505 Works

Data from: Degree of host susceptibility in the initial disease outbreak influences subsequent epidemic spread

Paul M. Severns, Laura K. Estep, Kathryn E. Sackett & Christopher C. Mundt
1. Disease epidemics typically begin as an outbreak of a relatively small, spatially explicit population of infected individuals (focus), in which disease prevalence increases and rapidly spreads into the uninfected, at-risk population. Studies of epidemic spread typically address factors influencing disease spread through the at-risk population, but the initial outbreak may strongly influence spread of the subsequent epidemic. 2. We initiated wheat stripe rust Puccinia striiformis f. sp. tritici epidemics to assess the influence of...

Data from: Infectious disease transmission and behavioral allometry in wild mammals

Barbara A. Han, Andrew W. Park, Anna Jolles, Sonia Altizer & Anna E. Jolles
1. Animal social and movement behaviors can impact the transmission dynamics of infectious diseases, especially for pathogens transmitted through close contact between hosts or through contact with infectious stages in the environment. 2. Estimating pathogen transmission rates and R0 from natural systems can be challenging. Because host behavioral traits that underlie the transmission process vary predictably with body size, one of the best-studied traits among animals, body size might therefore also predict variation in parasite...

Data from: Crossing the divide: gene flow produces intergeneric hybrid in feral transgenic creeping bentgrass population

María L. Zapiola & Carol A. Mallory-Smith
Gene flow is the most frequently expressed public concern related to the deregulation of transgenic events (Snow 2002; Ellstrand 2003). However, assessing the potential for transgene escape is complex because it depends on the opportunities for unintended gene flow, and establishment and persistence of the transgene in the environment (Warwick et al. 2008). Creeping bentgrass (Agrostis stolonifera L.), a turfgrass species widely used on golf courses, has been genetically engineered to be resistant to glyphosate,...

Data from: Phylogenetic signal detection from an ancient rapid radiation: effects of noise reduction, long-branch attraction, and model selection in crown clade Apocynaceae

Shannon C. K. Straub, Michael J. Moore, Pamela S. Soltis, Douglas E. Soltis, Aaron Liston, Tatyana Livshultz & Shannon C.K. Straub
Crown clade Apocynaceae comprise seven primary lineages of lianas, shrubs, and herbs with a diversity of pollen aggregation morphologies including monads, tetrads, and pollinia, making them an ideal group for investigating the evolution and function of pollen packaging. Traditional molecular systematic approaches utilizing small amounts of sequence data have failed to resolve relationships along the spine of the crown clade, a likely ancient rapid radiation. The previous best estimate of the phylogeny was a five-way...

Data from: Circumpolar diversity and geographic differentiation of mtDNA in the critically endangered Antarctic blue whale (Balaenoptera musculus intermedia)

Angela L. Sremba, Brittany Hancock-Hanser, Trevor A. Branch, Rick L. LeDuc & C. Scott Baker
The Antarctic blue whale (Balaenoptera musculus intermedia) was hunted to near extinction between 1904 and 1972, declining from an estimated initial abundance of more than 250,000 to fewer than 400. Here, we describe mtDNA control region diversity and geographic differentiation in the surviving population of the Antarctic blue whale, using 218 biopsy samples collected under the auspices of the International Whaling Commission (IWC) during research cruises from 1990–2009. Microsatellite genotypes and mtDNA sequences identified 166...

Data from: Rates of speciation and morphological evolution are correlated across the largest vertebrate radiation

Daniel L. Rabosky, Francesco Santini, Jonathan Eastman, Stephen A. Smtih, Brian Sidlauskas, Jonathan Chang & Michael E. Alfaro
Several evolutionary theories predict that rates of morphological change should be positively associated with the rate at which new species arise. For example, the theory of punctuated equilibrium proposes that phenotypic change typically occurs in rapid bursts associated with speciation events. However, recent phylogenetic studies have found little evidence linking these processes in nature. Here we demonstrate that rates of species diversification are highly correlated with the rate of body size evolution across the 30,000+...

Data from: Contrasting historical and recent gene flow among African buffalo herds in the Caprivi Strip of Namibia

Clinton W. Epps, Jessica A. Castillo, Anne Schmidt-Kuentzel, Pierre Du Preez, Greg Stuart-Hill, Mark Jago & Robin Naidoo
Population genetic structure is often used to infer population connectivity, but genetic structure may largely reflect historical rather than recent processes. We contrasted genetic structure with recent gene-flow estimates among 6 herds of African buffalo (Syncerus caffer) in the Caprivi Strip, Namibia, using 134 individuals genotyped at 10 microsatellite loci. We tested whether historical and recent gene flows were influenced by distance, potential barriers (rivers), or landscape resistance (distance from water). We also tested at...

Data from: Sex-determining chromosomes and sexual dimorphism: insights from genetic mapping of sex expression in a natural hybrid Fragaria × ananassa subsp. cuneifolia

Rajanikanth Govindarajulu, Aaron Liston & Tia-Lynn Ashman
We studied the natural hybrid (Fragaria × ananassa subsp. cuneifolia) between two sexually dimorphic octoploid strawberry species (Fragaria virginiana and Fragaria chiloensis) to gain insight into the dynamics of sex chromosomes and the genesis of sexual dimorphism. Male sterility is dominant in both the parental species and thus will be inherited maternally, but the chromosome that houses the sex-determining region differs. Thus, we asked whether (1) the cytotypic composition of hybrid populations represents one or...

Data from: Penalized likelihood methods improve parameter estimates in occupancy models

Rebecca A. Hutchinson, Jonathon J. Valente, Sarah C. Emerson, Matthew G. Betts & Thomas G. Dietterich
1. Occupancy models are employed in species distribution modelling to account for imperfect detection during field surveys. While this approach is popular in the literature, problems can occur when estimating the model parameters. In particular, the maximum likelihood estimates can exhibit bias and large variance for data sets with small sample sizes, which can result in estimated occupancy probabilities near 0 and 1 (‘boundary estimates’). 2. In this paper, we explore strategies for estimating parameters...

Data from: Landscape effects on gene flow for a climate-sensitive montane species, the American pika

Jessica A. Castillo, Clinton W. Epps, Anne R. Davis & Samuel A. Cushman
Climate change is arguably the greatest challenge to conservation of our time. Most vulnerability assessments rely on past and current species distributions to predict future persistence but ignore species' abilities to disperse through landscapes, which may be particularly important in fragmented habitats and crucial for long-term persistence in changing environments. Landscape genetic approaches explore the interactions between landscape features and gene flow and can clarify how organisms move among suitable habitats, but have suffered from...

Data from: Recombinant DNA modification of gibberellin metabolism alters growth rate and biomass allocation in Populus

Haiwei Lu, Venkatesh Viswanath, Cathleen Ma, Elizabeth Etherington, Palitha Dharmawardhana, Olga Shevchenko, Steven H. Strauss, David W. Pearce, Stewart B. Rood & Victor Busov
Overexpression of genes that modify gibberellin (GA) metabolism and signaling have been previously shown to produce trees with improved biomass production but highly disturbed development. To examine if more subtle types of genetic modification of GA could improve growth rate and modify tree architecture, we transformed a model poplar genotype (Populus tremula × P. alba) with eight genes, including two cisgenes (intact copies of native genes), four intragenes (modified copies of native genes), and two...

Data from: Invasiveness of plant pathogens depends on the spatial scale of host distribution

Alexey Mikaberidze, Christopher C. Mundt & Sebastian Bonhoeffer
Plant diseases often cause serious yield losses in agriculture. A pathogen’s invasiveness can be quantified by the basic reproductive number, R0. Since pathogen transmission between host plants depends on the spatial separation between them, R0 is strongly influenced by the spatial scale of the host distribution.We present a proof of principle of a novel approach to estimate the basic reproductive number, R0, of plant pathogens as a function of the size of a field planted...

Data from: Predator-guided sampling reveals biotic structure in the bathypelagic

Kelly J. Benoit-Bird, Brandon L. Southall & Mark A. Moline
We targeted habitat used differentially by deep-diving, air-breathing predators to empirically sample their prey’s distributions off southern California. Fine-scale measurements of the spatial variability of potential prey animals from the surface to 1200 m were obtained using conventional fisheries echosounders aboard a surface ship and uniquely integrated into a deep-diving autonomous vehicle. Significant spatial variability in the size, composition, total biomass, and spatial organization of biota was evident over all spatial scales examined and was...

Data from: Populations of aspen (Populus tremuloides Michx.) with different evolutionary histories differ in their climate occupancy

Burke T. Greer, Christopher Still, Glenn T. Howe, Christina Tague & Dar A. Roberts
Quaking aspens (Populus tremuloides Michx.) are found in diverse habitats throughout North America. While the biogeography of aspens' distribution has been documented, the drivers of the phenotypic diversity of aspen are still being explored. In our study, we examined differences in climate between northern and southwestern populations of aspen, finding large-scale differences between the populations. Our results suggest that northern and southwestern populations live in distinct climates and support the inclusion of genetic and phenotypic...

Data from: Timber harvest and tree size near nests explains variation in nest site occupancy but not productivity in northern goshawks (Accipiter gentilis)

Sabrina A. Rodriguez, Patricia L. Kennedy & Timothy H. Parker
Conservation concern for the northern goshawk (Accipiter gentilis) reflects evidence that goshawks may abandon nest sites or suffer from reduced nesting success in response to some forms of timber harvest. However, this evidence is mixed and has yet to be reviewed systemically and quantitatively. Therefore, we conducted a meta-analysis to assess the extent to which timber harvest and tree size explain variation in goshawk productivity and site occupancy. Goshawk productivity was not significantly explained by...

Data from: Experimental insight into the process of parasite community assembly

Sarah A. Budischak, Eric P. Hoberg, Art Abrams, Anna E. Jolles & Vanessa O. Ezenwa
1.Community assembly is a fundamental process that has long been a central focus in ecology. Extending community assembly theory to communities of co-infecting parasites, we used a gastrointestinal nematode removal experiment in free-ranging African buffalo to examine community assembly patterns and processes. 2.We first asked whether reassembled communities differ from undisturbed communities by comparing anthelmintic-treated and control hosts. Next, we examined the temporal dynamics of assembly using a cross-section of communities that reassembled for different...

Data from: Evaluating carbon storage, timber harvest, and habitat possibilities for a western Cascades (US) forest landscape

Jeffrey Kline, Mark Harmon, Thomas Spies, Anita Morzillo, Robert Pabst, Brenda McComb, Frank Schnekenburger, Keith Olsen, Blair Csuti, Jody Vogeler, Jeffrey D. Kline, Thomas A. Spies, Brenda C. McComb, Anita T. Morzillo, Mark E. Harmon, Robert J. Pabst, Keith A. Olsen & Jody C. Vogeler
Forest policymakers and managers have long sought ways to evaluate the capability of forest landscapes to jointly produce timber, habitat, and other ecosystem services in response to forest management. Currently, carbon is of particular interest as policies for increasing carbon storage on federal lands are being proposed. However, a challenge in joint production analysis of forest management is adequately representing ecological conditions and processes that influence joint production relationships. We used simulation models of vegetation...

Data from: Closing a gap in tropical forest biomass estimation: taking crown mass variation into account in pantropical allometries

Pierre Ploton, Nicholas Barbier, Stéphane Takoudjou Momo, Maxime Réjou-Méchain, Faustin Boyemba Bosela, Georges Chuyong, Gilles Dauby, Vincent Droissart, Adeline Fayolle, Rosa Calisto Goodman, Mathieu Henry, Narcisse Guy Kamdem, John Katembo Mukirania, David Kenfack, Moses Libalah, Alfred Ngomanda, Vivien Rossi, Bonaventure Sonké, Nicolas Texier, Duncan Thomas, Donatien Zebaze, Pierre Couteron, Uta Berger & Raphaël Pélissier
Accurately monitoring tropical forest carbon stocks is an outstanding challenge. Allometric models that consider tree diameter, height and wood density as predictors are currently used in most tropical forest carbon studies. In particular, a pantropical biomass model has been widely used for approximately a decade, and its most recent version will certainly constitute a reference in the coming years. However, this reference model shows a systematic bias for the largest trees. Because large trees are...

Data from: Genetic signatures of ecological diversity along an urbanization gradient

Ryan P. Kelly, James L. O'Donnell, Natalie C. Lowell, Andrew O. Shelton, Jameal F. Samhouri, Shannon M. Hennessey, Blake E. Feist & Gregory D. Williams
Despite decades of work in environmental science and ecology, estimating human influences on ecosystems remains challenging. This is partly due to complex chains of causation among ecosystem elements, exacerbated by the difficulty of collecting biological data at sufficient spatial, temporal, and taxonomic scales. Here, we demonstrate the utility of environmental DNA (eDNA) for quantifying associations between human land use and changes in an adjacent ecosystem. We analyze metazoan eDNA sequences from water sampled in nearshore...

Data from: Interactive influences of climate change and agriculture on aquatic habitat in a Pacific Northwestern watershed

Sandra J. DeBano, David. E. Wooster, Jonathan R. Walker, Laura E. McMullen, Donald A. Horneck & David E. Wooster
Climate change and agricultural intensification are two potential stressors that may pose significant threats to aquatic habitats in the inland Pacific Northwest over the next century. Climate change may impact running water through numerous pathways, including effects on water temperature and stream flow. In certain regions of the Pacific Northwest, agricultural activities, such as crop production, may become more profitable if water projects result in more irrigation water. If so, riparian buffers in these areas...

Data from: Female behavior and the interaction of male and female genital traits mediate sperm transfer during mating.

Christopher R. Friesen, Emily J. Uhrig, Robert T. Mason & Patricia L.R. Brennan
Natural selection and post-copulatory sexual selection, including sexual conflict, contribute to genital diversification. Fundamental first steps in understanding how these processes shape the evolution of specific genital traits are to determine their function experimentally and to understand the interactions between female and male genitalia during copulation. Our experimental manipulations of male and female genitalia in red-sided garter snakes (Thamnophis sirtalis parietalis) reveal that copulation duration and copulatory plug deposition, as well as total and oviductal/vaginal...

Data from: Host immunity, nutrition and coinfection alter longitudinal infection patterns of schistosomes in a free ranging African buffalo population

Mireya Smith, Anna E. Jolles, Paul L. A. M. Corstjens, Brianna R. Beechler, Govert J. Van Dam, Robert S. Spaan, Sarah A. Budischak, Michelle L. Steinauer & Vanessa O. Ezenwa
Schistosomes are trematode parasites of global importance, causing infections in millions of people, livestock, and wildlife. Most studies on schistosomiasis, involve human subjects; as such, there is a paucity of longitudinal studies investigating parasite dynamics in the absence of intervention. As a consequence, despite decades of research on schistosomiasis, our understanding of its ecology in natural host populations is centered around how environmental exposure and acquired immunity influence acquisition of parasites, while very little is...

Data from: Contrasting genetic metrics and patterns among naturalized rainbow trout (Oncorhynchus mykiss) in two Patagonian lakes differentially impacted by trout aquaculture

Cristian B. Canales-Aguirre, Lisa W. Seeb, James E. Seeb, Maria I. Cadiz, Selim S. Musleh, Ivan Arismendi, Gonzalo Gajardo, Ricardo Galleguillos & Daniel Gomez-Uchida
Different pathways of propagation and dispersal of non-native species into new environments may have contrasting demographic and genetic impacts on established populations. Repeated introductions of rainbow trout (Oncorhynchus mykiss) to Chile in South America, initially through stocking and later through aquaculture escapes, provide a unique setting to contrast these two pathways. Using a panel of single nucleotide polymorphisms, we found contrasting genetic metrics and patterns among naturalized trout in Lake Llanquihue, Chile’s largest producer of...

Data from: Genetic mapping and phylogenetic analysis reveal intraspecific variation in sex chromosomes of the Virginian strawberry

Na Wei, Rajanikanth Govindarajulu, Jacob A. Tennessen, Aaron Liston & Tia-Lynn Ashman
With their extraordinary diversity in sexual systems, flowering plants offer unparalleled opportunities to understand sex determination and to reveal generalities in the evolution of sex chromosomes. Comparative genetic mapping of related taxa with good phylogenetic resolution can delineate the extent of sex chromosome diversity within plant groups, and lead the way to understanding the evolutionary drivers of such diversity. The North American octoploid wild strawberries provide such an opportunity. We performed linkage mapping using targeted...

Data from: Cryptic species in the mountaintops: species delimitation and taxonomy of the Bembidion breve species group (Coleoptera: Carabidae) aided by genomic architecture of a century-old type specimen

John S. Sproul & David R. Maddison
The breve species group includes closely related Bembidion Latreille ground beetles commonly found at high elevation in the mountains of western North America. For several decades, the group has been considered to consist of two species. Here, we present evidence from morphological, molecular and geographic data that the group contains nine species: Bembidion ampliatum, B. breve, B. geopearlis, B. laxatum, B. lividulum, B. oromaia, B. saturatum, B. testatum and B. vulcanix. We describe three species...

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