246 Works

Data from: Take this broken tail and learn to jump: the ability to recover from reduced in-air stability in tailless green anole lizards (Anolis carolinensis [Squamata: Dactyloidae])

Chi-Yun Kuo, Gary B. Gillis & Duncan J. Irschick
Locomotion is involved in various fitness related tasks, such as foraging, acquiring mates and escaping from predators. Despite the importance of locomotor performance in determining fitness, animals often encounter situations in nature during which their locomotor performance is severely compromised. For animals that actively discard appendages as an antipredator strategy, the loss of appendages can cause a severe reduction in locomotor performance. However, whether animals can compensate for the impact on locomotor performance after autotomy...

Data from: Joined at the hip: linked characters and the problem of missing data in studies of disparity

Andrew John Smith, Michael V. Rosario, Thomas P. Eiting & Elizabeth R. Dumont
Paleontological investigations into morphological diversity, or disparity, are often confronted with large amounts of missing data. We illustrate how missing discrete data effects disparity using a novel simulation for removing data based on parameters from published datasets that contain both extinct and extant taxa. We develop an algorithm that assesses the distribution of missing characters in extinct taxa, and simulates data loss by applying that distribution to extant taxa. We term this technique ‘linkage’. We...

Data from: Vertebral evolution and the diversification of squamate reptiles

Philip J. Bergmann & Duncan J. Irschick
Taxonomic, morphological and functional diversity are often discordant and independent components of diversity. A fundamental and largely unanswered question in evolutionary biology is why some clades diversify primarily in some of these components and not others. Dramatic variation in trunk vertebral numbers (14 to >300) among squamate reptiles coincides with different body shapes, and snake-like body shapes have evolved numerous times. However, whether increased evolutionary rates or numbers of vertebrae underlie body shape and taxonomic...

Data from: Modularity and scaling in fast movements: power amplification in mantis shrimp

Thomas Claverie, Elliot Chan & Sheila N. Patek
Extremely fast animal actions are accomplished with mechanisms that reduce the duration of movement. This process is known as power amplification. While many studies have examined the morphology and performance of power-amplified systems, little is known about their development and evolution. Here we examine scaling and modularity in the powerful predatory appendages of a mantis shrimp, Gonodactylaceus falcatus (Crustacea, Stomatopoda). We propose that power-amplified systems can be divided into three units: an engine (e.g., muscle),...

Data from: Modularity and rates of evolutionary change in a power-amplified prey capture system

Thomas Claverie & S. N. Patek
The dynamic interplay among structure, function and phylogeny form a classic triad of influences on the patterns and processes of biological diversification. While these dynamics are widely recognized as important, quantitative analyses of their interactions have infrequently been applied to biomechanical systems. Here we analyze these factors using a fundamental biomechanical mechanism: power amplification. Power-amplified systems use springs and latches to generate extremely fast and powerful movements. This study focuses specifically on the power amplification...

Data from: How much does nasal cavity morphology matter? Patterns and rates of olfactory airflow in phyllostomid bats

Thomas P. Eiting, J. Blair Perot & Elizabeth R. Dumont
The morphology of the nasal cavity in mammals with a good sense of smell includes features that are thought to improve olfactory airflow, such as a dorsal conduit that delivers odours quickly to the olfactory mucosa, an enlarged olfactory recess at the back of the airway, and a clear separation of the olfactory and respiratory regions of the nose. The link between these features and having a good sense of smell has been established by...

Data from: Developmental plasticity affects sexual size dimorphism in an anole lizard

Camille Bonneaud, Erin Marnocha, Anthony Herrel, Bieke Vanhooydonck, Duncan J. Irschick & Thomas B. Smith
While developmental plasticity has been shown to contribute to sexual size dimorphism (SSD) in laboratory studies, its role in shaping SSD variation in wild vertebrate populations is unclear. Here we use a field study and a laboratory experiment to show that resource availability influences the degree of SSD among insular populations of Anolis sagrei lizards in the Bahamas. Total amounts of food biomass explained variation in male, but not female, body size on six Bahamian...

Data from: Dietary hardness, loading behavior, and the evolution of skull form in bats

Sharlene E. Santana, Ian R. Grosse & Elizabeth R. Dumont
The morphology and biomechanics of the vertebrate skull reflect the physical properties of diet and behaviors used in food acquisition and processing. We use phyllostomid bats, the most diverse mammalian dietary radiation, to investigate if and how changes in dietary hardness and loading behaviors during feeding shaped the evolution of skull morphology and biomechanics. When selective regimes of food hardness are modeled, we found that species consuming harder foods have evolved skull shapes that allow...

Data from: Geckos as springs: mechanics explain across-species scaling of adhesion

Casey A. Gilman, Michael J. Imburgia, Michael D. Bartlett, Daniel R. King, Alfred J. Crosby & Duncan J. Irschick
One of the central controversies regarding the evolution of adhesion concerns how adhesive force scales as animals change in size, either among or within species. A widely held view is that as animals become larger, the primary mechanism that enables them to climb is increasing pad area. However, prior studies show that much of the variation in maximum adhesive force remains unexplained, even when area is accounted for. We tested the hypothesis that maximum adhesive...

Data from: A characterization of autumn nocturnal migration detected by weather surveillance radars in the northeastern US

Andrew Farnsworth, Benjamin Mark Van Doren, Wesley M. Hochachka, Daniel Sheldon, Kevin Winner, Jed Irvine, Jeffrey Geevarghese & Steve Kelling
Billions of birds migrate at night over North America each year. However, few studies have described the phenology of these movements, such as magnitudes, directions, and speeds, for more than one migration season and at regional scales. In this study, we characterize density, direction, and speed of nocturnally migrating birds using data from 13 weather surveillance radars in the autumns of 2010 and 2011 in the northeastern US. After screening radar data to remove precipitation,...

Data from: The comparative hydrodynamics of rapid rotation by predatory appendages

Mathew J. McHenry, Philip S. L. Anderson, Sam Van Wassenbergh, David Matthews, Adam Summers & S. N. Patek
Countless aquatic animals rotate appendages through the water, yet fluid forces are typically modeled with translational motion. To elucidate the hydrodynamics of rotation, we analyzed the raptorial appendages of mantis shrimp (Stomatopoda) using a combination of flume experiments, mathematical modeling and phylogenetic comparative analyses. We found that computationally efficient blade-element models offered an accurate first-order approximation of drag, when compared with a more elaborate computational fluid-dynamic model. Taking advantage of this efficiency, we compared the...

Data from: Common evolutionary trends underlie the four-bar linkage systems of sunfish and mantis shrimp

Yinan Hu, Nathan Nelson-Maney, Philip S.L. Anderson & Philip S. L. Anderson
Comparative biomechanics offers an opportunity to explore the evolution of disparate biological systems that share common underlying mechanics. Four-bar linkage modelling has been applied to various biological systems such as fish jaws and crustacean appendages to explore the relationship between biomechanics and evolutionary diversification. Mechanical sensitivity states that the functional output of a mechanical system will show differential sensitivity to changes in specific morphological components. We document similar patterns of mechanical sensitivity in two disparate...

Data from: Trpc2 Pseudogenization dynamics in bats reveal ancestral vomeronasal signaling, then pervasive loss

Laurel R. Yohe, Ramatu Abubakar, Christina Giordano, Elizabeth Dumont, Karen Sears, Stephen J. Rossiter, Liliana M. Davalos & Karen E. Sears
Comparative methods are often used to infer loss or gain of complex phenotypes, but few studies take advantage of genes tightly linked with complex traits to test for shifts in the strength of selection. In mammals vomerolfaction detects chemical cues mediating many social and reproductive behaviors and is highly conserved, but all bats exhibit degraded vomeronasal structures with the exception of two families (Phyllostomidae and Miniopteridae). These families either regained vomerolfaction after ancestral loss, or...

Data from: Co-occurrence and hybridization of anther-smut pathogens specialized on Dianthus hosts

Elsa Petit, Casey Silver, Amandine Cornille, Pierre Gladieux, Lisa Rosenthal, Emily Bruns, Sarah Yee, Janis Antonovics, Tatiana Giraud & Michael Hood
Host specialization has important consequences for the diversification and ecological interactions of obligate pathogens. The anther-smut disease of natural plant populations, caused by Microbotryum fungi, has been characterized by specialized host-pathogen interactions, which contribute in part to the isolation among these numerous fungal species. This study investigated the molecular variation of Microbotryum pathogens within the geographic and host-specific distributions on wild Dianthus species in southern European Alps. In contrast to prior studies on this pathogen...

Data from: Adaptive developmental plasticity in rhesus macaques: the serotonin transporter gene interacts with maternal care to affect juvenile social behaviour

Jesus E. Madrid, Tara M. Mandalaywala, Sean P. Coyne, Jamie Ahloy-Dallaire, Joseph P. Garner, Christina S. Barr, Dario Maestripieri & Karen J. Parker
Research has increasingly highlighted the role that developmental plasticity-the ability of a particular genotype to produce variable phenotypes in response to different early environments-plays as an adaptive mechanism. One of the most widely studied genetic contributors to developmental plasticity in humans and rhesus macaques is a serotonin transporter gene-linked polymorphic region (5-HTTLPR), which determines transcriptional efficiency of the serotonin transporter gene in-vitro and modifies the availability of synaptic serotonin in these species. A majority of...

Data from: A local evaluation of the individual state-space to scale up Bayesian spatial capture recapture

Cyril Milleret, Pierre Dupont, Christophe Bonenfant, Henrik Brøseth, Øystein Flagstad, Chris Sutherland & Richard Bischof
1. Spatial capture-recapture models (SCR) are used to estimate animal density and to investigate a range of problems in spatial ecology that cannot be addressed with traditional non-spatial methods. Bayesian approaches in particular offer tremendous flexibility for SCR modelling. Increasingly, SCR data are being collected over very large spatial extents making analysis computational intensive, sometimes prohibitively so. 2. To mitigate the computational burden of large-scale SCR models, we developed an improved formulation of the Bayesian...

Data from: Large mammal declines and the incipient loss of mammal-bird mutualisms in an African savanna ecosystem

Nathan Diplock, Kate Johnston, Antoine Mellon, Laura Mitchell, Madison Moore, Daniel Schneider, Alyssa Taylor, Jess Whitney, Kera Zegar, John Kioko & Christian Kiffner
Over the past half-century, large mammal populations have declined substantially throughout East Africa, mainly due to habitat loss and unsustainable direct exploitation. While it has been acknowledged that the loss of large mammals can have direct and cascading effects on community composition and ecosystem characteristics, limited quantitative work has been done on how declines of large herbivore populations impacts the abundance of mutualistic symbionts. Using a space-for-time observational approach, we quantified the large mammal community...

Data from: Conserved but flexible modularity in the zebrafish skull: implications for craniofacial evolvability

Kevin J. Parsons, Young H. Son, Amelie Crespel, Davide Thambithurai, Shaun Killen, Matthew P. Harris & R. Craig Albertson
Morphological variation is the outward manifestation of development and provides fodder for adaptive evolution. Because of this contingency, evolution is often thought to be biased by developmental processes and functional interactions among structures, which are statistically detectable through forms of covariance among traits. This can take the form of substructures of integrated traits, termed modules, which together comprise patterns of variational modularity. While modularity is essential to an understanding of evolutionary potential, biologists currently have...

Data from: Pre-infection effects of nectar secondary compounds on a bumble bee gut pathogen

Kristen Michaud, Rebecca Irwin, Nicholas Barber & Lynn Adler
Bumble bee pollinators can be exposed to pathogens when foraging on flowers previously visited by infected individuals. Infectious cells may be deposited in floral nectar, providing a site for pathogens to interact with nectar secondary compounds prior to infecting bees. Some nectar secondary compounds can reduce pathogen counts in infected bumble bees, but we know less about how exposure to these compounds directly affects pathogens prior to being ingested by their host. We exposed the...

Source data for \"Writing with librarians: Reporting back on turning your poster or presentation into an article.\"

Kristin Lee & Thea Atwood

Something old, something new: evolution of Colombian weedy rice (Oryza spp.) through de novo de-domestication, exotic gene flow, and hybridization

Veronica Hoyos, Guido Plaza & Ana L. Caicedo
Weedy rice (Oryza spp.) is a worldwide weed of domesticated rice (O. sativa), considered particularly problematic due to its strong competition with the crop, which leads to reduction of yields and harvest quality. Several studies have established multiple independent origins for weedy rice populations in the U.S. and various parts of Asia; however, the origins of weedy rice in South America have not been examined in a global context. We evaluated the genetic variation of...

Dam Impoundments Sediment Mass – Tributaries to the Hudson River

Brian Yellen & Jonathan Woodruff
This repository contains data from sediment cores collected during 2017-2018 from 17 impoundments that are located on tributaries to the tidal portion of the Hudson River as part of a larger NERRs collaborative project entitled Dams and Sediment on the Hudson (DaSH). A companion dataset that contains sediment core data from Hudson tidal marshes is archived at UMass Scholarworks data repository. Sediment cores collected from impoundments behind dams were recovered via piston push coring, which...

Quantum supremacy using a programmable superconducting processor

John M. Martinis, Sergio Boixo, Hartmut Neven, Frank Arute, Kunal Arya, Ryan Babbush, Dave Bacon, Joseph C. Bardin, Rami Barends, Rupak Biswas, Fernando G. S. L. Brandao, David A. Buell, Brian Burkett, Yu Chen, Zijun Chen, Ben Chiaro, Roberto Collins, William Courtney, Andrew Dunsworth, Edward Farhi, Brooks Foxen, Austin Fowler, Craig Gidney, Marissa Giustina, Rob Graff … & Adam Zalcman
The tantalizing promise of quantum computers is that certain computational tasks might be executed exponentially faster on a quantum processor than on a classical processor. A fundamental challenge is to build a high-fidelity processor capable of running quantum algorithms in an exponentially large computational space. Here, we report using a processor with programmable superconducting qubits to create quantum states on 53 qubits, corresponding to a computational state-space of dimension 2^53 ∼ 10^16. Measurements from repeated...

Data and analyses from: Herbivory and time since flowering shape floral rewards and pollinator-pathogen interactions

Luis A. Aguirre, Julie K. Davis, Philip C. Stevenson & Lynn S. Adler
Herbivory can induce chemical changes throughout plant tissues including flowers, which could affect pollinator-pathogen interactions. Pollen is highly defended compared to nectar, but no study has examined whether herbivory affects pollen chemistry. We assessed the effects of leaf herbivory on nectar and pollen alkaloids in Nicotiana tabacum, and how herbivory-induced changes in nectar and pollen affect pollinator-pathogen interactions. We damaged leaves of Nicotiana tabacum using the specialist herbivore Manduca sexta and compared nicotine and anabasine...

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  • University of Massachusetts Amherst
  • University of California, Berkeley
  • Cornell University
  • University of California, Merced
  • Lawrence Berkeley National Laboratory
  • Lawrence Livermore National Laboratory
  • Pennsylvania State University
  • Joint Genome Institute
  • University of Arizona
  • North Carolina State University