212 Works

Data from: Explaining the ocean’s richest biodiversity hotspot and global patterns of fish diversity

Elizabeth Christina Miller, Kenji T. Hayashi, Dongyuan Song & John J. Wiens
For most marine organisms, species richness peaks in the Central Indo-Pacific region and declines longitudinally, a striking pattern that remains poorly understood. Here, we used phylogenetic approaches to address the causes of richness patterns among global marine regions, comparing the relative importance of colonization time, number of colonization events, and diversification rates (speciation minus extinction). We estimated regional richness using distributional data for almost all percomorph fishes (17,435 species total, including ~72% of all marine...

Data from: All-trans retinoic acid disrupts development in ex vivo cultured fetal rat testes. I: altered seminiferous cord maturation and testicular cell fate

Daniel J. Spade, Edward Dere, Susan J. Hall, Christoph Schorl, Richard N. Freiman & Kim Boekelheide
Exposure to excess retinoic acid disrupts the development of the mammalian testicular seminiferous cord. However, the molecular events surrounding retinoic acid-driven loss of cord structure have not previously been examined. To investigate the mechanisms associated with this adverse developmental effect, fetal rat testes were isolated on gestational day 15, after testis determination and the initiation of cord development, and cultured in media containing all-trans retinoic acid (ATRA; 10-8 to 10-6 M) or vehicle for 3...

Data from: Comparing forest structure and biodiversity on private and public land: secondary tropical dry forests in Costa Rica

Moana McClellan, Rebecca Montgomery, Kristen Nelson & Justin Becknell
Secondary forests constitute a substantial proportion of tropical forestlands. These forests occur on both public and private lands and different underlying environmental variables and management regimes may affect post‐abandonment successional processes and resultant forest structure and biodiversity. We examined whether differences in ownership led to differences in forest structure, tree diversity, and tree species composition across a gradient of soil fertility and forest age. We collected soil samples and surveyed all trees in 82 public...

Data from: Measuring couple relationship quality in a rural African population: validation of a couple functionality assessment tool in Malawi

Allison Ruark, Rachel Chase, John Hembling, Valerie Rhoe Davis, Paul Clayton Perrin & Dorothy Brewster-Lee
Available data suggest that individual and family well-being are linked to the quality of women’s and men’s couple relationships, but few tools exist to assess couple relationship functioning in low and middle-income countries. In response to this gap, Catholic Relief Services has developed a Couple Functionality Assessment Tool (CFAT) to capture valid and reliable data on various domains of relationship quality. This tool is designed to be used by interventions which aim to improve couple...

Data from: Both morph- and species-dependent asymmetries affect reproductive barriers between heterostylous species

Barbara Keller, Jurriaan M. De Vos, Alexander N. Schmidt-Lebuhn, James D. Thomson & Elena Conti
The interaction between floral traits and reproductive isolation is crucial to explaining the extraordinary diversity of angiosperms. Heterostyly, a complex floral polymorphism that optimizes outcrossing, evolved repeatedly and has been shown to accelerate diversification in primroses, yet its potential influence on isolating mechanisms remains unexplored. Furthermore, the relative contribution of pre- versus postmating barriers to reproductive isolation is still debated. No experimental study has yet evaluated the possible effects of heterostyly on pre- and postmating...

Data from: Understanding angiosperm diversification using small and large phylogenetic trees

Stephen A. Smith, Jeremy M. Beaulieu, Alexandros Stamatakis & Michael J. Donoghue
How will the emerging possibility of inferring ultra-large phylogenies influence our ability to identify shifts in diversification rate? For several large angiosperm clades (Angiospermae, Monocotyledonae, Orchidaceae, Poaceae, Eudicotyledonae, Fabaceae, and Asteraceae), we explore this issue by contrasting two approaches: (1) using small backbone trees with an inferred number of extant species assigned to each terminal clade and (2) using a mega-phylogeny of 55473 seed plant species represented in GenBank. The mega-phylogeny approach assumes that the...

Data from: Fossils matter: improved estimates of divergence times in Pinus reveal older diversification

Bianca Saladin, Andrew B. Leslie, Rafael O. Wueest, Glenn Litsios, Elena Conti, Nicolas Salamin & Niklaus E. Zimmermann
Background: The taxonomy of pines (genus Pinus) is widely accepted and a robust gene tree based on entire plastome sequences exists. However, there is a large discrepancy in estimated divergence times of major pine clades among existing studies, mainly due to differences in fossil placement and dating methods used. We currently lack a dated molecular phylogeny that makes use of the rich pine fossil record, and this study is the first to estimate the divergence...

Trophic rewilding revives biotic resistance to shrub invasion

Jennifer Guyton, Johan Pansu, Tyler Kartzinel, Tyler Coverdale, Arjun Potter, Joshua Daskin, Matthew Hutchinson, Ana Gledis Da Conceição, Mike Peel, Marc Stalmans & Robert Pringle
Trophic rewilding seeks to rehabilitate degraded ecosystems by repopulating them with large animals, thereby reestablishing strong top-down interactions. Yet there are vanishingly few tests of whether such initiatives can restore ecosystem structure and functions, and on what timescales. Here we show that war-induced collapse of large-mammal populations in Mozambique’s Gorongosa National Park exacerbated woody encroachment by the invasive shrub Mimosa pigra—one of the world’s ‘100 worst’ invasive species—and that one decade of concerted trophic rewilding...

Data from: Optimizing Coastal Restoration with the Stress Gradient Hypothesis

Hallie Fischman, Sinead M. Crotty & Christine Angelini
Restoration efforts have been escalating worldwide in response to widespread habitat degradation. However, coastal restoration attempts notoriously vary in their ability to establish resilient, high-functioning ecosystems. Conventional restoration attempts disperse transplants in competition-minimizing arrays, yet recent studies suggest that clumping transplants to maximize facilitative, intraspecific interactions improves restoration success. Here, we modify the Stress Gradient Hypothesis to generate predictions about where each restoration design will perform best across environmental stress gradients. We then test the...

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...

A common endocrine signature marks convergent evolution of an elaborate dance display in frogs

Nigel K. Anderson
Unrelated species often evolve similar phenotypic solutions to the same environmental problem, a phenomenon known as convergent evolution. But, how do these ‘common traits’ arise? We address this question from a physiological perspective by assessing how convergence of an elaborate gestural display in frogs (“foot flagging”) is linked to changes in the androgenic hormone systems that underlie it. We show that the emergence of this rare display in unrelated anuran taxa is marked by a...

Woodpecker drum evolution: an analysis of covariation in elements of a multicomponent acoustic display among and within species

Nicole M Moody, Emma K Vivlamore & Matthew J Fuxjager
Multicomponent signals are found throughout the animal kingdom, but how these elaborate displays evolve and diversify is still unclear. Here, we explore the evolution of the woodpecker drum display. Two components of this territorial, sexually selected signal, drum speed and drum length, are used by territory holders to assess the threat level of an intruding drummer. We explore the coevolution of these display components both among and within species. Among species, we find evidence for...

Dual function of epaxial musculature for swimming and suction feeding in largemouth bass

Yordano Jimenez & Elizabeth Brainerd
The axial musculature of many fishes generates the power for both swimming and suction feeding. In the case of the epaxial musculature, unilateral activation bends the body laterally for swimming, and bilateral activation bends the body dorsally to elevate the neurocranium for suction feeding. But how does a single muscle group effectively power these two distinct behaviors? Prior electromyographic (EMG) studies have identified fishes’ ability to activate dorsal and ventral epaxial regions independently, but no...

Pigmentation biosynthesis influences the microbiome associated with sea urchins

Gary Wessel, Masato Kiyomoto, Adam Reitzel & Tyler Carrier
Organisms living on the seafloor are subject to encrustations by a wide variety of animal, plants, and microbes. Sea urchins, however, thwart this covering. Despite having a sophisticated immune system, there is no clear mechanism that allows sea urchins to remain clean. Here, by using CRISPR/Cas9, we test the hypothesis that pigmentation biosynthesis in sea urchin spines influences their interactions with microbes in vivo. We have three primary findings. First, the microbiome of sea urchin...

At a Heightened Level of Intensity: A Discussion of the Philosophy and Politics of Language in John Cayley’s Digital Poetics

John Cayley & Scott Rettberg
A conversation at a heightened level of intensity, ranging from the aleatory tradition of Emmett Williams, Jackson Mac Low, and John Cage, through post-Poundian poetry and its Chinese influences, kinetic poetry or programmable media where the poem itself is performing, not just the poet. Attention is also given to the Internet as these two literary artists knew it for a very brief moment, before Google and Facebook, circa 2004, ¨figured out that everybody needed an...

Data from: Resolving the evolutionary relationships of molluscs with phylogenomic tools

Stephen A. Smith, Casey W. Dunn, Nerida G. Wilson, Freya E. Goetz, Caitlin Feehery, Sónia C. S. Andrade, Greg W. Rouse & Gonzalo Giribet
Molluscs (snails, octopuses, clams, and relatives) have great body plan disparity, and among animals only arthropods surpass them in species number. This diversity has made Mollusca one of the best-studied groups of animals, yet their evolutionary relationships remain poorly resolved. Open questions have important implications for the origin of Mollusca and morphological evolution within the group. These include whether the shell-less vermiform aplacophoran molluscs diverged prior to the origin of the shelled molluscs (Conchifera), or...

Data from: Different clades and traits yield similar grassland functional responses

Elisabeth J. Forrestel, Michael J. Donoghue, Erika J. Edwards, Walter Jetz, Justin C. O. Du Toit & Melinda D. Smith
Plant functional traits are viewed as key to predicting important ecosystem and community properties across resource gradients within and among biogeographic regions. Vegetation dynamics and ecosystem processes, such as aboveground net primary productivity (ANPP), are increasingly being modeled as a function of the quantitative traits of species, which are used as proxies for photosynthetic rates, and nutrient and water-use efficiency. These approaches rely on an assumption that a certain trait value consistently confers a specific...

Data from: Phenological and fitness responses to climate warming depend upon genotype and competitive neighborhood in Arabidopsis thaliana

Mark A. Taylor, Martha D. Cooper & Johanna Schmitt
1. Increasing temperatures during climate change are known to alter the phenology across diverse plant taxa, but the evolutionary outcomes of these shifts are poorly understood. Moreover, plant temperature-sensing pathways are known to interact with competition-sensing pathways, yet there remains little experimental evidence for how genotypes varying in temperature responsiveness react to warming in realistic competitive settings. 2. We compared flowering time and fitness responses to warming and competition for two near isogenic lines (NILs)...

Data from: Structure and composition of altered riparian forests in an agricultural Amazonian landscape

R. Chelsea Nagy, Stephen Porder, Christopher Neill, Paulo Brando, Raimundo Mota Quintino & Sebastiâo Aviz Do Nascimento
Deforestation and fragmentation influence the microclimate, vegetation structure, and composition of remaining patches of tropical forest. In the southern Amazon, at the frontier of cropland expansion, forests are converted and fragmented in a pattern that leaves standing riparian forests whose dimensions are mandated by the Brazilian National Forest Code. These altered riparian forests share many characteristics of well-studied upland forest fragments, but differ because they remain connected to larger areas of forest downstream, and because...

Testing Message Framing to Promote Exercise

Lauren Connell Bohlen, David Williams & Omar Galárraga
The primary aim of this project is to examine the effects of (a) incentives versus no incentives; (b) incentive amount ($100 versus $200), and (c) loss-framed versus gain-framed incentive messages on motivation to attend a fitness facility. A secondary aim is to examine the effects of different aspects of loss-framed messages on exercise motivation. Another secondary aim is to examine mediators and moderators of main effects. A tertiary aim is to pilot the questionnaire packet...

Selection in the city: Rapid and fine scale evolution of urban eastern water dragons

Nicola Jackson, Bethan Littleford-Colquhoun, Kasha Strickland, Barbara Class & Celine Frere
Oceanic archipelagos have long been treated as a petri dish for studies of evolutionary and ecological processes. Like archipelagos, cities exhibit similar patterns and processes, such as the rapid phenotypic divergence of a species between urban and non-urban environments. However, on a local scale, cities can be highly heterogenous, where geographically close populations can experience dramatically different environmental conditions. Nevertheless, we are yet to understand the evolutionary and ecological implications for populations spread across a...

Data for: Analogous computations in working memory input, output and motor gating: Electrophysiological and computational modeling evidence

Rachel Ratz-Lubashevsky & Michael Frank
Adaptive cognitive-control involves a hierarchical cortico-striatal gating system that supports selective updating, maintenance, and retrieval of useful cognitive and motor information. Here, we developed a task that independently manipulates selective gating operations into working-memory (input gating), from working-memory (output gating), and of responses (motor gating) and tested the neural dynamics and computational principles that support them. Increases in gating demands, captured by gate switches, were expressed by distinct EEG correlates at each gating level that...

Ecological consequences of large herbivore exclusion in an African savanna: 12 years of data from the UHURU experiment

Jesse Alston, Courtney Reed, Leo Khasoha, Bianca Brown, Gilbert Busienei, Nathaniel Carlson, Tyler Coverdale, Megan Dudenhoeffer, Marissa Dyck, John Ekeno, Abdikadir Hassan, Rhianna Hohbein, Rhiannon Jakopak, Buas Kimiti, Samson Kurukura, Peter Lokeny, Allison Louthan, Simon Musila, Paul Musili, Tosca Tindall, Sarah Weiner, Tyler Kartzinel, Todd Palmer, Robert Pringle & Jacob Goheen
Diverse communities of large mammalian herbivores (LMH), once widespread, are now rare. LMH exert strong direct and indirect effects on community structure and ecosystem functions, and measuring these effects is important for testing ecological theory and for understanding past, current, and future environmental change. This in turn requires long-term experimental manipulations, owing to the slow and often nonlinear responses of populations and assemblages to LMH removal. Moreover, the effects of particular species or body-size classes...

Seeking Coherence in a COVID-19 Context: The Maltese Islands During the Pandemic

Maximilian Bonnici, Isabelle Bonnici, Brett Miller, Jack Victory, Parth Panchal & Nathan Williams

Predicting Seasonal Influenza Hospitalizations Using an Ensemble Super Learner: A Simulation Study

Jason Gantenberg
Analysis code underlying Gantenberg, J.R., McConeghy, K.W., Howe, C.J., Steingrimsson, J., van Aalst, R., Chit, A. and Zullo A.R. Predicting seasonal influenza hospitalizations using an ensemble super learner: a simulation study. American Journal of Epidemiology (in press).

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