170 Works

Data from: Pathogens manipulate the preference of vectors, slowing disease spread in a multi-host system

Lauren G. Shoemaker, Evelyn Hayhurst, Christopher P. Weiss-Lehman, Alexander T. Strauss, Anita Porath-Krause, Elizabeth T. Borer, Eric W. Seabloom & Allison K. Shaw
The spread of vector‐borne pathogens depends on a complex set of interactions among pathogen, vector, and host. In single‐host systems, pathogens can induce changes in vector preferences for infected vs. healthy hosts. Yet it is unclear if pathogens also induce changes in vector preference among host species, and how changes in vector behaviour alter the ecological dynamics of disease spread. Here, we couple multi‐host preference experiments with a novel model of vector preference general to...

An experimental test of community-based strategies for mitigating human-wildlife conflict around protected areas

Ryan Long, Paola Branco, Jerod Merkle, Robert Pringle, Lucy King, Tosca Tindall & Marc Stalmans
Natural habitats are rapidly being converted to cultivated croplands, and crop-raiding by wildlife threatens both wildlife conservation and human livelihoods worldwide. We combined movement data from GPS-collared elephants with camera-trap data and local reporting systems in a before-after-control-impact design to evaluate community-based strategies for reducing crop raiding outside Mozambique’s Gorongosa National Park. All types of experimental fences tested (beehive, chili, beehive and chili combined, and procedural controls) significantly reduced the number of times elephants left...

Data from: Machine learning to classify animal species in camera trap images: applications in ecology

Micheal A. Tabak, Mohammad Sadegh Norouzzadeh, Michael A. Tabak, David W. Wolfson, Steven J. Sweeney, Paul A. Di Salvo, Ryan S. Miller, Jesse S. Lewis, Jeff Clune, Ryan K. Brook, Elizabeth G. Mandeville, Paul M. Lukacs, Anna K. Moeller, Raoul K. Boughton, Bethany Wight, James C. Beasley & Peter E. Schlichting
Motion‐activated cameras (“camera traps”) are increasingly used in ecological and management studies for remotely observing wildlife and are amongst the most powerful tools for wildlife research. However, studies involving camera traps result in millions of images that need to be analysed, typically by visually observing each image, in order to extract data that can be used in ecological analyses. We trained machine learning models using convolutional neural networks with the ResNet‐18 architecture and 3,367,383 images...

Data from: Plant host identity and soil macronutrients explain little variation in sapling endophyte community composition: is disturbance an alternative explanation?

Eric A. Griffin, Joshua G. Harrison, Steven W. Kembel, Alyssa A. Carrell, S. Joseph Wright & Walter P. Carson
1. Bacterial endophytes may be fairly host specific; nonetheless, an important subset of taxa may be shared among numerous host species forming a community-wide core microbiome. Moreover, other key factors, particularly the supply of limiting macronutrients and disturbances, may supersede the importance of host identity. 2. We tested the following four non-mutually exclusive hypotheses: 1. The Host Identity Hypothesis: endophytes vary substantially among different host plant species. 2. The Core Microbiome Hypothesis: a subset of...

Data from: A comprehensive analysis of autocorrelation and bias in home range estimation

Michael J. Noonan, Marlee A. Tucker, Christen H. Fleming, Tom S. Akre, Susan C. Alberts, Abdullahi H. Ali, Jeanne Altmann, Pamela C. Antunes, Jerrold L. Belant, Dean Beyer, Niels Blaum, Katrin Böhning-Gaese, , Rogerio De Paula Cunha, Jasja Dekker, Jonathan Drescher-Lehman, Nina Farwig, Claudia Fichtel, Christina Fischer, Adam T. Ford, Jacob R. Goheen, René Janssen, Florian Jeltsch, Matthew Kauffman, Peter M. Kappeler … & Justin M. Calabrese
Home range estimation is routine practice in ecological research. While advances in animal tracking technology have increased our capacity to collect data to support home range analysis, these same advances have also resulted in increasingly autocorrelated data. Consequently, the question of which home range estimator to use on modern, highly autocorrelated tracking data remains open. This question is particularly relevant given that most estimators assume independently sampled data. Here, we provide a comprehensive evaluation of...

Functional traits of avian frugivores have shifted following species extinction and introduction in the Hawaiian Islands

Samuel Case & Corey Tarwater
The extinction and introduction of species can alter ecological processes owing to the loss or gain of species roles. In vertebrate-dependent seed dispersal, mutualisms between frugivores and fruiting plants depend, in part, on matching of functional traits. High species turnover of frugivores has occurred on the Hawaiian Islands, owing to both the loss of native frugivores and the introduction of a new suite of frugivores. How this turnover has altered the functional traits of frugivores...

Infection status as the basis for habitat choices in a wild amphibian

Gabriel Barrile, Anna Chalfoun & Annika Walters
Animals challenged with disease may select specific habitat conditions that help prevent or reduce infection. Whereas pre-infection avoidance of habitats with a high risk of disease exposure has been documented in both captive and free-ranging animals, evidence of post-infection habitat switching to conditions that promote the clearing of infection is limited to laboratory experiments. The extent to which wild animals proximately modify habitat choices in response to infection status therefore remains unclear. We investigated pre-infection...

Data from: The value of the species interaction-abiotic stress hypothesis (SIASH) for invasion biology: using native latitude to explain non-native latitudinal range sizes

Mark Kirk, Brandon Hays & Chris Petranek
Establishment and spread of introduced species are difficult to predict because they are subject to a myriad of factors. A hypothesis which integrates multiple ecological processes, such as the species interaction-abiotic stress hypothesis (SIASH), may improve our ability to predict introduction success (i.e. establishment and spread). SIASH postulates that, along an environmental gradient, species’ range limits are set by abiotic stress at the environmentally harsh end of that gradient and by species interactions at the...

Data from: Elk migration influences the risk of disease spillover in the Greater Yellowstone Ecosystem

Nathaniel Rayl, Jerod Merkle, Kelly Proffitt, Emily Almberg, Jennifer Jones, Justin Gude & Paul Cross
Wildlife migrations provide important ecosystem services, but they are declining. Within the Greater Yellowstone Ecosystem (GYE) some elk (Cervus canadensis) herds are losing migratory tendencies, which may increase spatiotemporal overlap between elk and livestock (domestic bison [Bison bison] and cattle [Bos taurus]), potentially exacerbating pathogen transmission risk. We combined disease, movement, demographic, and environmental data from eight elk herds in the GYE to examine the differential risk of brucellosis transmission (through aborted fetuses) from migrant...

Finescale dace occurrence and abiotic and biotic covariates for the Belle Fourche River and Niobrara River basins

Evan Booher & Annika Walters
Aim The factors that set range limits for animal populations can inform management plans aimed at maintaining regional biodiversity. We examine abiotic and biotic drivers of the distribution of finescale dace (Chrosomus neogaeus) in two Great Plains basins to identify limiting factors for a threatened freshwater fish population at the edge of their range. Location Great Plains, Nebraska, South Dakota, and Wyoming, USA Methods We investigated abiotic and biotic factors influencing the contemporary distribution of...

Implications for evolutionary trends from the pairing frequencies among golden-winged and blue-winged warblers and their hybrids

John Confer, Cody Porter, Kyle Aldinger, Ronald Canterbury, Jeffery Larkin & Darin McNeil
Extensive range loss for the Golden-winged Warbler (Vermivora chrysoptera) has occurred in areas of intrusion by the Blue-winged Warbler (V. cyanoptera) potentially related to their close genetic relationship. We compiled data on social pairing from nine studies for 2,679 resident Vermivora to assess evolutionary divergence. Hybridization between pure phenotypes occurred with 1.2% of resident males for sympatric populations. Pairing success rates for Golden-winged Warblers was 83% and for Blue-winged Warblers was 77%. Pairing success for...

Data from: Enhanced seed defenses potentially relax selection by seed predators against serotiny in lodgepole pine

Craig Benkman & Anna Parker
Serotiny, the retention of seeds in a canopy seed bank until high temperatures cause seeds to be released, is an important life history trait for many woody plants in fire-prone habitats. Serotiny provides a competitive advantage after fire but increases vulnerability to predispersal seed predation, due to the seeds being retained in clusters in predictable locations for extended periods. This creates opposing selection pressures. Serotiny is favored in areas of high fire frequency, but is...

Data and code for: Rocky Mountain subalpine forests now burning more than any time in recent millennia

Philip Higuera, Bryan Shuman & Kyra Wolf
The 2020 fire season punctuated a decades-long trend of increased fire activity across the western United States, nearly doubling the total area burned in the central Rocky Mountains since 1984. Understanding the causes and implications of such extreme fire seasons, particularly in subalpine forests that have historically burned infrequently, requires a long-term perspective not afforded by observational records. We place 21st century fire activity in subalpine forests in the context of climate and fire history...

Air temperatures overpredict changes to stream fish assemblages with climate warming compared to water temperatures

Mark Kirk & Frank Rahel
Studies predicting how the distribution of aquatic organisms will shift with climate change often use projected increases in air temperature or water temperature. However, the assumed correlations between water temperature change and air temperature change can be problematic, especially for mountainous, high elevation streams. Using stream fish assemblage data from 1,442 surveys across a mountain - plains gradient (Wyoming, USA; 1990-2018), we compared the responsiveness of thermal guilds, native status groups, and assemblage structure to...

Worldwide evidence of a unimodal relationship between productivity and plant species richness

Lauchlan H. Fraser, Jason Pither, Anke Jentsch, Marcelo Sternberg, Martin Zobel, Diana Askarizadeh, Sandor Bartha, Carl Beierkuhnlein, Jonathan A. Bennett, Alex Bittel, Bazartseren Boldgiv, Ilsi I. Boldrini, Edward Bork, Leslie Brown, Marcelo Cabido, James Cahill, Cameron N. Carlyle, Giandiego Campetella, Stefano Chelli, Ofer Cohen, Anna-Maria Csergo, Sandra Diaz, Lucas Enrico, David Ensing, Alessandra Fidelis … & Szilárd Szentes
The search for predictions of species diversity across environmental gradients has challenged ecologists for decades. The humped-back model (HBM) suggests that plant diversity peaks at intermediate productivity; at low productivity few species can tolerate the environmental stresses, and at high productivity a few highly competitive species dominate. Over time the HBM has become increasingly controversial, and recent studies claim to have refuted it. Here, by using data from coordinated surveys conducted throughout grasslands worldwide and...

Data from: Unexpected ancestry of Populus seedlings from a hybrid zone implies a large role for postzygotic selection in the maintenance of species

Dorothea Lindtke, Zachariah Gompert, Christian Lexer & C. Alex Buerkle
In the context of potential interspecific gene flow, the integrity of species will be maintained by reproductive barriers that reduce genetic exchange, including traits associated with prezygotic isolation or poor performance of hybrids. Hybrid zones can be used to study the importance of different reproductive barriers, particularly when both parental species and hybrids occur in close spatial proximity. We investigated the importance of barriers to gene flow that act early versus late in the life...

Data from: The genomic consequences of adaptive divergence and reproductive isolation between species of manakins

Thomas L. Parchman, Zachariah Gompert, Michael J. Braun, Robb T. Brumfield, D. B. McDonald, J. Albert C. Uy, G. Zhang, Erich D. Jarvis, B. A. Schlinger & C. A. Buerkle
The processes of adaptation and speciation are expected to shape genomic variation within and between diverging species. Here we analyze genomic heterogeneity of genetic differentiation and introgression in a hybrid zone between two bird species (Manacus candei and M. vitellinus) using 59 100 SNPs, a whole genome assembly, and Bayesian models. Measures of genetic differentiation (inline image) and introgression (genomic cline center [α] and rate [β]) were highly heterogeneous among loci. We identified thousands of...

Data from: The evolutionary origins of modularity

Jeff Clune, Jean-Baptiste Mouret & Hod Lipson
A central biological question is how natural organisms are so evolvable (capable of quickly adapting to new environments). A key driver of evolvability is the widespread modularity of biological networks--their organization as functional, sparsely connected subunits--but there is no consensus regarding why modularity itself evolved. While most hypotheses assume indirect selection for evolvability, here we demonstrate that the ubiquitous, direct selection pressure to reduce the cost of connections between network nodes causes the emergence of...

Data from: Demographic drivers of a refugee species: large-scale experiments guide strategies for reintroductions of hirola

Abdullahi H. Ali, Matthew J. Kauffman, Rajan Amin, Amos Kibara, Juliet King, David Mallon, Charles Musyoki & Jacob R. Goheen
Effective reintroduction strategies require accurate estimates of vital rates and the factors that influence them. We estimated vital rates of hirola (Beatragus hunteri) populations exposed to varying levels of predation and rangeland quality from 2012 to 2015, and then built population matrices to estimate the finite rate of population change (λ) and demographic sensitivities. Mean survival for all age classes and population growth was highest in the low predation/high-rangeland quality setting (λ = 1.08 ±...

Recent hybrids recapitulate ancient hybrid outcomes

Zachariah Gompert, Samridhi Chaturvedi, Lauren Lucas, C. Alex Buerkle, James Fordyce, Matthew Forister & Chris Nice
Genomic outcomes of hybridization depend on selection and recombination in hybrids. Whether these processes have similar effects on hybrid genome composition in contemporary hybrid zones versus ancient hybrid lineages is unknown. Here we show that patterns of introgression in a contemporary hybrid zone in Lycaeides butterflies predict patterns of ancestry in geographically adjacent, older hybrid populations. We find a particularly striking lack of ancestry from one of the hybridizing taxa, Lycaeides melissa, on the Z...

Data from: Negative frequency-dependent foraging behaviour in a generalist herbivore (Alces alces) and its stabilizing influence on food-web dynamics

Sarah R. Hoy, John A. Vucetich, Rongsong Liu, Don L. DeAngelis, Rolf O. Peterson, Leah M. Vucetich & John J. Henderson
1.Resource selection is widely appreciated to be context‐dependent and shaped by both biological and abiotic factors. However, few studies have empirically assessed the extent to which selective foraging behaviour is dynamic and varies in response to environmental conditions for free‐ranging animal populations. 2.Here, we assessed the extent that forage selection fluctuated in response to different environmental conditions for a free‐ranging herbivore, moose (Alces alces) in Isle Royale National Park, over a 10‐year period. More precisely,...

Data from: Migrating bison engineer the green wave

Chris Geremia, Jerod Merkle, Daniel Eacker, Rick Wallen, P.J. White, Mark Hebblewhite & Matthew Kauffman
Newly emerging plants provide the best forage for herbivores. To exploit this fleeting resource, migrating herbivores align their movements to surf the wave of spring green-up. With new technology to track migrating animals, the Green Wave Hypothesis has steadily gained empirical support across a diversity of migratory taxa. This hypothesis assumes the green wave is controlled by variation in climate, weather, and topography, and its progression dictates the timing, pace, and extent of migrations. However,...

Accuracy of de novo assembly of DNA sequences from double‐digest libraries varies substantially among software

Melanie E. F. LaCava, Ellen O. Aikens, Libby C. Megna, Gregg Randolph, Charley Hubbard & C. Alex Buerkle
Advances in DNA sequencing have made it feasible to gather genomic data for non-model organisms and large sets of individuals, often using methods for sequencing subsets of the genome. Several of these methods sequence DNA associated with endonuclease restriction sites (various RAD and GBS methods). For use in taxa without a reference genome, these methods rely on de novo assembly of fragments in the sequencing library. Many of the software options available for this application...

Novel hybrid finds a peri-urban niche: Allen’s Hummingbirds in southern California

Braden L. Godwin, Melanie E. F. LaCava, Beth Mendelsohn, Roderick B. Gagne, Kyle D. Gustafson, Sierra M. Love Stowell, Andrew Engilis, Lisa A. Tell & Holly B. Ernest
Species range expansions and contractions can have ecological and genetic consequences, and thus are important areas of study for conservation. Hybridization and introgression are not uncommon in closely related populations that experience secondary contact during a range expansion. Allen’s Hummingbird (Selasphorus sasin) in California comprises two subspecies: the migratory S. s. sasin, which winters in central Mexico and breeds in central and northern California, and the resident S. s. sedentarius, which lives and breeds year-round...

Data from: Population genomics of divergence among extreme and intermediate color forms in a polymorphic insect

Jeffrey D. Lozier, Jason M. Jackson, Michael E. Dillon & James P. Strange
Geographic variation in insect coloration is among the most intriguing examples of rapid phenotypic evolution and provides opportunities to study mechanisms of phenotypic change and diversification in closely related lineages. The bumble bee Bombus bifarius comprises two geographically disparate color groups characterized by red-banded and black-banded abdominal pigmentation, but with a range of spatially and phenotypically intermediate populations across western North America. Microsatellite analyses have revealed that B. bifarius in the USA are structured into...

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