212 Works

Data from: Dispersal increases the resilience of tropical savanna and forest distributions

Nikunj Goel, Vishwesha Guttal, Simon Levin & Carla Staver
Global change may induce changes in savanna and forest distributions, but the dynamics of these changes remain unclear. Classical biome theory suggests that climate is predictive of biome distributions, such that shifts will be continuous and reversible. This view, however, cannot explain the overlap in the climatic ranges of tropical biomes, which some argue may result from fire-vegetation feedbacks, maintaining savanna and forest as bistable states. Under this view, biome shifts are argued to be...

Amplitude modulations of cortical sensory responses in pulsatile evidence accumulation

Sue Ann Koay
Condensed neural and behavioral data, included secondary results from model fits and analyses. This dataset contains all information required to recreate figures from the paper.

Vaccine driven virulence evolution: Consequences of unbalanced reductions in mortality and transmission and implications for pertussis vaccines

Ian Miller & C. Jessica Metcalf
Many vaccines have heterogenous effects across individuals. Additionally, some vaccines do not prevent infection, but reduce disease-associated mortality and transmission. Both of these factors will alter selection pressures on pathogens, and thus shape the evolution of pathogen virulence. We use a mathematical modeling framework to show that 1. the balance of how vaccines reduce transmission vs. mortality, and 2. individual variability in protection conferred, both shape the evolution of pathogen virulence. Epidemiological (burden of disease)...

Data from: Low-dimensional spatio-temporal dynamics underlie cortex-wide neural activity

Timothy Buschman & Camden MacDowell
Cognition arises from the dynamic flow of neural activity through the brain. To capture these dynamics, we used mesoscale calcium imaging to record neural activity across the dorsal cortex of awake mice. We found that the large majority of variance in cortex-wide activity (~75%) could be explained by a limited set of ~14 ‘motifs’ of neural activity. Each motif captured a unique spatio-temporal pattern of neural activity across the cortex. These motifs generalized across animals...

Data from: Social bonds do not mediate the relationship between early adversity and adult glucocorticoids in wild baboons

Stacy Rosenbaum, Shuxi Zeng, Fernando Campos, Laurence Gesquiere, Jeanne Altmann, Susan Alberts, Fan Li & Elizabeth Archie
In humans and other animals, harsh conditions in early life can have profound effects on adult physiology, including the stress response. This relationship may be mediated by a lack of supportive relationships in adulthood. That is, early life adversity may inhibit the formation of supportive social ties, and weak social support is itself often linked to dysregulated stress responses. Here we use prospective, longitudinal data from wild baboons in Kenya to test the links between...

Data from: Canine length in wild male baboons: maturation, aging and social dominance rank

Jordi Galbany, Jenny Tung, Jeanne Altmann & Susan C. Alberts
Canines represent an essential component of the dentition for any heterodont mammal. In primates, like many other mammals, canines are frequently used as weapons. Hence, tooth size and wear may have significant implications for fighting ability, and consequently for social dominance rank, reproductive success, and fitness. We evaluated sources of variance in canine growth and length in a well-studied wild primate population because of the potential importance of canines for male reproductive success in many...

Data from: A daily global mesoscale ocean eddy dataset from satellite altimetry

James H. Faghmous, Ivy Frenger, Yuanshun Yao, Robert Warmka, Aron Lindell & Vipin Kumar
Mesoscale ocean eddies are ubiquitous coherent rotating structures of water with radial scales on the order of 100 kilometers. Eddies play a key role in the transport and mixing of momentum and tracers across the World Ocean. We present a global daily mesoscale ocean eddy dataset that contains ~45 million mesoscale features and 3.3 million eddy trajectories that persist at least two days as identified in the AVISO dataset over a period of 1993–2014. This...

Data from: DNA metabarcoding illuminates dietary niche partitioning by African large herbivores

Tyler R. Kartzinel, Patricia A. Chen, Tyler C. Coverdale, David L. Erickson, W. John Kress, Maria L. Kuzmina, Daniel I. Rubenstein, Wei Wang & Robert M. Pringle
Niche partitioning facilitates species coexistence in a world of limited resources, thereby enriching biodiversity. For decades, biologists have sought to understand how diverse assemblages of large mammalian herbivores (LMH) partition food resources. Several complementary mechanisms have been identified, including differential consumption of grasses versus nongrasses and spatiotemporal stratification in use of different parts of the same plant. However, the extent to which LMH partition food-plant species is largely unknown because comprehensive species-level identification is prohibitively...

Data from: Frequent and seasonally variable sublethal anthrax infections are accompanied by short-lived immunity in an endemic system

Carrie A. Cizauskas, Steven E. Bellan, Wendy C. Turner, Russell E. Vance & Wayne M. Getz
1. Few studies have examined host-pathogen interactions in wildlife from an immunological perspective, particularly in the context of seasonal and longitudinal dynamics. In addition, though most ecological immunology studies employ serological antibody assays, endpoint titer determination is usually based on subjective criteria and needs to be made more objective. 2. Despite the fact that anthrax is an ancient and emerging zoonotic infectious disease found worldwide, its natural ecology is not well understood. In particular, little...

Data from: Genetic subdivision and candidate genes under selection in North American gray wolves

Rena M. Schweizer, Bridgett M. VonHoldt, Ryan Harrigan, James C. Knowles, Marco Musiani, David Coltman, John Novembre & Robert K. Wayne
Previous genetic studies of the highly mobile gray wolf (Canis lupus) found population structure that coincides with habitat and phenotype differences. We hypothesized that these ecologically distinct populations (ecotypes) should exhibit signatures of selection in genes related to morphology, coat color, and metabolism. To test these predictions, we quantified population structure related to habitat using a genotyping array to assess variation in 42,036 SNPs in 111 North American gray wolves. Using these SNP data and...

Data from: Ecological legacies of civil war: 35-year increase in savanna tree cover following wholesale large-mammal declines

Joshua H. Daskin, Marc Stalmans & Robert M. Pringle
1. Large mammalian herbivores (LMH) exert strong effects on plants in tropical savannas, and many wild LMH populations are declining. However, predicting the impacts of these declines on vegetation structure remains challenging. 2. Experiments suggest that tree cover can increase rapidly following LMH exclusion. Yet it is unclear whether these results scale up to predict ecosystem-level impacts of LMH declines, which often alter fire regimes, trigger compensatory responses of other herbivores, and accompany anthropogenic land-use...

Data from: Ribosome profiling reveals pervasive and regulated stop codon readthrough in Drosophila melanogaster

Joshua G. Dunn, Catherine K. Foo, Nicolette G. Belletier, Elizabeth R. Gavis & Jonathan S. Weissman
Ribosomes can read through stop codons in a regulated manner, elongating rather than terminating the nascent peptide. Stop codon readthrough is essential to diverse viruses, and phylogenetically predicted to occur in a few hundred genes in Drosophila melanogaster, but the importance of regulated readthrough in eukaryotes remains largely unexplored. Here, we present a ribosome profiling assay (deep sequencing of ribosome-protected mRNA fragments) for Drosophila melanogaster, and provide the first genome-wide experimental analysis of readthrough. Readthrough...

Data from: Transformation of stimulus correlations by the retina

Kristina D. Simmons, Jason S. Prentice, Gašper Tkačik, Jan Homann, Heather K. Yee, Stephanie E. Palmer, Philip C. Nelson & Vijay Balasubramanian
Redundancies and correlations in the responses of sensory neurons may seem to waste neural resources, but they can also carry cues about structured stimuli and may help the brain to correct for response errors. To investigate the effect of stimulus structure on redundancy in retina, we measured simultaneous responses from populations of retinal ganglion cells presented with natural and artificial stimuli that varied greatly in correlation structure; these stimuli and recordings are publicly available online....

Data from: Termite mounds can increase the robustness of dryland ecosystems to climatic change

Juan A. Bonachela, Robert M. Pringle, Efrat Sheffer, Tyler C. Coverdale, Jennifer A. Guyton, Kelly K. Caylor, Simon A. Levin & Corina E. Tarnita
Self-organized spatial vegetation patterning is widespread and has been described using models of scale-dependent feedback between plants and water on homogeneous substrates. As rainfall decreases, these models yield a characteristic sequence of patterns with increasingly sparse vegetation, followed by sudden collapse to desert. Thus, the final, spot-like pattern may provide early warning for such catastrophic shifts. In many arid ecosystems, however, termite nests impart substrate heterogeneity by altering soil properties, thereby enhancing plant growth. We...

Data from: Incomplete loss of a conserved trait: function, latitudinal cline, and genetic constraints

Anne M. Royer, Colin Kremer, Kola George, Samuel G. Pérez, Douglas W. Schemske & Jeffrey K. Conner
Retention of nonfunctional traits over evolutionary time is puzzling, because the cost of trait production should drive loss. Indeed, several studies have found nonfunctional traits are rapidly eliminated by selection. However, theory suggests that complex genetic interactions and a lack of genetic variance can constrain evolution, including trait loss. In the mustard family Brassicaceae the conserved floral condition includes four long and two short stamens, but we show that short stamens in the highly self-pollinating...

Data from: Sexual dimorphism and retinal mosaic diversification following the evolution of a violet receptor in butterflies

Kyle J. McCulloch, Furong Yuan, Ying Zhen, Matthew L. Aardema, Gilbert Smith, Jorge Llorente-Bousquets, Peter Andolfatto & Adriana D. Briscoe
Numerous animal lineages have expanded and diversified the opsin-based photoreceptors in their eyes underlying color vision behavior. However, the selective pressures giving rise to new photoreceptors and their spectral tuning remain mostly obscure. Previously, we identified a violet receptor (UV2) that is the result of a UV opsin gene duplication specific to Heliconius butterflies. At the same time the violet receptor evolved, Heliconius evolved UV-yellow coloration on their wings, due to the pigment 3-hydroxykynurenine (3-OHK)...

Data from: Experimental and statistical reevaluation provides no evidence for Drosophila courtship song rhythms

David L. Stern, Jan Clemens, Philip Coen, Adam J. Calhoun, John B. Hogenesch, Ben J. Arthur & Mala Murthy
From 1980 to 1992, a series of influential papers reported on the discovery, genetics, and evolution of a periodic cycling of the interval between Drosophila male courtship song pulses. The molecular mechanisms underlying this periodicity were never described. To reinitiate investigation of this phenomenon, we previously performed automated segmentation of songs but failed to detect the proposed rhythm [Arthur BJ, et al. (2013) BMC Biol 11:11; Stern DL (2014) BMC Biol 12:38]. Kyriacou et al....

Data from: Determining epistatic selection in admixed populations

Molly Schumer & Yaniv Brandvain
When two diverging species begin hybridizing, selection against hybridization is likely driven not by single substitutions, but by interactions between incompatible mutations. To identify these incompatibilities in natural populations, researchers examine the extent of non-random associations between ancestry at physically unlinked loci in admixed populations. In this approach, which we call “AD scans”, locus-pairs with significantly positive “ancestry disequilibrium” (AD, i.e. locus-pairs that positively covary by ancestry) represent incompatible alleles. Past research has uniformly revealed...

Data from: Predator-induced collapse of niche structure and coexistence on islands

Robert M. Pringle, Tyler R. Kartzinel, Todd M. Palmer, Timothy J. Thurman, Kena Fox-Dobbs, Charles C. Y. Xu, Matthew C. Hutchinson, Tyler C. Coverdale, Joshua H. Daskin, Dominic A. Evangelista, Kiyoko M. Gotanda, , Johanna E. Wegener, Jason J. Kolbe, Thomas W. Schoener, David A. Spiller, Jonathan B. Losos & Rowan D. H. Barrett
Biological invasions represent both a pressing environmental challenge and an opportunity to investigate fundamental ecological processes, such as the role of top predators in regulating species diversity and food-web structure. In whole-ecosystem manipulations of small Caribbean islands where brown anole lizards (Anolis sagrei) were the native top predator, we experimentally staged invasions by competitors (green anoles, A. smaragdinus) and/or novel top predators (curly-tailed lizards, Leiocephalus carinatus). We show that curly-tails destabilized coexistence of competing prey...

Data from: Immigration of susceptible hosts triggers the evolution of alternative parasite defence strategies

Hélène Chabas, Van Houte Stineke, Molin Hoyland-Kroghsbo Nina, Buckling Angus, Westra R. Edze, Nina Molin Høyland-Kroghsbo, Angus Buckling, Stineke Van Houte & Edze R. Westra
Migration of hosts and parasites can have a profound impact on host–parasite ecological and evolutionary interactions. Using the bacterium Pseudomonas aeruginosa UCBPP-PA14 and its phage DMS3vir, we here show that immigration of naive hosts into coevolving populations of hosts and parasites can influence the mechanistic basis underlying host defence evolution. Specifically, we found that at high levels of bacterial immigration, bacteria switched from clustered regularly interspaced short palindromic repeats (CRISPR-Cas) to surface modification-mediated defence. This...

Data from: Stigmergy, collective actions and animal social spacing

Luca Giuggioli, Jonathan R. Potts, Daniel I. Rubenstein & Simon A. Levin
Collective animal behavior studies have led the way in developing models that account for a large number of individuals, but have mostly considered situations where alignment and attraction play a key role, such as in schooling and flocking. By quantifying how animals react to each others' presence, when interaction is via conspecific avoidance rather than alignment or attraction, we present a mechanistic insight that enables us to link individual behavior and space use patterns. As...

Data from: Epiphytes improve host plant water use by microenvironment modification

Daniel E. Stanton, Jackelyn Huallpa Chávez, Luis Villegas, Francisco Villasante, Juan Armesto, Lars O. Hedin & Henry Horn
1. Epiphytes have the potential to modify the canopy environments in which they grow. Accurately evaluating the impact of epiphytes can be challenging, since plants without epiphytes may also otherwise differ from host plants, and experimental removal is impractical and difficult to replicate in many forests. 2. We studied the impacts of epiphytes (primarily fruticose lichens and Tillandsia spp.) on host plants (Eulychnia saint-pieana and Caesalpinia spinosa) in two fog ecosystems in Chile (Pan de...

Data from: Timing malaria transmission with mosquito fluctuations

Romain Pigeault, Quentin Caudron, Nicot Antoine, Ana Rivero, Sylvain Gandon & Antoine Nicot
Temporal variations in the activity of arthropod vectors can dramatically affect the epidemiology and evolution of vector-borne pathogens. Here we explore the “Hawking hypothesis” stating that these pathogens may evolve the ability to time investment in transmission to match the activity of their vectors. First, we use a theoretical model to identify the conditions promoting the evolution of time-varying transmission strategies in pathogens. Second, we experimentally test the “Hawking hypothesis” by monitoring the within-host dynamics...

Data from: Optogenetic dissection of descending behavioral control in Drosophila

Jessica Cande, Shigehiro Namiki, Jirui Qiu, Wyatt Korff, Gwyneth M. Card, Joshua W. Shaevitz, David L. Stern & Gordon J. Berman
In most animals, the brain makes behavioral decisions that are transmitted by descending neurons to the nerve cord circuitry that produces behaviors. In insects, only a few descending neurons have been associated with specific behaviors. To explore how descending neurons control an insect's movements, we developed a novel method to systematically assay the behavioral effects of activating individual neurons on freely behaving terrestrial D. melanogaster. We calculated a two-dimensional representation of the entire behavior space...

Data from: An extensive suite of functional traits distinguishes wet and dry Hawaiian forests and enables prediction of species vital rates

Camila D. Medeiros, Christine Scoffoni, Grace John, Megan Bartlett, Faith Inman-Narahari, Rebecca Ostertag, Susan Cordell, Christian Giardina, Lawren Sack, Megan K. Bartlett & Grace P. John
1. The application of functional traits to predict and explain plant species’ distributions and vital rates has been a major direction in functional ecology for decades, yet numerous physiological traits have not yet been incorporated into the approach. 2. Using commonly measured traits such as leaf mass per area (LMA) and wood density (WD), and additional traits related to water transport, gas exchange and resource economics, including leaf vein, stomatal, and wilting traits, we tested...

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