263 Works

Data from: Range-wide population genomics of the Mexican fruit fly: towards development of pathway analysis tools

Julian R. Dupuis, Raul Ruiz-Arce, Norman B. Barr, Donald B. Thomas & Scott M. Geib
Recurrently invading pests provide unique challenges for pest management, but also present opportunities to utilize genomics to understand invasion dynamics and inform regulatory management through pathway analysis. In the southern United States, the Mexican fruit fly Anastrepha ludens is such a pest, and its incursions into Texas and California represent major threats to the agricultural systems of those regions. We developed a draft genome assembly for A. ludens, conducted range-wide population genomics using restriction-site associated...

Relative reproductive phenology and synchrony affect neonate survival in a nonprecocial ungulate

Eric Michel, Bronson Strickland, Stephen Demarais, Jerrold Belant, Todd Kautz, Jared Duquette, Dean Beyer, Michael Chamberlain, Karl Miller, Rebecca Shuman, John Kilgo, Duane Diefenbach, Bret Wallingford, Justin Vreeland, Steve Ditchkoff, Christopher DePerno, Christopher Moorman, Michael Chitwood & Marcus Lashley
1. Degree of reproductive synchronization in prey is hypothesized as a predator defense strategy reducing prey risk via predator satiation or predator avoidance. Species with precocial young, especially those exposed to specialist predators, should be highly synchronous to satiate predators (predator satiation hypothesis), while prey with nonprecocial (i.e., altricial) young, especially those exposed to generalist predators, should become relatively asynchronous to avoid predator detection (predator avoidance hypothesis). The white-tailed deer (Odocoileus virginianus) in North America...

Globally, plant-soil feedbacks are weak predictors of plant abundance

Kurt Reinhart, Jonathan Bauer, Sarah McCarthy-Neumann, Andrew MacDougall, José Hierro, Mariana Chiuffo, Scott Mangan, Johannes Heinze, Joana Bergmann, Jasmin Joshi, Richard Duncan, Jeff Diaz, Paul Kardol, Gemma Rutten, Markus Fischer, Wim Van Der Putten, T. Bezemer & John Klironomos
Plant-soil feedbacks (PSFs) have been shown to strongly affect plant performance under controlled conditions, and PSFs are thought to have far reaching consequences for plant population dynamics and the structuring of plant communities. However, thus far the relationship between PSF and plant species abundance in the field is not consistent. Here, we synthesize PSF experiments from tropical forests to semiarid grasslands, and test for a positive relationship between plant abundance in the field and PSFs...

Species complex diversification by host plant use in an herbivorous insect: The source of Puerto Rican cactus mealybug pest and implications for biological control

Daniel Poveda-Martínez, María Aguirre, Guillermo Logarzo, Stephen D. Hight, Serguei Triapitsyn, Hilda Diaz-Soltero, Marcelo Vitorino & Esteban Hasson
Cryptic taxa have often been observed in the form of host‐associated species that diverged as the result of adaptation to alternate host plants. Untangling cryptic diversity in species complexes that encompass invasive species is a mandatory task for pest management. Moreover, investigating the evolutionary history of a species complex may help to understand the drivers of their diversification. The mealybug Hypogeococcus pungens was believed to be a polyphagous species from South America and has been...

Genomic regions influencing aggressive behavior in honey bees are defined by colony allele frequencies

Arián Avalos, Miaoquan Fang, Hailin Pan, Aixa Ramirez Lluch, Alexander E. Lipka, Sihai Dave Zhao, Tugrul Giray, Gene E. Robinson, Guojie Zhang & Matthew E. Hudson
For social animals, the genotypes of group members affect the social environment, and thus individual behavior, often indirectly. We used genome-wide association studies (GWAS) to determine the influence of individual vs. group genotypes on aggression in honey bees. Aggression in honey bees arises from the coordinated actions of colony members, primarily nonreproductive “soldier” bees, and thus, experiences evolutionary selection at the colony level. Here, we show that individual behavior is influenced by colony environment, which...

Extinct plants of North America north of Mexico

Wesley Knapp, Anne Frances, Reed Noss, Robert Naczi, Alan Weakley, George Gann, Bruce Baldwin, James Miller, Patrick McIntyre, Brent Mishler, Gerry Moore, Richard Olmstead, Anna Strong, Daniel Gluesenkamp & Kathryn Kennedy
The recent study by Humphreys et al., reporting extinction of almost 600 plant species globally, represents a groundbreaking effort at compiling direct data on seed plants. We applaud Humphreys et al. for quantifying plant extinctions because they formulate an important and testable hypothesis. However, their study missed many extinctions and rediscoveries of seed plants in the United States and Canada. Our team of experts has been compiling a list of extinct plants of North America...

A spatially explicit model to simulate the population dynamics of gypsy moth (Lymantria dispar)

Mandy C. Barron, Andrew M. Liebhold, John M. Kean, Brian Richardson & Eckehard G. Brockerhoff
Removal of host plants is a 'tool' that can be used for the eradication of invasive alien plant pests. We developed a spatially explicit agent-based population model to simulate the population dynamics of the European strain of gypsy moth, Lymantria dispar, based on Robinet et al. (2008 - Journal of Animal Ecology 77, 966–973. doi:10.1111/j.1365-2656.2008.01417.x). The model was coded in the R language (R Core Team, 2017) and is deposited in this Dryad record. A...

Data from: Trade-offs in parasitism efficiency and brood size mediate parasitoid coexistence, with implications for biological control of the invasive emerald ash borer

Xiao-Yi Wang, David E. Jennings & Jian J. Duan
1. Parasitoids often are selected for use as biological control agents because of their high host specificity, yet such host specificity can result in strong interspecific competition. Few studies have examined whether and how various extrinsic factors (such as parasitism efficiency, i.e. the ability to optimize host-finding attack rates) influence the outcome of competition between parasitoids, even though they could have profound effects on the implementation of classical biological control programmes. 2. To determine the...

Data from: Quantifying \"apparent\" impact and distinguishing impact from invasiveness in multispecies plant invasions

Dean E. Pearson, Yvette K. Ortega, Ozkan Eren & Jose L. Hierro
The quantification of invader impacts remains a major hurdle to understanding and managing invasions. Here, we demonstrate a method for quantifying the community-level impact of multiple plant invaders by applying Parker et al.'s (1999) equation (impact = range x local abundance x per capita effect or per unit effect) using data from 620 survey plots from 31 grasslands across west-central Montana, USA. In testing for interactive effects of multiple invaders on native plant abundance (percent...

Data from: Ecotypes of an ecologically dominant prairie grass (Andropogon gerardii) exhibit genetic divergence across the U.S. Midwest grasslands environmental gradient

Miranda M. Gray, Paul St. Amand, Nora M. Bello, Mary Knapp, Karen A. Garrett, Theodore J. Morgan, Sara G. Baer, Brian R. Maricle, Eduard D. Akhunov, Loretta C. Johnson & Matthew B. Galliart
Big bluestem (Andropogon gerardii) is an ecologically dominant grass with wide distribution across the environmental gradient of U.S. Midwest grasslands. This system offers an ideal natural laboratory to study the nature of population divergence and adaptation in spatially varying climates. Objectives were to: (i) characterize neutral genetic diversity and structure within and among three regional ecotypes derived from 11 prairies across the U.S. Midwest environmental gradient, (ii) distinguish between the relative roles of isolation-by-distance (IBD)...

Data from: Emergence timing and fitness consequences of variation in seed oil composition in Arabidopsis thaliana

Sandra E. Pelc & C. Randal Linder
Early seedling emergence can increase plant fitness under competition. Seed oil composition (the types and relative amounts of fatty acids in the oils) may play an important role in determining emergence timing and early growth rate in oilseeds. Saturated fatty acids provide more energy per carbon atom than unsaturated fatty acids but have substantially higher melting points (when chain length is held constant). This characteristic forms the basis of an adaptive hypothesis that lower melting...

Data from: Cattle sex-specific recombination and genetic control from a large pedigree analysis

Li Ma, Jeffrey R. O'Connell, Paul M. Vanraden, Botong Shen, Abinash Padhi, Chuanyu Sun, Derek M. Bickhart, John B. Cole, Daniel J. Null, George E. Liu, Yang Da & George R. Wiggans
Meiotic recombination is an essential biological process that generates genetic diversity and ensures proper segregation of chromosomes during meiosis. From a large USDA dairy cattle pedigree with over half million genotyped animals, we extracted 186,927 three-generation families, identified over 8.5 million maternal and paternal recombination events, and constructed sex-specific recombination maps for 59,309 autosomal SNPs. The recombination map spans for 25.5 Morgans in males and 23.2 Morgans in females, for a total studied region of...

Data from: Enhanced diversity and aflatoxigenicity in interspecific hybrids of Aspergillus flavus and Aspergillus parasiticus

Rodrigo A. Olarte, Carolyn J. Worthington, Bruce W. Horn, Geromy G. Moore, Rakhi Singh, James T. Monacell, Joe W. Dorner, Eric A. Stone, De-Yu Xie & Ignazio Carbone
Aspergillus flavus and A. parasiticus are the two most important aflatoxin-producing fungi responsible for the contamination of agricultural commodities worldwide. Both species are heterothallic and undergo sexual reproduction in laboratory crosses. Here we examine the possibility of interspecific matings between A. flavus and A. parasiticus. These species can be distinguished morphologically and genetically, as well as by their mycotoxin profiles. Aspergillus flavus produces both B aflatoxins and cyclopiazonic acid (CPA), B aflatoxins or CPA alone,...

Data from: An integrated occupancy and space-use model to predict abundance of imperfectly detected, territorial vertebrates

Morgan W. Tingley, Robert L. Wilkerson, Christine A. Howell & Rodney B. Siegel
It is often highly desirable to know not only where species are likely to occur (i.e., occupancy) but also how many individuals are supported by a given habitat (i.e., density). For many animals, occupancy and density may be determined by distinct ecological processes. Here we develop a novel abundance model as the product of landscape-scale occupancy probability and habitat-scale density given occupancy. One can conceptualize our model as fully packing a landscape with home ranges...

Data from: Past tree influence and prescribed fire mediate biotic interactions and community reassembly in a grassland-restoration experiment

Charles B. Halpern, Joseph A. Antos, Donald McKenzie & Annette M. Olson
Woody plant encroachment of grasslands is occurring globally, with profound ecological consequences. Attempts to restore herbaceous dominance may fail if the woody state is resilient or if intervention leads to an alternate, undesirable state. Restoration outcomes often hinge on biotic interactions – particularly on priority effects that inhibit or promote community reassembly. Following experimental tree removal from conifer-invaded grasslands, we documented substantial variation in community reassembly associated with the changing abundance of the native clonal...

Data from: Spatio-temporal dynamics of a tree-killing beetle and its predator

Aaron S. Weed, Matthew P. Ayres, Andrew M. Liebhold & Ronald F. Billings
Resolving linkages between local-scale processes and regional-scale patterns in abundance of interacting species is important for understanding long-term population stability across spatial scales. Landscape patterning in consumer population dynamics may be largely the result of interactions between consumers and their predators, or driven by spatial variation in basal resources. Empirical testing of these alternatives has been limited by the lack of suitable data. In this study, we analyzed an extensive network of spatially replicated time...

Data from: Genetic diversity of the two commercial tetraploid cotton species in the Gossypium Diversity Reference Set

Lori L. Hinze, Elodie Gazave, Michael A. Gore, David D. Fang, Brian E. Scheffler, John Z. Yu, Don C. Jones, James Frelichowski & Richard G. Percy
A diversity reference set has been constructed for the Gossypium accessions in the U.S. National Cotton Germplasm Collection to facilitate more extensive evaluation and utilization of accessions held in the Collection. A set of 105 mapped simple sequence repeat markers were used to study the allelic diversity of 1,933 tetraploid Gossypium accessions representative of the range of diversity of the improved and wild accessions of G. hirsutum and G. barbadense. The reference set contained 410...

Data from: Naturally occurring variation in tadpole morphology and performance linked to predator regime

James B. Johnson, Daniel Saenz, Cory K. Adams & Toby J. Hibbitts
Divergent natural selection drives a considerable amount of the phenotypic and genetic variation observed in natural populations. For example, variation in the predator community can generate conflicting selection on behavioral, life-history, morphological, and performance traits. Differences in predator regime can subsequently increase phenotypic and genetic variations in the population and result in the evolution of reproductive barriers (ecological speciation) or phenotypic plasticity. We evaluated morphology and swimming performance in field collected Bronze Frog larvae (Lithobates...

Data from: Confirmation of independent introductions of an exotic plant pathogen of Cornus species, Discula destructiva, on the east and west coasts of North America

Kristie Mantooth, Denita Hadziabdic, Sarah Boggess, Mark Windham, Stephen Miller, Cai Guohong, Joseph Spatafora, Ning Zhang, Meg Staton, Bonnie Ownley, Robert Trigiano & Guohong Cai
Cornus florida (flowering dogwood) and C. nuttallii (Pacific dogwood) are North American native tree species that belong to the big-bracted group of dogwoods. Cornus species are highly valued for their ornamental characteristics, and have fruits that contain high fat content for animals. Also, they are an important understory tree in natural forests. Dogwood anthracnose, caused by Discula destructiva, was observed in the late 1970s on the east and west coasts of the United States and...

Data from: Vegetation cover in relation to socioeconomic factors in a tropical city assessed from sub-meter resolution imagery

Sebastián Martinuzzi, Olga M. Ramos-González, Tischa A. Muñoz-Erickson, Dexter H. Locke, Ariel E. Lugo & Volker C. Radeloff
Fine-scale information about urban vegetation and social-ecological relationships is crucial to inform both urban planning and ecological research, and high spatial resolution imagery is a valuable tool for assessing urban areas. However, urban ecology and remote sensing have largely focused on cities in temperate zones. Our goal was to characterize urban vegetation cover with sub-meter resolution aerial imagery, and identify social-ecological relationships of urban vegetation patterns in a tropical city, the San Juan Metropolitan Area,...

Data from: Pre-dispersal seed predation and pollen limitation constrain population growth across the geographic distribution of Astragalus utahensis

Kathryn C. Baer & John L. Maron
1. A central focus of ecology is to understand the conditions under which biotic interactions affect species’ abundance and distribution. Classic and recent studies have shown that biotic interactions can strongly impact local or regional patterns of species abundance, but two fundamental questions remain largely unaddressed for non-competitive biotic interactions. First, do the effects of these interactions on population performance change predictably with environmental context? Second, to what extent do population-scale effects contribute to limiting...

Data from: The role of hybridization during ecological divergence of southwestern white pine (Pinus strobiformis) and limber pine (P. flexilis)

Mitra Menon, Justin C. Bagley, Christopher J. Friedline, Amy V. Whipple, Anna W. Schoettle, Alejandro Lael-Saenz, Christian Wehenkel, Francisco Molina-Freaner, Lluvia Flores-Renteria, M. Socorro Gonzalez-Elizondo, Richard A. Sniezko, Samuel A. Cushman, Kristen M. Waring & Andrew J. Eckert
Interactions between extrinsic factors, such as disruptive selection, and intrinsic factors, such as genetic incompatibilities among loci, often contribute towards the maintenance of species boundaries. The relative roles of these factors in the establishment of reproductive isolation can be examined using species pairs characterized by gene flow throughout their divergence history. We investigated the process of speciation and the maintenance of species boundaries between Pinus strobiformis and P. flexilis. Utilizing ecological niche modeling, demographic modeling,...

Data from: Applying ecological site concepts and state-and-transition models to a grazed riparian rangeland

Felix Ratcliff, James Bartolome, Luke Macaulay, Sheri Spiegal & Michael D. White
Ecological sites and state-and-transition models are useful tools for generating and testing hypotheses about drivers of vegetation composition in rangeland systems. These models have been widely implemented in upland rangelands, but comparatively little attention has been given to developing ecological site concepts for rangeland riparian areas, and additional environmental criteria may be necessary to classify riparian ecological sites. Between 2013 and 2016, fifteen study reaches on five creeks were studied at Tejon Ranch in southern...

Data from: Design of cinnamaldehyde amino acid Schiff base compounds based on the quantitative structure–activity relationship

Hui Wang, Mingyue Jiang, Shujun Li, ChungYun Hse, Chunde Jin, Fangli Sun, Zhuo Li & Chung-Yun Hse
Cinnamaldehyde amino acid Schiff base (CAAS) is a new class of safe, bioactive compounds which could be developed as potential antifungal agents for fungal infections. To design new cinnamaldehyde amino acid Schiff base compounds with high bioactivity, the quantitative structure–activity relationships (QSARs) for CAAS compounds against Aspergillus niger (A. niger) and Penicillium citrinum (P. citrinum) were analysed. The QSAR models (R2 = 0.9346 for A. niger, R2 = 0.9590 for P. citrinum,) were constructed and...

Data from: Long-term climate and competition explain forest mortality patterns under extreme drought

Derek J. N. Young, Jens T. Stevens, J. Mason Earles, Jeffrey Moore, Adam Ellis, Amy L. Jirka & Andrew M. Latimer
Rising temperatures are amplifying drought-induced stress and mortality in forests globally. It remains uncertain, however, whether tree mortality across drought-stricken landscapes will be concentrated in particular climatic and competitive environments. We investigated the effects of long-term average climate [i.e. 35-year mean annual climatic water deficit (CWD)] and competition (i.e. tree basal area) on tree mortality patterns, using extensive aerial mortality surveys conducted throughout the forests of California during a 4-year statewide extreme drought lasting from...

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  • United States Department of Agriculture
  • Cornell University
  • University of Florida
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