232 Works

Paraphyletic species no more – genomic data resolve a Pleistocene radiation and validate morphological species of the Melanoplus scudderi complex (Insecta: Orthoptera)

Jen-Pan Huang, JoVonn G. Hill, Joaquín Ortego & L. Lacey Knowles
Rapid speciation events, with taxa generated over a short time period, are among the most investigated biological phenomena. However, molecular systematics often reveals contradictory results compared with morphological/phenotypical diagnoses of species under scenarios of recent and rapid diversification. In this study, we used molecular data from an average of over 29,000 loci per sample from RADseq to reconstruct the diversification history and delimit the species boundary in a short-winged grasshopper species complex (Melanoplus Scudderi group),...

Common barriers, but temporal dissonance: genomic tests suggest ecological and paleo-landscape sieves structure a coastal riverine fish community

Andrea Thomaz & L. Lacey Knowles
Assessments of spatial and temporal congruency across taxa from genetic data provide insights into the extent to which similar processes structure communities. However, for coastal regions that are affected continuously by cyclical sea-level changes over the Pleistocene, congruent interspecific response will not only depend upon co-distributions, but also on similar dispersal histories among taxa. Here, we use SNPs to test for concordant genetic structure among four co-distributed taxa of freshwater fishes (Teleostei: Characidae) along the...

Data from: Gender diversity of editorial boards and gender differences in the peer review process at six journals of ecology and evolution.

Charles Fox, Meghan Duffy, Daphne Fairbairn & Jennifer Meyer
Despite substantial progress for women in science, women remain underrepresented in many aspects of the scholarly publication process. We examined how the gender diversity of editors and reviewers changed over time for six journals in ecology and evolution (2003-2015 for four journals, 2007-2015 or 2009-2015 for the other two), and how several aspects of the peer review process differed between female and male editors and reviewers. We found that, for five of the six journals,...

Higher rates of liana regeneration after canopy fall drives species abundance patterns in central Amazonia

Elisangela Rocha, Juliana Schietti, Caian Gerolamo, Robyn Burnham & Anselmo Nogueira
In tropical rainforest, most vascular plants have some capacity to resprout, and lianas are often effective resprouters after canopy fall. However, the diversity of resprouting responses of liana species and the consequence for plant persistence is poorly understood. We hypothesized that variation in regeneration among liana species causes differences in liana species abundance in tropical rainforest through differential resprouting capacity, such that liana species with higher densities produce more resprouts after canopy falls. We applied...

Motion and heart rate from a wrist-worn wearable and labeled sleep from polysomnography

Olivia Walch
This project contains acceleration (in units of g) and heart rate (bpm, measured from photoplethysmography) recorded from the Apple Watch, as well as labeled sleep scored from gold-standard polysomnography. Data were collected at the University of Michigan from June 2017 to March 2019, and there are 31 subjects in total. Code to read and process these files is available on GitHub. The paper corresponding to the work is Walch et al., "Sleep stage prediction with...

Effective Strategies for Recording Interviewer Observations: Evidence from the PASS Study in Germany

Brady T. West & Mark Trappmann

Trophic-specific responses to migration in empirical metacommunities

Zachary Hajian-Forooshani
The metacommunity, as it evolved from Levins’s metapopulation, provides a framework to consider the spatial organization of species interactions. A defining feature of metapopulations and metacommunities is that organisms (populations or communities) are connected via migration. An important result from Levins’s metapopulation work—that increasing migration lowers regional extinction probability—is often incorporated into conceptions of metacommunities; however, this may not hold true for multiple interacting metapopulations (metacommunities). We report results from a metacommunity field experiment conducted...

Multi-dimensional biodiversity hotspots and the future of taxonomic, ecological, and phylogenetic diversity: a case study of North American rodents

Tara Smiley, Pascal Title, Miriam Zelditch & Rebecca Terry
Aim: We investigate geographic patterns across taxonomic, ecological, and phylogenetic diversity to test for spatial (in)congruency and identify aggregate diversity hotspots in relation to present land-use and future climate. Simulating extinctions of imperiled species, we demonstrate where losses across diversity dimensions and geography are predicted. Location: North America Time period: Present-day, future Major taxa studied: Rodentia Methods: Using geographic range maps for rodent species, we quantified spatial patterns for eleven dimensions of diversity: taxonomic (species,...

Shared morphological consequences of global warming in North American migratory birds

Brian Weeks, David Willard, Marketa Zimova, Aspen Ellis, Max Witynski, Mary Hennen & Ben Winger
Increasing temperatures associated with climate change are predicted to cause reductions in body size, a key determinant of animal physiology and ecology. Using a four-decade specimen series of 70,716 individuals of 52 North American migratory bird species, we demonstrate that increasing annual summer temperature over the 40-year period predicts consistent reductions in body size across these diverse taxa. Concurrently, wing length—an index of body shape that impacts numerous aspects of avian ecology and behavior—has consistently...

Belowground competition can influence the evolution of root traits

Sara Colom & Regina Baucom
Although root traits play a critical role in mediating plant-plant interactions and resource acquisition from the soil environment, research examining if and how belowground competition can influence the evolution of root traits remains largely unexplored. Here we examine the potential that root traits may evolve as a target of selection from interspecific competition using Ipomoea purpurea and I. hederacea, two closely related morning glory species that commonly co-occur in the United States as a model...

TypeTE: a tool to genotype mobile element insertions from whole genome resequencing data

Clément Goubert, Jainy Thomas, Lindsay Payer, Jeffrey Kidd, Julie Feusier, W. Scott Watkins, Kathleen Burns, Lynn Jorde & Cédric Feschotte
Alu retrotransposons account for more than 10% of the human genome, and insertions of these elements create structural variants segregating in human populations. Such polymorphic Alu are powerful markers to understand population structure, and they represent variants that can greatly impact genome function, including gene expression. Accurate genotyping of Alu and other mobile elements has been challenging. Indeed, we found that Alu genotypes previously called for the 1000 Genomes Project are sometimes erroneous, which poses...

Evaluating the boundaries of marine biogeographic regions of the Southwestern Atlantic using halacarid mites (Halacaridae), meiobenthic organisms with a low dispersal potential

Almir Pepato, Pavel Klimov & Teofânia Vidigal
Aim We evaluated traditional biogeographic boundaries of coastal marine regions in SW Atlantic using DNA sequence data from common, rocky-shore inhabiting, marine mites of the genera Agauopsis and Rhombognathus, family Halacaridae. Methods We investigated geographic population genetic structure using CO1 gene sequences, estimated divergence times using a multigene dataset and absolute time-calibrated molecular clock analyses, and performed environmental niche modeling (ENM) of common marine mite species. Results Agauopsis legionium has a shallow history (2.01 Ma)...

Data from: The contribution of host cell-directed vs. parasite-directed immunity to the disease and dynamics of malaria infections

Nina Wale, Matthew J. Jones, Derek G. Sim, Andrew F. Read & Aaron A. King
Hosts defend themselves against pathogens by mounting an immune response. Fully understanding the immune response as a driver of host disease and pathogen evolution requires a quantitative account of its impact on parasite population dynamics. Here, we use a data-driven modeling approach to quantify the birth and death processes underlying the dynamics of infections of the rodent malaria parasite, Plasmodium chabaudi, and the red blood cells (RBCs) it targets. We decompose the immune response into...

Similar but different: Revealing the relative roles of species‐traits versus biome properties structuring genetic variation in South American marsh rats

Joyce Rodrigues Do Prado, Joyce R. Prado, Alexandre R. Percequillo, Andréa T. Thomaz & L. Lacey Knowles
Aim: Wetland habitats, and the ecological restrictions imposed by them, structure patterns of genetic variation in constituent taxa. As such, genetic variation may reflect properties of the specific biomes species inhabit, or shared life history traits among species may result in similar genetic structure. We evaluated these hypotheses jointly by quantifying the similarity of genetic structure in three South American marsh rat species (Holochilus), and test how genetic variation in each species relates to biome‐specific...

Sex differences in IV thrombolysis treatment for stroke: a systematic review and meta-analysis

Brent Strong, Lynda Lisabeth & Mathew Reeves
Objective: A prior meta-analysis of reports published between 2000 and 2008 found that women were 30% less likely to receive IV rt-PA treatment for stroke than men; we updated this meta-analysis to determine if this sex difference still persisted. Methods: We identified studies that reported sex-specific IV rt-PA treatment rates for acute ischemic stroke published between 2008 and 2018. Eligible studies included representative populations of ischemic stroke patients from hospital-based, registry-based, or administrative data. Random...

Data from: Long-term dynamics of liana seedlings suggest decelerating increases in liana relative abundance over time

Maria Natalia Umaña, Eric Manzané-Pinzón & Liza Comita
Over the past decades, tropical forests have experienced both compositional and structural changes. In the Neotropics, researchers at multiple sites have observed significant increases in the abundance and biomass of lianas (i.e. woody vines) relative to trees. However, the role of dynamics at early life stages in contributing to increasing liana abundance remains unclear. We took advantage of a unique dataset on seedling dynamics over 16 years in ~20,000 1-m2plots in a tropical forest in...

A new species of croton (Euphorbiaceae) from a Madagascan lineage discovered in coastal Kenya

Veronicah Ngumbau, Mwadime Nyange, Neng Wei, Benjamin Van Ee, Paul Berry, Itambo Malombe, Guang-Wan Hu & Qing-Feng Wang
Croton kinondoensis, a new species from Kenya, is described and illustrated here with photographs. It is found in the sacred Kaya Kinondo Forest, one of the last remaining coastal forests patches in Kenya. Its morphology and systematic position based on ITS and trnL-F DNA sequence data clearly place it within the Adenophorus Group of Croton, a clade of ca. 15 species otherwise known only from Madagascar and the Comoros Archipelago. Its closest affinities appear to...

The diverse nature of island isolation and its effect on land-bridge insular faunas

Yuval Itescu, Johannes Foufopoulos, Panayiotis Pafilis & Shai Meiri
Aim Isolation is a key factor in island biology. It is usually defined as the distance to the geographically nearest mainland, but multiple alternatives exist. We explored how testing different isolation indices affects the inference of isolation effects on faunal characteristics. We focused on land-bridge islands and compared the relationships of multiple spatial and temporal (i.e., through time) isolation indices with community-, population-, and individual-level characteristics (species richness, population density, and body size, respectively). Location...

Data from: Physician champions’ perspectives and practices on electronic health records implementation: challenges and strategies

Xinning Gui, Yunan Chen, Xiaomu Zhou, Tera L. Reynolds, Kai Zheng & David A. Hanauer
Objective: Physician champions are “boots on the ground” physician leaders who facilitate the implementation of, and transition to, new health information technology (HIT) systems within an organization. They are commonly cited as key personnel in HIT implementations, yet little research has focused on their practices and perspectives. Methods: We addressed this research gap through a qualitative study of physician champions that aimed to capture their challenges and strategies during a large-scale HIT implementation. Email interviews...

Fluorescent biomarkers demonstrate prospects for spreadable vaccines to control disease transmission in wild bats

Kevin Bakker, Tonie Rocke, Rachel Abbott, Carlos Tello, Jorge Carrera, William Valderrama, Carlos Shiva, Nestor Falcon, Jorge Osorio & Daniel Streicker
Vaccines that autonomously transfer among individuals have been proposed as a strategy to control infectious diseases within wildlife populations. However, understanding rates of spread and epidemiological efficacy in real world systems remain elusive. Here, we investigated whether topical vaccines that transfer among bats through social contacts can control vampire bat rabies, a medically and economically important zoonosis in Latin America. Field experiments in 3 Peruvian bat colonies which used fluorescent biomarkers as a proxy for...

Data from: Functional traits, not productivity, predict openness to seedling recruitment in alpine plant communities under climatic warming

Eric Meineri, Kari Klanderud, John Guittar, Deborah Goldberg & Vigdis Vandvik
Understanding the degree to which plant communities are open to seedling recruitment is key to predicting how they will be impacted by climate change. We experimentally assessed whether communities assembled under colder climates were inherently more open to recruitment than warmer-climate communities, after controlling for differences in the current climate under which the communities were growing. We then tested whether variation in openness to recruitment could be explained by community biomass or by the plant...

Data from: A phylogenomic framework for pelagiarian fishes (Acanthomorpha: Percomorpha) highlights mosaic radiation in the open ocean

Matthew Friedman, Kara Feilich, Hermione Beckett, Michael Alfaro, Brant Faircloth, David Černý, Masaki Miya, Thomas Near & Richard Harrington
The fish clade Pelagiaria, which includes tunas as its most famous members, evolved remarkable morphological and ecological variety in a setting not generally considered conducive to diversification: the open ocean. Relationships within Pelagiaria have proven elusive due to short internodes subtending major lineages suggestive of rapid early divergences. Using a novel sequence dataset of over 1000 ultraconserved DNA elements (UCEs) for 94 of the 286 species of Pelagiaria (more than 70% of genera), we provide...

Data from: Environmental filtering structures fungal endophyte communities in tree bark

Peter Pellitier, Donald Zak & Sydney Salley
The factors that control the assembly and composition of endophyte communities across plant hosts remains poorly understood. This is especially true for endophyte communities inhabiting inner tree bark, one of the least studied components of the plant microbiome. Here, we test the hypothesis that bark of different tree species acts as an environmental filter structuring endophyte communities, as well as the alternative hypothesis, that bark acts as a passive reservoir that accumulates a diverse assemblage...

Data from: Testing main Amazonian rivers as barriers across time and space within widespread taxa

Renata Pirani, Fernanda Werneck, Andréa Thomaz, Mariah Kenney, Marcelo Sturaro, Teresa Cristina Avila-Pires, Pedro Peloso, Miguel Rodrigues & L. Lacey Knowles
Aim: Present Amazonian diversity patterns can result from many different mechanisms and, consequently, the factors contributing to divergence across regions and/or taxa may differ. Nevertheless, the river-barrier hypothesis (RBH) is still widely invoked as a causal process in divergence of Amazonian species. Here we use model-based phylogeographic analyses to test the extent to which major Amazonian rivers act similarly as barriers across time and space in two broadly distributed Amazonian taxa. Local: Amazon rainforest. Taxon:...

Quantum supremacy using a programmable superconducting processor

John Martinis, Sergio Boixo, Hartmut Neven, Frank Arute, Kunal Arya, Ryan Babbush, Dave Bacon, Joseph C. Bardin, Rami Barends, Rupak Biswas, Fernando G. S. L. Brandao, David A. Buell, Brian Burkett, Yu Chen, Zijun Chen, Ben Chiaro, Roberto Collins, William Courtney, Andrew Dunsworth, Edward Farhi, Brooks Foxen, Austin Fowler, Craig Gidney, Marissa Giustina, Rob Graff … & John M. Martinis
The tantalizing promise of quantum computers is that certain computational tasks might be executed exponentially faster on a quantum processor than on a classical processor. A fundamental challenge is to build a high-fidelity processor capable of running quantum algorithms in an exponentially large computational space. Here, we report using a processor with programmable superconducting qubits to create quantum states on 53 qubits, corresponding to a computational state-space of dimension 2^53 ∼ 10^16. Measurements from repeated...

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