451 Works

Data from: Locating evolutionary precursors on a phylogenetic tree

Brigitte Marazzi, Cecile M. Ane, Marcelo F. Simon, Melissa A. Luckow, Alfonso Delgado-Salinas & Michael J. Sanderson
Conspicuous innovations in the history of life are often preceded by more cryptic genetic and developmental precursors. In many cases, these appear to be associated with recurring origins of very similar traits in close relatives (parallelisms) or striking convergences separated by deep time (“deep homologies”). Although the phylogenetic distribution of gain and loss of traits hints strongly at the existence of such precursors, no models of trait evolution currently permit inference about their location on...

Data from: Drivers of nocturnal water flux in a tallgrass prairie

Kimberly O'Keefe & Jesse B. Nippert
1. Nocturnal transpiration can impact water balance from the local community to earth-atmosphere fluxes. However, the dynamics and drivers of nocturnal transpiration among coexisting plant functional groups in herbaceous ecosystems are unknown. 2. Here, we addressed the following questions: (1) How do nocturnal (Enight) and diurnal (Eday) transpiration vary among coexisting grasses, forbs, and shrubs in a tallgrass prairie? (2) What environmental variables drive Enight and do these differ from the drivers of Eday? (3)...

Data from: Reverse genetics in the tidepool: knockdown of target gene expression via RNA interference in the copepod Tigriopus californicus

Felipe S. Barreto, Sean D. Schoville & Ronald S. Burton
Reverse genetic tools are essential for characterizing phenotypes of novel genes and testing functional hypotheses generated from next-generation sequencing studies. RNA interference (RNAi) has been a widely used technique for describing or quantifying physiological, developmental or behavioural roles of target genes by suppressing their expression. The marine intertidal copepod Tigriopus californicus has become an emerging model for evolutionary and physiological studies, but this species is not amenable to most genetic manipulation approaches. As crustaceans are...

Data from: Post-fire changes in forest carbon storage over a 300-year chronosequence of Pinus contorta-dominated forests

Daniel M. Kashian, William H. Romme, Daniel Tinker, Monica G. Turner, Michael G. Ryan & Daniel B. Tinker
A warming climate may increase the frequency and severity of stand-replacing wildfires, reducing carbon (C) storage in forest ecosystems. Understanding the variability of post-fire C cycling on heterogeneous landscapes is critical for predicting changes in C storage with more frequent disturbance. We measured C pools and fluxes for 77 lodgepole pine (Pinus contorta Dougl. ex Loud var. latifolia Engelm.) stands in and around Yellowstone National Park (YNP) along a 300-year chronosequence to examine how quickly...

Data from: Pumping ions: rapid parallel evolution of ionic regulation following habitat invasions

Carol Eunmi Lee, Michael Kiergaard, Gregory William Gelembiuk, Brian Donovan Eads & Marijan Posavi
Marine to freshwater colonizations constitute among the most dramatic evolutionary transitions in the history of life. This study examined evolution of ionic regulation following saline-to-freshwater transitions in an invasive species. In recent years, the copepod Eurytemora affinis has invaded freshwater habitats multiple times independently. We found parallel evolutionary shifts in ion-motive enzyme activity (V-type H+ ATPase, Na+/K+-ATPase) across independent invasions and in replicate laboratory selection experiments. Freshwater populations exhibited increased V-type H+ ATPase activity in...

Data from: Recognizing cross-ecosystem responses to changing temperatures: soil warming impacts pelagic food webs

Samuel B. Fey, Andrew N. Mertens, Lucas J. Beversdorf, Katherine D. McMahon & Kathryn L. Cottingham
The energy and materials that move across ecosystem boundaries influence food web structure and key ecosystem functions. Despite the acknowledged importance of such ecological subsidies, surprisingly little information is available regarding the role of environmental temperature in influencing subsidy quality and the response of the recipient ecosystem. We evaluated the impacts of temperature-mediated changes in leaves from deciduous trees, an important subsidy from terrestrial to freshwater ecosystems, on both the producer-based and detritivore-based components of...

Data from: Disentangling the genetic effects of refugial isolation and range expansion in a trans-continentally distributed species

Brendan N. Reid, Jamie M. Kass, Seth Wollney, Evelyn L. Jensen, Michael A. Russello, Ella M. Viola, Jenna Pantophlet, John B. Iverson, Marcus Z. Peery, Christopher J. Raxworthy & Eugenia Naro-Maciel
In wide-ranging taxa with historically dynamic ranges, past allopatric isolation and range expansion can both influence the current structure of genetic diversity. Considering alternate historical scenarios involving expansion from either a single refugium or from multiple refugia can be useful in differentiating the effects of isolation and expansion. Here, we examined patterns of genetic variability in the trans-continentally distributed painted turtle (Chrysemys picta). We utilized an existing phylogeographic dataset for the mitochondrial control region and...

Data from: An evaluation of a novel estimator of linkage disequilibrium

Daniel Gianola, Saber Qanbari & Henner Simianer
The analysis of systems involving many loci is important in population and quantitative genetics. An important problem is the study of linkage disequilibrium (LD), a concept relevant in genome-enabled prediction of quantitative traits and in exploration of marker-phenotype associations. This article introduces a new estimator of a LD parameter (ρ^2) that is much easier to compute than a maximum likelihood (or Bayesian) estimate of a tetra-choric correlation. We examined the conjecture that the sampling distribution...

Data from: Linking plant genes to insect communities: identifying the genetic bases of plant traits and community composition

Hilary L. Barker, Jennifer F. Riehl, Carolina Bernhardsson, Kennedy Rubert-Nason, Liza Holeski, Pär K. Ingvarsson & Richard L. Lindroth
Community genetics aims to understand the effects of intraspecific genetic variation on community composition and diversity, thereby connecting community ecology with evolutionary biology. Thus far, research has shown that plant genetics can underlie variation in the composition of associated communities (e.g., insects, lichen, endophytes), and those communities can therefore be considered as extended phenotypes. This work, however, has been conducted primarily at the plant genotype level and has not identified the key underlying genes. To...

Data from: Tracking temporal shifts in area, biomes, and pollinators in the radiation of Salvia (sages) across continents: leveraging anchored hybrid enrichment and targeted sequence data

Ricardo Kriebel, Bryan T. Drew, Chloe P. Drummond, Jesús Guadalupe González Gallegos, Ferhat Celep, Mohamed M. Mahdjoub, Jeffrey P. Rose, Chun-Lei Xiang, Guo-Xiong Hu, Jay B. Walker, Emily M. Lemmon, Alan R. Lemmon & Kenneth J. Sytsma
Premise of the Study: A key question in evolutionary biology is why some clades are more successful by being widespread geographically, biome diverse, or species‐rich. To extend understanding of how shifts in area, biomes, and pollinators impact diversification in plants, we examined the relationships of these shifts to diversification across the mega‐genus Salvia. Methods: A chronogram was developed from a supermatrix of anchored hybrid enrichment genomic data and targeted sequence data for over 500 of...

Data from: Downscaled and debiased climate simulations for North America from 21,000 years ago to 2100AD

David J. Lorenz, Diego Nieto-Lugilde, Jessica L. Blois, Matthew C. Fitzpatrick & John W. Williams
Increasingly, ecological modellers are integrating paleodata with future projections to understand climate-driven biodiversity dynamics from the past through the current century. Climate simulations from earth system models are necessary to this effort, but must be debiased and downscaled before they can be used by ecological models. Downscaling methods and observational baselines vary among researchers, which produces confounding biases among downscaled climate simulations. We present unified datasets of debiased and downscaled climate simulations for North America...

Water uptake, cloud condensation nuclei and surface tension: results from the MadFACTS campaign

Sara Forestieri, Sean Staudt, Thomas Kuborn, Christopher Ruehl, Timothy Bertram & Christopher Cappa
This data set is associated with the manuscript “Establishing the Impact of Model Surfactants on Cloud Condensation Nuclei Activity of Sea Spray Aerosols” by Forestieri et al. that has been submitted to Atmospheric Chemistry and Physics. The abstract to this manuscript is provided below. By reducing surface tension (σ), surfactants present in aerosols can increase their cloud condensation nuclei (CCN) activation efficiency. However, the importance of this effect is poorly constrained. Here we present estimates...

Data from: Natal dispersal of tree sloths in a human-dominated landscape: implications for tropical biodiversity conservation

Mario F. Garces-Restrepo, Jonathan N. Pauli & M. Zachariah Peery
1. Habitat loss and fragmentation resulting from the conversion of tropical forests are among the most important threats to biodiversity globally. Habitat specialists and species with low dispersal capacity are expected to be the most sensitive to such changes. Relatively little is known, however, about how habitat change and life history interact to impact natal dispersal and population viability in tropical species. 2. Here, we characterized natal dispersal patterns, habitat selection, and survival rates in...

Data from: Rapid divergence of genome architectures following the origin of an ectomycorrhizal symbiosis in the genus Amanita

Jaqueline Hess, Inger Skrede, Maryam Chaib De Mares, Matthieu Hainaut, Bernard Henrissat & Anne Pringle
Fungi are evolutionary shape shifters and adapt quickly to new environments. Ectomycorrhizal (EM) symbioses are mutualistic associations between fungi and plants and have evolved repeatedly and independently across the fungal tree of life, suggesting lineages frequently reconfigure genome content to take advantage of open ecological niches. To date analyses of genomic mechanisms facilitating EM symbioses have involved comparisons of distantly related species, but here, we use the genomes of three EM and two asymbiotic (AS)...

Data from: Reproductive aging patterns in primates reveal that humans are distinct

Susan C. Alberts, Jeanne Altmann, Diane K. Brockman, Marina Cords, Linda M. Fedigan, Anne Pusey, Tara S. Stoinski, Karen B. Strier, William F. Morris & Anne M. Bronikowski
Women rarely give birth after approximately 45 years of age, and they experience the cessation of reproductive cycles – menopause – at approximately 50 years of age, after a fertility decline lasting almost two decades. Such reproductive senescence in mid-lifespan is an evolutionary puzzle of enduring interest because it should be inherently disadvantageous. Further, comparative data on reproductive senescence from other primates, or indeed other mammals, remains relatively rare. Here we carried out the first...

Data from: Genetic drivers of pancreatic islet function

Mark P. Keller, Daniel M. Gatti, Kathryn L. Schueler, Mary E. Rabaglia, Donnie S. Stapleton, Peter Simecek, Matthew Vincent, Sadie Allen, Aimee Teo Broman, Rhonda Bacher, Christina Kendziorski, Karl W. Broman, Brian S. Yandell, Gary A. Churchill, Alan D. Attie & Petr Simecek
Nearly all gene loci that have been associated with type 2 diabetes play a role in pancreatic islet function. To evaluate the role of islet gene expression in the etiology of diabetes, we sensitized a genetically diverse mouse population with a Western diet and carried out genome-wide association mapping of diabetes-related phenotypes. We quantified mRNA abundance in the islets, and identified 18,775 expression quantitative trait loci. We applied mediation analysis to identify candidate causal driver...

Data from: Population dynamics of a northern-adapted mammal: disentangling the influence of predation and climate change

John W. Pokallus, Jonathan N. Pauli &
Community structure and interspecific interactions are particularly vulnerable to rapidly changing climatic regimes. Recent changes in both climate and vertebrate community assemblages have created a unique opportunity to examine the impacts of two dynamic forces on population regulation. We examined the effects of warming winter conditions and the reestablishment of a previously extirpated predator, the fisher (Martes pennanti), on regulatory mechanisms in a northern-adapted mammal, the porcupine (Erethizon dorsatum), along their southern range boundary. Using...

Data from: What are the prospects for citizen science in agriculture? Evidence from three continents on motivation and mobile telephone use of resource-poor farmers

Eskender Beza, Jonathan Steinke, Jacob Van Etten, Pytrik Reidsma, Carlo Fadda, Sarika Mittra, Prem Mathur & Lammert Kooistra
As the sustainability of agricultural citizen science projects depends on volunteer farmers who contribute their time, energy and skills, understanding their motivation is important to attract and retain participants in citizen science projects. The objectives of this study were to assess 1) farmers' motivations to participate as citizen scientists and 2) farmers' mobile telephone usage. Building on motivational factors identified from previous citizen science studies, a questionnaire based methodology was developed which allowed the analysis...

Data from: Hibernation alters the diversity and composition of mucosa-associated bacteria while enhancing antimicrobial defense in the gut of 13-lined ground squirrels

Kimberly A. Dill-McFarland, Katie L. Neil, Austin Zeng, Ryan J. Sprenger, Courtney C. Kurtz, Garret Suen & Hannah V. Carey
The gut microbiota plays important roles in animal nutrition and health. This relationship is particularly dynamic in hibernating mammals where fasting drives the gut community to rely on host-derived nutrients instead of exogenous substrates. We used 16S rRNA pyrosequencing and cecal tissue protein analysis to investigate the effects of hibernation on the mucosa-associated bacterial microbiota and host responses in 13-lined ground squirrels. The mucosal microbiota was less diverse in winter hibernators than in actively feeding...

Data from: Host social behavior decreases exposure to vector-borne disease: a field experiment in a “hotspot” of West Nile virus transmission

Bethany L. Krebs, Tavis K. Anderson, Tony L. Goldberg, Gabriel L. Hamer, Uriel D. Kitron, Christina M. Newman, Marilyn O. Ruiz, Edward D. Walker & J. D. Brawn
Animals can decrease their individual risk of predation by forming groups. The encounter-dilution hypothesis extends the potential benefits of gregariousness to biting insects and vector-borne disease by predicting that the per capita number of insect bites should decrease within larger host groups. Although vector-borne diseases are common and can exert strong selective pressures on hosts, there have been few tests of the encounter-dilution effect in natural systems. We conducted an experimental test of the encounter-dilution...

Data from: Predator experience overrides learned aversion to heterospecifics in stickleback species pairs

Genevieve M. Kozak & Janette W. Boughman
Predation risk can alter female mating decisions because the costs of mate searching and selecting attractive mates increase when predators are present. In response to predators, females have been found to plastically adjust mate preference within species, but little is known about how predators alter sexual isolation and hybridization among species. We tested the effects of predator exposure on sexual isolation between benthic and limnetic threespine sticklebacks (Gasterosteus spp.). Female discrimination against heterospecific mates was...

Data from: Emergence of long-term balanced polymorphism under cyclic selection of spatially variable magnitude

Davorka Gulisija & Yuseob Kim
A fundamental question in evolutionary biology is what promotes genetic variation at non-neutral loci, a major precursor to adaptation in changing environments. In particular, balanced polymorphism under realistic evolutionary models of temporally varying environments in finite natural populations remains to be demonstrated. Here, we propose a novel mechanism of balancing selection under temporally varying fitnesses. Using forward-in-time computer simulations and mathematical analysis, we show that cyclic selection that spatially varies in magnitude, such as along...

Data from: Temperature effects on long-term population dynamics in a parasitoid-host system

Anthony R. Ives, Matthew H. Meisner & Jason P. Harmon
Long-term environmental changes will likely alter the strengths of interactions between species and consequently their population dynamics, leading to changes in the stability of ecological systems. While an increasing number of empirical studies have shown that environmental changes can alter the strengths of species interactions, these studies are typically short (<1–2 generations) and therefore give only partial information about longer term population dynamics. To focus on longer term dynamics, we investigated population cycles of pea...

Data from: Extensive genetic diversity is present within North American switchgrass germplasm

Joseph Evans, Millicent D. Sanciangco, Kin H. Lau, Emily Crisovan, Kerrie Barry, Chris Daum, Hope Hundley, Jerry Jenkins, Megan Kennedy, Govindarajan Kunde-Ramamoorthy, Brieanne Vaillancourt, Ananta Acharya, Jeremy Schmutz, Malay Saha, Shawn M. Kaeppler, E. Charles Brummer, Michael D. Casler & C. Robin Buell
Switchgrass (Panicum virgatum L.) is a perennial native North American grass present in two ecotypes: upland, found primarily in the northern range of switchgrass habitats, and lowland, found largely in the southern reaches of switchgrass habitats. Previous studies focused on a diversity panel of primarily northern switchgrass, so to expand our knowledge of genetic diversity in a broader set of North American switchgrass, exome capture sequence data were generated for 632 additional, primarily lowland individuals....

Data from: Modality interactions alter the shape of acoustic mate preference functions in gray treefrogs

Michael S. Reichert & Gerlinde Höbel
Sexual selection takes place in complex environments where females evaluating male mating signals are confronted with stimuli from multiple sources and modalities. The pattern of expression of female preferences may be influenced by interactions between modalities, changing the shape of female preference functions, and thus ultimately altering the selective landscape acting on male signal evolution. We tested the hypothesis that the responses of female gray treefrogs, Hyla versicolor, to acoustic male advertisement calls are affected...

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