30 Works

Data from: Phylogenetic clustering of origination and extinction across the Late Ordovician mass extinction

Andrew Z. Krug & Mark E. Patzkowsky
Mass extinctions can have dramatic effects on the trajectory of life, but in some cases the effects can be relatively small even when extinction rates are high. For example, the Late Ordovician mass extinction is the second most severe in terms of the proportion of genera eliminated, yet is noted for the lack of ecological consequences and shifts in clade dominance. By comparison, the end-Cretaceous mass extinction was less severe but eliminated several major clades...

Data from: Tc-MYBPA an Arabidopsis TT2-like transcription factor and functions in the regulation of proanthocyanidin synthesis in Theobroma cacao

Yi Liu, Zi Shi, Siela N. Maximova, Mark J. Payne & Mark J. Guiltinan
Background: The flavan-3-ols catechin and epicatechin, and their polymerized oligomers, the proanthocyanidins (PAs, also called condensed tannins), accumulate to levels of up to 15 % of the total weight of dry seeds of Theobroma cacao L. These compounds have been associated with several health benefits in humans. They also play important roles in pest and disease defense throughout the plant. In Arabidopsis, the R2R3 type MYB transcription factor TT2 regulates the major genes leading to...

Data from: Do humans optimally exploit redundancy to control step variability in walking?

Jonathan B. Dingwell, Joby John & Joseph P. Cusumano
It is widely accepted that humans and animals minimize energetic cost while walking. While such principles predict average behavior, they do not explain the variability observed in walking. For robust performance, walking movements must adapt at each step, not just on average. Here, we propose an analytical framework that reconciles issues of optimality, redundancy, and stochasticity. For human treadmill walking, we defined a goal function to formulate a precise mathematical definition of one possible control...

Data from: Evaluation of Blue Crab, Callinectes sapidus, megalopal settlement and condition during the Deepwater Horizon oil spill

Erin K. Grey, Susan C. Chiasson, Hannah G. Williams, Victoria J. Troeger & Caz M. Taylor
The Blue Crab, Callinectes sapidus, is a commercially, culturally, and ecologically significant species in the Gulf of Mexico (GOM), whose offshore stages were likely impacted by the Deepwater Horizon oil spill (DWH). To test for DWH effects and to better understand the planktonic ecology of this species, we monitored Callinectes spp. megalopal settlement and condition at sites within and outside of the spill extent during and one year after the DWH. We tested for DWH...

Data from: Molecular dynamic simulations reveal the structural determinants of fatty acid binding to oxy-myoglobin

Sree V. Chintapalli, Gaurav Bhardwaj, Reema Patel, Natasha Shah, Randen L. Patterson, Damian B. Van Rossum, Andriy Anishkin & Sean H. Adams
The mechanism(s) by which fatty acids are sequestered and transported in muscle have not been fully elucidated. A potential key player in this process is the protein myoglobin (Mb). Indeed, there is a catalogue of empirical evidence supporting direct interaction of globins with fatty acid metabolites; however, the binding pocket and regulation of the interaction remains to be established. In this study, we employed a computational strategy to elucidate the structural determinants of fatty acids...

Data from: Does high-dose antimicrobial chemotherapy prevent the evolution of resistance?

Troy Day & Andrew F. Read
High-dose chemotherapy has long been advocated as a means of controlling drug resistance in infectious diseases but recent empirical studies have begun to challenge this view. We develop a very general framework for modeling and understanding resistance emergence based on principles from evolutionary biology. We use this framework to show how high-dose chemotherapy engenders opposing evolutionary processes involving the mutational input of resistant strains and their release from ecological competition. Whether such therapy provides the...

Data from: Deadwood structural properties may influence aye-aye (Daubentonia madagascariensis) extractive foraging behavior

Katharine E. T. Thompson, Richard J. Bankoff, Edward E. Louis & George H. Perry
The identification of critical, limited natural resources for different primate species is important for advancing our understanding of behavioral ecology and toward future conservation efforts. The aye-aye (Daubentonia madagascariensis) is an Endangered nocturnal lemur with adaptations for accessing structurally defended foods: continuously growing incisors; an elongated, flexible middle finger; and a specialized auditory system. In some seasons, ca. 90% of the aye-aye’s diet consists of two structurally defended resources: 1) the larvae of wood boring...

Data from: Symbiodinium population genetics: testing for species boundaries and analyzing samples with mixed genotypes

Drew C. Wham & Todd C. LaJeunesse
Population genetic markers are increasingly being used to study the diversity, ecology, and evolution of Symbiodinium, a group of eukaryotic microbes that are often mutualistic with reef-building corals. Population genetic markers can resolve individual clones, or strains, from samples of host tissue, however samples may comprise different species that may confound interpretations of gene flow and genetic structure. Here we propose a method for resolving species from population genetic data using tests of genetic recombination....

Data from: Biotic invasion, niche stability, and the assembly of regional biotas in deep time: comparison between faunal provinces

Mark E. Patzkowsky & Steven M. Holland
Biotic invasions in the fossil record provide natural experiments for testing hypotheses of niche stability, speciation, and the assembly and diversity of regional biotas. We compare ecologic parameters (preferred environment, occupancy, median abundance, rank abundance) of genera shared between faunal provinces during the Richmondian Biotic Invasion in the Late Ordovician on the Laurentian continent. Genera that spread from one faunal province to the other during the invasion (invading shared genera) have high Spearman rank correlations...

Data from: Conservation and modification of genetic and physiological toolkits underpinning diapause in bumble bee queens

Etya Amsalem, David A. Galbraith, Jonathan Cnaani, Peter E. A. Teal & Christina M. Grozinger
Diapause is the key adaptation allowing insects to survive unfavorable conditions and inhabit an array of environments. Physiological changes during diapause are largely conserved across species, and are hypothesized to be regulated by a conserved suite of genes (a “toolkit”). Furthermore, it is hypothesized that in social insects, this toolkit was co-opted to mediate caste differentiation between long-lived, reproductive, diapause-capable queens and short-lived, sterile workers. Using Bombus terrestris queens we examined the physiological and transcriptomic...

Data from: The stratigraphy of mass extinction

Steven M. Holland, Mark E. Patzkowksy & Mark E. Patzkowsky
Patterns of last occurrences of fossil species are often used to infer the tempo and timing of mass extinction, even though last occurrences generally precede the time of extinction. Numerical simulations with constant extinction demonstrate that last occurrences are not randomly distributed, but tend to cluster at subaerial unconformities, surfaces of forced regression, flooding surfaces and intervals of stratigraphical condensation, all of which occur in predictable stratigraphical positions. This clustering arises not only from hiatuses...

Data from: Persistent chaos of measles epidemics in the prevaccination United States caused by a small change in seasonal transmission patterns

Benjamin D. Dalziel, Ottar N. Bjornstad, Willem G. Van Panhuis, Donald S. Burke, C. Jessica E. Metcalf, Bryan T. Grenfell & Ottar N. Bjørnstad
Epidemics of infectious diseases often occur in predictable limit cycles. Theory suggests these cycles can be disrupted by high amplitude seasonal fluctuations in transmission rates, resulting in deterministic chaos. However, persistent deterministic chaos has never been observed, in part because sufficiently large oscillations in transmission rates are uncommon. Where they do occur, the resulting deep epidemic troughs break the chain of transmission, leading to epidemic extinction, even in large cities. Here we demonstrate a new...

Data from: Detecting spatial genetic signatures of local adaptation in heterogeneous landscapes

Brenna R. Forester, Matthew R. Jones, Stéphane Joost, Erin L. Landguth & Jesse R. Lasky
The spatial structure of the environment (e.g., the configuration of habitat patches) may play an important role in determining the strength of local adaptation. However, previous studies of habitat heterogeneity and local adaptation have largely been limited to simple landscapes, which poorly represent the multi-scale habitat structure common in nature. Here, we use simulations to pursue two goals: (1) we explore how landscape heterogeneity, dispersal ability, and selection affect the strength of local adaptation, and...

Data from: Covariation in abscission force and terminal velocity of wind-borne sibling seeds alters long distance dispersal projections

Brittany J. Teller, James H. Marden & Katriona Shea
1. Despite the fact that seeds are unlikely to be identical—even among siblings within a maternal individual—dispersal models typically use one mean trait value to represent the ability of an entire species to disperse. Previous work has shown that the environmental conditions under which individuals leave the maternal site strongly affect how far seeds will travel. However, less is known about how trait variation within individuals contributes to dispersal or how such variation might interact...

Data from: Immune response and insulin signalling alter mosquito feeding behaviour to enhance malaria transmission potential

Jose E. Pietri, Lauren J. Cator, Courtney C. Murdock, Johanna R. Ohm, Edwin E. Lews, Andrew F. Read, Shirley Luckhart & Matthew B. Thomas
Malaria parasites alter mosquito feeding behaviour in a way that enhances parasite transmission. This is widely considered a prime example of manipulation of host behaviour to increase onward transmission, but transient immune challenge in the absence of parasites can induce the same behavioural phenotype. Here, we show that alterations in feeding behaviour depend on the timing and dose of immune challenge relative to blood ingestion and that these changes are functionally linked to changes in...

Data from: Population and genetic outcomes 20 years after reintroducing bobcats (Lynx rufus) to Cumberland Island, Georgia USA

Duane Diefenbach, Leslie Hansen, Justin Bohling & Cassandra Miller-Butterworth
In 1988–1989, 32 bobcats Lynx rufus were reintroduced to Cumberland Island (CUIS), Georgia, USA, from which they had previously been extirpated. They were monitored intensively for 3 years immediately post-reintroduction, but no estimation of the size or genetic diversity of the population had been conducted in over 20 years since reintroduction. We returned to CUIS in 2012 to estimate abundance and effective population size of the present-day population, as well as to quantify genetic diversity...

Data from: Testing the depth-differentiation hypothesis in a deepwater octocoral

Andrea M. Quattrini, Iliana B. Baums, Timothy M. Shank, Cheryl L. Morrison & Erik E. Cordes
The depth-differentiation hypothesis proposes that the bathyal region is a source of genetic diversity and an area where there is a high rate of species formation. Genetic differentiation should thus occur over relatively small vertical distances, particularly along the upper continental slope (200–1000 m) where oceanography varies greatly over small differences in depth. To test whether genetic differentiation within deepwater octocorals is greater over vertical rather than geographical distances, Callogorgia delta was targeted. This species...

Data from: Amyloid precursor protein translation is regulated by a 3'UTR guanine quadruplex

Ezekiel Crenshaw, Brian P. Leung, Chun Kit Kwok, Michal Sharoni, Kalee Olson, Neeraj P. Sebastian, Sara Ansaloni, Reinhard Schweitzer-Stenner, Michael R. Akins, Philip C. Bevilacqua & Aleister J. Saunders
A central event in Alzheimer’s disease is the accumulation of amyloid β (Aβ) peptides generated by the proteolytic cleavage of the amyloid precursor protein (APP). APP overexpression leads to increased Aβ generation and Alzheimer’s disease in humans and altered neuronal migration and increased long term depression in mice. Conversely, reduction of APP expression results in decreased Aβ levels in mice as well as impaired learning and memory and decreased numbers of dendritic spines. Together these...

Data from: Phosphorus amendment mitigates nitrogen addition-induced phosphorus limitation in two plant species in a desert steppe, China

Huang Juying, Hailong Yu, Henry Lin, Yu Zhang, Eric B. Searle, Zhiyou Yuan & Juying Huang
Background and aims: The increasing deposition of atmospheric nitrogen (N) due to anthropogenic activities has significantly enhanced N inputs to ecosystems, resulting in an imbalance in the N: phosphorus (P) ratios in plants and soils. This study aimed to determine whether, and to what extent, P addition alleviates N-induced P limitation in a desert steppe ecosystem. Methods: We conducted a multi-level N:P supply experiment (i.e., constant N with varied P-addition levels) for a grass species,...

Data from: Effects of land use on lake nutrients: the importance of scale, hydrologic connectivity, and region

Patricia A. Soranno, Kendra Spence Cheruvelil, Tyler Wagner, Katherine E. Webster & Mary Tate Bremigan
Catchment land uses, particularly agriculture and urban uses, have long been recognized as major drivers of nutrient concentrations in surface waters. However, few simple models have been developed that relate the amount of catchment land use to downstream freshwater nutrients. Nor are existing models applicable to large numbers of freshwaters across broad spatial extents such as regions or continents. This research aims to increase model performance by exploring three factors that affect the relationship between...

Data from: Energetic constraint of non-monotonic mass change during offspring growth: a general hypothesis and application of a new tool

Jennifer M. Arnold, Ian C. Nisbet & Stephen A. Oswald
1. Postnatal growth is an important life-history trait and can be a sensitive indicator of ecological stress. For over 50 years, monotonic (never-decreasing) growth has been viewed as the predominant trajectory of postnatal mass change in most animal species, notably among birds. However, prevailing analytical approaches and energetic constraints may limit detection of non-monotonic (or multi-phasic), determinate growth patterns, such as mass recession in birds (weight-loss prior to fledging, preceded by overshooting adult mass), which...

Data from: The potential for fungal biopesticides to reduce malaria transmission under diverse environmental conditions

Rebecca L. Heinig, Krijn P. Paaijmans, Penelope A. Hancock & Matthew B. Thomas
1.The effectiveness of conventional malaria vector control is being threatened by the spread of insecticide resistance. One promising alternative to chemicals is the use of naturally-occurring insect-killing fungi. Numerous laboratory studies have shown that isolates of fungal pathogens such as Beauveria bassiana can infect and kill adult mosquitoes, including those resistant to chemical insecticides. 2. Unlike chemical insecticides, fungi may take up to a week or more to kill mosquitoes following exposure. This slow kill...

Data from: Detecting recent selective sweeps while controlling for mutation rate and background selection

Christian D. Huber, Michael DeGiorgio, Ines Hellmann & Rasmus Nielsen
A composite likelihood ratio test implemented in the program SweepFinder is a commonly used method for scanning a genome for recent selective sweeps. SweepFinder uses information on the spatial pattern (along the chromosome) of the site frequency spectrum (SFS) around the selected locus. To avoid confounding effects of background selection and variation in the mutation process along the genome, the method is typically applied only to sites that are variable within species. However, the power...

Data from: Home bodies and wanderers: sympatric lineages of the deep-sea black coral Leiopathes glaberrima

Dannise V. Ruiz-Ramos, Miles G. Saunders, Charles R. Fisher, Iliana B. Baums & Miles Saunders
Colonial corals occur in a wide range of marine benthic habitats from the shallows to the deep ocean, often defining the structure of their local community. The black coral Leiopathes glaberrima is a long-lived foundation species occurring on carbonate outcrops in the Northern Gulf of Mexico (GoM). Multiple color morphs of L. glaberrima grow sympatrically in the region. Morphological, mitochondrial and nuclear ribosomal markers supported the hypothesis that color morphs constituted a single biological species...

Data from: Microbial invasion of the Caribbean by an Indo-Pacific coral zooxanthella

D. Tye Pettay, Drew C. Wham, Robin T. Smith, Roberto Iglesias-Prieto & Todd C. LaJeunesse
Human-induced environmental changes have ushered in the rapid decline of coral reef ecosystems, particularly by disrupting the symbioses between reef-building corals and their photosymbionts. However, escalating stressful conditions enable some symbionts to thrive as opportunists. We present evidence that a stress-tolerant “zooxanthella” from the Indo-Pacific Ocean, Symbiodinium trenchii, has rapidly spread to coral communities across the Greater Caribbean. In marked contrast to populations from the Indo-Pacific, Atlantic populations of S. trenchii contained exceptionally low genetic...

Registration Year

  • 2015

Resource Types

  • Dataset


  • Pennsylvania State University
  • National Institutes of Health
  • University of Georgia
  • University of California, Berkeley
  • University of Florida
  • University of California, Davis
  • North West Agriculture and Forestry University
  • University of Montana
  • The Bronx Defenders
  • Utah State University