32 Works

Data from: The multispecies coalescent model outperforms concatenation across diverse phylogenomic

Xiaodong Jiang, Scott Edwards & Liang Liu
A statistical framework of model comparison and model validation is essential to resolving the debates over concatenation and coalescent models in phylogenomic data analysis. A set of statistical tests are here applied and developed to evaluate and compare the adequacy of substitution, concatenation, and multispecies coalescent (MSC) models across 47 phylogenomic data sets collected across tree of life. Tests for substitution models and the concatenation assumption of topologically concordant gene trees suggest that a poor...

Warmer nights offer no respite for a defensive mutualism

Clesson Higashi, Brandon Barton & Kerry Oliver
1. Ecologically-relevant symbioses are widespread in terrestrial arthropods but based on recent findings these specialized interactions are likely to be especially vulnerable to climate warming. Importantly, empirical data and climate models indicate that warming is occurring asynchronously, with nighttime temperatures increasing faster than daytime temperatures. Daytime (DTW) and nighttime warming (NTW) may impact ectothermic animals and their interactions differently as DTW results in greater daily temperature variation and moves organisms nearer to their thermal limits,...

Data from: Joint phylogenetic estimation of geographic movements and biome shifts during the global diversification of Viburnum

Michael Landis, Deren Eaton, Wendy Clement, Brian Park, Elizabeth Spriggs, Patrick Sweeney, Erika Edwards & Michael Donoghue
Phylogeny, molecular sequences, fossils, biogeography, and biome occupancy are all lines of evidence that reflect the singular evolutionary history of a clade, but they are most often studied separately, by first inferring a fossil-dated molecular phylogeny, then mapping on ancestral ranges and biomes inferred from extant species. Here we jointly model the evolution of biogeographic ranges, biome affinities, and molecular sequences, incorporating fossils to estimate a dated phylogeny for all of the 163 extant species...

Deep evolutionary analysis reveals the design principles of fold A glycosyltransferases

Rahil Taujale, Aarya Venkat, Liang-Chin Huang, Zhongliang Zhou, Wayland Yeung, Khaled Rasheed, Sheng Li, Arthur Edison, Kelley Moremen & Natarajan Kannan
Glycosyltransferases (GTs) are prevalent across the tree of life and regulate nearly all aspects of cellular functions. The evolutionary basis for their complex and diverse modes of catalytic functions remain enigmatic. Here, based on deep mining of over half million GT-A fold sequences, we define a minimal core component shared among functionally diverse enzymes. We find that variations in the common core and emergence of hypervariable loops extending from the core contributed to GT-A diversity....

Data from: Spatial and temporal variation in nest temperatures forecasts sex ratio skews in a crocodilian with environmental sex determination

Samantha L. Bock, Russell H. Lowers, Thomas R. Rainwater, Eric Stolen, John M. Drake, Philip M. Wilkinson, Stephanie Weiss, Back Brenton, Louis Guillette & Benjamin B. Parrott
Species displaying temperature-dependent sex determination (TSD) are especially vulnerable to the effects of a rapidly changing global climate due to their profound sensitivity to thermal cues during development. Predicting the consequences of climate change for these species, including skewed offspring sex ratios, depends on understanding how climatic factors interface with features of maternal nesting behavior to shape the developmental environment. Here, we measure thermal profiles in 86 nests at two geographically distinct sites in the...

Virulence-mediated infectiousness and activity trade-offs and their impact on transmission potential of patients infected with influenza

Brian McKay, Mark Ebell, Ariella Dale, Ye Shen & Andreas Handel
Communicable diseases are often virulent, i.e., they cause morbidity symptoms in those infected. While some symptoms may be transmission-enhancing, other symptoms are likely to reduce transmission potential. For human diseases, the reduction in transmission opportunities is commonly caused by reduced activity. There is limited data regarding the potential impact of virulence on transmission potential. We performed an exploratory data analysis of 324 influenza patients at a university health center during the 2016/2017 influenza season. We...

Data from: Age influences the thermal suitability of Plasmodium falciparum transmission in the Asian malaria vector Anopheles stephensi

Courtney Murdock, Kerri Miazgowicz, Erin Mordecai, Sadie Ryan, Richard Hall, Harry Owen, Temitayo Adanlawo, Kavya Balaji, Marta Shocket, Oswaldo Villena & Leah Johnson
Models predicting disease transmission are vital tools for long-term planning of malaria reduction efforts, particularly for mitigating impacts of climate change. We compared temperature-dependent malaria transmission models when mosquito life history traits were estimated from a truncated portion of the lifespan (a common practice) to traits measured across the full lifespan. We conducted an experiment on adult female Anopheles stephensi, the Asian urban malaria mosquito, to generate daily per capita values for mortality, egg production,...

Data from: Comparing traditional and Bayesian approaches to ecological meta-analysis

Paula Pappalardo, Kiona Ogle, Elizabeth Hamman, James Bence, Bruce Hungate & Craig Osenberg
1. Despite the wide application of meta-analysis in ecology, some of the traditional methods used for meta-analysis may not perform well given the type of data characteristic of ecological meta-analyses. 2. We reviewed published meta-analyses on the ecological impacts of global climate change, evaluating the number of replicates used in the primary studies (ni) and the number of studies or records (k) that were aggregated to calculate a mean effect size. We used the results...

Collective Effect of Landfills and Landscape Composition on Bird-Aircraft Collisions

Morgan B. Pfeiffer, Bradley F. Blackwell & Travis L. DeVault
Ninety-three percent of all reported bird strikes occur below 1,067 m, which based on the typical approach and departure angles of aircraft is within 8–13 km of an airport. Concomitantly, the Federal Aviation Administration and the International Civil Aviation Organization recommend that any feature that would attract hazardous wildlife to the approach and departure airspace be restricted. Thus, preventing the establishment of wildlife attractants, such as municipal solid waste landfills (MSWLFs) within 8 km or...

There’s More to Groove than Bass in Electronic Dance Music

Brian Wesolowski & Alex Hofmann
The purpose of this study was to explore the relationship between audio descriptors for groove-based electronic dance music (EDM) and raters’ perceived cognitive, affective, and psychomotor responses. From 198 musical excerpts (length: 15 sec.) representing 11 subgenres of EDM, 19 low-level audio feature descriptors were extracted. A principal component analysis of the feature vectors indicated that the musical excerpts could effectively be classified using five complex measures, describing the rhythmical properties of: (a) the high-frequency...

Ecological and evolutionary drivers of hemoplasma infection and genotype sharing in a Neotropical bat community

Daniel Becker, Kelly Speer, Alexis Brown, Alex Washburne, Brock Fenton, Sonia Altizer, Daniel Streicker, Raina Plowright, Vladimir Chizhikov, Nancy Simmons & Dmitriy Volokhov
Most emerging pathogens can infect multiple species, underscoring the importance of understanding the ecological and evolutionary factors that allow some hosts to harbor greater infection prevalence and share pathogens with other species. However, our understanding of pathogen jumps is primarily based around viruses, despite bacteria accounting for the greatest proportion of zoonoses. Because bacterial pathogens in bats (Order: Chiroptera) can have conservation and human health consequences, studies that examine the ecological and evolutionary drivers of...

Data from: Patterns of annual and seasonal immune investment in a temporal reproductive opportunist

Elizabeth Schultz, Christian Gunning, Jamie Cornelius, Dustin Reichard, Kirk Klasing & Thomas Hahn
Historically, investigations of how organismal investments in immunity fluctuate in response to environmental and physiological changes have focused on seasonally breeding organisms that confine reproduction to seasons with mild environmental conditions and abundant resources. The red crossbill, Loxia curvirostra, is a songbird that can breed opportunistically if conifer seeds are abundant, on both short, cold, and long, warm days, providing an ideal system to investigate interactions between immunity, reproduction, and environmental fluctuations. In this study,...

Assessing the effects of elephant foraging on the structure and diversity of an Afrotropical forest

Cooper Rosin, Kendall Beals, Michael Belovitch, Ruby Harrison, Megan Pendred, Megan Sullivan, Nicolas Yao & John Poulsen
African forest elephants (Loxodonta cyclotis) are ecosystem engineers that browse and damage large quantities of vegetation during their foraging and movement. Though elephant trail networks and clearings are conspicuous features of many African forests, the consequences of elephant foraging for forest structure and diversity are poorly documented. In this study in northeastern Gabon, we compare stem size, stem density, proportional damage, species diversity, and species relative abundance of seedlings and saplings in the vicinity of...

Landscape context mediates the physiological stress response of birds to farmland diversification

Christopher Latimer, Olivia Smith, Joseph Taylor, Amanda Edworthy, Jeb Owen, William Snyder & Christina M. Kennedy
1. Farmland diversification practices are increasingly adopted to help reverse biodiversity declines in agroecosystems. However, evidence for the effectiveness of this approach often comes from documenting the species attracted to particular farming systems or landscapes, rather than their underlying physiological states that ultimately determine population growth or decline over the longer term. 2. Across 38 organic, mixed-produce farms spanning the U.S. west coast, we quantified three physiological biomarkers that are widely used to capture variation...

More than DNA methylation: does pleiotropy drive the complex pattern of evolution of Dnmt1?

Patricia Moore, Ashley Amukamara, Joshua Washington, Zachary Sanchez, Elizabeth McKinney, Allen Moore & Robert Schmitz
DNA methylation is an important chromatin modification that can stably alter gene expression in cells and maintain genome integrity in plants and vertebrates. The function of DNA methylation outside of these well-studied systems, however, is unclear. Insects, in particular, represent an understudied group. Variation in the level of DNA methylation and gains and losses in the maintenance methyltransferase, DNMT1, across the insect tree of life suggests that there is much we don’t understand about DMNT1...

Experimental N and P additions relieve stoichiometric constraints on organic-matter flows through five stream food webs

Lee Demi, Jonathan Benstead, Amy Rosemond & John Maerz
1. Human activities have dramatically altered global patterns of nitrogen (N) and phosphorus (P) availability. This pervasive nutrient pollution is changing basal resource quality in food webs, thereby affecting rates of biological productivity and the pathways of energy and material flow to higher trophic levels. 2. Here, we investigate how the stoichiometric quality of basal resources modulates patterns of material flow through food webs by characterizing the effects of experimental N and P enrichment on...

Freeze-tolerance of poleward-spreading mangrove species weakened by soil properties of resident salt marsh competitor

Enjian Chen, Julie Blaze, Rachel Smith, Shaolin Peng & James Byers
1. Background: Increasing temperatures associated with climate change are shifting plant species to higher latitudes. Soil communities could aid the plants’ shift into novel areas by harbouring fewer soil-borne antagonists or more mutualists that influence the fitness and stress tolerance of the shifting species. Alternatively, they could contain novel antagonists or fewer mutualists. Thus, soil communities could positively or negatively affect plant range expansion, particularly if they influence plants’ responses to climate, such as freeze...

Data-driven models reveal mutant cell behaviors important for myxobacterial aggregation

Oleg Igoshin, Zhaoyang Zhang, Christopher R. Cotter, Lawrence J. Shimkets & Zhe Lyu
Single mutations frequently alter several aspects of cell behavior but rarely reveal whether a particular statistically significant change is biologically significant. To determine which behavioral changes are most important for multicellular self-organization, we devised a new methodology using Myxococcus xanthus as a model system. During development, myxobacteria coordinate their movement to aggregate into spore-filled fruiting bodies. We investigate how aggregation is restored in two mutants, csgA and pilC, that cannot aggregate unless mixed with wild...

Data from: Oxidative killing of encapsulated and nonencapsulated Streptococcus pneumoniae by lactoperoxidase-generated hypothiocyanite

Balazs Rada
Streptococcus pneumoniae (Pneumococcus) infections affect millions of people worldwide, cause serious mortality and represent a major economic burden. Despite recent successes due to pneumococcal vaccination and antibiotic use, Pneumococcus remains a significant medical problem. Airway epithelial cells, the primary responders to pneumococcal infection, orchestrate an extracellular antimicrobial system consisting of lactoperoxidase (LPO), thiocyanate anion and hydrogen peroxide (H2O2). LPO oxidizes thiocyanate using H2O2 into the final product hypothiocyanite that has antimicrobial effects against a wide...

Do Synthesis Centers Synthesize? A Semantic Analysis of Topical Diversity in Research

Edward Hackett, Erin Leahy, John Parker, Ismael Rafols, Stephanie Hampton, Ugo Corte, Diego Chavarro, John Drake, Bart Penders, Laura Sheble, Niki Vermeulen & Todd Vision
Synthesis centers are a form of scientific organization that catalyzes and supports research that integrates diverse theories, methods and data across spatial or temporal scales to increase the generality, parsimony, applicability, or empirical soundness of scientific explanations. Synthesis working groups are a distinctive form of scientific collaboration that produce consequential, high-impact publications. But no one has asked if synthesis working groups synthesize: are their publications substantially more diverse than others, and if so, in what...

Social trematodes parasites increase standing army size in areas of greater invasion threat

Emlyn Resetarits, Mark Torchin & Ryan Hechinger
Organisms or societies are resource limited, causing important trade-offs between reproduction and defence. Given such trade-offs, optimal allocation theory predicts that, for animal societies with a soldier caste, allocation to soldiers should reflect local external threats. Although both threat intensity and soldier allocation can vary widely in nature, we currently lack strong evidence that spatial variation in threat can drive corresponding variation in soldier allocation. The diverse guild of trematode parasites of the California horn...

Data from: An initial comparative genomic autopsy of wasting disease in sea stars

Dannise V. Ruiz‐Ramos, Lauren M. Schiebelhut, Katharina J. Hoff, John P. Wares & Michael N. Dawson
Beginning in 2013, sea stars throughout the Eastern North Pacific were decimated by wasting disease, also known as ‘asteroid idiopathic wasting syndrome’ (AIWS) due to its elusive etiology. The geographic extent and taxonomic scale of AIWS meant events leading up to the outbreak were heterogeneous, multifaceted, and oftentimes unobserved; progression from morbidity to death was rapid, leaving few tell-tale symptoms. Here we take a forensic genomic approach to discover candidate genes that may help explain...

Ambient temperature and female body condition are related to night incubation behavior in wood ducks (Aix sponsa)

Alexander Grimaudo, Sydney Hope, Sarah DuRant, Robert Kennamer, John Hallagan & William Hopkins
For many animals, parental care behavior is an important aspect of their life history that affects both parents and offspring. In birds, one of the most important parental care behaviors is incubation, which is costly to the parent but directly influences embryonic development and fitness of offspring. Some birds exhibit the intriguing behavior of partially incubating their eggs prior to clutch completion for only a portion of each day. This partial incubation is characterized by...

Data from: A comparison of diversity estimators applied to a database of host-parasite associations

Claire Teitelbaum, Caroline Amoroso, Shan Huang, T. Jonathan Davies, Julie Rushmore, John Drake, Patrick Stephens, James Byers, Ania Majewska & Charles Nunn
Understanding the drivers of biodiversity is important for forecasting changes in the distribution of life on earth. However, most studies of biodiversity are limited by uneven sampling effort, with some regions or taxa better sampled than others. Numerous methods have been developed to account for differences in sampling effort, but most methods were developed for systematic surveys in which all study units are sampled using the same design and assemblages are sampled randomly. Databases compiled...

No net insect abundance and diversity declines across US Long Term Ecological Research sites

Michael Crossley, Amanda Meier, Emily Baldwin, Lauren Berry, Leah Crenshaw, Glen Hartman, Doris Lagos-Kutz, David Nichols, Krishna Patel, Sofia Varriano, Matthew Moran & William Snyder
Recent reports of dramatic declines in insect abundance suggest grave consequences for global ecosystems and human society. Most evidence comes from Europe, however, leaving uncertainty about insect population trends worldwide. We used > 5,300 time series for insects and other arthropods, collected over 4-36 years at monitoring sites representing 68 different natural and managed areas, to search for evidence of declines across the United States. Some taxa and sites showed decreases in abundance and diversity...

Registration Year

  • 2020
    32

Resource Types

  • Dataset
    29
  • Text
    3

Affiliations

  • University of Georgia
    32
  • University of Wisconsin-Madison
    2
  • Indiana University Bloomington
    2
  • Mississippi State University
    2
  • Washington State University
    2
  • University of California, Davis
    2
  • University of Music and Performing Arts Vienna
    1
  • China Food and Drug Administration
    1
  • University of Georgia Press
    1
  • Sun Yat-sen University
    1