198 Works

Data from: A generalized K statistic for estimating phylogenetic signal from shape and other high-dimensional multivariate data

Dean C. Adams
Phylogenetic signal is the tendency for closely related species to display similar trait values due to their common ancestry. Several methods have been developed for quantifying phylogenetic signal in univariate traits and for sets of traits treated simultaneously, and the statistical properties of these approaches have been extensively studied. However, methods for assessing phylogenetic signal in high-dimensional multivariate traits like shape are less well developed, and their statistical performance is not well characterized. In this...

Data from: Application of CRISPR/Cas9 to Tragopogon (Asteraceae), an evolutionary model for the study of polyploidy

Shengchen Shan, Evgeny V. Mavrodiev, Riqing Li, Zhengzhi Zhang, Bernard A. Hauser, Pamela S. Soltis, Douglas E. Soltis & Bing Yang
Tragopogon (Asteraceae) is an excellent natural system for studies of recent polyploidy. Development of an efficient CRISPR/Cas9-based genome editing platform in Tragopogon will facilitate novel studies of the genetic consequences of polyploidy. Here, we report our initial results of developing CRISPR/Cas9 in Tragopogon. We have established a feasible tissue culture and transformation protocol for Tragopogon. Through protoplast transient assays, use of the TragCRISPR system (i.e. the CRISPR/Cas9 system adapted for Tragopogon) was capable of introducing...

Data from: Seed polyphenols in a diverse tropical plant community

Sofia Gripenberg, Jadranka Rota, Jorma Kim, S. Joseph Wright, Nancy C. Garwood, Evan C. Fricke, Paul-Camilo Zalamea & Juha-Pekka Salminen
1. Polyphenols are one of the most common groups of secondary metabolites in plants and thought to play a key role in enhancing plant fitness by protecting plants against enemies. Although enemy-inflicted mortality at the seed stage can be an important regulator of plant populations and a key determinant of community structure, few studies have assessed community-level patterns of polyphenol content in seeds. 2. We describe the distribution of the main seed polyphenol groups across...

Data from: Potential rapid evolution of foot morphology in Italian plethodontid salamanders (Hydromantes strinatii) following the colonization of an artificial cave

Sebastiano Salvidio, Federico Crovetto & Dean C. Adams
How organisms respond to environmental change is a long-standing question in evolutionary biology. Species invading novel habitats provide an opportunity to examine contemporary evolution in action, and decipher the pace of evolutionary change over short time scales. Here we characterized phenotypic evolution in the Italian plethodontid salamander, Hydromantes strinatii following the recent colonization of an artificial cave by a forest floor population. When compared with a nearby and genetically related population in the natural forest...

Data from: Rapid molecular evolution across amniotes of the IIS/TOR network

Suzanne E. McGaugh, Anne M. Bronikowski, Chih-Horng Kuo, Dawn M. Reding, Elizabeth A. Addis, Lex E. Flagel, Fredric J. Janzen & Tonia S. Schwartz
Comparative analyses of central molecular networks uncover variation that can be targeted by biomedical research to develop insights and interventions into disease. The insulin/insulin-like signaling and target of rapamycin (IIS/TOR) molecular network regulates metabolism, growth, and aging. With the development of new molecular resources for reptiles, we show that genes in IIS/TOR are rapidly evolving within amniotes (mammals and reptiles, including birds). Additionally, we find evidence of natural selection that diversified the hormone-receptor binding relationships...

Data from: Leaf nutrients, not specific leaf area, are consistent indicators of elevated nutrient inputs

Jennifer Firn, James M. McGree, Eric Harvey, Habacuc Flores-Moreno, Martin Schütz, Yvonne M. Buckley, Elizabeth T. Borer, Eric W. Seabloom, Kimberly J. La Pierre, Andrew M. MacDougall, Suzanne M. Prober, Carly J. Stevens, Lauren L. Sullivan, Erica Porter, Emma Ladouceur, Charlotte Allen, Karine H. Moromizato, John W. Morgan, W. Stanley Harpole, Yann Hautier, Nico Eisenhauer, Justin P. Wright, Peter B. Adler, Carlos Alberto Arnillas, Jonathan D. Bakker … & Anita C. Risch
Leaf traits are frequently measured in ecology to provide a ‘common currency’ for predicting how anthropogenic pressures impact ecosystem function. Here, we test whether leaf traits consistently respond to experimental treatments across 27 globally distributed grassland sites across 4 continents. We find that specific leaf area (leaf area per unit mass)—a commonly measured morphological trait inferring shifts between plant growth strategies—did not respond to up to four years of soil nutrient additions. Leaf nitrogen, phosphorus...

Data from: More salt, please: global patterns, responses, and impacts of foliar sodium in grasslands

Elizabeth T. Borer, Eric M. Lind, Jennifer Firn, Eric W. Seabloom, T. Michael Anderson, Elizabeth S. Bakker, Lori Biederman, Kimberly J. La Pierre, Andrew S. MacDougall, Joslin L. Moore, Anita C. Risch, Martin Schutz & Carly J. Stevens
Sodium is unique among abundant elemental nutrients, because most plant species do not require it for growth or development, whereas animals physiologically require sodium. Foliar sodium influences consumption rates by animals and can structure herbivores across landscapes. We quantified foliar sodium in 201 locally abundant, herbaceous species representing 32 families and, at 26 sites on four continents, experimentally manipulated vertebrate herbivores and elemental nutrients to determine their effect on foliar sodium. Foliar sodium varied taxonomically...

Data from: Insights into the ecology and evolution of polyploid plants through network analysis

Joseph P. Gallagher, Corinne E. Grover, Guanjing Hu, Jonathan F. Wendel & Corrinne E. Grover
Polyploidy is a widespread phenomenon throughout eukaryotes, with important ecological and evolutionary consequences. Although genes operate as components of complex pathways and networks, polyploid changes in genes and gene expression have typically been evaluated as either individual genes or as a part of broad-scale analyses. Network analysis has been fruitful in associating genomic and other 'omic'-based changes with phenotype for many systems. In polyploid species, network analysis has the potential not only to facilitate a...

Data from: Pleistocene and ecological effects on continental-scale genetic differentiation in the bobcat (Lynx rufus)

Dawn M. Reding, Anne M. Bronikowski, Warren E. Johnson & William R. Clark
The potential for widespread, mobile species to exhibit genetic structure without clear geographic barriers is a topic of growing interest. Yet the patterns and mechanisms of structure – particularly over broad spatial scales – remain largely unexplored for these species. Bobcats occur across North America and possess many characteristics expected to promote gene flow. To test whether historical, topographic, or ecological factors have influenced genetic differentiation in this species, we analyzed 1 KB mtDNA sequence...

Data from: Evaluating modularity in morphometric data: challenges with the RV coefficient and a new test measure

Dean C. Adams
Modularity describes the case where patterns of trait covariation are unevenly dispersed across traits. Specifically, trait correlations are high and concentrated within subsets of variables (modules), but the correlations between traits across modules are relatively weaker. For morphometric data sets, hypotheses of modularity are commonly evaluated using the RV coefficient, an association statistic used in a wide variety of fields. In this article, I explore the properties of the RV coefficient using simulated data sets....

Data from: Segmental allotetraploidy generates extensive homeologous expression rewiring and phenotypic diversity at the population level in rice

Yue Sun, Ying Wu, Chunwu Yang, Shuai Sun, Xiuyun Lin, Lixia Liu, Chunming Xu, Jonathan F. Wendel, Lei Gong & Bao Liu
Allopolyploidization, i.e., concomitant merging and doubling of two or more divergent genomes in a common nucleus/cytoplasm, is known to instantly alter genome-wide transcriptome dynamics, a phenomenon referred to as “transcriptomic shock”. However, the immediate effects of transcriptomic alteration in generating phenotypic diversity at the population level remain under-investigated. Here, we employed the MassARRAY-based Sequenom platform to assess and compare orthologous, allelic, and homeologous gene expression status in two tissues (leaf and root) of a set...

Dominant native and non-native graminoids differ in key leaf traits irrespective of nutrient availability

Arthur Broadbent, Jennifer Firn, James McGree, Elizabeth Borer, Yvonne Buckley, W. Stanley Harpole, Kimberly Komatsu, Andrew MacDougall, Kate Orwin, Nicholas Ostle, Eric Seabloom, Jonathan Bakker, Lori Biedermann, Maria Caldeira, Nico Eisenhauer, Nicole Hagenah, Yann Hautier, Joslin Moore, Carla Nogueira, Pablo Peri, Anita Risch, Christiane Roscher, Martin Schuetz & Carly Stevens
Aim Nutrient enrichment is associated with plant invasions and biodiversity loss. Functional trait advantages may predict the ascendancy of invasive plants following nutrient enrichment but this is rarely tested. Here, we investigate 1) whether dominant native and non-native plants differ in important morphological and physiological leaf traits, 2) how their traits respond to nutrient addition, and 3) whether responses are consistent across functional groups. Location Australia, Europe, North America and South Africa Time period 2007...

Nitrogen budget data

Tan Zou, Xin Zhang, Luis Lassaletta, Nathaniel Mueller, Francesco Tubiello, Matthew Lisk, Chaoqun Lu, Richard Conant, Christopher Dorich, James Gerber, Hanqin Tian, Tom Bruulsema, Tai Maaz, Kazuya Nishina, Benjamin Bodirsky, Alexander Popp, Lex Bouwman, Arthur Beusen, Jinfeng Chang, Petr Havlík, David Leclère, Josep Canadell, Robert Jackson, Patrick Heffer, Nathan Wanner … & Eric Davidson
Input-output estimates of nitrogen (N) on cropland are essential for improving N management and better understanding the global N cycle. Here, we compare 13 N budget datasets covering 115 countries and regions over 1961-2015. Though most datasets showed similar spatiotemporal patterns, some annual estimates varied widely among them, resulting in large ranges and uncertainty. In 2010, global medians (in Tg N yr-1) and associated min-max ranges were 73 (64-84) for global harvested crop N; 161...

Dual infection by respiratory syncytial virus and Streptococcus pneumoniae in an experimental lamb model

David Verhoeven
Respiratory syncytial virus (RSV) is the primary cause of viral bronchiolitis resulting in hospitalization and a frequent cause of secondary respiratory bacterial infection, especially by Streptococcus pneumoniae (Spn) in infants. While murine studies have demonstrated enhanced morbidity during a viral/bacterial co-infection, human meta-studies have conflicting results. Moreover, little knowledge about the pathogenesis of emerging Spn serotype 22F, especially the co-pathologies between RSV and Spn, is known. Here, colostrum-deprived neonate lambs were divided into four groups....

Construction of a chromosome-scale long-read reference genome assembly for potato

John Hamilton, Gina Pham, Joshua Wood, Joe Burke, Hainan Zhao, Brieanne Vaillancourt, Shujun Ou, Jiming Jiang & C. Robin Buell
Background: Worldwide, the cultivated potato, Solanum tuberosum L., is the number one vegetable crop and a critical food security crop. The genome sequence of DM1-3 516 R44, a doubled monoploid clone of S. tuberosum Group Phureja, was published in 2011 using a whole-genome shotgun sequencing approach with short read sequence data. Current advanced sequencing technologies now permit generation of near-complete, high-quality chromosome-scale genome assemblies at a minimal cost. Findings: Here, we present an updated version...

Frei Otto's Pneumatic Experiments for Humanitarian Design

This paper will explore the intersection of building technology and humanitarian design-science research by looking at Frei Otto’s pneumatic experiments. The purpose of the study is to contextualize our contemporary demands for humanitarian design work by reflecting upon the manner by which Otto integrated an ambitious design ideology with an elevated and innovative technical acumen. Constraining the investigation to Otto’s work, particularly his relatively unknown early work with pneus, provides a useful exploration of design-science...

Sheepnose mussel (P. cyphyus) microsatellite dataset for population genetic analysis

Sara Schwarz & Kevin Roe
North American freshwater mussel species have experienced substantial range fragmentation and population reductions. These impacts have the potential to reduce genetic connectivity among populations and increase the risk of losing genetic diversity. Thirteen microsatellite loci and an 883 bp fragment of the mitochondrial ND1 gene were used to assess genetic diversity, population structure, contemporary migration rates, and population size changes across the range of the Sheepnose mussel (Plethobasus cyphyus). Population structure analyses reveal five populations,...

Correcting parentage relationships in the endangered California condor: Improving mean kinship estimates for conservation management

Brigid M. Moran, Steven M. Thomas, Jessica M. Judson, Asako Navarro, Heidi Davis, Lindsay Sidak-Loftis, Marisa Korody, Michael Mace, Katherine Ralls, Taylor Callicrate, Oliver A. Ryder, Leona G. Chemnick & Cynthia C. Steiner
Maintaining the existing biodiversity of endangered species is a goal of conservation management programs, and a major component of many collaborative efforts undertaken by zoos, field biologists, and conservation scientists. Over the past three decades, the San Diego Zoo has performed long-term genetic studies in support of the recovery program for the critically endangered California condor (Gymnogyps californianus). This work has included sex determination of hatchlings and parentage confirmation using microsatellite genotyping. This paper describes...

Data and scripts for: Genetic dissection of seasonal vegetation index dynamics in maize through aerial based high-throughput phenotyping

Jinyu Wang, Guo Guo, Tingting Guo, Matthew Dzievit, Xiaoqing Xiaoqing, Peng Liu, Kevin Price & Jianming Yu
Plant phenotyping under field conditions plays an important role in agricultural research. Efficient and accurate high-throughput phenotyping strategies enable a better connection between genotype and phenotype. Unmanned aerial vehicle-based high-throughput phenotyping platforms (UAV-HTPPs) provide novel opportunities for large-scale proximal measurement of plant traits with high efficiency, high resolution, and low cost. The objective of this study was to use time series normalized difference vegetation index (NDVI) extracted from UAV-based multispectral imagery to characterize its pattern...

Reducing Construction Costs Through Effective Field Communication and Administration

Gabriel B. Dadi, Roy E., Jr. Sturgill, Steven Waddle & Steven Douglas Kreis
Falling Road Fund receipts have placed added strain on the Kentucky Transportation Cabinet’s (KYTC) already-underfunded highway program. Revenue declines have increased the urgency of improving the efficiency and cost-effectiveness of the Cabinet’s operations. One method KYTC can use to realize greater cost savings is improving the administration of construction projects. Effective field communication and administration helps control construction costs, enhances quality, and minimizes delays and claims. One challenge the Cabinet will need to confront to...

Data from: Anthelmintic drugs modulate the acute phase immune response but not the microbiota in wild Song Sparrows

Grace Vaziri, Michelle Jusino, Jon Palmer, Matthew Brewer & James Adelman
Co-infection with microparasites (e.g., bacteria) and macroparasites (e.g., helminths) is often the natural state for wild animals. Despite evidence that gut helminths can bias immune responses away from inflammatory processes, few field studies have examined the role that helminths, or their potential interactions with internal microbial communities, play in modulating immunity in free-living, wild birds. Here, we used anthelmintic drugs to treat wild Song Sparrows (Melospiza melodia) for helminth infections and measured markers of systemic...

Data from: Genomic analysis suggests KITLG is responsible for a roan pattern in two Pakistani goat breeds

Andrea Talenti, Francesca Bertolini, Jamie Williams, Muhammad Moaeen-Ud-Din, Stefano Frattini, Beatrice Coizet, Giulio Pagnacco, Jim Reecy, Max Rothschild, Paola Crepaldi, James Reecy & Max F Rothschild
The roan coat color pattern is described as the presence of white hairs intermixed with pigmented hairs. This kind of pigmentation pattern has been observed in many domestic species, including the goat. The molecular mechanisms and inheritance that underlie this pattern are known for some species and the KITLG gene has been shown associated with this phenotype. To date, no research effort has been done to find the gene(s) that controls roan coat color pattern...

Data from: Variation in home-field advantage and ability in leaf litter decomposition across successional gradients

G.F. Ciska Veen, Ashley D. Keiser, Wim H. Van Der Putten, David A. Wardle & G. F. Ciska Veen
1. It is increasingly recognized that interactions between plants and soil (a)biotic conditions can influence local decomposition processes. For example, decomposer communities may become specialized in breaking down litter of plant species that they are associated with, resulting in accelerated decomposition, known as ‘home-field advantage’ (HFA). Also, soils can vary inherently in their capacity to degrade organic compounds, known as ‘ability’. However, we have a poor understanding how environmental conditions drive the occurrence of HFA...

Data from: Cover crop root contributions to soil carbon in a no-till corn bioenergy cropping system

Emily E. Austin, Kyle Wickings, Marshall D. McDaniel, G. Philip Robertson & A. Stuart Grandy
Crop residues are potential biofuel feedstocks, but residue removal may reduce soil carbon (C). The inclusion of a cover crop in a corn bioenergy system could provide additional biomass, mitigating the negative effects of residue removal by adding to stable soil C pools. In a no-till continuous corn bioenergy system in the northern US Corn Belt, we used 13CO2 pulse labeling to trace plant C from a winter rye (Secale cereale) cover crop into different...

Data from: Experimental evolution of the Caenorhabditis elegans sex determination pathway

Christopher H. Chandler, Genna Elise Chadderdon, Patrick C. Phillips, Ian Dworkin & Fredric J. Janzen
Sex determination is a critical developmental decision with major ecological and evolutionary consequences, yet a large variety of sex determination mechanisms exist and we have a poor understanding of how they evolve. Theoretical and empirical work suggest that compensatory adaptations to mutations in genes involved in sex determination may play a role in the evolution of these pathways. Here, we directly address this problem using experimental evolution in Caenorhabditis elegans lines fixed for a pair...

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