162 Works

Data from: Evidence of lasting impact of the Deepwater Horizon oil spill on a deep Gulf of Mexico coral community

Pen-Yuan Hsing, Bo Fu, Elizabeth A. Larcom, Samantha P. Berlet, Timothy M. Shank, Annette Frese Govindarajan, Alexandra Julia Lukasiewicz, Philip M. Dixon & Charles R. Fisher
A coral community 11 km southwest of the site of the Deepwater Horizon blowout at 1,370 m water depth was discovered 3.5 months after the well was capped on 3 November 2010. Gorgonian corals at the site were partially covered by a brown flocculent material (floc) that contained hydrocarbons fingerprinted to the oil spill. Here we quantify the visible changes to the corals at this site during five visits over 17 months by digitizing images...

Data from: Extent and variability of interstitial telomeric sequences and their effects on estimates of telomere length

Christopher G. Foote, David Vleck & Carol M. Vleck
Telomeres often shorten with time, although this varies between tissues, individuals and species, and their length and/or rate of change may reflect fitness and rate of senescence. Measurement of telomeres is increasingly important to ecologists, yet the relative merits of different methods for estimating telomere length are not clear. In particular the extent to which interstitial telomere sequences (ITSs), telomere repeats located away from chromosomes ends, confound estimates of telomere length is unknown. Here we...

Data from: Dissecting genome-wide association signals for loss-of-function phenotypes in sorghum flavonoid pigmentation traits

Geoffrey P. Morris, Davina H. Rhodes, Zachary Brenton, Punna Ramu, Vinayan Madhumal Thayil, Santosh Deshpande, C. Thomas Hash, Charlotte Acharya, Sharon E. Mitchell, Edward S. Buckler, Jianming Yu & Stephen Kresovich
Genome-wide association studies (GWAS) are a powerful method to dissect the genetic basis of traits, though in practice the effects of complex genetic architecture and population structure remain poorly understood. To compare mapping strategies we dissect the genetic control of flavonoid pigmentation traits in the cereal grass sorghum using high-resolution genotyping-by-sequencing (GBS) SNP markers. Studying the grain tannin trait, we find that General Linear Models (GLM) are not able to precisely map tan1-a, a known...

A Document Analysis of Anti-Hazing Policy

Christobal Salinas, Michelle Boettcher & Jennifer Plagman-Galvin

Data from: Phylogenetic ANOVA: group-clade aggregation, biological challenges, and a refined permutation procedure

Dean C. Adams & Michael L. Collyer
Phylogenetic regression is frequently utilized in macroevolutionary studies, and its statistical properties have been thoroughly investigated. By contrast, phylogenetic ANOVA has received relatively less attention, and the conditions leading to incorrect statistical and biological inferences when comparing multivariate phenotypes among groups remains under-explored. Here we propose a refined method of randomizing residuals in a permutation procedure (RRPP) for evaluating phenotypic differences among groups while conditioning the data on the phylogeny. We show that RRPP displays...

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...

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: Are attractive male crickets better able to pay the costs of an immune challenge?

Clint D. Kelly, Melissa S. C. Telemeco, Lyric C. Bartholomay & Melissa S.C. Telemeco
Reproduction and immunity are fitness-related traits that trade-off with each other. Parasite-mediated theories of sexual selection suggest, however, that higher-quality males should suffer smaller costs to reproduction-related traits and behaviours (e.g., sexual display) from an immune challenge because these males possess more resources with which to deal with the challenge. We used Gryllus texensis field crickets to test the prediction that attractive males should better maintain the performance of fitness-related traits (e.g., calling effort) in...

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: 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...

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...

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: 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: 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: Plant connectivity underlies plant-pollinator-exploiter distributions in Ficus petiolaris and associated pollinating and non-pollinating fig wasps

Alexander Duthie, John D. Nason & A. Bradley Duthie
Mutualism is ubiquitous in nature, and nursery pollination mutualisms provide a system well suited to quantifying the benefits and costs of symbiotic interactions. In nursery pollination mutualisms, pollinators reproduce within the inflorescence they pollinate, with benefits and costs being measured in the numbers of pollinator offspring and seeds produced. This type of mutualism is also typically exploited by seed-consuming non-pollinators that obtain resources from plants without providing pollination services. Theory predicts that the rate at...

Data from: Female and male life tables for seven wild primate species

Anne M. Bronikowski, Marina Cords, Susan C. Alberts, Jeanne Altmann, Diane K. Brockman, Linda M. Fedigan, Anne Pusey, Tara Stoinski, Karen B. Strier & William F. Morris
We provide male and female census count data, age-specific survivorship, and female age-specific fertility estimates for populations of seven wild primates that have been continuously monitored for at least 29 years: sifaka (Propithecus verreauxi) in Madagascar; muriqui (Brachyteles hypoxanthus) in Brazil; capuchin (Cebus capucinus) in Costa Rica; baboon (Papio cynocephalus) and blue monkey (Cercopithecus mitis) in Kenya; chimpanzee (Pan troglodytes) in Tanzania; and gorilla (Gorilla beringei) in Rwanda. Using one-year age-class intervals, we computed point...

Data from: Altered spring phenology of North American freshwater turtles and the importance of representative populations

Fredric J. Janzen, Luke A. Hoekstra, Ronald J. Brooks, David M. Carroll, J. Whitfield Gibbons, Judith L. Greene, John B. Iverson, Jacqueline D. Litzgus, Edwin D. Michael, Steven G. Parren, Willem M. Roosenburg, Gabriel F. Strain, John K. Tucker & Gordon R. Ultsch
Globally, populations of diverse taxa have altered phenology in response to climate change. However, most research has focused on a single population of a given taxon, which may be unrepresentative for comparative analyses, and few long‐term studies of phenology in ectothermic amniotes have been published. We test for climate‐altered phenology using long‐term studies (10–36 years) of nesting behavior in 14 populations representing six genera of freshwater turtles (Chelydra, Chrysemys, Kinosternon, Malaclemys, Sternotherus, and Trachemys). Nesting...

Data from: Maternal effects influence phenotypes and survival during early life stages in an aquatic turtle

Timothy S. Mitchell, Jessica A. Maciel & Fredric J. Janzen
Offspring phenotypic variation can be substantially influenced by non-genetic factors such as maternal effects, which ultimately can influence organismal fitness. For oviparous organisms that lack parental care, oviposition-site choice and egg size are maternal effects that can greatly affect offspring traits. Yet, few studies examine the consequences of these traits in the wild. We manipulated the contents of natural painted turtle nests such that offspring spent two life stages (incubation and hibernation) in either maternally-selected...

Data from: A method for analysis of phenotypic change for phenotypes described by high-dimensional data

Michael L. Collyer, David J. Sekora & Dean C. Adams
The analysis of phenotypic change is important for several evolutionary biology disciplines, including phenotypic plasticity, evolutionary developmental biology, morphological evolution, physiological evolution, evolutionary ecology and behavioral evolution. It is common for researchers in these disciplines to work with multivariate phenotypic data. When phenotypic variables exceed the number of research subjects—data called ‘high-dimensional data’—researchers are confronted with analytical challenges. Parametric tests that require high observation to variable ratios present a paradox for researchers, as eliminating variables...

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: 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...

Data from: Herbivores safeguard plant diversity by reducing variability in dominance

Brent Mortensen, Brent Danielson, Stan W. Harpole, Juan Alberti, Carlos Alberto Arnillas, Lori Biederman, Elizabeth T. Borer, Marc W. Cadotte, John M. Dwyer, Nicole Hagenah, Yann Hautier, Pablo Luis Peri, Eric W. Seabloom & W. Stanley Harpole
1. Reductions in community evenness can lead to local extinctions as dominant species exclude subordinate species; however, herbivores can prevent competitive exclusion by consuming otherwise dominant plant species, thus increasing evenness. While these predictions logically result from chronic, gradual reductions in evenness, rapid, temporary pulses of dominance may also reduce species richness. Short pulses of dominance can occur as biotic or abiotic conditions temporarily favor one or a few species, manifested as increased temporal variability...

Data from: Inferring node dates from tip dates in fossil Canidae: the importance of tree priors

Nicholas J. Matzke & April Wright
Tip-dating methods are becoming popular alternatives to traditional node calibration approaches for building time-scaled phylogenetic trees, but questions remain about their application to empirical datasets. We compared the performance of the most popular methods against a dated tree of fossil Canidae derived from previously published monographs. Using a canid morphology dataset, we performed tip-dating using BEAST v. 2.1.3 and MrBayes v. 3.2.5. We find that for key nodes (Canis, approx. 3.2 Ma, Caninae approx. 11.7...

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: Molecular phylogenetics and biogeography of galaxiid fishes (Osteichthyes: Galaxiidae): dispersal, vicariance, and the position of Lepidogalaxias salamandroides

Jonathan M. Waters, J. Andrés López & Graham P. Wallis
The galaxiid fishes exhibit a gondwanan distribution. We use mitochondrial DNA sequences to test conflicting vicariant and dispersal biogeographic hypotheses regarding the southern hemisphere range of this freshwater group. Although phylogenetic resolution of cytochrome b and 16S rRNA sequences is largely limited to more recent divergences, our data indicate that the radiation can be interpreted as a number of relatively recent dispersal events superimposed on an ancient gondwanan radiation. Genetic relationships contradict the findings of...

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