80 Works

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...

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...

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 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...

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...

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...

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...

Equiprobable Mappings in Weighted Constraint Grammars

Arto Topani Anttila, Scott Borgeson & Giorgio Magri

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...

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...

DialectGram: Detecting Dialectal Variation at Multiple Geographic Resolutions

Hang Jiang, Haoshen Hong, Yuxing Chen & Vivek Kulkarni

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...

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...

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...

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...

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...

Repeated fire shifts carbon and nitrogen cycling by changing plant inputs and soil decomposition across ecosystems

Adam Francis Pellegrini, Sarah Hobbie, Peter Reich, Ari Jumpponen, Jack Brookshire, Anthony Caprio, Corli Coetsee & Robert Jackson
Fires shape the biogeochemistry and functioning of many ecosystems, and fire frequencies are changing across much of the globe. Frequent fires can change soil carbon (C) and nitrogen (N) storage by altering the quantity and chemistry of plant inputs through changes in plant biomass and composition as well as altering decomposition of soil organic matter. How decomposition rates change with shifting inputs remains uncertain because most studies focus on the effects of single fires, where...

Data from: Seasonal changes in diet and toxicity in the Climbing Mantella frog (Mantella laevigata)

Nora A. Moskowitz, Alexandre B. Roland, Eva K. Fischer, Ndimbintsoa Ranaivorazo, Charles Vidoudez, Marianne T. Aguilar, Sophia M. Caldera, Jackie Chea, Miruna G. Cristus, Jett P. Crowdis, Bluyé DeMessie, Caroline R. Desjardins-Park, Audrey H. Effenberger, Felipe Flores, Michael Giles, Emma Y. He, Nike S. Izmaylov, ChangWon C. Lee, Nicholas A. Pagel, Krystal K. Phu, Leah U. Rosen, Danielle A. Seda, Yong Shen, Santiago Vargas, Hadley S. Weiss … & Lauren A. O’Connell
Poison frogs acquire chemical defenses from the environment for protection against potential predators. These defensive chemicals are lipophilic alkaloid toxins that are sequestered by poison frogs from dietary arthropods and stored in skin glands. Despite decades of research focusing on identifying poison frog toxins, we know relatively little about how environmental variation and subsequent arthropod availability impacts toxicity in poison frogs. We investigated how seasonal environmental variation influences poison frog toxin profiles through changes in...

Magnitude and predictability of pH fluctuations shape plastic responses to ocean acidification

Mark Bitter, Lydia Kapsenberg, Katherine Silliman, Jean-Pierre Gattuso & Catherine Pfister
Phenotypic plasticity is expected to facilitate the persistence of natural populations as global change progresses. The attributes of fluctuating environments that favor the evolution of plasticity have received extensive theoretical investigation, yet empirical validation of these findings is still in its infancy. Here, we combine high-resolution environmental data with a laboratory-based experiment to explore the influence of habitat pH fluctuation dynamics on the plasticity of gene expression in two populations of the Mediterranean mussel, Mytilus...

Interspecific variation and elevated CO2 influence the relationship between plant chemical resistance and regrowth tolerance

Leslie Decker & Mark D. Hunter
To understand how comprehensive plant defense phenotypes will respond to global change, we investigated the legacy effects of elevated CO2 on the relationships between chemical resistance (constitutive and induced via mechanical damage) and regrowth tolerance in four milkweed species (Asclepias). We quantified potential resistance and tolerance tradeoffs at the physiological level following simulated clipping/mowing, which are relevant to milkweed ecology and conservation. We examined the legacy effects of elevated CO2 on four hypothesized tradeoffs between:...

Data from: Shark movement strategies influence poaching risk and can guide enforcement decisions in a large, remote Marine Protected Area

David Jacoby, Francesco Ferretti, Robin Freeman, Aaron Carlisle, Taylor Chapple, David Curnick, Jonathan Dale, Robert Schallert, David Tickler & Barbara Block
Large, remote marine protected areas (MPAs) containing both reef and pelagic habitats, have been shown to offer considerable refuge to populations of reef-associated sharks. Many large MPAs are, however, impacted by illegal fishing activity conducted by unlicensed vessels. While enforcement of these reserves is often expensive, it would likely benefit from the integration of ecological data on the mobile animals they are designed to protect. Consequently, shark populations in some protected areas continue to decline,...

A kaleidoscopic view of ovarian genes associated with infertility, subfertility and senescence

Aaron Hsueh
Ovarian infertility and subfertility presenting with premature ovarian insufficiency (POI) and diminished ovarian reserve are major issues facing in the developed world due to the trend of delaying child birth. Polycystic ovary syndrome (PCOS) is a common endocrine and metabolic disorder affecting 6-10% of women in reproductive age. Based on advances in whole exome sequencing, evaluation of gene copy variants, together with family-based and genome-wide association studies (GWAS), we discussed genes responsible for the POI,...

Data from: Nonlinearities between inhibition and T-type calcium channel activity bidirectionally regulate thalamic oscillations

Adam Lu, Christine Lee, Max Kleiman-Weiner, Brian Truong, Megan Wang, John Huguenard & Mark Beenhakker
Absence seizures result from 3-5 Hz generalized thalamocortical oscillations that depend on highly regulated inhibitory neurotransmission in the thalamus. Efficient reuptake of the inhibitory neurotransmitter GABA is essential, and reuptake failure worsens seizures. Here, we show that blocking GABA transporters (GATs) in acute brain slices containing key parts of the thalamocortical seizure network modulates epileptiform activity. As expected, we found that blocking either GAT1 or GAT3 prolonged oscillations. However, blocking both GATs unexpectedly suppressed oscillations....

Data from: The future of food from the sea

Tracey Mangin, Christopher Costello, Ling Cao, Stefan Gelcich, Miguel A. Cisneros-Mata, Christopher M. Free, Halley E. Froehlich, Christopher D. Golden, Gakushi Ishimura, Jason Maier, Ilan Macadam-Somer, Michael C. Melnychuk, Masanori Miyahara, Carryn L. De Moor, Rosamond Naylor, Linda Nøstbakken, Elena Ojea, Erin O’Reilly, Ana M. Parma, Andrew J. Plantinga, Shakuntala H. Thilsted & Jane Lubchenco
Global food demand is on the rise and serious questions remain about whether supply can increase sustainably. Land-based expansion is possible, but may exacerbate climate change and biodiversity loss and compromise the delivery of other ecosystem services. As food from the sea represents only 17% of current edible meat production, we ask: How much food can we expect the ocean to sustainably produce by 2050? We examine the main food-producing sectors in the ocean—wild fisheries,...

Data from: Foundation species promote local adaptation and fine-scale distribution of herbaceous plants

Michael O'Brien, Elisa Carbonell, Gianalberto Losapio, Philipp Schlüter & Christian Schöb
1) Interactions among neighbors can alter demography and traits of commingled species via adaptation or plasticity in phenotypic expression and understanding these two mechanisms in diverse communities is important for determining the ecological and evolutionary consequences of plant–plant interactions. 2) We reciprocally transplanted perennial species (Arenaria armerina and Festuca indigesta) among patches of two foundation shrub species and open ground to assess whether origin microsite (defined as the spatially distinct abiotic and biotic conditions associated...

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