13 Works

Data from: An ecosystem services perspective on brush management: research priorities for competing land use objectives

Steve R. Archer, Katharine I. Predick & Steven R. Archer
1. The vegetation of semi-arid and arid landscapes is often comprised of mixtures of herbaceous and woody vegetation. Since the early 1900s, shifts from herbaceous to woody plant dominance, termed woody plant encroachment and widely regarded as a state change, have occurred world-wide. This shift presents challenges to the conservation of grassland and savanna ecosystems and to animal production in commercial ranching systems and pastoral societies. 2. Dryland management focused on cattle and sheep grazing...

Data from: Geographical barriers and climate influence demographic history in narrowleaf cottonwoods

Luke M. Evans, Gerard J. Allan, Stephen P. DiFazio, Gancho T. Slavov, Jason A. Wilder, Kevin D. Floate, Stewart B. Rood & Thomas G. Whitham
Studies of genetic variation can clarify the role of geography and spatio-temporal variation of climate in shaping demography, particularly in temperate zone tree species with large latitudinal ranges. Here, we examined genetic variation in narrowleaf cottonwood, Populus angustifolia, a dominant riparian tree. Using multi-locus surveys of polymorphism in 363 individuals across the species’ 1800 km latitudinal range, we found that, first, P. angustifolia has stronger neutral genetic structure than many forest trees (simple sequence repeat...

Data from: Be meek or be bold? A colony-level behavioural syndrome in ants

Sarah E. Bengston & Anna Dornhaus
Consistent individual variation in animal behaviour is nearly ubiquitous and has important ecological and evolutionary implications. Additionally, suites of behavioural traits are often correlated, forming behavioural syndromes in both humans and other species. Such syndromes are often described by testing for variation in traits across commonly described dimensions (e.g. aggression and neophobia), independent of whether this variation is ecologically relevant to the focal species. Here, we use a variety of ecologically relevant behavioural traits to...

Data from: Disentangling methodological and biological sources of gene tree discordance on Oryza (Poaceae) chromosome 3

Derrick J. Zwickl, Joshua C. Stein, Rod A. Wing, Doreen Ware & Michael J. Sanderson
We describe new methods for characterizing gene tree discordance in phylogenomic datasets, which screen for deviations from neutral expectations, summarize variation in statistical support among gene trees, and allow comparison of the patterns of discordance induced by various analysis choices. Using an exceptionally complete set of genome sequences for the short arm of chromosome 3 in Oryza (rice) species, we applied these methods to identify the causes and consequences of differing patterns of discordance in...

Data from: Effect of lysyl oxidase inhibition on angiotensin II-induced arterial hypertension, remodeling, and stiffness

Lance S. Eberson, Pablo A. Sanchez, Beenish A. Majeed, Supannikar Tawinwung, Timothy W. Secomb & Douglas F. Larson
It is well accepted that angiotensin II (Ang II) induces altered vascular stiffness through responses including both structural and material remodeling. Concurrent with remodeling is the induction of the enzyme lysyl oxidase (LOX) through which ECM proteins are cross-linked. The study objective was to determine the effect of LOX mediated cross-linking on vascular mechanical properties. Three-month old mice were chronically treated with Ang II with or without the LOX blocker, β -aminopropionitrile (BAPN), for 14...

Data from: Tissue storage and primer selection influence pyrosequencing-based inferences of diversity and community composition of endolichenic and endophytic fungi

Jana M. U'Ren, Jakob M. Riddle, James T. Monacell, Ignazio Carbone, Jolanta Miadlikowska & A. Elizabeth Arnold
Next-generation sequencing technologies have provided unprecedented insights into fungal diversity and ecology. However, intrinsic biases and insufficient quality control in next-generation methods can lead to difficult-to-detect errors in estimating fungal community richness, distributions, and composition. The aim of this study was to examine how tissue storage prior to DNA extraction, primer design, and various quality-control approaches commonly used in 454 amplicon pyrosequencing might influence ecological inferences in studies of endophytic and endolichenic fungi. We first...

Data from: Genotyping of Coxiella burnetii from domestic ruminants and human in Hungary: indication of various genotypes

Kinga M. Sulyok, Zsuzsa Kreizinger, Heidie M. Hornstra, Talima Pearson, Alexandra Szigeti, Ádám Dán, Eszter Balla, Paul S. Keim & Miklós Gyuranecz
Background: Information about the genotypic characteristic of Coxiella burnetii from Hungary is lacking. The aim of this study is to describe the genetic diversity of C. burnetii in Hungary and compare genotypes with those found elsewhere. A total of 12 samples: (cattle, n = 6, sheep, n = 5 and human, n = 1) collected from across Hungary were studied by a 10-loci multispacer sequence typing (MST) and 6-loci multiple-locus variable-number of tandem repeat analysis...

Data from: Diversity and abundance of phyllosphere bacteria are linked to insect herbivory

Parris T. Humphrey, Trang T. Nguyen, Martha M. Villalobos & Noah K. Whiteman
Simultaneous or sequential attack by herbivores and microbes is common in plants. Many seed plants exhibit a defence trade-off against chewing herbivorous insects and leaf-colonizing (‘phyllosphere’) bacteria, which arises from cross-talk between the phytohormones jasmonic acid (JA, induced by many herbivores) and salicylic acid (SA, induced by many bacteria). This cross-talk may promote reciprocal susceptibility in plants between phyllosphere bacteria and insect herbivores. In a population of native bittercress (Cardamine cordifolia, Brassicaceae), we tested whether...

Data from: Machine learning-based differential network analysis: a study of stress-responsive transcriptomes in Arabidopsis thaliana

Chuang Ma, Mingming Xin, Kenneth A. Feldmann & Xiangfeng Wang
Machine learning (ML) is an intelligent data mining technique that builds a prediction model based on the learning of prior knowledge to recognize patterns in large-scale data sets. We present an ML-based methodology for transcriptome analysis via comparison of gene coexpression networks, implemented as an R package called machine learning–based differential network analysis (mlDNA) and apply this method to reanalyze a set of abiotic stress expression data in Arabidopsis thaliana. The mlDNA first used a...

Data from: Viral tagging reveals discrete populations in Synechococcus viral genome sequence space

Li Deng, J. Cesar Ignacio-Espinoza, Ann C. Gregory, Bonnie T. Poulos, Joshua S. Weitz, Philip Hugenholtz & Matthew B. Sullivan
Microbes and their viruses drive myriad processes across ecosystems ranging from oceans and soils to bioreactors and humans. Despite this importance, microbial diversity is only now being mapped at scales relevant to nature, while the viral diversity associated with any particular host remains little researched. Here we quantify host-associated viral diversity using viral-tagged metagenomics, which links viruses to specific host cells for high-throughput screening and sequencing. In a single experiment, we screened 107 Pacific Ocean...

Data from: Programmed death in a unicellular organism has species-specific fitness effects

Pierre M. Durand, Rajdeep Choudhury, Armin Rashidi & Richard E. Michod
Programmed cell death (PCD) is an ancient phenomenon and its origin and maintenance in unicellular life is unclear. We report that programmed death provides differential fitness effects that are species specific in the model organism Chlamydomonas reinhardtii. Remarkably, PCD in this organism not only benefits others of the same species, but also has an inhibitory effect on the growth of other species. These data reveal that the fitness effects of PCD can depend upon genetic...

Data from: A gateway for phylogenetic analysis powered by grid computing featuring GARLI 2.0

Adam L. Bazinet, Derrick J. Zwickl & Michael P. Cummings
We introduce molecularevolution.org, a publicly available gateway for high-throughput, maximum likelihood phylogenetic analysis powered by grid computing. The gateway features a garli 2.0 web service that enables a user to quickly and easily submit thousands of maximum likelihood tree searches or bootstrap searches that are executed in parallel on distributed computing resources. The garli web service allows one to easily specify partitioned substitution models using a graphical interface, and it performs sophisticated post-processing of phylogenetic...

Data from: Phenotypic constraints and community structure: linking trade-offs within and among species

Amy L. Angert, Sarah Kimball, Megan Peterson, Travis E. Huxman & D. Lawrence Venable
Trade-offs are central to many topics in biology, from the evolution of life histories to ecological mechanisms of species coexistence. Trade-offs observed among species may reflect pervasive constraints on phenotypes that are achievable given biophysical and resource limitations. If so, then among-species trade-offs should be consistent with trade-offs within species. Alternatively, trait variation among co-occurring species may reflect historical contingencies during community assembly rather than within-species constraints. Here, we test whether a key trade-off between...

Registration Year

  • 2014

Resource Types

  • Dataset


  • University of Arizona
  • Duke University
  • University of Queensland
  • West Virginia University
  • Georgia Institute of Technology
  • University of British Columbia
  • University of the Witwatersrand
  • University of California, Santa Cruz
  • University of Lethbridge
  • University of Maryland, College Park