220 Works

Data from: Fishing, fast growth, and climate variability increase the risk of collapse

Malin L. Pinsky & David Byler
Species around the world have suffered collapses, and a key question is why some populations are more vulnerable than others. Traditional conservation biology and evidence from terrestrial species suggest that slow-growing populations are most at risk, but interactions between climate variability and harvest dynamics may alter or even reverse this pattern. Here, we test this hypothesis globally. We use boosted regression trees to analyse the influences of harvesting, species traits and climate variability on the...

Data from: Molecular detection of invertebrate prey in vertebrate diets: trophic ecology of Caribbean island lizards

Tyler R. Kartzinel & Robert M. Pringle
Understanding community assembly and population dynamics frequently requires detailed knowledge of food web structure. For many consumers, obtaining precise information about diet composition has traditionally required sacrificing animals or other highly invasive procedures, generating tension between maintaining intact study populations and knowing what they eat. We developed 16S mitochondrial DNA sequencing methods to identify arthropods in the diets of generalist vertebrate predators without requiring a blocking primer. We demonstrate the utility of these methods for...

Data from: Climatic variation modulates the indirect effects of large herbivores on small-mammal habitat use

Ryan A. Long, Alois Wambua, Jacob R. Goheen, Todd M. Palmer & Robert M. Pringle
Large mammalian herbivores (LMH) strongly shape the composition and architecture of plant communities. A growing literature shows that negative direct effects of LMH on vegetation frequently propagate to suppress the abundance of smaller consumers. Indirect effects of LMH on the behaviour of these consumers, however, have received comparatively little attention despite their potential ecological significance. We sought to understand (i) how LMH indirectly shape small-mammal habitat use by altering the density and distribution of understorey...

Data from: The effect of atomoxetine on random and directed exploration in humans

Christopher M. Warren, Robert C. Wilson, Nic J. Van Der Wee, Eric J. Giltay, Martijn S. Van Noorden, Jonathan D. Cohen & Sander Nieuwenhuis
The adaptive regulation of the trade-off between pursuing a known reward (exploitation) and sampling lesser-known options in search of something better (exploration) is critical for optimal performance. Theory and recent empirical work suggest that humans use at least two strategies for solving this dilemma: a directed strategy in which choices are explicitly biased toward information seeking, and a random strategy in which decision noise leads to exploration by chance. Here we examined the hypothesis that...

Data from: Sexually dimorphic gene expression and transcriptome evolution provides mixed evidence for a fast‐Z effect in Heliconius

Ana Pinharanda, Marjolaine Rousselle, Simon H. Martin, Joseph J. Hanly, John W. Davey, Sujai Kumar, Nicolas Galtier & Chris D. Jiggins
Sex chromosomes have different evolutionary properties compared to autosomes due to their hemizygous nature. In particular, recessive mutations are more readily exposed to selection, which can lead to faster rates of molecular evolution. Here, we report patterns of gene expression and molecular evolution for a group of butterflies. First, we improve the completeness of the Heliconius melpomene reference annotation, a neotropical butterfly with a ZW sex determination system. Then, we analyse RNA from male and...

Data from: Mapping the imprint of biotic interactions on β-diversity

Marc Ohlmann, Florent Mazel, Loïc Chalmandrier, Stéphane Bec, Eric Coissac, Ludovic Gielly, Johan Pansu, Vincent Schilling, Pierre Taberlet, Lucie Zinger, Jerome Chave & Wilfried Thuiller
Investigating how trophic interactions influence the β-diversity of meta-communities is of paramount importance to understanding the processes shaping biodiversity distribution. Here, we apply a statistical method for inferring the strength of spatial dependencies between pairs of species groups. Using simulated community data generated from a multi-trophic model, we showed that this method can approximate biotic interactions in multi-trophic communities based on β-diversity patterns across groups. When applied to soil multi-trophic communities along an elevational gradient...

Data from: Effects of mis-alignment between dispersal traits and landscape structure on dispersal success in fragmented landscapes

Justine A. Atkins, George L. W. Perry & Todd E. Dennis
Dispersal is fundamental to population dynamics and hence extinction risk. The dispersal success of animals depends on the biophysical structure of their environments and their biological traits; however, comparatively little is known about how evolutionary trade-offs among suites of biological traits affect dispersal potential. We developed a spatially explicit agent-based simulation model to evaluate the influence of trade-offs among a suite of biological traits on the dispersal success of vagile animals in fragmented landscapes. We...

Data from: When hawks give rise to doves: the evolution and transition of enforcement strategies

Omar Tonsi Eldakar, Andrew C. Gallup & William Wallace Driscoll
The question of how altruism can evolve despite its local disadvantage to selfishness has produced a wealth of theoretical and empirical research capturing the attention of scientists across disciplines for decades. One feature that has remained consistent through this outpouring of knowledge has been that researchers have looked to the altruists themselves for mechanisms by which altruism can curtail selfishness. An alternative perspective may be that just as altruists want to limit selfishness in the...

Data from: Genetic architecture and adaptive significance of the selfing syndrome in Capsella

Tanja Slotte, Khaled Michel Hazzouri, David L Stern, Peter Andolfatto & Stephen I. Wright
The transition from outcrossing to predominant self-fertilization is one of the most common evolutionary transitions in flowering plants. This shift is often accompanied by a suite of changes in floral and reproductive characters termed the selfing syndrome. Here, we characterize the genetic architecture and evolutionary forces underlying evolution of the selfing syndrome in Capsella rubella following its recent divergence from the outcrossing ancestor Capsella grandiflora. We conduct genotyping by multiplexed shotgun sequencing and map floral...

Data from: Community-wide changes in inter-taxonomic temporal co-occurrence resulting from phenological shifts

Fangyuan Hua, Junhua Hu, Yang Liu, Xingli Giam, Tien Ming Lee, Hao Luo, Jia Wu, Qiaoyi Liang, Jian Zhao, Xiaoyan Long, Hong Pang, Biao Wang, Wei Liang, Zhengwang Zhang, Xuejie Gao & Jiang Zhu
Global climate change is known to affect the assembly of ecological communities by altering species’ spatial distribution patterns, but little is known about how climate change may affect community assembly by changing species’ temporal co-occurrence patterns, which is highly likely given the widely observed phenological shifts associated with climate change. Here we analyzed a 29-year phenological data set comprising community-level information on the timing and span of temporal occurrence in 11 seasonally occurring animal taxon...

Data from: The Achilles' heel hypothesis: misinformed keystone individuals impair collective learning and reduce group success

Jonathan Pruitt, Colin Wright, Carl Keiser, Alexander DeMarco, Matt Grobis, Noa Pinter-Wollman, Matthew M. Grobis, Alex E. DeMarco, Carl N. Keiser, Jonathan N. Pruitt & Colin M. Wright
Many animal societies rely on highly influential keystone individuals for proper functioning. When information quality is important for group success, such keystone individuals have the potential to diminish group performance if they possess inaccurate information. Here we test whether information quality (accurate or inaccurate) influences collective outcomes when keystone individuals are the first to acquire it. We trained keystone or generic individuals to attack or avoid novel stimuli and implanted these seed individuals within groups...

Data from: Machine learning for characterization of insect vector feeding

Denis S. Willett, Justin George, Nora S. Willett, Lukasz L. Stelinski & Stephen L. Lapointe
Insects that feed by ingesting plant and animal fluids cause devastating damage to humans, livestock, and agriculture worldwide, primarily by transmitting pathogens of plants and animals. The feeding processes required for successful pathogen transmission by sucking insects can be recorded by monitoring voltage changes across an insect-food source feeding circuit. The output from such monitoring has traditionally been examined manually, a slow and onerous process. We taught a computer program to automatically classify previously described...

Data from: Environmental heterogeneity generates opposite gene-by-environment interactions for two fitness-related traits within a population

Zachary Wyatt Culumber, Molly Schumer, Scott Monks & Michael Tobler
Theory predicts that environmental heterogeneity offers a potential solution to the maintenance of genetic variation within populations, but empirical evidence remains sparse. The livebearing fish Xiphophorus variatus exhibits polymorphism at a single locus, with different alleles resulting in up to five distinct melanistic “tailspot” patterns within populations. We investigated the effects of heterogeneity in two ubiquitous environmental variables (temperature and food availability) on two fitness-related traits (upper thermal limits and body condition) in two different...

Data from: Woody plant biomass and carbon exchange depend on elephant-fire interactions across a productivity gradient in African savanna

Adam F. A. Pellegrini, Robert M. Pringle, Navashni Govender, Lars O. Hedin & Lars. O. Hedin
Elephants and fire are individually well-known disturbance agents within savanna ecosystems, but their interactive role in governing tree-cover dynamics and savanna–forest biome boundaries remains unresolved. Of central importance are the mechanisms by which elephants vs. fire affect tree biomass and cover, and how – over long time periods – both factors interact with rainfall and soils to govern tree biomass and carbon dynamics. Here, we evaluated the response of woody vegetation to 56 years of...

Data from: The within-host dynamics of infection in trans-generationally primed flour beetles

Ann T. Tate, Peter Andolfatto, Jeffery P. Demuth & Andrea L. Graham
Many taxa exhibit plastic immune responses initiated after primary microbial exposure that provide increased protection against disease-induced mortality and the fitness costs of infection. In several arthropod species, this protection can even be passed from parents to offspring through a phenomenon called trans-generational immune priming. Here, we first demonstrate that trans-generational priming is a repeatable phenomenon in flour beetles (Tribolium castaneum) primed and infected with Bacillus thuringiensis (Bt). We then quantify the within-host dynamics of...

Data from: Evolution of mammalian migrations for refuge, breeding, and food

Gitanjali E. Gnanadesikan, William D. Pearse & Allison K. Shaw
Many organisms migrate between distinct habitats, exploiting variable resources while profoundly affecting ecosystem services, disease spread, and human welfare. However, the very characteristics that make migration captivating and significant also make it difficult to study, and we lack a comprehensive understanding of which species migrate and why. Here we show that, among mammals, migration is concentrated within Cetacea and Artiodactyla but also diffusely spread throughout the class (found in 12 of 27 orders). We synthesize...

Data from: Estimating infection prevalence: best practices and their theoretical underpinnings

Ian F. Miller, India Schneider-Crease, Charles L. Nunn & Michael P. Muehlenbein
Accurately estimating infection prevalence is fundamental to the study of population health, disease dynamics, and infection risk factors. Prevalence is estimated as the proportion of infected individuals (“individual-based estimation”), but is also estimated as the proportion of samples from which the disease-causing organisms are recovered (“anonymous estimation”). The latter method is often used when researchers lack information on individual host identity, which can occur during noninvasive sampling of wild populations or when the individual that...

Data from: Natural selection interacts with recombination to shape the evolution of hybrid genomes

Molly Schumer, Chenling Xu, Daniel L Powell, Arun Durvasula, Laurits Skov, Chris Holland, John C Blazier, Sriram Sankararaman, Peter Andolfatto, Gil G Rosenthal & Molly Przeworski
To investigate the consequences of hybridization between species, we studied three replicate hybrid populations that formed naturally between two swordtail fish species, estimating their fine-scale genetic map and inferring ancestry along the genomes of 690 individuals. In all three populations, ancestry from the “minor” parental species is more common in regions of high recombination and where there is linkage to fewer putative targets of selection. The same patterns are apparent in a reanalysis of human...

Domestication phenotype linked to vocal behavior in marmoset monkeys

Asif Ghazanfar, Lauren Kelly, Daniel Takahashi, Sandra Winters, Rebecca Terrett & James Higham
The domestication syndrome refers to a set of traits that are the incidental by-products of artificial selection for increased tolerance towards humans. One hypothesis is that some species like humans and bonobos “self domesticated”, that they have been under selection for that same suite of domesticated phenotypes. However, the evidence for this has been largely circumstantial. Here, we provide evidence that in marmoset monkeys, the size of a domestication phenotype—a white facial fur patch—is linked...

Data from: Upper tidal flats are disproportionately important for the conservation of migratory shorebirds

Tong Mu & David S. Wilcove
Migratory animals are crucial for global ecosystems, yet many species are threatened by human activities. Coastal shorebirds along the East Asian-Australasian Flyway have experienced precipitous declines over the past three decades, primarily due to the rapid development of the tidal flats, their major stopover habitat. However, populations of several species have declined must faster than the rate of habitat loss. To explain this discrepancy, we quantified the foraging distribution of 17 migratory shorebirds throughout the...

Data from: Covariation of diet and gut microbiome in African megafauna

Tyler R. Kartzinel, Julianna C. Hsing, Paul M. Musili, Bianca R. P. Brown & Robert M. Pringle
A major challenge in biology is to understand how phylogeny, diet, and environment shape the mammalian gut microbiome. Yet most studies of non-human microbiomes have relied on relatively coarse dietary categorizations and have focused either on individual wild populations or on captive animals that are sheltered from environmental pressures, which may obscure the effects of dietary and environmental variation on microbiome composition in diverse natural communities. We analyzed plant and bacterial DNA in fecal samples...

Fruit syndromes in Viburnum: correlated evolution of color, nutritional content, and morphology in bird-dispersed fleshy fruits

Miranda Sinnott-Armstrong, Chong Lee, Wendy Clement & Michael Donoghue
Premise A key question in plant dispersal via animal vectors is where and why fruit colors vary between species and how color relates to other fruit traits. To better understand the factors shaping the evolution of fruit color diversity, we tested for the existence of syndromes of traits (color, morphology, and nutrition) in the fruits of Viburnum. We placed these results in a larger phylogenetic context and reconstructed ancestral states to assess how Viburnum fruit...

Data from: Dry-season decline in tree sapflux is correlated with leaf turgor loss point in a tropical rainforest

Isabelle Maréchaux, Damien Bonal, Megan K. Bartlett, Benoît Burban, Sabrina Coste, Elodie A. Courtois, Maguy Dulormne, Jean-Yves Goret, Eléonore Mira, Ariane Mirabel, Lawren Sack, Clément Stahl & Jerome Chave
1. Water availability is a key determinant of forest ecosystem function and tree species distributions. While droughts are increasing in frequency in many ecosystems, including in the tropics, plant responses to water supply vary with species and drought intensity, and are therefore difficult to model. Based on physiological first principles, we hypothesized that trees with a lower turgor loss point (πtlp), i.e., a more negative leaf water potential at wilting, would maintain water transport for...

Data from: Tropical tree height and crown allometries for the Barro Colorado Nature Monument, Panama: a comparison of alternative hierarchical models incorporating interspecific variation in relation to life history traits

Isabel Martinez Cano, Helene C. Muller-Landau, S. Joseph Wright, Stephanie A. Bohlman & Stephen W. Pacala
Tree allometric relationships are widely employed for estimating forest biomass and production and are basic building blocks of dynamic vegetation models. In tropical forests, allometric relationships are often modeled by fitting scale-invariant power functions to pooled data from multiple species, an approach that fails to capture changes in scaling during ontogeny and physical limits to maximum tree size and that ignores interspecific differences in allometry. Here, we analyzed allometric relationships of tree height (9884 individuals)...

Data from: Vocal state change through laryngeal development

Yisi S. Zhang, Daniel Y. Takahashi, Diana A. Liao, Asif A. Ghazanfar & Coen P. H. Elemans
Across vertebrates, progressive changes in vocal behavior during postnatal development are typically attributed solely to developing neural circuits. How the changing body influences vocal development remains unknown. Here we show that state changes in the contact vocalizations of infant marmoset monkeys, which transition from noisy, low frequency cries to tonal, higher pitched vocalizations in adults, are caused partially by laryngeal development. Combining analyses of natural vocalizations, motorized excised larynx experiments, tensile material tests and high-speed...

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