115 Works

Data from: Gene transfer from bacteria and archaea facilitated evolution of an extremophilic eukaryote

Gerald Schönknecht, Wei-Hua Chen, Chad M. Ternes, Guillaume G. Barbier, Roshan P. Shrestha, Mario Stanke, Andrea Bräutigam, Brett J. Baker, Jillian F. Banfield, R. Michael Garavito, Kevin Carr, Curtis Wilkerson, Stefan A. Rensing, David Gagneul, Nicholas E. Dickenson, Christine Oesterhelt, Martin J. Lercher & Andreas P. M. Weber
Some microbial eukaryotes, such as the extremophilic red alga Galdieria sulphuraria, can live in hot, toxic metal-rich, acidic environments. To elucidate the underlying molecular mechanisms of adaptation, we sequenced the 13.7 Mb genome of G. sulphuraria. This alga shows an enormous metabolic flexibility, growing either photoautotrophically or heterotrophically on more than 50 carbon sources. Environmental adaptation seems to have been facilitated by horizontal gene transfer from various bacteria and archaea, often followed by gene family...

Data from: Eutrophication and predation risk interact to affect sexual trait expression and mating success

Rickey Duane Cothran, Andy R Stiff, Punidan D Jeyasingh & Rick A Relyea
Sexual traits are especially sensitive to low food resources. Other environmental parameters (e.g., predation) should also affect sexual trait expression by favoring investment in viability traits rather than sexual traits. We know surprisingly little about how predators alter investment in sexual traits, or how predator and resource environments interact to affect sexual trait investment. We explored how increasing phosphorous (P) availability, at a level mimicking cultural eutrophication, affects the development of sexual, non-sexual, and viability...

Data from: Selection from parasites favors immunogenetic diversity but not divergence among locally adapted host populations

Michael Tobler, Martin Plath, Rüdiger Riesch, Ingo Schlupp, Anna Grasse, Gopi K. Munimanda, Claudia Setzer, Dustin J. Penn & Yoshan Moodley
The unprecedented polymorphism in the major histocompatibility complex (MHC) genes is thought to be maintained by balancing selection from parasites. However, do parasites also drive divergence at MHC loci between host populations, or do the effects of balancing selection maintain similarities among populations? We examined MHC variation in populations of the livebearing fish Poecilia mexicana and characterized their parasite communities. Poecilia mexicana populations in the Cueva del Azufre system are locally adapted to darkness and...

Data from: Effect of microsatellite selection on individual and population genetic inferences: an empirical study using cross-specific and species-specific amplifications

Joao Queiros, Raquel Godinho, Susana Lopes, Christian Gortazar, Jose De La Fuente & Paulo C. Alves
Although whole-genome sequencing is becoming more accessible and feasible for nonmodel organisms, microsatellites have remained the markers of choice for various population and conservation genetic studies. However, the criteria for choosing microsatellites are still controversial due to ascertainment bias that may be introduced into the genetic inference. An empirical study of red deer (Cervus elaphus) populations, in which cross-specific and species-specific microsatellites developed through pyrosequencing of enriched libraries, was performed for this study. Two different...

Data from: Systems biology of tissue-specific response to Anaplasma phagocytophilum reveals differentiated apoptosis in the tick vector Ixodes scapularis

Nieves Ayllón, Margarita Villar, Ruth C. Galindo, Katherine M. Kocan, Radek Sima, Juan A. López, Jesús Vázquez, Pilar Alberdi, Alejandro Cabezas-Cruz, Petr Kopáček & José De La Fuente
Anaplasma phagocytophilum is an emerging pathogen that causes human granulocytic anaplasmosis. Infection with this zoonotic pathogen affects cell function in both vertebrate host and the tick vector, Ixodes scapularis. Global tissue-specific response and apoptosis signaling pathways were characterized in I. scapularis nymphs and adult female midguts and salivary glands infected with A. phagocytophilum using a systems biology approach combining transcriptomics and proteomics. Apoptosis was selected for pathway-focused analysis due to its role in bacterial infection...

Data from: Restoring fire to grasslands is critical for migrating shorebird populations

Torre J. Hovick, J. Matthew Carroll, R. Dwayne Elmore, Craig A. Davis & Samuel D. Fuhlendorf
Fire is a disturbance process that maintains the structure and function of grassland ecosystems while sustaining grassland biodiversity. Conversion of grasslands to other land uses coupled with altered disturbance regimes have greatly diminished the habitat available to many grassland dependent species. These changes have been linked to declines in breeding bird populations, but may also be critical for migrating bird populations such as those shorebird species that depend on mesic grasslands during migration. We examined...

Data from: Does prey encounter and nutrient content affect prey selection in wolf spiders inhabiting Bt cotton fields?

Dalila Rendon, Phillip W. Taylor, Shawn M. Wilder & Mary E.A. Whitehouse
Wolf spiders are abundant and voracious predators at the soil-plant interface in cotton crops. Among other prey, they attack late-instar larvae of the cotton bollworm Helicoverpa spp., an economically important pest. Consequently, wolf spiders in transgenic Bt cotton could provide significant biological control of Bt-resistant Helicoverpa larvae that descend to the soil to pupate. The predator-prey interactions between wolf spiders and Helicoverpa could, however, be constrained by the presence of alternative prey and intraguild predators....

Data from: Perinatal and juvenile social environments interact to shape cognitive behaviour and neural phenotype in prairie voles

George S. Prounis, Lauren Foley, Asad Rehman & Alexander G. Ophir
Social environments experienced at different developmental stages profoundly shape adult behavioural and neural phenotypes, and may have important interactive effects. We asked if social experience before and after weaning influenced adult social cognition in male prairie voles. Animals were raised either with or without fathers and then either housed singly or in sibling pairs. Males that were socially deprived before (fatherless) and after (singly housed) weaning did not demonstrate social recognition or dissociate spatial from...

Associated data for: Disease and weather induce rapid shifts in a rangeland ecosystem mediated by a keystone species (Cynomys ludovicianus)

Courtney Duchardt
Habitat loss and changing climate have direct impacts on native species but can also interact with disease pathogens to influence wildlife communities. In the North American Great Plains, black-tailed prairie dogs (Cynomys ludovicianus) are a keystone species that create important grassland habitat for numerous species and serve as prey for predators, but lethal control driven by agricultural conflict has severely reduced their abundance. Novel disease dynamics caused by epizootic plague (Yersinia pestis) within prairie dog...

Soil Moisture Data for the Red River and Rio Grande Basins from 2015-2019

Tyson Ochsner, Matthew Levi & Grant Snitker
Modeled soil moisture raster maps (4km-pixels) displaying volumetric water content (VWC) and fraction of available water (FAW) in 10-cm depth increments for the 2015-2019 period for the Red River and Rio Grande basins.

Differential Proteomic Expression of Equine Cardiac and Lamellar Tissue During Insulin-Induced Laminitis

Allison Campolo, Matthew Frantz, Melody De Laat, Steven Hartson, Martin Furr & Veronique Lacombe
Endocrinopathic laminitis is pathologically similar to the multi-organ dysfunction and peripheral neuropathy found in human patients with metabolic syndrome. Similarly, endocrinopathic laminitis has been shown to partially result from vascular dysfunction. However, despite extensive research, the pathogenesis of this disease is not well elucidated and laminitis remains without an effective treatment. Here, we sought to identify novel proteins and pathways underlying the development of equine endocrinopathic laminitis. Healthy Standardbred horses (n=4/group) were either given an...

A Dataset on the influence of air voids and fluid absorption on salt-induced calcium oxychloride damage

Rita M. Ghantous, Keegan Zetterberg, Hope Hall Becker, Amir Behravan, M. Tyler Ley, O. Burkan Isgor & W. Jason Weiss
This dataset aims to display damage induced by calcium oxychloride formation with respect to concrete air void content, and boundary conditions. The purpose of this data set is to complete the data in the paper submitted to Cement and Concrete Composites Journal. The citation for this journal paper is : [1] Rita M. Ghantous, K. Zetterberg, H. H. Becker, A. Behravan, M. T. Ley, O. B. Isgor, W. J. Weiss (2022). “The influence of air...

A time-lagged association between the gut microbiome, nestling weight and nestling survival in wild great tits

Gabrielle Davidson, Shane Somers, Niamh Wiley, Crystal Johnson, Micheal Reichert, R. Paul Ross, Catherine Stanton & John Quinn
Natal body mass is a key predictor of viability and fitness in many animals. While variation in body mass and therefore viability of juveniles may be explained by genetic and environmental factors, emerging evidence points to the gut microbiota as an important factor influencing host health. The gut microbiota is known to change during development, but it remains unclear whether the microbiome predicts fitness, and if it does, at which developmental stage it affects fitness...

The roles of recombination and selection in shaping genomic divergence in an incipient ecological species complex

Matthew Wersebe, Ryan Sherman, Punidan Jeyasingh & Lawrence Weider
Speciation genomic studies have revealed that genomes of diverging lineages are shaped jointly by the actions of gene flow and selection. These evolutionary forces acting in concert with processes such as recombination and genome features such as gene density shape a mosaic landscape of divergence. We investigated the roles of recombination and gene density in shaping the patterns of differentiation and divergence between the cyclically parthenogenetic ecological sister-taxa, Daphnia pulicaria and Daphnia pulex. First, we...

Data from: Prediction accuracies for growth and wood attributes of interior spruce in space using genotyping-by-sequencing

Omnia Gamal El-Dien, Blaise Ratcliffe, Jaroslav Klápste, Charles Chen, Ilga Porth & Yousry A. El-Kassaby
Background: Genomic selection (GS) in forestry can substantially reduce the length of breeding cycle and increase gain per unit time through early selection and greater selection intensity, particularly for traits of low heritability and late expression. Affordable next-generation sequencing technologies made it possible to genotype large numbers of trees at a reasonable cost. Results: Genotyping-by-sequencing was used to genotype 1,126 Interior spruce trees representing 25 open-pollinated families planted over three sites in British Columbia, Canada....

Data from: Patterns of diversity and adaptation in Glomeromycota from three prairie grasslands

Baoming Ji, Catherine A. Gehring, Gail W. T. Wilson, R. M. Miller, Lluvia Flores-Rentería & Nancy Collins Johnson
Arbuscular mycorrhizal (AM) fungi are widespread root symbionts that often improve the fitness of their plant hosts. We tested whether local adaptation in mycorrhizal symbioses would shape the community structure of these root symbionts in a way that maximizes their symbiotic functioning. We grew a native prairie grass (Andropogon gerardii) with all possible combinations of soils and AM fungal inocula from three different prairies that varied in soil characteristics and disturbance history (two native prairie...

Data from: Resurrected “ancient” Daphnia genotypes show reduced thermal stress tolerance compared to modern descendants

Aimee M. Yousey, Priyanka Roy Chowdhury, Nicole Biddinger, Jennifer H. Shaw, Punidan D. Jeyasingh, Lawrence J. Weider & Aime'e M. Yousey
Understanding how populations adapt to rising temperatures has been a challenge in ecology. Research often evaluates multiple populations to test whether local adaptation to temperature regimes is occurring. Space-for-time substitutions are common, as temporal constraints limit our ability to observe evolutionary responses. We employed a resurrection ecology approach to understand how thermal tolerance has changed in a Daphnia pulicaria population over time. Temperatures experienced by the oldest genotypes were considerably lower than the youngest. We...

Data from: Biotic and abiotic factors shape the microbiota of wild-caught populations of the arbovirus vector Culicoides imicola

Sandra Díaz-Sánchez, Angélica Hernández-Jarguín, Alessandra Torina, Isabel G Fernández De Mera, Agustín Estrada-Peña, Margarita Villar, Francesco La Russa, Valeria Blanda, Joaquín Vicente, Santo Caracappa, Christian Gortazar & José De La Fuente
Biting midges of the genus Culicoides are known vectors of arboviruses affecting human and animal health. However, little is known about Culicoides imicola microbiota and its influence on this insect’s biology. In this study, the impact of biotic and abiotic factors on C. imicola microbiota was characterized using shotgun-metagenomic sequencing of whole body DNA samples. Wild-caught C. imicola adult nulliparous females were sampled in two locations from Sicily, Italy. The climatic variables of temperature and...

Data from: Phylogenetic patterns of trait and trait plasticity evolution: Insights from amphibian embryos

Rick Relyea, Patrick R. Stephens, Lisa N. Barrow, Andrew Blaustein, Paul Bradley, Julia Buck, Ann Chang, Brian I Crother, James Collins, Julia Earl, Stephanie S. Gervasi, Jason T. Hoverman, Olliver Hyman, Emily Claire Moriarty Lemmon, Thomas Luhring, Moses Michelsohn, Christopher M. Murray, Steven Price, Raymond Semlitsch, Andy Sih, Aaron Stoler, Nick VandenBroek, Alexa Warwick, Greta Wengert, John Hammond … & Aaron B. Stoler
Environmental variation favors the evolution of phenotypic plasticity. For many species, we understand the costs and benefits of different phenotypes, but we lack a broad understanding of how plastic traits evolve across large clades. Using identical experiments conducted across North America, we examined prey responses to predator cues. We quantified five life history traits and the magnitude of their plasticity for 23 amphibian species/populations (spanning three families and five genera) when exposed to no cues,...

Data from: A ground-nesting Galliform’s response to thermal heterogeneity: Implications for ground-dwelling birds

J. Matthew Carroll, Craig A. Davis, R. Dwayne Elmore & Samuel D. Fuhlendorf
The habitat selection choices that individuals make in response to thermal environments influence both survival and reproduction. Importantly, the way that organisms behaviorally respond to thermal environments depends on the availability and juxtaposition of sites affording tolerable or preferred microclimates. Although, ground nesting birds are especially susceptible to heat extremes across many reproductive stages (i.e., breeding, nesting, brood rearing), the mechanistic drivers of nest site selection for these species are not well established from a...

Data from: Trade-offs among locomotor performance, reproduction, and immunity in lizards

Jerry F. Husak, Haley A. Ferguson & Matthew B. Lovern
Life-history theory predicts that investment of acquired energetic resources to a particular trait denies those same resources from being allocated to a different trait, resulting in life-history trade-offs. Dynamic, whole-organism performance traits, including locomotor capacity, are key to fitness and fit within this framework. Such performance traits are typically energetically expensive, but are seldom integrated into life-history studies. We manipulated diet and allocation of resources to performance, via exercise training, to examine trade-offs among endurance...

Data from: Ionome and elemental transport kinetics shaped by parallel evolution in threespine stickleback

Seth M. Rudman, Jared M. Goos, Joseph B. Burant, Kevin V. Brix, Taylor C. Gibbons, Colin J. Brauner & Punidan D. Jeyasingh
Evidence that organisms evolve rapidly enough to alter ecological dynamics necessitates investigation of the reciprocal links between ecology and evolution. Data that link genotype to phenotype to ecology are needed to understand both the process and ecological consequences of rapid evolution. Here we quantified the suite of elements in individuals (i.e., ionome) and the fluxes of key nutrients across populations of threespine stickleback. We find that allelic variation associated with freshwater adaptation that controls bony...

Herbaceous production and soil nitrogen after mesquite mortality

Jim Ansley
In the mixed C3/C4 grassland of the southern Great Plains, USA, the invasive woody legume, honey mesquite (Prosopis glandulosa), affects grass production and composition differently beneath the canopy (subcanopy) than in spaces between trees (intercanopy) due in part to the dominant presence of C3 Texas wintergrass (Nassella leucotricha) beneath the mesquite canopy and soil enrichment from N-fixation by mesquite. This arrangement, unlike most Prosopis systems worldwide that have C4 grass or C3 subshrub understories, uniquely...

Age predicts risky investment better than residual reproductive value

David Delaney, Luke Hoekstra & Fredric Janzen
Life-history theory predicts that investment into reproduction should increase as future reproductive opportunities (i.e., residual reproductive value, RRV) decrease. Researchers have thus intuitively used age as a proxy for RRV and assume RRV decreases with age when interpreting age-specific investment. Yet, age is an imperfect proxy for RRV and may even be a poor correlate in some systems. We used a 30-year study of the nesting ecology of painted turtles ( Chrysemys picta ) to...

Data from: Evolution of dispersal, habit, and pollination in Africa pushed Apocynaceae diversification after the Eocene-Oligocene climate transition

Nicolai M. Nürk, Cássia Bitencourt, Alessandro Rapini, Mark Fishbein, André O. Simões, David J. Middleton, Ulrich Meve, Mary E. Endress & Sigrid Liede-Schumann
Apocynaceae (the dogbane and milkweed family) is one of the ten largest flowering plant families, with approximately 5,350 species and diverse morphology and ecology, ranging from large trees and lianas that are emblematic of tropical rainforests, to herbs in temperate grasslands, to succulents in dry, open landscapes, and to vines in a wide variety of habitats. Despite a specialized and conservative basic floral architecture, Apocynaceae are hyperdiverse in flower size, corolla shape, and especially derived...

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  • Oklahoma State University
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  • University of California, Berkeley
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