49 Works

Data from: Phylogenomic analyses of Sabal (Arecaceae) species relationships using targeted sequence capture

Karolina Heyduk, Dorset W. Trapnell, Craig F. Barrett & Jim Leebens-Mack
With the increasing availability of high-throughput sequencing, phylogenetic analyses are no longer constrained by the limited availability of a few loci. Here, we describe a sequence capture methodology, which we used to collect data for analyses of diversification within Sabal (Arecaceae), a palm genus native to the south-eastern USA, Caribbean, Bermuda and Central America. RNA probes were developed and used to enrich DNA samples for putatively low copy nuclear genes and the plastomes for all...

Data from: Resolving relationships within the palm subfamily Arecoideae (Arecaceae) using next-gen derived plastid sequences

Jason R. Comer, Wendy B. Zomlefer, Craig F. Barrett, Jerrold I. Davis, Dennis W. Stevenson, Karolina Heyduk & James H. Leebens-Mack
Premise of the study: Several studies have incorporated molecular and morphological data to study the phylogeny of the palms (Arecaceae), but some relationships within the family remain ambiguous—particularly those within Arecoideae, the most diverse subfamily including coconut and oil palm. Here, two next-generation, targeted plastid-enrichment methods were compared and used to elucidate Arecoideae phylogeny. Methods: Next-generation sequencing techniques were used to generate a plastid genome data set. Long range PCR and hybrid gene capture were...

Data from: Specificity and strain-typing capabilities of Nanorod Array-Surface Enhanced Raman Spectroscopy for Mycoplasma pneumoniae detection

Kelley C. Henderson, Alvaro J. Benitez, Amy E. Ratliff, Donna M. Crabb, Edward S. Sheppard, Jonas M. Winchell, Richard A. Dluhy, Ken B. Waites, T. Prescott Atkinson & Duncan C. Krause
Mycoplasma pneumoniae is a cell wall-less bacterial pathogen of the human respiratory tract that accounts for > 20% of all community-acquired pneumonia (CAP). At present the most effective means for detection and strain-typing is quantitative polymerase chain reaction (qPCR), which can exhibit excellent sensitivity and specificity but requires separate tests for detection and genotyping, lacks standardization between available tests and between labs, and has limited practicality for widespread, point-of-care use. We have developed and previously...

Data from: How a GNSS receiver is held may affect static horizontal position accuracy

Steven A. Weaver, Zennure Ucar, Pete Bettinger & Krista Merry
The static horizontal position accuracy of a mapping-grade GNSS receiver was tested in two forest types over two seasons, and subsequently was tested in one forest type against open sky conditions in the winter season. The main objective was to determine whether the holding position during data collection would result in significantly different static horizontal position accuracy. Additionally, we wanted to determine whether the time of year (season), forest type, or environmental variables had an...

Data from: Species tree estimation of diploid Helianthus (Asteraceae) using target enrichment

Jessica D. Stephens, Willie L. Rogers, Chase M. Mason, Lisa A. Donovan & Russell L. Malmberg
Premise of the study: The sunflower genus Helianthus has long been recognized as economically significant, containing species of agricultural and horticultural importance. Additionally, this genus displays a large range of phenotypic and genetic variation, making Helianthus a useful system for studying evolutionary and ecological processes. Here we present the most robust Helianthus phylogeny to date, laying the foundation for future studies of this genus. Methods: We used a target enrichment approach across 37 diploid Helianthus...

Data from: Resolving phylogenetic relationships of the recently radiated carnivorous plant genus Sarracenia using target enrichment

Jessica D. Stephens, Willie L. Rogers, Karolina Heyduk, Jennifer M. Cruse-Sanders, Ron O. Determann, Travis C. Glenn & Russell L. Malmberg
The North American carnivorous pitcher plant genus Sarracenia (Sarraceniaceae) is a relatively young clade (<3 million years ago) displaying a wide range of morphological diversity in complex trapping structures. This recently radiated group is a promising system to examine the structural evolution and diversification of carnivorous plants; however, little is known regarding evolutionary relationships within the genus. Previous attempts at resolving the phylogeny have been unsuccessful, most likely due to few parsimony-informative sites compounded by...

Data from: Controlled measurement and comparative analysis of cellular components in E. coli reveals broad regulatory changes in response to glucose starvation

John R. Houser, Craig Barnhart, Daniel R. Boutz, Sean M. Carrol, Aurko Dasgupta, Joshua K. Michener, Brittany D. Needham, Ophelia Papoulas, Viswanadham Sridhara, Dariya K. Sydykova, Christopher J. Marx, M. Stephen Trent, Jeffery E. Barrick, Edward M. Marcotte, Claus O. Wilke, Jeffrey E. Barrick & Sean M. Carroll
How do bacteria regulate their cellular physiology in response to starvation? Here, we present a detailed characterization of Escherichia coli growth and starvation over a time-course lasting two weeks. We have measured multiple cellular components, including RNA and proteins at deep genomic coverage, as well as lipid modifications and flux through central metabolism. Our study focuses on the physiological response of E. coli in stationary phase as a result of being starved for glucose, not...

Data from: Phylogenomics and historical biogeography of the monocot order Liliales: out of Australia and through Antarctica

Thomas J. Givnish, Alejandro Zuluaga, Isabel Marques, Vivienne K. Y. Lam, Marybel Soto Gomez, William J. D. Iles, Mercedes Ames, Daniel Spalink, Jackson R. Moeller, Barbara G. Briggs, Stephanie P. Lyon, Dennis W. Stevenson, Wendy Zomlefer, Sean W. Graham & Marybel Soto Gomez
We present the first phylogenomic analysis of relationships among all ten families of Liliales, based on 75 plastid genes from 35 species in 29 genera, and 97 additional plastomes stratified across angiosperm lineages. We used a supermatrix approach to extend our analysis to 58 of 64 genera of Liliales, and calibrated the resulting phylogeny against 17 fossil dates to produce a new timeline for monocot evolution. Liliales diverged from other monocots 124 Mya and began...

Data from: Macroevolution of leaf defenses and secondary metabolites across the genus Helianthus

Chase M. Mason, Alan W. Bowsher, Breanna L. Crowell, Rhodesia M. Celoy, Chung-Jui Tsai & Lisa A. Donovan
Leaf defenses are widely recognized as key adaptations and drivers of plant evolution. Across environmentally diverse habitats, the macroevolution of leaf defenses can be predicted by the univariate trade-off model, which predicts that defenses are functionally redundant and thus trade off, and the resource availability hypothesis, which predicts that defense investment is determined by inherent growth rate and that higher defense will evolve in lower resource environments. Here, we examined the evolution of leaf physical...

Data from: Phylogenetic signals in host-parasite associations for Neotropical bats and Nearctic desert rodents

Steven J. Presley, Tad Dallas, Brian T. Klingbeil & Michael R. Willig
Hosts and their parasites have strong ecological and evolutionary relationships, with hosts representing habitats and resources for parasites. In the present study, we use approaches developed to evaluate the statistical dependence of species trait values on phylogenetic relationships to determine whether host–parasite relationships (i.e. parasite infections) are contingent on host phylogeny. If host–parasite relationships are contingent on the ability of hosts to provide habitat or resources to parasites, and if host phylogeny is an effective...

Data from: Impacts of degraded DNA on restriction enzyme associated DNA sequencing (RADSeq)

Carly F. Graham, Travis C. Glenn, Andrew G. McArthur, Douglas R. Boreham, Troy Kieran, Stacey Lance, Richard G. Manzon, Jessica A. Martino, Todd Pierson, Sean M. Rogers, Joanna Y. Wilson & Christopher M. Somers
Degraded DNA from suboptimal field sampling is common in molecular ecology. However, its impact on techniques that use restriction site associated next-generation DNA sequencing (RADSeq, GBS) is unknown. We experimentally examined the effects of in situDNA degradation on data generation for a modified double-digest RADSeq approach (3RAD). We generated libraries using genomic DNA serially extracted from the muscle tissue of 8 individual lake whitefish (Coregonus clupeaformis) following 0-, 12-, 48- and 96-h incubation at room...

Data from: Phylogenetic comparative methods for evaluating the evolutionary history of function-valued traits

Eric W. Goolsby
Phylogenetic comparative methods offer a suite of tools for studying trait evolution. However, most models inherently assume fixed trait values within species. Although some methods can incorporate error around species means, few are capable of accounting for variation driven by environmental or temporal gradients, such as trait responses to abiotic stress or ontogenetic trajectories. Such traits, often referred to as function-valued or infinite-dimensional, are typically expressed as reaction norms, dose–response curves, or time plots and...

Data from: Occupancy models for data with false positive and false negative errors and heterogeneity across sites and surveys

Paige F. B. Ferguson, Michael J. Conroy, Jeffrey Hepinstall-Cymerman & Paige F.B. Ferguson
False positive detections, such as species misidentifications, occur in ecological data, although many models do not account for them. Consequently, these models are expected to generate biased inference. The main challenge in an analysis of data with false positives is to distinguish false positive and false negative processes while modeling realistic levels of heterogeneity in occupancy and detection probabilities without restrictive assumptions about parameter spaces. Building on previous attempts to account for false positive and...

Data from: Male burying beetles extend, not reduce, parental care duration when reproductive competition is high

Paul E. Hopwood, Allen J. Moore, Tom Tregenza, Nick J. Royle, A. J. Moore, P. E. Hopwood, T. Tregenza & N. J. Royle
Male parents spend less time caring than females in many species with biparental care. The traditional explanation for this pattern is that males have lower confidence of parentage, so they desert earlier in favor of pursuing other mating opportunities. However, one recent alternative hypothesis is that prolonged male parental care might also evolve if staying to care actively improves paternity. If this is the case, an increase in reproductive competition should be associated with increased...

Data from: Facultative endosymbionts mediate dietary breadth in a polyphagous herbivore

Steven M. Wagner, Adam J. Martinez, Yong-Ming Ruan, Kyungsun L. Kim, Paul A. Lenhart, Allison C. Dehnel, Kerry M. Oliver & Jennifer A. White
1. Intraspecific variation in dietary breadth can influence important ecological and evolutionary processes, yet the mechanisms generating this variation are usually unknown. Maternally-transmitted bacterial symbionts frequently infect insect herbivores, and many have been shown to mediate key ecological interactions. For polyphagous herbivores, infection with particular symbionts is often strongly correlated with feeding on particular plant species, suggesting that facultative symbionts might directly determine herbivore food plant specificity. However, previous tests of this hypothesis have returned...

Data from: Reconstructing changes in the genotype, phenotype, and climatic niche of an introduced species

Daniel Z. Atwater, U. Uzay Sezen, Valorie Goff, Wenqian Kong, Andrew H. Paterson & Jacob N. Barney
An introduced species must contend with enormous environmental variation in its introduced range. In this study, we use niche models and ordination analyses to reconstruct changes in genotype, phenotype, and climatic niche of Johnsongrass (Sorghum halepense), which is regarded as one of the world's most threatening invasive plants. In the United States, Johnsongrass has rapidly evolved within- and among-population genetic diversity; our results show that genetic differentiation in expanding Johnsongrass populations has resulted in phenotypic...

Data from: Honey bee colonies headed by hyperpolyandrous queens have improved brood rearing efficiency and lower infestation rates of parasitic Varroa mites

Keith S. Delaplane, Stéphane Pietravalle, Mike A. Brown & Giles E. Budge
A honey bee queen mates on wing with an average of 12 males and stores their sperm to produce progeny of mixed paternity. The degree of a queen’s polyandry is positively associated with measures of her colony’s fitness, and observed distributions of mating number are evolutionary optima balancing risks of mating flights against benefits to the colony. Effective mating numbers as high as 40 have been documented, begging the question of the upper bounds of...

Data from: Quantifying direct vs. indirect effects of nectar robbers on male and female components of plant fitness

Rebecca E. Irwin, Paige Howell & Candace Galen
1. Plants interact simultaneously with both mutualists and antagonists. While webs of plant-animal interactions in natural systems can be highly complex, most interactions can be simplified into those that are either direct (mediated through pairwise interactions) or indirect (mediated through third-party species). Mechanistic studies of the direct and indirect pathways by which foliar herbivores affect plants have been well explored; however, mechanistic explorations of how floral herbivores, such as nectar robbers, affect total plant fitness...

Data from: Large wildlife removal drives immune defense increases in rodents

Hillary S. Young, Rodolfo Dirzo, Kristofer M. Helgen, Douglas J. McCauley, Charles L. Nunn, Paul Snyder, Kari E. Veblen, Serena Zhao & Vanessa O. Ezenwa
Anthropogenic disturbances involving land use change, climate disruption, pollution, and invasive species have been shown to impact immune function of wild animals. These immune changes have direct impacts on the fitness of impacted animals and, also, potentially indirect effects on other species and on ecological processes, notably involving the spread of infectious disease. Here, we investigate whether the selective loss of large wildlife can also drive changes in immune function of other consumer species. Using...

Data from: Evolution of the leaf economics spectrum in herbs: evidence from environmental divergences in leaf physiology across Helianthus (Asteraceae)

Chase M. Mason, Lisa Alayne Donovan & Lisa A. Donovan
The leaf economics spectrum (LES) describes a major axis of plant functional trait variation worldwide, defining suites of leaf traits aligned with resource-acquisitive to resource-conservative ecological strategies. The LES has been interpreted to arise from leaf-level trade-offs among ecophysiological traits common to all plants. However, it has been suggested that the defining leaf-level trade-offs of the LES may not hold within specific functional groups (e.g., herbs) nor within many groups of closely-related species, which challenges...

Data from: Behavioral plasticity and GxE of reproductive tactics in Nicrophorus vespilloides burying beetles

Mauricio J. Carter, Megan L. Head, Allen J. Moore & Nick J. Royle
Phenotypic plasticity is important in the evolution of traits and facilitates adaptation to rapid environmental changes. However, variation in plasticity at the individual level, and the heritable basis underlying this plasticity is rarely quantified for behavioral traits. Alternative behavioral reproductive tactics are key components of mating systems but are rarely considered within a phenotypic plasticity framework (i.e., as reaction norms). Here, using lines artificially selected for repeated mating rate, we test for genetic (GxE) sources...

Data from: Fine root tradeoffs between nitrogen concentration and xylem vessel traits preclude unified whole-plant resource strategies in Helianthus

Alan W. Bowsher, Chase M. Mason, Eric W. Goolsby & Lisa A. Donovan
Recent work suggests variation in plant growth strategies is governed by a tradeoff in resource acquisition and use, ranging from a rapid resource acquisition strategy to a resource-conservative strategy. While evidence for this tradeoff has been found in leaves, knowledge of root trait strategies, and whether they reflect adaptive differentiation across environments, is limited. In the greenhouse, we investigated variation in fine root morphology (specific root length and tissue density), chemistry (nitrogen concentration and carbon:nitrogen),...

Data from: Maternal effects and maternal selection arising from variation in allocation of free amino acid to eggs

Devi Newcombe, John Hunt, Christopher Mitchell & Allen J. Moore
Maternal provisioning can have profound effects on offspring phenotypes, or maternal effects, especially early in life. One ubiquitous form of provisioning is in the makeup of egg. However, only a few studies examine the role of specific egg constituents in maternal effects, especially as they relate to maternal selection (a standardized selection gradient reflecting the covariance between maternal traits and offspring fitness). Here, we report on the evolutionary consequences of differences in maternal acquisition and...

Data from: An examination of fitness costs of glyphosate resistance in the common morning glory, Ipomoea purpurea

Catherine L. Debban, Sara Okum, Kathleen E. Pieper, Ariana Wilson & Regina S. Baucom
Fitness costs are frequently invoked to explain the presence of genetic variation underlying plant defense across many types of damaging agents. Despite the expectation that costs of resistance are prevalent, however, they have been difficult to detect in nature. To examine the potential that resistance confers a fitness cost, we examined the survival and fitness of genetic lines of the common morning glory, Ipomoea purpurea, that diverged in the level of resistance to the herbicide...

Data from: The effect of hydroperiod and predation on the diversity of temporary pond zooplankton communities

Marcus Zokan & John M. Drake
In temporary pond ecosystems, it is hypothesized that the two dominant structuring forces on zooplankton communities are predation and demographic constraints due to wetland drying. Both of these forces are deterministic processes that act most strongly at opposing ends of a hydroperiod gradient. Our objective was to test how these two processes affect α- and β-diversity of zooplankton communities derived from a diverse temporary pond system. We hypothesized that decreased hydroperiod length and the presence...

Registration Year

  • 2015

Resource Types

  • Dataset


  • University of Georgia
  • University of Exeter
  • Oregon State University
  • Cornell University
  • The University of Texas at Austin
  • University of Michigan–Ann Arbor
  • University of California System
  • Duke University
  • University of Wisconsin–Madison
  • McMaster University
  • University of Missouri
  • University of Regina
  • Harvard University
  • University of Calgary
  • Northern Ontario School of Medicine