175 Works

Data from: Genomic sequence capture of haemosporidian parasites: methods and prospects for enhanced study of host-parasite evolution

Lisa N. Barrow, Julie M. Allen, Xi Huang, Staffan Bensch & Christopher C. Witt
Avian malaria and related haemosporidians (Plasmodium, [Para]Haemoproteus, and Leucocytoozoon) represent an exciting multi-host, multi-parasite system in ecology and evolution. Global research in this field accelerated after 1) the publication in 2000 of PCR protocols to sequence a haemosporidian mitochondrial (mtDNA) barcode, and 2) the development in 2009 of an open-access database to document the geographic and host ranges of parasite mtDNA haplotypes. Isolating haemosporidian nuclear DNA from bird hosts, however, has been technically challenging, slowing...

Data from: Rarity does not limit genetic variation or preclude subpopulation structure in the geographically restricted desert forb Astragalus lentiginosus var. piscinensis

Joshua G. Harrison, Matthew L. Forister, Stephanie R. Mcknight, Erin Nordin & Thomas L. Parchman
Premise of the study: Characteristics of rare taxa include small population sizes and limited geographical ranges. The genetic consequences of rarity are poorly understood for most taxa. A small geographical range could result in reduced opportunity for isolation by distance or environment, thereby limiting genetic structure and variation, but few studies explore genetic structure at small spatial scales with sufficient resolution to test this hypothesis. Moreover, few comparative genetic studies exist among infrataxa differing in...

Data from: Desiccation and rehydration of mosses greatly increases resource fluxes that alter soil carbon and nitrogen cycling

Mandy L. Slate, Benjamin W. Sullivan & Ray M. Callaway
1. Mosses often have positive effects on soil carbon and nitrogen cycling, but we know little about how environmentally determined cycles of desiccation and rehydration in mosses influence these processes. 2. In this context, we compared carbon and nitrogen in throughfall after precipitation passed through eight moss species that were either hydrated continuously or desiccated and rehydrated. Also, the throughfall of four moss species was added to soil and used to determine the net effect...

Data from: Stick insect genomes reveal natural selection's role in parallel speciation

Victor Soria-Carrasco, Zachariah Gompert, Aaron A. Comeault, Timothy E. Farkas, Thomas L. Parchman, J. Spencer Johnston, C. Alex Buerkle, Jeffrey L. Feder, Jens Bast, Tanja Schwander, Scott P. Egan, Bernard J. Crespi & Patrik Nosil
Natural selection can drive the repeated evolution of reproductive isolation, but the genomic basis of parallel speciation remains poorly understood. We analyzed whole-genome divergence between replicate pairs of stick insect populations that are adapted to different host plants and undergoing parallel speciation. We found thousands of modest-sized genomic regions of accentuated divergence between populations, most of which are unique to individual population pairs. We also detected parallel genomic divergence across population pairs involving an excess...

Data from: Integrated population models: bias and inference

Thomas V. Riecke, Perry J. Williams, Tessa L. Behnke, Daniel Gibson, Alan G. Leach, Benjamin S. Sedinger, Phillip A. Street & James S. Sedinger
Integrated population models (hereafter, IPMs) have become increasingly popular for the modeling of populations, as investigators seek to combine survey and demographic data to understand processes governing population dynamics. These models are particularly useful for identifying and exploring knowledge gaps within datasets, because they allow investigators to estimate biologically meaningful parameters, such as immigration and reproduction, that are uninformed by data. As IPMs have been developed relatively recently, model behavior remains relatively poorly understood. Much...

Data from: Cascading effects of mammalian herbivores on ground-dwelling arthropods: variable responses across arthropod groups, habitats and years

Eric M. Cecil, Marko J. Spasojevic & J. Hall Cushman
1. Large mammalian herbivores are well known to shape the structure and function of ecosystems worldwide and these effects can in turn cascade through systems to indirectly influence other animal species. A wealth of studies have explored the effects of large mammals on arthropods, but to date they have reported such widely varying results that generalizations have been elusive. Three factors are likely drivers of this variability: the widely varying life-history characteristics of different arthropod...

Spectral data for quaking aspen (Populus tremuloides) clones of different ploidy levels

B. Blonder, B.J. Graae, B. Greer, M. Haagsma, K. Helsen, R.E. Kapás, H. Pai, J. Rieksta, D. Sapena, C.J. Still & R. Strimbeck
Data comprise measurements of spectral reflectance for quaking aspen (Populus tremuloides Michx.) trees at a range of sites in southwestern Colorado near the town of Crested Butte. Spectra were measured in three different ways: hyperspectral measurements of leaves, hyperspectral measurements of bark, and multispectral measurements of canopies. The first two measurements were made using a handheld spectrometer, while the latter were made via airborne imaging from an unmanned aerial system. In addition to these reflectance...

Data from: Return of a giant: DNA from archival museum samples helps to identify a unique cutthroat trout lineage formerly thought to be extinct

Mary M. Peacock, Evon R. Hekkala, Veronica S. Kirchoff & Lisa G. Heki
Currently one small, native population of the culturally and ecologically important Lahontan cutthroat trout (Oncorhynchus clarkii henshawi, LCT, Federally listed) remains in the Truckee River watershed of northwestern Nevada and northeastern California. The majority of populations in this watershed were extirpated in the 1940’s due to invasive species, overharvest, anthropogenic water consumption and changing precipitation regimes. In 1977, a population of cutthroat trout discovered in the Pilot Peak Mountains in the Bonneville basin of Utah,...

Data from: The global distribution of diet breadth in insect herbivores

Matthew L. Forister, Vojtech Novotny, Anna K. Panorska, Leontine Baje, Yves Basset, Philip T. Butterill, Lukas Cizek, Phyllis D. Coley, Francesca Dem, Ivone R. Diniz, Pavel Drozd, Mark Fox, Andrea E. Glassmire, Rebecca Hazen, Jan Hrcek, Joshua P. Jahner, Ondrej Kaman, Tomasz J. Kozubowski, Thomas Kursar, Owen T. Lewis, John Lill, Robert J. Marquis, Scott E. Miller, Helena C. Morais, Masashi Murakami … & Lee A. Dyer
Understanding variation in resource specialization is important for progress on issues that include coevolution, community assembly, ecosystem processes, and the latitudinal gradient of species richness. Herbivorous insects are useful models for studying resource specialization, and the interaction between plants and herbivorous insects is one of the most common and consequential ecological associations on the planet. However, uncertainty persists regarding fundamental features of herbivore diet breadth, including its relationship to latitude and plant species richness. Here...

Data from: Phenotypic differentiation is associated with divergent sexual selection among closely related barn swallow populations

Matthew R. Wilkins, Hakan Karaardıç, Yoni Vortman, Thomas L. Parchman, Tomáš Albrecht, Adéla Petrželková, Leyla Özkan, Peter L. Pap, Joanna K. Hubbard, Amanda K. Hund & Rebecca J. Safran
Sexual selection plays a key role in the diversification of numerous animal clades and may accelerate trait divergence during speciation. However, much of our understanding of this process comes from phylogenetic comparative studies, which rely on surrogate measures such as dimorphism that may not represent selection in wild populations. In this study, we assess sexual selection pressures for multiple male visual signals across four barn swallow (Hirundo rustica) populations. Our sample encompassed 2400 linear km...

Data from: Whole-plant metabolic allocation under water stress

Fabiane M. Mundim & Elizabeth G. Pringle
Trade-offs between plant growth and defense depend on environmental resource availability. Plants are predicted to prioritize growth when environmental resources are abundant and defense when environmental resources are scarce. Nevertheless, such predictions lack a whole-plant perspective-they do not account for potential differences in plant allocation above- and belowground. Such accounting is important because leaves and roots, though both critical to plant survival and fitness, differ in their resource-uptake roles and, often, in their vulnerability to...

Data from: The mismatch in distributions of vertebrates and the plants that they disperse

Jacob W. Dittel, Christopher M. Moore & Stephen B. Vander Wall
Little is known about how mutualistic interactions affect the distribution of species richness on broad geographic scales. Because mutualism positively affects the fitness of all species involved in the interaction, one hypothesis is that the richness of species involved should be positively correlated across their range, especially for obligate relationships. Alternatively, if mutualisms are facilitative (e.g., involving multiple mutualistic partners), the distribution of mutualists should not necessarily be related, and patterns in species distributions might...

Data from: Stressful city sounds: glucocorticoid responses to experimental traffic noise are environmentally dependent

Scott Davies, Nicole Haddad & Jenny Q. Ouyang
A major challenge in urban ecology is to identify the environmental factors responsible for phenotypic differences between urban and rural individuals. However, the intercorrelation between the factors that characterise urban environments, combined with a lack of experimental manipulations of these factors in both urban and rural areas, hinder efforts to identify which aspects of urban environments are responsible for phenotypic differences. Among the factors modified by urbanisation, anthropogenic sound, particularly traffic noise, is especially detrimental...

Data from: Experimental effects of early-life corticosterone on the HPA axis and pre-migratory behaviour in a wild songbird

Jesse J. Pakkala, D. Ryan Norris, James S. Sedinger & Amy E. M. Newman
1.Although laboratory studies have shown that chronic exposure to elevated glucocorticoids during development can have profound effects on the physiology and behaviour of animals, we still have a poor understanding of the proximate and ultimate consequences of early-life stress on individuals in the wild. 2. In an island population of Savannah sparrows (Passerculus sandwichensis), we examined multiple hypotheses to explain how elevated glucocorticoid exposure during the nestling period influenced both hypothalamic-pituitary-adrenal (HPA) axis function during...

Data from: Ecological segregation in a small mammal hybrid zone: habitat-specific mating opportunities and selection against hybrids restrict gene flow on a fine spatial scale

Quinn Rodney Shurtliff, Peter J. Murphy & Marjorie D. Matocq
The degree to which closely related species interbreed is determined by a complex interaction of ecological, behavioral, and genetic factors. We examine the degree of interbreeding between two woodrat species, Neotoma bryanti and N. lepida, at a sharp ecological transition. We identify the ecological association of each genotypic class, assess the opportunity for mating between these groups, and test whether they have similar patterns of year-to-year persistence on our study site. We find that 13%...

Data from: Estimating species richness using environmental DNA

Brett P. Olds, Christopher L. Jerde, Mark A. Renshaw, Yiyuan Li, Nathan T. Evans, Cameron R. Turner, Kristy Deiner, Andrew R. Mahon, Michael A. Brueseke, Patrick D. Shirey, Michael E. Pfrender, David M. Lodge & Gary A. Lamberti
The foundation for any ecological study and the for effective management of biodiversity in natural systems requires knowing what species are present in an ecosystem. We assessed fish communities in a stream using two methods, depletion-based electrofishing and environmental DNA metabarcoding (eDNA) from water samples, to test the hypothesis that eDNA provides an alternative means of determining species richness and species identities for a natural ecosystem. In a northern Indiana stream, electrofishing yielded a direct...

Data from: Phylogeographic diversification of antelope squirrels (Ammospermophilus) across North American deserts

Stacy J. Mantooth, David J. Hafner, , Brett R. Riddle & Robert W. Bryson
We investigated the biogeographic history of antelope squirrels, genus Ammospermophilus, which are widely distributed across the deserts and other arid lands of western North America. We combined range-wide sampling of all currently recognized species of Ammospermophilus with a multilocus data set to infer phylogenetic relationships. We then estimated divergence times within identified clades of Ammospermophilus using fossil-calibrated and rate-calibrated molecular clocks. Lastly, we explored generalized distributional changes of Ammospermophilus since the last glacial maximum using...

Data from: Identifying biases at different spatial and temporal scales of diversification: a case study in the Neotropical parrotlet genus Forpus

Brian Tilston Smith, Camila C. Ribas, Bret M. Whitney, Blanca E. Hernández-Baños & John Klicka
The temporal origins of the extraordinary biodiversity of the Neotropical region are highly debated. Recent empirical work has found support for alternative models on the tempo of speciation in Neotropical species further fuelling the debate. However, relationships within many Neotropical lineages are poorly understood and it is unclear how this uncertainty impacts inferences on the evolution of taxa in the region. We examined the robustness of diversification patterns in the avian genus Forpus by testing...

Data from: Patterns in parasitism frequency explained by diet and immunity

Alyssa C. Hansen, Andrea E. Glassmire, Lee A. Dyer & Angela M. Smilanich
We sought to explain patterns in parasitism frequency of two specialist herbivores (Geometridae) by investigating the influence of plant diet as a source of variation in immune response variables important for defense against parasitism. Field collected caterpillars (Eois apyraria and Eois nympha) were assigned to one of two species in the plant genus Piper (Piperaceae): 1) a host species with high diversity of defensive chemistry, P. cenocladum C.DC., or 2) a host species with lower...

Data from: Genomic regions with a history of divergent selection affect fitness of hybrids between two butterfly species

Zachariah Gompert, Lauren K. Lucas, Chris Clark Nice, James Andrew Fordyce, Matthew L. Forister & C. Alex Buerkle
Speciation is the process by which reproductively isolated lineages arise, and is one of the fundamental means by which the diversity of life increases. Whereas numerous studies have documented an association between ecological divergence and reproductive isolation, relatively little is known about the role of natural selection in genome divergence during the process of speciation. Here we use genome-wide DNA sequences and Bayesian models to test the hypothesis that loci under divergent selection between two...

Data from: Host species, pathogens, and disease associated with divergent nasal microbial communities in tortoises

Chava L. Weitzman, Franziska C. Sandmeier & C. Richard Tracy
Diverse bacterial communities are found on every surface of macro-organisms, and they play important roles in maintaining normal physiological functions in their hosts. While the study of microbiomes has expanded with the influx of data enabled by recent technological advances, microbiome research in reptiles lags behind other organisms. We sequenced the nasal microbiomes in a sample of four North American tortoise species, and we found differing community compositions among tortoise species and sampling sites, with...

Data from: Genetic source-sink dynamics among naturally structured and anthropogenically fragmented puma populations

Kyle D. Gustafson, Roderick B. Gagne, T. Winston Vickers, Seth P.D. Riley, Christopher C. Wilmers, Vernon C. Bleich, Becky M. Pierce, Marc Kenyon, Tracy L. Drazenovich, Jeff A. Sikich, Walter M. Boyce & Holly B. Ernest
Fragmentation of wildlife populations is increasing on a global scale and understanding current population genetic structure, genetic diversity, and genetic connectivity is key to informing wildlife management and conservation. We genotyped 992 pumas (Puma concolor) at 42 previously developed microsatellite loci and identified 10 genetic populations throughout the states of California and Nevada, USA. Although some genetic populations had large effective population sizes, others were small and inbred. Genetic diversity was extremely variable (heterozygosity, uHe...

Data from: Community analysis of microbial sharing and specialization in a Costa Rican ant–plant–hemipteran symbiosis

Elizabeth G. Pringle & Corrie S. Moreau
Ants have long been renowned for their intimate mutualisms with trophobionts and plants and more recently appreciated for their widespread and diverse interactions with microbes. An open question in symbiosis research is the extent to which environmental influence, including the exchange of microbes between interacting macroorganisms, affects the composition and function of symbiotic microbial communities. Here we approached this question by investigating symbiosis within symbiosis. Ant–plant–hemipteran symbioses are hallmarks of tropical ecosystems that produce persistent...

Data from: Modeling spatiotemporal abundance of mobile wildlife in highly variable environments using boosted GAMLSS hurdle models

Adam Smith, Benjamin Hofner, Juliet S. Lamb, Jason Osenkowski, Taber Allison, Giancarlo Sadoti, Scott McWilliams & Peter Paton
1. Modeling organism distributions from survey data involves numerous statistical challenges, including zero-inflation, overdispersion, and selection and incorporation of environmental covariates. In environments with high spatial and temporal variability, addressing these challenges often requires numerous assumptions regarding organism distributions and their relationships to biophysical features. These assumptions may limit the resolution or accuracy of predictions resulting from survey-based distribution models. 2. We propose an iterative modeling approach that incorporates a negative binomial hurdle, followed by...

Data from: On the importance of having a good mother: maternal investment affects duckling mortality risk in wood ducks

Benjamin S. Sedinger, Christopher A. Nicolai, Kelley M. Stewart & Kelly M. Stewart
Most avian populations experience more variation in recruitment than adult survival, and twhich drives much of the change in population growth rates from year to year. In duck species, the probability of duckling survival is an important component of recruitment into the breeding population. We investigated how variation in maternal investment in offspring by nesting female wood duck Aix sponsa affected duckling mortality (1‐survival) to 60 days of age using capture‐mark‐recapture techniques. Our primary sample...

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