96 Works

Detoxification-related gene expression accompanies anhydrobiosis in the foliar nematode (Aphelenchoides fragariae)

Zhen Fu, Paula Agudelo & Christina Wells
The foliar nematode (Aphelenchoides fragariae) is a quarantined pest that infects a broad range of herbaceous and woody plants. Previous work has demonstrated its remarkable ability to survive rapid and extreme desiccation, although the specific mechanisms underlying its anhydrobiotic response have not been characterized. We used RNA sequencing and de novo transcriptome assembly to compare patterns of gene expression between hydrated and 24-hr desiccated nematodes. Two thousand eighty-three and 953 genes were significantly up- and...

The effect of influenza vaccination for the elderly on hospitalization and mortality: an observational study with a regression-discontinuity design

, Carlos Dobkin & Devon Gorry
Replication files for "The Effect of Influenza Vaccination for the Elderly on Hospitalization and Mortality: An Observational Study with a Regression-Discontinuity Design", published in the Annals of Internal Medicine.

Cape ground squirrel site comparison dataset

Mary Manjerovic, Eric Hoffman, Christopher Parkinson & Jane Waterman
Male mating strategies respond to female availability such that variation in resources that affect spatial distribution can also alter cost-benefit tradeoffs within a population. In arid-adapted species, rainfall alters reproduction, behavior, morphology, and population density such that populations differing in resource availability may also differ in successful reproductive strategies. Here we compare two populations of Cape ground squirrels (Xerus inauris), a sub-Saharan species with year-round breeding and intense mating competition. Unlike most mammals where males...

Sex differences in the plasticity of life history in response to social environment

Elizabeth Lange, Margaret Ptacek, Joseph Travis & Kimberly Hughes
Predicting how social environment affects life history variation is critical to understanding if, and when, selection favors alternative life history development, especially in systems in which social interactions change over time or space. While sexual selection theory predicts that males and females should respond differently to variation in the social environment, few studies have examined the responses of both male and female phenotypes to the same gradient of social environment. In this study, we used...

A multi-species approach to manage effects of land cover and weather on upland game birds

Alexander Schindler, David Haukos, Christian Hagen & Beth Ross
Loss and degradation of grasslands in the Great Plains region has resulted in major declines in abundance of grassland bird species. To ensure future viability of grassland bird populations, it is crucial to evaluate specific effects of environmental factors among species to determine drivers of population decline and develop effective conservation strategies. We used threshold models to quantify effects of land cover and weather changes on lesser and greater prairie-chickens (Tympanuchus pallidicinctus and T. cupido,...

The effects of climate change on floral anthocyanin polymorphisms

Matthew Koski & Cierra Sullivan
Pigmentation affords resistance to abiotic stressors, and thus can respond adaptively or plastically to drought and extreme temperatures associated with global change. Plants frequently display variability in flower coloration that is underlain by anthocyanin pigmentation. While anthocyanin polymorphisms impact plant-animal interactions, they also impact reproductive performance under abiotic stress. We used descriptions of population-level flower color from >1900 herbarium records representing 12 North American species spanning 124 years to test whether flower color responded to...

Diversification of a polyploid complex: the biogeography and acoustic communication evolution of North American gray treefrogs throughout the Quaternary

William Booker, Emily Lemmon, Alan Lemmon, Margaret Ptacek, Alyssa Hassinger, Johannes Schul & H. Carl Gerhardt
Polyploid speciation and whole genome duplications are major drivers of biological diversity. After polyploid species are formed, the interactions between diploid and polyploid lineages may generate additional diversity in novel cytotypes and phenotypes. In anurans, mate choice by acoustic communication is the primary method by which individuals identify their own species and assess suitable mates. As such, the evolution of acoustic signals is an important mechanism for contributing to reproductive isolation and diversification in this...

Data from: Community-level responses of African carnivores to prescribed burning

Laura Gigliotti, Goncalo Curveira-Santos, Rob Slotow, Craig Sholto-Douglas, Lourens Swanepoel & David Jachowski
Fires are common in many ecosystems worldwide, and are frequently used as a management tool. Although the responses of herbivores to fire have been well-studied, the responses of carnivores to fire remain unclear. In particular, post-fire habitat changes, and the associated changes in prey availability, might affect the coexistence or competition of carnivore species within the larger carnivore community, but few studies have focused on how fires influence multiple carnivore species simultaneously. Using South African...

Dataset for Raman enhanced four-wave mixing in silicon core fibers

Shiyu Sun, Meng Huang, Dong Wu, Li Shen, Haonan Ren, Thomas Hawkins, John Ballato, Ursula J. Gibson, Goran Mashanovich & Anna Peacock
This dataset supports the publication "Raman enhanced four-wave mixing in silicon core fibers" published in Optics Letters, including four Excel files and a Readme.txt.

Context dependency of top‐down, bottom‐up and density‐dependent influences on cheetah demography

Laura C. Gigliotti, Rob Slotow, Luke T. B. Hunter, Julien Fattebert, Craig Sholto-Douglas & David S. Jachowski
1. Research on drivers of demographic rates has mostly focused on top predators and their prey, and comparatively less research has considered the drivers of mesopredator demography. Of those limited studies, most focused on top-down effects of apex predators on mesopredator population dynamics, whereas studies investigating alternative mechanisms are less common. 2. In this study, we tested hypotheses related to top-down, bottom-up, and density-dependent regulation of demographic rates in an imperiled mesopredator, the cheetah (Acinonyx...

Data from: Genetic analyses in Lake Malawi cichlids identify new roles for Fgf signaling in scale shape variation

R. Craig Albertson, Kenta Kawasaki, Emily Tetrault & Kara Powder
Elasmoid scales are the most common epithelial appendage among vertebrates, however an understanding of the genetic mechanisms that underlie variation in scale shape is lacking. Using an F2 mapping cross between morphologically distinct cichlid species, we identified >40 QTL for scale shape at different body positions. We show that while certain regions of the genome regulate variation in multiple scales, most are specific to scales at distinct positions. This suggests a degree of regional modularity...

FishShapes v1: functionally relevant measurements of teleost shape and size on three dimensions

Samantha Price, Sarah Friedman, Katherine Corn, Olivier Larouche, Kasey Brockelsby, Anna Lee, Nick Bertrand, Mailee Danao, Megan Coyne, John Estrada, Rachel Friedman, Evan Hoeft, Mikayla Iwan, Dominique Gross, Jo Hsuan Kao, Brian Landry, Monica Linares, Carley McGlinn, Jennifer Nguyen, Allison Proffitt, Sierra Rodriguez, Maxwell Rupp, Erin Shen, Victoria Susman, Angelly Tovar … & Peter Wainwright
Teleost fishes account for 96% of all fish species and exhibit a spectacular variety of body forms. Teleost lineages range from deep-bodied to elongate (e.g. eels, needlefish), laterally compressed (e.g. ribbonfish) to globular (e.g. pufferfish) and include uniquely shaped lineages such as seahorses, flatfishes and ocean sunfishes. Adaptive body shape convergence within fishes has long been hypothesized but the nature of the relationships between fish form and ecological and environmental variables remain largely unknown at...

Data from: Prenatal acoustic programming of mitochondrial function for high temperatures in an arid-adapted bird

Eve Udino, Julia George, Matthew McKenzie, Anaïs Pessato, Ondi Crino, Katherine Buchanan & Mylene Mariette
Sound is an essential source of information in many taxa and can notably be used by embryos to program their phenotypes for postnatal environments. While underlying mechanisms are mostly unknown, there is growing evidence for the implication of mitochondria – main source of cellular energy (i.e. ATP) – in developmental programming processes. Here, we tested whether prenatal sound programs mitochondrial metabolism. In the arid-adapted zebra finch, prenatal exposure to “heat-calls” – produced by parents incubating...

SNP genotypes for healthy and CIM-affected GSDs

Leigh Anne Clark, Sarah Bell, Jacquelyn Evans, Katy Evans, Kate Tsai, Rooksana Noorai, Thomas Famula & Dolores Holle
German shepherd dogs (GSDs) are predisposed to an inherited motility disorder of the esophagus, termed congenital idiopathic megaesophagus (CIM), in which swallowing is ineffective and the esophagus is enlarged. Affected puppies are unable to properly pass food into their stomachs and consequently regurgitate their meals and show a failure to thrive, often leading to euthanasia. Here, we generated genome-wide SNP profiles for healthy and CIM-affected GSDs using the Illumina CanineHD BeadChip, containing 220,853 SNPs.

Data from: Ancestral polyploidy in seed plants and angiosperms

Yuannian Jiao, Norman J. Wickett, Ayyampalayam Saravanaraj, André S. Chanderbali, Lena Landherr, Paula E. Ralph, Lynn P. Tomsho, Yi Hu, Haiying Liang, Pamela S. Sotis, Douglas E. Soltis, Sandra W. Clifton, Scott E. Schlarbaum, Stephan C. Schuster, Hong Ma, Jim Leebens-Mack & Claude W. DePamphilis
Whole-genome duplication (WGD), or polyploidy, followed by gene loss and diploidization has long been recognized as an important evolutionary force in animals, fungi and other organisms1, 2, 3, especially plants. The success of angiosperms has been attributed, in part, to innovations associated with gene or whole-genome duplications4, 5, 6, but evidence for proposed ancient genome duplications pre-dating the divergence of monocots and eudicots remains equivocal in analyses of conserved gene order. Here we use comprehensive...

Data from: Humeral loads during swimming and walking in turtles: implications for morphological change during aquatic reinvasions

Vanessa K. Hilliard Young, Charlotte E. Wienands, Brittany P. Wilburn & Richard W. Blob
During evolutionary reinvasions of water by terrestrial vertebrates, ancestrally tubular limb bones often flatten to form flippers. Differences in skeletal loading between land and water might have facilitated such changes. In turtles, femoral shear strains are significantly lower during swimming than during walking, potentially allowing a release from loads favoring tubular shafts. However, flipper-like morphology in specialized tetrapod swimmers is most accentuated in the forelimbs. To test if the forelimbs of turtles also experience reduced...

Data from: Shared phylogeographical breaks in a Caribbean coral reef sponge and its invertebrate commensals

Melissa B. DeBiasse, Vincent P. Richards, Mahmood S. Shivji & Michael E. Hellberg
Aim: To test whether phylogeographical barriers in the brooding sponge Callyspongia vaginalis match breaks previously identified in the Caribbean. We also compared patterns of subdivision in the sponge to those of three of its commensals, the broadcast spawning brittle star Ophiothrix suensonii and the brooding amphipods Leucothoe ashleyae and L. kensleyi, and tested whether any shared breaks arose simultaneously. Location: Florida, Bahamas and the Caribbean. Methods: Subdivision of C. vaginalis populations was inferred from one...

Data from: Mycelia-derived C contributes more to nitrogen cycling than root-derived C in ectomycorrhizal alpine forests

Ziliang Zhang, Richard P. Phillips, Wenqiang Zhao, Yuanshuang Yuan, Qing Liu & Huajun Yin
1. Plant roots and their associated microbial symbionts impact carbon (C) and nutrient cycling in ecosystems, but estimates of the relative contributions of root- versus microbe-derived dynamic inputs are highly uncertain. Roots release C into soil via exudation and turnover (i.e., root-derived C), but also by allocating C to mycorrhizal fungal mycelia, which exude C and undergo turnover (i.e., mycelia-derived C). Given that the relative contributions of root- and mycelia-derived C inputs are unknown, a...

Data from: A novel, bounding gait in swimming turtles: implications for aquatic locomotor diversity

Christopher J. Mayerl & Richard W. Blob
Turtles are an iconic lineage in studies of animal locomotion, typifying the use of slow, alternating footfalls during walking. Alternating movements of contralateral limbs are also typical during swimming gaits for most freshwater turtles. Here, we report a novel gait in turtles, in which the pleurodire Emydura subglobosa swims using a bounding gait that coordinates bilateral protraction of both forelimbs with bilateral retraction of both hindlimbs. Use of this bounding gait is correlated with increased...

Data from: Mouthpart conduit sizes of fluid-feeding insects determine the ability to feed from pores

Matthew S. Lehnert, Andrew Bennett, Kristen E. Reiter, Patrick D. Gerard, Qi-Huo Wei, Miranda Byler, Huan Yan & Wah-Keat Lee
Fluid-feeding insects, such as butterflies, moths and flies (20% of all animal species), are faced with the common selection pressure of having to remove and feed on trace amounts of fluids from porous surfaces. Insects able to acquire fluids that are confined to pores during drought conditions would have an adaptive advantage and increased fitness over other individuals. Here, we performed feeding trials using solutions with magnetic nanoparticles to show that butterflies and flies have...

Data from: A genome-wide analysis of MADS-box genes in peach [Prunus persica (L.) Batsch]

Christina E. Wells, Elisa Vendramin, Sergio Jimenez Tarodo, Ignazio Verde & Douglas G. Bielenberg
BACKGROUND: MADS-box genes encode a family of eukaryotic transcription factors distinguished by the presence of a highly-conserved ~58 amino acid DNA-binding and dimerization domain (the MADS-box). The central role played by MADS-box genes in peach endodormancy regulation led us to examine this large gene family in more detail. We identified the locations and sequences of 79 MADS-box genes in peach, separated them into established subfamilies, and broadly surveyed their tissue-specific and dormancy-induced expression patterns using...

Data from: Reticulate evolution in nuclear Middle America causes discordance in the phylogeny of palm‐pitvipers (Viperidae: Bothriechis)

Andrew J. Mason, Felipe G. Grazziotin, Hussam Zaher, Alan R. Lemmon, Emily Moriarty Lemmon & Christopher L. Parkinson
Aim: A number of processes can lead to weak or conflicting phylogenetic signals, especially in geographically dynamic regions where unstable landscapes and climates promote complex evolutionary histories. The Middle American pitviper genus Bothriechis has a complex biogeographic distribution and previous phylogenetic analyses have recovered conflicting topologies based on the data type used. Here, we tested whether historic conflicts in the phylogeny were the result of reticulate evolution and whether the inferred biogeographic history of the...

Data from: White shark genome reveals ancient elasmobranch adaptations associated with wound healing and the maintenance of genome stability

Nicholas J. Marra, Michael J. Stanhope, Nathaniel K. Jue, Minghui Wang, Qi Sun, Paulina P. Bitar, Vincent P. Richards, Aleksey Komissarov, Mike Rayko, Sergey Kliver, Bryce J. Stanhope, Chuck Winkler, Stephen J. O'Brien, Agostinho Antunes, Salvador J. Jorgensen & Mahmood S. Shivji
The white shark (Carcharodon carcharias; Chondrichthyes, Elasmobranchii) is one of the most publicly recognized marine animals. Here we report the genome sequence of the white shark and comparative evolutionary genomic analyses to the chondrichthyans, whale shark (Elasmobranchii) and elephant shark (Holocephali), as well as various vertebrates. The 4.63-Gbp white shark genome contains 24,520 predicted genes, and has a repeat content of 58.5%. We provide evidence for a history of positive selection and gene-content enrichments regarding...

Divergent processes drive parallel evolution in marine and freshwater fishes

Sarah Friedman, Mike Collyer, Samantha Price & Peter Wainwright
Evolutionary comparisons between major environmental divides, such as between marine and freshwater systems, can reveal the fundamental processes governing diversification dynamics. Although processes may differ due to the different scales of their biogeographic barriers, freshwater and marine environments nevertheless offer similar opportunities for diversification in benthic, demersal, and pelagic habitats. Here, we compare the evolutionary patterns and processes shaping teleost diversity in each of these three habitats and between marine and freshwater systems. Using specimens...

Effect of soil carbon amendments in reversing the legacy effect of plant invasion

Vidya Suseela, Ziliang Zhang & Prasanta Bhowmik
1. Invasive plant species are key drivers of global environmental changes leading to the disruption of ecosystems they invade. Many invasive species engage in novel niche construction through plant-soil feedbacks facilitated by the input of secondary compounds, which help their further spread and survival. These compounds can persist in soil even after the removal of the invader thus creating a legacy effect that inhibits the return of native flora and fauna. Thus, formulating active intervention...

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  • Clemson University
  • University of California, Davis
  • University of Virginia
  • University of Georgia
  • United States Department of Agriculture
  • University of Massachusetts Amherst
  • Columbia University
  • University of California, Berkeley
  • Agricultural Research Service
  • Chinese Academy of Sciences