180 Works

Data from: An upper bound for accuracy of prediction using GBLUP

Emre Karaman, Hao Cheng, Mehmet Z. Firat, Dorian J. Garrick & Rohan L. Fernando
This study aims at characterizing the asymptotic behavior of genomic prediction R2 as the size of the reference population increases for common or rare QTL alleles through simulations. Haplotypes derived from whole-genome sequence of 85 Caucasian individuals from the 1,000 Genomes Project were used to simulate random mating in a population of 10,000 individuals for at least 100 generations to create the LD structure in humans for a large number of individuals. To reduce computational...

Data from: A garter snake transcriptome: pyrosequencing, de novo assembly, and sex-specific differences

Tonia S. Schwartz, Hongseok Tae, Youngik Yang, Keithanne Mockaitis, John L. Van Hemert, Stephen R. Proulx, Jeong-Hyeon Choi & Anne M. Bronikowski
Background: The reptiles, characterized by both diversity and unique evolutionary adaptations, provide a comprehensive system for comparative studies of metabolism, physiology, and development. However, molecular resources for ectothermic reptiles are severely limited, hampering our ability to study the genetic basis for many evolutionarily important traits such as metabolic plasticity, extreme longevity, limblessness, venom, and freeze tolerance. Here we use massively parallel sequencing (454 GS-FLX Titanium) to generate a transcriptome of the western terrestrial garter snake...

Data from: Phenology differences between native and novel exotic-dominated grasslands rival the effects of climate change

Brian J. Wilsey, Leanne M. Martin & Andrew D. Kaul
1. Novel ecosystems can differ from the native systems they replaced. We used phenology measures to compare ecosystem functioning between novel exotic-dominated and native-dominated grasslands in the central US. 2. Phenology, or timing of biological events, is affected by climate and land use changes. We assessed how phenology shifts are being altered by exotic species dominance by comparing remotely sensed Normalized Difference Vegetation Index (NDVI) within growing seasons at exotic- and native-dominated sites along a...

Data from: Offspring dispersal ability covaries with nest-site choice

David M. Delaney & Fredric J. Janzen
Optimal maternal investment is often a tradeoff between conflicting pressures and varies depending upon environmental context and intrinsic female traits. Yet, offspring phenotype might also interact with such factors to influence investment. In aquatic turtles, terrestrial nests constructed farther from shore often have higher survival because nest predators tend to forage along environmental edges. However, offspring from eggs deposited farther inland must migrate farther to water upon emergence. We released hatchling common snapping turtles (Chelydra...

Data from: Episodic radiations in the fly tree of life

Brian M. Wiegmann, Michelle D. Trautwein, Isaac S. Winkler, Norman B. Barr, Jung-Wook Kim, Christine Lambkin, Matthew A. Bertone, Brian K. Cassel, Keith M. Bayless, Alysha M. Heimberg, Benjamin M. Wheeler, Kevin J. Peterson, Thomas Pape, Bradley J. Sinclair, Jeffrey H. Skevington, Vladimir Blagoderov, Jason Caravas, Sujatha Narayanan Kutty, Urs Schmidt-Ott, Gail E. Kampmeier, F. Christian Thompson, David A. Grimaldi, Andrew T. Beckenbach, Gregory W. Courtney, Markus Friedrich … & J.-W. Kim
Flies are one of four superradiations of insects (along with beetles, wasps, and moths) that account for the majority of animal life on Earth. Diptera includes species known for their ubiquity (Musca domestica house fly), their role as pests (Anopheles gambiae malaria mosquito), and their value as model organisms across the biological sciences (Drosophila melanogaster). A resolved phylogeny for flies provides a framework for genomic, developmental, and evolutionary studies by facilitating comparisons across model organisms,...

Data from: Prophylactic digoxin treatment reduces IL-17 production in vivo in the neonatal calf and moderates RSV-associated disease

Jodi L. McGill, Mariana Guerra-Maupome & Sarah Schneider
Respiratory syncytial virus (RSV) is a leading cause of morbidity and mortality in human infants. Bovine RSV infection of neonatal calves is pathologically and immunologically similar to RSV infection in infants, and is therefore a useful preclinical model for testing novel therapeutics. Treatment of severe RSV bronchiolitis relies on supportive care and may include use of bronchodilators and inhaled or systemic corticosteroids. Interleukin-17A (IL-17) is an inflammatory cytokine that plays an important role in neutrophil...

Data from: Signatures of selection and environmental adaptation across the goat genome post-domestication

Licia Colli, Marco Milanesi, Andrea Talenti, Francesca Bertolini, Minhui Chen, Alessandra Crisà, Kevin Daly, Marcello Del Corvo, Bernt Guldbrandtsen, Johannes A. Lenstra, Ben D. Rosen, Elia Vajana, Gennaro Catillo, Stéphane Joost, Ezequiel Luis Nicolazzi, Estelle Rochat, Max F. Rothschild, Bertrand Servin, Tad S. Sonstegard, Roberto Steri, Curtis P. Van Tassel, Paolo Ajmone-Marsan, Paola Crepaldi, Alessandra Stella & AdaptMap Consortium
Background: Since goat was domesticated 10,000 years ago, many factors have contributed to the differentiation of goat breeds and these are classified mainly into two types: (i) adaptation to different breeding systems and/or purposes and (ii) adaptation to different environments. As a result, approximately 600 goat breeds have developed worldwide; they differ considerably from one another in terms of phenotypic characteristics and are adapted to a wide range of climatic conditions. In this work, we...

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: Variability in community productivity: mediating effects of vegetation attributes

Wayne H. Polley & Brian J. Wilsey
1. Plant productivity varies though time in response to environmental fluctuations. Reducing variability in productivity requires an improved understanding of how plant community attributes interact with environmental fluctuations to influence plant growth dynamics. We evaluated links between two community attributes, species diversity and abundance-weighted values of specific leaf area (SLA), and temporal variability in grassland productivity at patch (local) and aggregate (multi-patch) spatial scales. 2. Aggregate communities were created by combining patches of spatially-distinct communities...

Data from: Maintenance of genetic diversity in an introduced island population of Guanacos after seven decades and two severe demographic bottlenecks: implications for camelid conservation

Benito A. González, Pablo Orozco-TerWengel, Rainer Von Borries, Warren E. Johnson, William L. Franklin & Juan C. Marín
Fifteen Guanacos were introduced to Staats Island in Falklands/Malvinas archipelago from Patagonia in the 1930s. After introduction, the Guanaco population increased to almost 400 animals that retained a footprint of the founding effect and bottleneck reflected in the genetic status of this isolated population. The goals of this study were to (i) make a genetic assessment of this island population through comparisons with mainland populations and simulation, and (ii) assess the likely source population of...

Data from: Hormonal and metabolic responses to upper temperature extremes in divergent life-history ecotypes of a garter snake

Eric J. Gangloff, Kaitlyn G. Holden, Rory S. Telemeco, Lance H. Baumgard & Anne M. Bronikowski
Extreme temperatures constrain organismal physiology and impose both acute and chronic effects. Additionally, temperature-induced hormone-mediated stress response pathways and energetic trade-offs are important drivers of life-history variation. This study employs an integrative approach to quantify acute physiological responses to high temperatures in divergent life-history ecotypes of the western terrestrial garter snake (Thamnophis elegans). Using wild-caught animals, we measured oxygen consumption rate and physiological markers of hormonal stress response, energy availability, and anaerobic respiration in blood...

Data from: The low but uncertain measured benefits of U.S. water quality policy

David A. Keiser, Catherine L. Kling & Joseph S. Shapiro
US investment to decrease pollution in rivers, lakes, and other surface waters has exceeded $1.9 trillion since 1960, and has also exceeded the cost of most other US environmental initiatives. These investments come both from the 1972 Clean Water Act and the largely voluntary efforts to control pollution from agriculture and urban runoff. This paper reviews the methods and conclusions of about 20 recent evaluations of these policies. Surprisingly, most analyses estimate that these policies’...

Data from: Vegetation type controls root turnover in global grasslands

Jinsong Wang, Jian Sun, Zhen Yu, Yong Li, Dashuan Tian, Bingxue Wang, Zhaolei Li & Shuli Niu
Abstract: Aim: Root turnover is an important process determining carbon and nutrient cycling in terrestrial ecosystems. It is an established fact that root turnover is jointly regulated by climatic, edaphic, and biotic factors. However, the relative importance of these forces in determining the global patterns of root turnover time is far from clear. Location: Global. Time period: 1946–2017. Major taxa studied: Grasslands. Methods: We compiled a database of 141 sites with 433 observations on root...

Data from: Monarch butterfly population decline in North America: identifying the threatening processes

Wayne E. Thogmartin, Ruscena Wiederholt, Karen Oberhauser, Ryan G. Drum, Jay E. Diffendorfer, Sonia Altizer, Orley R. Taylor, John Pleasants, Darius Semmens, Brice Semmens, Richard Erickson, Kaitlin Libby & Laura Lopez-Hoffman
The monarch butterfly (Danaus plexippus) population in North America has sharply declined over the last two decades. Despite rising concern over the monarch butterfly's status, no comprehensive study of the factors driving this decline has been conducted. Using partial least-squares regressions and time-series analysis, we investigated climatic and habitat-related factors influencing monarch population size from 1993 to 2014. Potential threats included climatic factors, habitat loss (milkweed and overwinter forest), disease and agricultural insecticide use (neonicotinoids)....

Data from: Hallauer's Tusón: a decade of selection for tropical- to-temperate phenological adaptation in maize

Juliana E. C. Teixeira, Teclemariam Weldekidan, Natalia De Leon, Sherry Flint-Garcia, James B. Holland, Nick Lauter, Seth C. Murray, Wenwei Xu, David A. Hessel, Adrienne E. Kleintop, James A. Hawk, Arnel R. Hallauer & Randall J. Wisser
Crop species exhibit an astounding capacity for environmental adaptation, but genetic bottlenecks resulting from intense selection for adaptation and productivity can lead to a genetically vulnerable crop. Improving the genetic resiliency of temperate maize depends upon the use of tropical germplasm, which harbors a rich source of natural allelic diversity. Here, the adaptation process was studied in a tropical maize population subjected to 10 recurrent generations of directional selection for early flowering in a single...

Data from: Pleiotropy can be effectively estimated without counting phenotypes through the rank of genotype-phenotype map

Xun Gu
Though pleiotropy, the capability of a gene affecting multiple phenotypes, has been well-known as one of common gene properties, a quantitative estimation remains a great challenge, simply because of the phenotype complexity. Not surprisingly, it is hard for general readers to understand how, without counting phenotypes, gene pleiotropy can be effectively estimated from the genetics data. In this article we extensively discussed the Gu-2007-method (Genetics 175: 1813-1822) that estimated pleiotropy from the protein sequence analysis....

Data from: The Sarracenia alata pitcher plant system and obligate arthropod inquilines should be considered an evolutionary community

Jordan D. Satler & Bryan C. Carstens
Aim: The Sarracenia alata pitcher plant and inquiline species comprise an ecological community. These inquilines span the continuum in their ecological association with the host pitcher plant, from species that contain little-to-no interaction with the plant to species that are completely dependent on the plant for their entire life cycle. We are interested in testing if degree of ecological dependence is positively correlated with a shared evolutionary history, and in identifying members of this community...

Assessing the impact of incomplete species sampling on estimates of speciation and extinction rates

Rachel C. M. Warnock, Tracy A. Heath & Tanja Stadler
Estimating speciation and extinction rates is essential for understanding past and present biodiversity, but is challenging given the incompleteness of the rock and fossil records. Interest in this topic has led to a divergent suite of independent methods—paleontological estimates based on sampled stratigraphic ranges and phylogenetic estimates based on the observed branching times in a given phylogeny of living species. The fossilized birth–death (FBD) process is a model that explicitly recognizes that the branching events...

Data from: Nutrient availability controls the impact of mammalian herbivores on soil carbon and nitrogen pools in grasslands

Judith Sitters, E.R. Jasper Wubs, Elisabeth S. Bakker, Thomas W. Crowther, Peter B. Adler, Sumanta Bagchi, Jonathan D. Bakker, Lori Biederman, Elizabeth T. Borer, Elsa E. Cleland, Nico Eisenhauer, Jennifer Firn, Laureano Gherardi, Nicole Hagenah, Yann Hautier, Sarah E. Hobbie, Johannes M.H. Knops, Andrew S. MacDougall, Rebecca L. McCulley, Joslin L. Moore, Brent Mortensen, Pablo L. Peri, Suzanne M. Prober, Charlotte Riggs, Anita C. Risch … &
Grasslands have been subject to considerable alteration due to human activities globally, including widespread changes in populations and composition of large mammalian herbivores and elevated supply of nutrients. Grassland soils remain important reservoirs of carbon (C) and nitrogen (N). Herbivores may affect both C and N pools and these changes likely interact with increases in soil nutrient availability. Given the scale of grassland soil fluxes, such changes can have striking consequences for atmospheric C concentrations...

Data from: Outcrossing mating system of the early-divergent moonwort fern (Botrychium lunaria, Ophioglossaceae) revealed in the European Alps

Benjamin Dauphin, Jason Grant & Donald Farrar
Premise of the Research. Vascular plants depend on sexual recombination for generating new genetic variability to meet environmental needs. Nevertheless, members of the early-divergent fern genus Botrychium (Ophioglossaceae) typically maintain gametophytic selfing and show strong inbreeding within populations. To explain this evolutionary anomaly, the existence of previous or current but undiscovered outcrossing, genetically rich, precursors of the existing genetically depauperate taxa has been hypothesized. Methodology. Using allele expression at thirteen independently assorting enzyme loci, we...

Honey bee virus causes context-dependent changes in host social behavior

Adam Dolezal, Tim Gernat, Geffre Amy, Gyan Harwood, Beryl Jones, Adam Hamilton, Bryony Bonning, Amy Toth, Gene Robinson & Deisy Morselli Gysi
Anthropogenic changes create evolutionarily novel environments that present opportunities for emerging diseases, potentially changing the balance between host and pathogen. Honey bees provide essential pollination services, but intensification and globalization of honey bee management has coincided with increased pathogen pressure, primarily due to a parasitic mite/virus complex. Here, we investigated how honey bee individual and social phenotypes are altered by a virus of concern, Israeli acute paralysis virus (IAPV). Using automated and manual behavioral monitoring...

Efficient targeted integration directed by short homology in zebrafish and mammalian cells

Jeffrey Essner & Maura McGrail
Efficient precision genome engineering requires high frequency and specificity of integration at the genomic target site. Here, we describe a set of resources to streamline precision gene targeting in zebrafish and demonstrate the broader utility of the method in mammalian cells. Our approach uses short homology of 24-48 bp to drive targeted integration of DNA reporter cassettes by homology-mediated end joining (HMEJ) at high frequency. Our vector series, pGTag (plasmids for Gene Tagging), contains reporters...

Strategies for the utilization of USDA mungbean germplasm collection for breeding outcomes

Kulbir Sandhu & Arti Singh
Global and mid-west U.S. agriculture requires diversification and new sources of protein for sustainable crop production. Mungbean as a legume crop has a long cultivation history in Asia; however, its potential lays hitherto underexplored in the U.S. As a first step towards exploring mungbean for crop diversification in northern latitudes, crop germplasm centers that harbor worldwide crop resources need to be utilized. This study explores the potential of mungbean in the U.S. northern latitudes through...

Comparing the strength of modular signal, and evaluating alternative modular hypotheses, using covariance ratio effect sizes with morphometric data

Adams Dean & Michael Collyer
The study of modularity is paramount for understanding trends of phenotypic evolution, and for determining the extent to which covariation patterns are conserved across taxa and levels of biological organization. However, biologists currently lack quantitative methods for statistically comparing the strength of modular signal across datasets, and a robust approach for evaluating alternative modular hypotheses for the same dataset. As a solution to these challenges, we propose an effect size measure (Z_CR) derived from the...

Climate effects on nesting phenology in Nebraska turtles

John Iverson, Ashley Hedrick, Daniel Greene, Erin Lewis, Andrew Hood & John Iverson
A frequent response of organisms to climate change is altering the timing of reproduction. In particular, advancement of reproductive timing has been a common response to warming temperatures in temperate regions. Over the past three decades in Nebraska, USA, the timing of nesting of the Common Snapping Turtle (Chelydra serpentina) was negatively correlated with mean December maximum temperatures of the preceding year and mean May minimum and maximum temperatures in the nesting year, and positively...

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