283 Works

Elephant agricultural use metrics in Mara-Serengeti ecosystem

Nathan Hahn
Agricultural use metrics were calculated for 66 elephants as part of a study to characterize crop use tactics in the Mara-Serengeti ecosystem in Kenya and Tanzania. Metrics were calculated to capture mean agricultural use, maximum use from a moving average, and the difference between mean and max use. These metrics were used to classify agricultural use tactics for each elephant using Gaussian mixture models. Tables are provided with metrics and tactic classifications for the lifetime...

Phylogenomic data reveal widespred introgression across the range of an alpine and arctic specialist

Erik Funk, Garth Spellman, Kevin Winker, Jack Withrow, Erika Zavaleta, Kristen Ruegg & Scott Taylor
Understanding how gene flow affects population divergence and speciation remains challenging. Differentiating one evolutionary process from another can be difficult because multiple processes can produce similar patterns, and more than one process can occur simultaneously. While simple population models produce predictable results, how these processes balance in taxa with patchy distributions and complicated natural histories is less certain. These types of populations might be highly connected through migration (gene flow), but can experience stronger effects...

Mass ratio effects underlie ecosystem responses to environmental change

Melinda Smith, Sarah Koerner, Alan K. Knapp, Meghan Avolio, Francis Chaves, Elsie Denton, John Dietrich, David Gibson, Jesse Gray, Ava Hoffman, David Hoover, Kimberly La Pierre, Andrea Silletti, Kevin Wilcox, Qiang Yu & John Blair
1. Random species loss has been shown experimentally to reduce ecosystem function, sometimes more than other anthropogenic environmental changes. Yet, controversy surrounds the importance of this finding for natural systems where species loss is non-random. 2. We compiled data from 16 multi-year experiments located at a single site in native tallgrass prairie. These experiments included responses to 11 anthropogenic environmental changes, as well as non-random biodiversity loss - either the removal of uncommon/rare plant species...

Dataset associated with Long-Term Effects of Fuel Reduction Treatments on Surface Fuel Loading in the Blue Mountains of Oregon

Kat Morici
Dataset contains a 2015 partial re-measurement of the Blue Mountains Fire and Fire Surrogate study. 8 plots were measured from each of the 16 units, selected randomly from all plots in each unit. Species are recorded using USDA plant codes, "UNKN" is unknown species. For fine fuels, 3 Brown's transects were collected per plot. The length varied based on fuel size class. The "hr1/hr10/hr100" columns include the count of fuel particles within each size class...

Data from: Gene expression differs in codominant prairie grasses under drought

Ava M. Hoffman & Melinda D. Smith
Grasslands of the Central US are expected to experience severe droughts and other climate extremes in the future, yet we know little about how these grasses will respond in terms of gene expression. We compared gene expression in Andropogon gerardii and Sorghastrum nutans, two closely related co-dominant C4 grasses responsible for the majority of ecosystem function, using RNA-seq. We compared Trinity assemblies within each species to determine annotated functions of transcripts responding to drought. Subsequently,...

Data from: Cryptic species diversity reveals biogeographic support for the ‘mountain passes are higher in the tropics’ hypothesis

Brian A. Gill, B. C. Kondratieff, K. L. Casner, A. C. Encalada, A. S. Flecker, D. G. Gannon, C. K. Ghalambor, J. M. Guayasamin, N. L. Poff, M. P. Simmons, S. A. Thomas, K. R. Zamudio & W. C. Funk
The ‘mountain passes are higher in the tropics’ (MPHT) hypothesis posits that reduced climate variability at low latitudes should select for narrower thermal tolerances, lower dispersal and smaller elevational ranges compared with higher latitudes. These latitudinal differences could increase species richness at low latitudes, but that increase may be largely cryptic, because physiological and dispersal traits isolating populations might not correspond to morphological differences. Yet previous tests of the MPHT hypothesis have not addressed cryptic...

Data from: Gene expression and drought response in an invasive thistle

Kathryn G. Turner, Kristin A. Nurkowski & Loren H. Rieseberg
Though rapid phenotypic evolution has been observed in many invasive plant species, less is known about the associated genetic mechanisms. Some hypotheses invoke the evolution of trade-offs in resource allocation to explain phenotypic differences between the native and invaded ranges of a species. Alternately, invasive species may benefit from a generalist strategy and perform well in many environments. Identification of the molecular changes associated with successful invasions can offer clues regarding the mechanistic basis of...

Data from: Cross-biome metagenomic analyses of soil microbial communities and their functional attributes

Noah Fierer, Jonathan W. Leff, Byron J. Adams, Uffe N. Nielsen, Scott Thomas Bates, Christian L. Lauber, Sarah Owens, Jack A. Gilbert, Diana H. Wall & J. Gregory Caporaso
For centuries ecologists have studied how the diversity and functional traits of plant and animal communities vary across biomes. In contrast, we have only just begun exploring similar questions for soil microbial communities despite soil microbes being the dominant engines of biogeochemical cycles and a major pool of living biomass in terrestrial ecosystems. We used metagenomic sequencing to compare the composition and functional attributes of 16 soil microbial communities collected from cold deserts, hot deserts,...

Data from: Balancing selection maintains sex determining alleles in multiple-locus complementary sex determination

Jerome J. Weis, Paul J. Ode & George E. Heimpel
Hymenopteran species in which sex is determined through a haplo-diploid mechanism known as complementary sex determination (CSD) are vulnerable to a unique form of inbreeding depression. Diploids heterozygous at one or more CSD loci develop into females but diploids homozygous at all loci develop into diploid males, which are generally sterile or inviable. Species with multiple polymorphic CSD loci (ml-CSD) may have lower rates of diploid male production than species with a single CSD locus...

Data from: Geosmithia associated with bark beetles and woodborers in the western USA: taxonomic diversity and vector specificity

Miroslav Kolařík, Steven J. Seybold, Ned Tisserat, Wilhelm De Beer, David M. Rizzo, Jiri Hulcr & Martin Kostovčík
Fungi in the genus Geosmithia (Ascomycota: Hypocreales) are frequent associates of bark beetles and woodborers that colonize hardwood and coniferous trees. One species, Geosmithia morbida, is an economically damaging invasive species. The authors surveyed the Geosmithia species of California and Colorado, USA, to (i) provide baseline data on taxonomy of Geosmithia and beetle vector specificity across the western USA; (ii) investigate the subcortical beetle fauna for alternative vectors of the invasive G. morbida; and (iii)...

Data from: Fine scale genetic correlates to condition and migration in a wild Cervid

Joseph M. Northrup, Aaron B. A. Shafer, , David W. Coltman, George Wittemyer & Charles R. Anderson
The relationship between genetic variation and phenotypic traits is fundamental to the study and management of natural populations. Such relationships often are investigated by assessing correlations between phenotypic traits and heterozygosity or genetic differentiation. Using an extensive data set compiled from free-ranging mule deer (Odocoileus hemionus), we combined genetic and ecological data to (i) examine correlations between genetic differentiation and migration timing, (ii) screen for mitochondrial haplotypes associated with migration timing, and (iii) test whether...

Data from: Hybridization of an invasive shrub affects tolerance and resistance to defoliation by a biological control agent

Wyatt I. Williams, Jonathan M. Friedman, John F. Gaskin & Andrew P. Norton
Evolution has contributed to the successful invasion of exotic plant species in their introduced ranges, but how evolution affects particular control strategies is still under evaluation. For instance, classical biological control, a common strategy involving the utilization of highly specific natural enemies to control exotic pests, may be negatively affected by host hybridization because of shifts in plant traits, such as root allocation or chemical constituents. We investigated introgression between two parent species of the...

Data from: The relationship between female brooding and male nestling provisioning: does climate underlie geographic variation in sex roles?

Jongmin Yoon, Helen R. Sofaer, T. Scott Sillett, Scott A. Morrison & Cameron K. Ghalambor
Comparative studies of populations occupying different environments can provide insights into the ecological conditions affecting differences in parental strategies, including the relative contributions of males and females. Male and female parental strategies reflect the interplay between ecological conditions, the contributions of the social mate, and the needs of offspring. Climate is expected to underlie geographic variation in incubation and brooding behavior, and can thereby affect both the absolute and relative contributions of each sex to...

Data from: Interactions among herbivory, climate, topography, and plant age shape riparian willow dynamics in northern Yellowstone National Park, USA

Kristin N. Marshall, David J. Cooper & N. Thompson Hobbs
Understanding how the environmental context modifies the strength of trophic interactions within food webs forms a central challenge in community ecology. Here, we demonstrate the necessity of considering the influence of climate, landscape heterogeneity and demographics for understanding trophic interactions in a well-studied food web in Yellowstone National Park, USA. We studied riparian willow (Salix spp.) establishment and stem growth reconstructed from tree rings on the northern range of Yellowstone over a 30-year period that...

Data from: Female preference for novel males constrains contemporary evolution of assortative mating in guppies

Felipe Dargent, Lisa Chen, Gregor F. Fussmann, Cameron K. Ghalambor & Andrew P. Hendry
Progress toward local adaptation is expected to be enhanced when divergent selection is multi-dimensional, because many simultaneous sources of selection can increase the total strength of selection and enhance the number of independent traits under selection. Yet, whether local adaptation ensues from multi-dimensional selection also depends on its potential to cause the build-up of reproductive barriers such as sexual signals and preference for these signals. We used replicate experimental introductions of guppies (Poecilia reticulata) in...

Data from: Factors influencing ocelot occupancy in Brazilian Atlantic Forest reserves

Rodrigo Lima Massara, Ana Maria De Oliveira Paschoal, Larissa Lynn Bailey, , André Hirsch, Adriano Garcia Chiarello & Paul F. Doherty
Over 80% of Atlantic Forest remnants are <50 ha and protected areas are embedded in a matrix dominated by human activities, undermining the long-term persistence of carnivores. The ocelot (Leopardus pardalis) is an opportunistic species, but little is known about its tolerance to habitat alterations and the influence of other species on its occupancy in Atlantic Forest remnants. We used camera traps to assess ocelot occupancy in protected areas of Atlantic Forest in southeastern Brazil....

Data from: Simulating the distribution of individual livestock farms and their populations in the united states: an example using domestic swine (Sus scrofa domesticus) farms

Christopher L. Burdett, Brian R. Kraus, Sarah J. Garza, Ryan S. Miller & Kathe E. Bjork
Livestock distribution in the United States (U.S.) can only be mapped at a county-level or worse resolution. We developed a spatial microsimulation model called the Farm Location and Agricultural Production Simulator (FLAPS) that simulated the distribution and populations of individual livestock farms throughout the conterminous U.S. Using domestic pigs (Sus scrofa domesticus) as an example species, we customized iterative proportional-fitting algorithms for the hierarchical structure of the U.S. Census of Agriculture and imputed unpublished state-...

Data from: Deterministic and stochastic processes lead to divergence in plant communities 25 years after the 1988 Yellowstone fires

William H. Romme, Timothy G. Whitby, Daniel B. Tinker & Monica G. Turner
Young, recently burned forests are increasingly widespread throughout western North America, but forest development after large wildfires is not fully understood, especially regarding effects of variable burn severity, environmental heterogeneity, and changes in drivers over time. We followed development of subalpine forests after the 1988 Yellowstone fires by periodically re-sampling permanent plots established soon after the fires. We asked two questions about patterns and processes over the past 25 years: (1) Are plant species richness...

Data from: Precipitation and environmental constraints on three aspects of flowering in three dominant tallgrass species

Nathan P. Lemoine, John D. Dietrich & Melinda D. Smith
Flower production can comprise up to 70% of aboveground primary production in grasslands. Yet we know relatively little about how the environment and timing of rainfall determine flower productivity. Evidence suggests that deficits or additions of rainfall during phenlologically relevant periods (i.e. growth, storage, initiation of flowering, and reproduction) can determine flower production in grasslands. We used long-term data from the Konza Prairie LTER to test how fire, soil topography, and precipitation amounts during four...

Data from: Nonselective bottlenecks control the divergence and diversification of phase-variable bacterial populations

Jack Aidley, Shweta Rajopadhye, Nwanekka M. Akinyemi, Lea Lango-Scholey & Christopher D. Bayliss
Phase variation occurs in many pathogenic and commensal bacteria and is a major generator of genetic variability. A putative advantage of phase variation is to counter reductions in variability imposed by nonselective bottlenecks during transmission. Genomes of Campylobacter jejuni, a widespread food-borne pathogen, contain multiple phase-variable loci whose rapid, stochastic variation is generated by hypermutable simple sequence repeat tracts. These loci can occupy a vast number of combinatorial expression states (phasotypes) enabling populations to rapidly...

Data from: De novo genome assembly of Geosmithia morbida, the causal agent of thousand cankers disease

Taruna A. Schuelke, Anthony Westbrook, Kirk Broders, Keith Woeste & Matthew D. MacManes
Geosmithia morbida is a filamentous ascomycete that causes thousand cankers disease in the eastern black walnut tree. This pathogen is commonly found in the western U.S.; however, recently the disease was also detected in several eastern states where the black walnut lumber industry is concentrated. G. morbida is one of two known phytopathogens within the genus Geosmithia, and it is vectored into the host tree via the walnut twig beetle. We present the first de...

Data from: Blood mercury levels of zebra finches are heritable: implications for the evolution of mercury resistance

Kenton A. Buck, Claire W. Varian-Ramos, Daniel A. Cristol & John P. Swaddle
Mercury is a ubiquitous metal contaminant that negatively impacts reproduction of wildlife and has many other sub-lethal effects. Songbirds are sensitive bioindicators of mercury toxicity and may suffer population declines as a result of mercury pollution. Current predictions of mercury accumulation and biomagnification often overlook possible genetic variation in mercury uptake and elimination within species and the potential for evolution in affected populations. We conducted a study of dietary mercury exposure in a model songbird...

Data from: Partial support for the central–marginal hypothesis within a population: reduced genetic diversity but not increased differentiation at the range edge of an island endemic bird

Kathryn M. Langin, T. Scott Sillett, W. Chris Funk, Scott A. Morrison & Cameron K. Ghalambor
Large-scale population comparisons have contributed to our understanding of the evolution of geographic range limits and species boundaries, as well as the conservation value of populations at range margins. The central–marginal hypothesis (CMH) predicts a decline in genetic diversity and an increase in genetic differentiation toward the periphery of species’ ranges due to spatial variation in genetic drift and gene flow. Empirical studies on a diverse array of taxa have demonstrated support for the CMH....

Data from: Ecological correlates of the distribution limits of two poeciliid species across a salinity gradient

Julián Torres-Dowdall, Felipe Dargent, Corey A. Handelsman, Indar W. Ramnarine & Cameron K. Ghalambor
Identifying the environmental factors responsible for the formation of a species' distribution limit is challenging because organisms interact in complex ways with their environments. However, the use of statistical niche models in combination with the analysis of phenotypic variation along environmental gradients can help to reduce such complexity and identify a subset of candidate factors. In the present study, we used such approaches to describe and identify factors responsible for the parapatric distribution of two...

Data from: Hybridization and invasion: an experimental test with diffuse knapweed (Centaurea diffusa Lam.)

Amy C Blair, Dana Blumenthal & Ruth A Hufbauer
A number of studies have suggested a link between hybridization and invasion. In this study, we experimentally test the potential for hybridization to influence invasion through a greenhouse common garden study. Diffuse knapweed (Centaurea diffusa Lam.) was introduced to North America with admixture from spotted knapweed (Centaurea stoebe subsp. stoebe L.). Comparisons between North American diffuse knapweed (including hybrid phenotypes) and native (European) diffuse knapweed in a common garden did not reveal enhanced performance or...

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