarchical clustering analyses were used to determine DNA methylome signatures. Results: Hypomethylated CpGs were significantly more common in VHL-related versus sporadic and MEN1-related NETs (P <...

Data from: Fate of internal waves on a shallow shelf

Kristen Davis, Robert Arthur, Emma Reid, Thomas DeCarlo, Anne Cohen, Oliver Fringer & Justin Rogers
Internal waves strongly influence the physical and chemical environment of coastal ecosystems worldwide. We report novel observations from a distributed temperature sensing (DTS) system that tracked the transformation of internal waves from the shelf break to the surf zone over a narrow shelf-slope region in the South China Sea. The spatially-continuous view of temperature fields provides a perspective of physical processes commonly available only in laboratory settings or numerical models, including internal wave reflection off...

Footprints of local adaptation span hundreds of linked genes in the Atlantic silverside genome

Aryn Wilder, Stephen Palumbi, David Conover & Nina Overgaard Therkildsen
The study of local adaptation in the presence of ongoing gene flow is the study of natural selection in action, revealing the functional genetic diversity most relevant to contemporary pressures. In addition to individual genes, genome-wide architecture can itself evolve to enable adaptation. Distributed across a steep thermal gradient along the east coast of North America, Atlantic silversides (Menidia menidia) exhibit an extraordinary degree of local adaptation in a suite of traits, and the capacity...

The evolutionary dynamics and fitness landscape of clonal hematopoiesis

Caroline J. Watson, A.L. Papula, Gladys Y.P. Poon, Wing H. Wong, Andrew L. Young, Todd E. Druley, Daniel S. Fisher & Jamie R. Blundell
Somatic mutations acquired in healthy tissues as we age are major determinants of cancer risk. Whether variants confer a fitness advantage or rise to detectable frequencies by change remains largely unknown. Blood sequencing data from ∼50,000 individuals reveals how mutation, genetic drift and fitness shape the genetic diversity of healthy blood (clonal hematopoiesis). We show that positive selection, not drift, is the major force shaping clonal hematopoiesis, provide bounds on the number of hematopoietic stem...

Comprehensive investigation of circulating biomarkers and their causal role in atherosclerosis-related risk factors and clinical events

Daniela Zanetti
Background: Circulating biomarkers have been previously associated with atherosclerosis-related risk factors, but the nature of these associations is incompletely understood. Methods: We performed multivariable-adjusted regressions and 2-sample Mendelian randomization analyses to assess observational and causal associations of 27 circulating biomarkers with 7 cardiovascular traits in up to 451 933 participants of the UK Biobank. Results: After multiple-testing correction (alpha=1.3Å~10−4), we found a total of 15, 9, 21, 22, 26, 24, and 26 biomarkers strongly associated...

Amyloid PET imaging in self-identified non-Hispanic Blacks from the Anti-Amyloid in Asymptomatic Alzheimer’s Disease (A4) Study – Supplementary Data

Kacie Deters, Valerio Napolioni, Reisa Sperling, Gabriel Kennedy, Michael Greicius, Richard Mayeux, Timothy Hohman & Elizabeth Mormino
The goal of the manuscript was to examine whether amyloid PET in CN individuals that were screened for the Anti-Amyloid in Asymptomatic AD (A4) study differed across self-identified, non-Hispanic White and Black (NHW and NHB) groups. We examined 3685 NHW and 144 NHB that passed initial screening for the A4 study and underwent amyloid PET. The effect of race on amyloid PET was examined using logistic (dichotomous groups) and linear (continuous values) regression controlling for...

Data and R code for: An experimental approach to assessing the impact of ecosystem engineers on biodiversity and ecosystem functions

Gianalberto Losapio, Bernhard Schmid, Jordi Bascompte, Richard Michalet, Pierfilippo Cerretti, Christoph Germann, Jean-Paul Haenni, Rainer Neumeyer, Francisco Javier Ortiz-Sánchez, Adrian C Pont, Pascal Rousse, Jürg Schmid, Daniele Sommaggio & Christian Schöb
Plants acting as ecosystem engineers create habitats and facilitate biodiversity maintenance within plant communities. Furthermore, biodiversity research has demonstrated that plant diversity enhances the productivity and functioning of ecosystems. However, these two fields of research developed in parallel and independent from one another, with the consequence that little is known about the role of ecosystem engineers in the relationship between biodiversity and ecosystem functioning across trophic levels. Here, we present an experimental framework to study...

Hormonal and neural correlates of care in active versus observing poison frog parents

Eva K. Fischer & Lauren A. O'Connell
The occasional reversal of sex-typical behavior suggests that many of the neural circuits underlying behavior are conserved between males and females and can be activated in response to the appropriate social condition or stimulus. Most poison frog species (Family Dendrobatidae) exhibit male uniparental care, but flexible compensation has been observed in some species, where females will take over parental care duties when males disappear. We investigated hormonal and neural correlates of sex-typical and sex-reversed parental...

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: The effects of ground-irregularity-cancelling prosthesis control on balance over uneven surfaces

Vincent Chiu, Alexandra Voloshina & Steven Collins
Over half of individuals with a lower-limb amputation are unable to walk on uneven terrain. Using a prosthesis emulator system, we developed an irregularity-cancelling controller intended to reduce the effect of disturbances resulting from uneven surfaces. This controller functions by changing the neutral angles of two forefoot digits in response to local terrain heights. To isolate the effects of the controller, we also programmed a spring-like controller that maintained fixed neutral angles. Five participants with...

Maps of northern peatland extent, depth, carbon storage and nitrogen storage

Gustaf Hugelius, Julie Loisel, Sarah Chadburn, Robert B. Jackson, Miriam Jones, Glen MacDonald, Maija Marushchak, David Olefeldt, Maara Packalen, Matthias B. Siewert, Claire Treat, Merritt Turestsky, Carolina Voigt & Zicheng Yu
This dataset is grids of peatland extent, peat depth, peatland organic carbon storage, peatland total nitrogen storage and approximate extent of ombrotrophic/minerotrophic peatlands. The grids are geotiff files in 10 km pixel resolution projected in the World Azimuthal Equidistant projection. Note that the peat depth grid shows potential peat depth everywhere,also where there is no peatland cover. For files on peatland organic carbon, total nitrogen extent and extent of ombrotrophic/minerotrophic peatlands, there are separate files...

Data from: Gene expression correlates of social evolution in coral reef butterflyfishes

Jessica Nowicki, Morgan Pratchett, Stefan Walker, Darren Coker & Lauren O'Connell
Animals display remarkable variation in social behavior. However, outside of rodents, little is known about the neural mechanisms of social variation, and whether they are shared across species and sexes, limiting our understanding of how sociality evolves. Using coral reef butterflyfishes, we examined gene expression correlates of social variation (i.e., pair bonding vs. solitary living) within and between species and sexes. In several brain regions, we quantified gene expression of receptors important for social variation...

Bio-optical Database of the Arctic Ocean

Kate Lewis, Gert Van Dijken & Kevin Arrigo
The Arctic bio-optical database assembles a diverse suite of biological and optical data from 34 expeditions throughout the Arctic Ocean. Data combined into a single AO database following the OBPG criteria (Pegau et al. 2003), as was done in the development of the global NASA Bio-optical Marine Algorithm Data Set (NOMAD) (Werdell 2005, Werdell & Bailey 2005). This Arctic database combines coincident in situ observations of IOPs, apparent optical properties (AOPs), Chl a, environmental data...

Versatile simulations of admixture and accurate local ancestry inference with mixnmatch and ancestryinfer

Molly Schumer, Daniel Powell & Russell Corbett-Detig
It is now clear that hybridization between species is much more common than previously recognized. As a result, we now know that the genomes of many modern species, including our own, are a patchwork of regions derived from past hybridization events. Increasingly researchers are interested in disentangling which regions of the genome originated from each parental species using local ancestry inference methods. Due to the diverse effects of admixture, this interest is shared across disparate...

Raw images of targeted gearshifting in actin-based active nematic liquid crystals

Steven Redford, Rui Zhang, Paul Ruijgrok, Nitin Kumar, Ali Mozaffari, Sasha Zemsky, Aaron Dinner, Vincenzo Vitelli, Zev Bryant, Margaret Gardel & Juan De Pablo
Active materials are capable of converting free energy into mechanical work to produce autonomous motion, and exhibit striking collective dynamics that biology relies on for essential functions. Controlling those dynamics and transport in synthetic systems has been particularly challenging. Here, we introduce the concept of spatially structured activity as a means to control and manipulate transport in active nematic liquid crystals consisting of actin filaments and light-sensitive myosin motors. Simulations and experiments are used to...

Landscape simplification increases vineyard pest outbreaks and insecticide use

Daniel Paredes, Jay Rosenheim, Rebecca Chaplin-Kramer, Silvia Winter & Daniel Karp
Diversifying agricultural landscapes may mitigate biodiversity declines and improve pest management. Yet landscapes are rarely managed to suppress pests, in part because researchers seldom measure key variables related to pest outbreaks and insecticides that drive management decisions. We used a 13-year government database to analyze landscape effects on European grapevine moth (Lobesia botrana) outbreaks and insecticides across ~400 Spanish vineyards. At harvest, we found pest outbreaks increased four-fold in simplified, vineyard-dominated landscapes compared to complex...

Analysis of measles-mumps-rubella (MMR) titers of recovered COVID-19 patients

Jeffrey Gold, William Baumgartl, Ramazan Okyay, Warren Licht, Paul Fidel, Mairi Noverr, Larry Tilley, David Hurley, Balázs Rada & John Ashford
The measles-mumps-rubella (MMR) vaccine has been theorized to provide protection against COVID-19. Our aim was to determine whether any MMR IgG titers are inversely correlated with severity in recovered COVID-19 patients previously vaccinated with MMR II. We divided 80 subjects into two groups, comparing MMR titers to recent COVID-19 severity. The MMR II group consisted of 50 subjects who would primarily have MMR antibodies from the MMR II vaccine, and a comparison group of 30...

Transmission of West Nile and five other temperate mosquito-borne viruses peaks at temperatures between 23-26ºC

Marta Shocket, Anna Verwillow, Mailo Numazu, Hani Slamani, Jeremy Cohen, Fadoua El Moustaid, Jason Rohr, Leah Johnson & Erin Mordecai
The temperature-dependence of many important mosquito-borne diseases has never been quantified. These relationships are critical for understanding current distributions and predicting future shifts from climate change. We used trait-based models to characterize temperature-dependent transmission of 10 vector–pathogen pairs of mosquitoes (Culex pipiens, Cx. quinquefascsiatus, Cx. tarsalis, and others) and viruses (West Nile, Eastern and Western Equine Encephalitis, St. Louis Encephalitis, Sindbis, and Rift Valley Fever viruses), most with substantial transmission in temperate regions. Transmission is...

Registration Year

  • 2020
    73

Resource Types

  • Dataset
    73

Affiliations

  • Stanford University
    72
  • Oregon State University
    4
  • University of Toronto
    4
  • University of California Los Angeles
    4
  • Columbia University
    3
  • University of California, Berkeley
    3
  • Virginia Tech
    3
  • Harvard University
    3
  • Cornell University
    3
  • SLAC National Accelerator Laboratory
    3