104 Works

Data from: Consistently positive effect of species diversity on ecosystem, but not population, temporal stability

Qianna Xu
Despite much recent progress, our understanding of diversity-stability relationships across different study systems remains incomplete. In particular, recent theory clarified that within-species population stability and among-species asynchronous population dynamics combine to determine ecosystem temporal stability, but their relative importance in modulating diversity-ecosystem temporal stability relationships in different ecosystems remains unclear. We addressed this issue with a meta-analysis of empirical studies of ecosystem and population temporal stability in relation to species diversity across a range of...

Breaking a species barrier by enabling hybrid recombination

G. Ozan Bozdag, Jasmine Ono, Jai A. Denton, Emre Karakoc, Neil Hunter, Jun-Yi Leu & Duncan Greig
Hybrid sterility maintains reproductive isolation between species by preventing them from exchanging genetic material. Anti-recombination can contribute to hybrid sterility when different species’ chromosome sequences are too diverged to cross-over efficiently during hybrid meiosis, resulting in chromosome mis-segregation and aneuploidy. The genome sequences of the yeasts Saccharomyces cerevisiae and Saccharomyces paradoxus have diverged by about 12% and their hybrids are sexually sterile: nearly all of their gametes are aneuploid and inviable. Previous methods to increase...

Data from: Diverse and complex muscle spindle afferent firing properties emerge from multiscale muscle mechanics

Kyle Blum, Brian Horslen, Kenneth Campbell, Brian Horslen, Paul Nardelli, Stephen Housley, Timothy Cope & Lena Ting
Despite decades of research, we lack a mechanistic framework capable of predicting how movement-related signals are transformed into the diversity of muscle spindle afferent firing patterns observed experimentally, particularly in naturalistic behaviors. Here, a biophysical model demonstrates that well-known firing characteristics of mammalian muscle spindle Ia afferents – including movement history dependence, and nonlinear scaling with muscle stretch velocity – emerge from first principles of muscle contractile mechanics. Further, mechanical interactions of the muscle spindle...

Heterogenous susceptibility to R-pyocins in populations of Pseudomonas aeruginosa sourced from cystic fibrosis lungs

Madeline Mei, Jacob Thomas & Stephen Diggle
Bacteriocins are proteinaceous antimicrobials produced by bacteria which are active against other strains of the same species. R-type pyocins are phage tail-like bacteriocins produced by Pseudomonas aeruginosa. Due to their anti-pseudomonal activity, R-pyocins have potential as therapeutics in infection. P. aeruginosa is a Gram-negative opportunistic pathogen and is particularly problematic for individuals with cystic fibrosis (CF). P. aeruginosa from CF lung infections develop increasing resistance to antibiotics, making new treatment approaches essential. P. aeruginosa populations...

Comparative study of snake lateral undulation kinematics in model heterogeneous terrain

Perrin Schiebel, Alex Hubbard & Daniel I. Goldman

Programming Mechanics in Knitted Materials, Stitch by Stitch Data

Krishma Singal, Michael Dimitriyev & Elisabetta A. Matsumoto

Genotypes at 10 microsatellite loci for 8 perennial, polygyne colonies of Vespula squamosa

Carl Dyson
Many highly social species show plasticity in their social structure in response to different environmental conditions. For example, typical colonies of the yellowjacket wasp Vespula squamosa are headed by a single reproductive queen and survive for only a single season. However, in warmer climates, V. squamosa colonies sometimes persist for multiple years and can grow to extremely large size. We used genetic markers to understand patterns of reproduction and recruitment within these perennial colonies. We...

Adaptive shifts underlie the divergence in wing morphology in bombycoid moths

Brett Aiello, Milton Tan, Usama Bin Sikandar, Alexis Alvey, Burhanuddin Bhinderwala, Katalina Kimball, Jesse Barber, Chris Hamilton, Akito Kawahara & Simon Sponberg
The evolution of flapping flight is linked to the prolific success of insects. Across Insecta, wing morphology diversified, strongly impacting aerodynamic performance. In the presence of ecological opportunity, discrete adaptive shifts and early bursts are two processes hypothesized to give rise to exceptional morphological diversification. Here, we use the diverse sister-families Sphingidae and Saturniidae to answer how the evolution of aerodynamically important traits is linked to clade divergence and through what process(es) these traits evolve....

Dataset from: Warming effects on grassland productivity depend on plant diversity

Junjiong Shao, Xuhui Zhou, Kees Van Groenigen, Guiyao Zhou, Huimin Zhou, Lingyan Zhou, Meng Lu, Jianyang Xia, Lin Jiang, Bruce Hungate, Yiqi Luo, Fangliang He & Madhav Thakur
Aim: Climate warming and biodiversity loss both alter plant productivity, yet we lack an understanding of how biodiversity regulates the responses of ecosystems to warming. In this study, we examine how plant diversity regulates the responses of grassland productivity to experimental warming using meta-analytic techniques. Location: Global Major taxa studied: Grassland ecosystems Methods: Our meta-analysis is based on warming responses of 40 different plant communities obtained from 20 independent studies on grasslands across five continents....

FRET imaging and curvature data of freely moving C. elegans

Daniel Porto
The force - induced unfolding and refolding of proteins is speculated to be a key mechanism in the sensing and transduction of mechanical signals in the living cell. Yet, little evidence has been gathered for its existence in vivo . Prominently, s tretch - induced unfolding is postulated to be the activation mechanism of the t witchin/titin family of autoinhibited sarcomeric kinases linked to the mechanical stress response of muscle. To test the occurrence of...

Time-series drinking water metagenomes: Assemblies & MAGs

Solize Vosloo, Linxuan Huo, Christopher Anderson, Maria Sevillano & Ameet Pinto
Reconstructing microbial genomes from metagenomic short-read data can be challenging due to the unknown and uneven complexity of microbial communities. This complexity encompasses highly diverse populations which often includes strain variants. Reconstructing high-quality genomes is a crucial part of the metagenomic workflow as subsequent ecological and metabolic inferences depend on their accuracy, quality and completeness. In contrast to microbial communities in other ecosystems, there has been no systematic assessment of genome-centric metagenomic workflows for drinking...

Warming effect on ecosystem stability

Quan Quan, Fangyue Zhang, Lin Jiang, Han Y. H. Chen, Jinsong Wang, Fangfang Ma, Bing Song & Shuli Niu
1. Ecosystem stability is essential to its sustainable functions and services to humanity. Although climate warming is projected to vary from 1-5ºC by the end of 21st century, how the temporal stability of plant community biomass production responds to different warming scenarios remains unclear. 2. To fill this knowledge gap, we conducted a 6-year field experiment with three levels of warming treatments (control, + 1.5oC, + 5oC) by using infrared radiators, in an alpine meadow...

Island biogeography of soil bacteria and fungi: similar patterns, but different mechanisms

Shaopeng Li, Pandeng Wang, Yongjian Chen, Maxwell Wilson, Xian Yang, Chao Ma, Jianbo Lu, Xiao-Yong Chen, Jianguo Wu, Wen-Sheng Shu & Lin Jiang
Microbes, similar to plants and animals, exhibit biogeographic patterns. However, in contrast with the considerable knowledge on the island biogeography of higher organisms, we know little about the distribution of microorganisms within and among islands. Here, we explored insular soil bacterial and fungal biogeography and underlying mechanisms, using soil microbiota from a group of land-bridge islands as a model system. Similar to island species-area relationships observed for many macroorganisms, both island-scale bacterial and fungal diversity...

Precise timing is ubiquitous, consistent and coordinated across a comprehensive, spike-resolved flight motor program

Joy Putney, Rachel Conn & Simon Sponberg
Sequences of action potentials, or spikes, carry information in the number of spikes and their timing. Spike timing codes are critical in many sensory systems, but there is now growing evidence that millisecond-scale changes in timing also carry information in motor brain regions, descending decision-making circuits, and individual motor units. Across all the many signals that control a behavior how ubiquitous, consistent, and coordinated are spike timing codes? Assessing these open questions ideally involves recording...

Data from: History-dependent perturbation response in limb muscle

Simon Sponberg, Chidinma Chukwueke & Thomas Libby
Muscle mediates movement but movement is typically unsteady and perturbed. Muscle is known to behave non-linearly and with history dependent properties during steady locomotion, but the importance of history dependence in mediating muscles function during perturbations remains less clear. To explore muscle's capacity to mitigate perturbations during locomotion, we constructed a series of perturbations that varied only in kinematic history, keeping instantaneous position, velocity and time from stimulation constant. We find that muscle's perturbation response...

Minnesota peat viromes reveal terrestrial and aquatic niche partitioning for local and global viral populations

Anneliek Ter Horst, Christian Santos-Medellín, Jackson Sorensen, Laura Zinke, Rachel Wilson, Eric Johnston, Gareth Trubl, Jennifer Pett-Ridge, Steven Blazewicz, Paul Hanson, Jeffrey Chanton, Christopher Schadt, Joel Kostka & Joanne Emerson
Background: Peatlands are expected to experience sustained yet fluctuating higher temperatures due to climate change, leading to increased microbial activity and greenhouse gas emissions. Despite mounting evidence for viral contributions to these processes in thawing permafrost, little is known about viruses in other peatlands. More generally, soil viral biogeography and its potential drivers are poorly understood at both local and global scales. Here, 87 metagenomes and five viral size-fraction metagenomes (viromes) from a boreal peatland...

Technology review and roadmap for inventorying complete streets for integration into pavement asset management systems

April Gadsby, & John Harvey
Complete Streets provide mobility for all modes of transportation including active transportation. Complete Streets are being implemented in the US and transportation agencies must maintain these assets, which requires bringing them into asset management systems. Many gaps exist to include Complete Streets in asset management, and there is no comprehensive plan for filling those gaps. This project developed a road map to fill those gaps. To create this roadmap, the study completed the following tasks:...

Data from: Experimental demonstration of the importance of keystone communities for maintaining metacommunity biodiversity and ecosystem functioning

Xian Yang, Jiaqi Tan, Kevin Harry Sun & Lin Jiang
As local communities within a metacommunity may differ considerably in their contributions to biodiversity and ecosystem functioning, it has been suggested that conservation priority should be given to disproportionately important local communities (i.e., keystone communities). However, we know little about what characterizes a keystone community. Using laboratory protist microcosms as the model system, we examined how the environmental uniqueness and location of a local community affect its contributions to the metacommunities. We found that the...

Data from: De novo active sites for resurrected Precambrian enzymes

Valeria A. Risso, Sergio Martinez Rodriguez, Adela M. Candel, Dennis M. Krüger, David Pantoja-Uceda, Mariano Ortega-Munoz, Francisco Santoyo-Gonzalez, Eric A. Gaucher, Shina Caroline Lynn Kamerlin, Marta Bruix, Jose A. Gavira & Jose M. Sanchez-Ruiz
Protein engineering studies often suggest the emergence of completely new enzyme functionalities to be highly improbable. However, enzymes likely catalysed many different reactions already in the last universal common ancestor. Mechanisms for the emergence of completely new active sites must therefore either plausibly exist or at least have existed at the primordial protein stage. Here, we use resurrected Precambrian proteins as scaffolds for protein engineering and demonstrate that a new active site can be generated...

Data from: Hawkmoth flight in the unsteady wakes of flowers

Megan Matthews & Simon Sponberg
Flying animals maneuver and hover through environments where wind gusts and flower wakes produce unsteady flow. Although both flight maneuvers and aerodynamic mechanisms have been studied independently, little is known about how these interact in an environment where flow is already unsteady. Moths forage from flowers by hovering in the flower’s wake.We investigated hawkmoths tracking a 3D-printed robotic flower in a wind tunnel.We visualized the flow in the wake and around the wings and compared...

Data from: CRISPR-induced distributed immunity in microbial populations

Lauren M. Childs, Whitney E. England, Mark J. Young, Joshua S. Weitz & Rachel J. Whitaker
In bacteria and archaea, viruses are the primary infectious agents, acting as virulent, often deadly pathogens. A form of adaptive immune defense known as CRISPR-Cas enables microbial cells to acquire immunity to viral pathogens by recognizing specific sequences encoded in viral genomes. The unique biology of this system results in evolutionary dynamics of host and viral diversity that cannot be fully explained by the traditional models used to describe microbe-virus coevolutionary dynamics. Here, we show...

Data from: Nitrogen addition does not reduce the role of spatial asynchrony in stabilizing grassland communities

Yunhai Zhang, Jinchao Feng, Michel Loreau, Nianpeng He, Xingguo Han & Lin Jiang
While nitrogen (N) amendment is known to affect the stability of ecological communities, whether this effect is scale‐dependent remains an open question. By conducting a field experiment in a temperate grassland, we found that both plant richness and temporal stability of community biomass increased with spatial scale, but N enrichment reduced richness and stability at the two scales considered. Reduced local‐scale stability under N enrichment arose from N‐induced reduction in population stability, which was partly...

Data from: Scale dependence of the diversity–stability relationship in a temperate grassland

Yunhai Zhang, Nianpeng He, Michel Loreau, Qingmin Pan & Xingguo Han
1. A positive relationship between biodiversity and ecosystem stability has been reported in many ecosystems; however, it has yet to be determined whether and how spatial scale affects this relationship. Here, for the first time, we assessed the effects of alpha, beta and gamma diversity on ecosystem stability and the scale dependence of the slope of the diversity–stability relationship. 2. By employing a long-term (33 years) dataset from a temperate grassland, northern China, we calculated...

Data from: Phylogenetic context determines the role of competition in adaptive radiation

Jiaqi Tan, Matthew R. Slattery, Xian Yang & Lin Jiang
Understanding ecological mechanisms regulating the evolution of biodiversity is of much interest to ecologists and evolutionary biologists. Adaptive radiation constitutes an important evolutionary process that generates biodiversity. Competition has long been thought to influence adaptive radiation, but the directionality of its effect and associated mechanisms remain ambiguous. Here, we report a rigorous experimental test of the role of competition on adaptive radiation using the rapidly evolving bacterium Pseudomonas fluorescens SBW25 interacting with multiple bacterial species...

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