24 Works

Data from: Multicopy single-stranded DNA directs intestinal colonization of enteric pathogens

Johanna R. Elfenbein, Leigh A. Knodler, Ernesto S. Nakayasu, Charles Ansong, Heather M. Brewer, Lydia Bogomolnaya, L. Garry Adams, Michael McClelland, Joshua N. Adkins & Helene L. Andrews-Polymenis
Multicopy single-stranded DNAs (msDNAs) are hybrid RNA-DNA molecules encoded on retroelements called retrons and produced by the action of retron reverse transcriptases. Retrons are widespread in bacteria but the natural function of msDNA has remained elusive despite 30 years of study. The major roadblock to elucidation of the function of these unique molecules has been the lack of any identifiable phenotypes for mutants unable to make msDNA. We report that msDNA of the zoonotic pathogen...

Data from: Limitations of climate data for inferring species boundaries: insights from speckled rattlesnakes

Jesse M. Meik, Jeffrey W. Streicher, A. Michelle Lawing, Oscar Flores-Villela & Matthew K. Fujita
Phenotypes, DNA, and measures of ecological differences are widely used in species delimitation. Although rarely defined in such studies, ecological divergence is almost always approximated using multivariate climatic data associated with sets of specimens (i.e., the “climatic niche”); the justification for this approach is that species-specific climatic envelopes act as surrogates for physiological tolerances. Using identical statistical procedures, we evaluated the usefulness and validity of the climate-as-proxy assumption by comparing performance of genetic (nDNA SNPs...

Data from: Effects of mating order and male size on embryo survival in a pipefish

Ines Braga Goncalves, Kenyon B. Mobley, Ingrid Ahnesjö, Gry Sagebakken, Adam G. Jones & Charlotta Kvarnemo
In species that provide parental care, individuals should invest adaptively in their offspring in relation to the pre- and post-zygotic care provided by their partners. In the broad-nosed pipefish, Syngnathus typhle L., females transfer large, nutrient-rich eggs into the male brood pouch during mating. The male broods and nourishes the embryos for several weeks before independent juveniles emerge at parturition. Given a choice, females clearly prefer large partners. Yet, females provide protein-richer eggs when the...

Data from: Polyceraty (multi-horns) in Damara sheep maps to ovine chromosome 2

Ockert F. C. Greyvenstein, Coralie M. Reich, Este Van Marle-Koster, David G. Riley & Ben J. Hayes
Polyceraty (presence of multiple horns) is rare in modern day ungulates. Although not found in wild sheep, polyceraty does occur in a small number of domestic sheep breeds covering a wide geographical region. Damara are fat-tailed hair sheep, from the south-western region of Africa, which display polyceraty, with horn number ranging from zero to four. We conducted a genome-wide association study for horn number with 43 Damara genotyped with 606 006 SNP markers. The analysis...

Data from: Species mtDNA genetic diversity explained by infrapopulation size in a host-symbiont system

Jorge Doña, Marina Moreno-García, Charles D. Criscione, David Serrano & Roger Jovani
Understanding what shapes variation in genetic diversity among species remains a major challenge in evolutionary ecology, and it has been seldom studied in parasites and other host-symbiont systems. Here, we studied mtDNA variation in a host-symbiont non-model system: 418 individual feather mites from 17 feather mite species living on 17 different passerine bird species. We explored how a surrogate of census size, the median infrapopulation size (i.e., the median number of individual parasites per infected...

Data from: Northern Bobwhite (Colinus virginianus) mitochondrial population genomics reveals structure, divergence, and evidence for heteroplasmy

Yvette A. Halley, David L. Oldeschulte, Eric K. Bhattarai, Joshua Hill, Richard P. Metz, Charles D. Johnson, Steven M. Presley, Rebekah E. Ruzicka, Dale Rollins, Markus J. Peterson, WIlliam J. Murphy & Christopher M. Seabury
Herein, we evaluated the concordance of population inferences and conclusions resulting from the analysis of short mitochondrial fragments (i.e., partial or complete D-Loop nucleotide sequences) versus complete mitogenome sequences for 53 bobwhites representing six ecoregions across TX and OK (USA). Median joining (MJ) haplotype networks demonstrated that analyses performed using small mitochondrial fragments were insufficient for estimating the true (i.e., complete) mitogenome haplotype structure, corresponding levels of divergence, and maternal population history of our samples....

Data from: Physiological status drives metabolic rate in Mediterranean geckos infected with pentastomes

Isabel C. Caballero, Andrew J. Sakla, Jillian T. Detwiler, Marion Le Gall, Spencer T. Behmer & Charles D. Criscione
Negative effects of parasites on their hosts are well documented, but the proximate mechanisms by which parasites reduce their host’s fitness are poorly understood. For example, it has been suggested that parasites might be energetically demanding. However, a recent meta-analysis suggests that they have statistically insignificant effects on host resting metabolic rate (RMR). It is possible, though, that energetic costs associated with parasites are only manifested during and/or following periods of activity. Here, we measured...

Data from: A Flippase-mediated GAL80/GAL4 intersectional resource for dissecting appendage development in Drosophila

Brittany N. Smith, Arash M. Ghazanfari, Rudolf A. Bohm, William P. Welch, Bing Zhang & John P. Masly
Drosophila imaginal discs provide an ideal model to study processes important for cell signaling and cell specification, tissue differentiation, and cell competition during development. One challenge to understanding genetic control of cellular processes and cell interactions is the difficulty in effectively targeting a defined subset of cells in developing tissues in gene manipulation experiments. A recently developed Flippase-induced intersectional GAL80/GAL4 repression method incorporates several gene manipulation technologies in Drosophila to enable such fine-scale dissection in...

Data from: Phylogenomic evidence for ancient hybridization in the genomes of living cats (Felidae)

Gang Li, Brian W. Davis, Eduardo Eizirik & William J. Murphy
Interspecies hybridization has been recently recognized as potentially common in wild animals, but the extent to which it shapes modern genomes is still poorly understood. Distinguishing historical hybridization events from other processes leading to phylogenetic discordance among different markers requires a well-resolved species tree that considers all modes of inheritance, and overcomes systematic problems due to rapid lineage diversification by sampling large genomic character sets. Here we assessed genome-wide phylogenetic variation across a diverse mammalian...

Data from: Evolutionary consequence of a change in life cycle complexity: a link between precocious development and evolution towards female-biased sex allocation in a hermaphroditic parasite

Emily L. Kasl, Chris T. McAllister, Henry W. Robison, Matthew B. Connior, William F. Font & Charles D. Criscione
The evolutionary consequences of changes in the complex life cycles of parasites are not limited to the traits that directly affect transmission. For instance, mating systems that are altered due to precocious sexual maturation in what is typically regarded as an intermediate host may impact opportunities for outcrossing. In turn, reproductive traits may evolve to optimize sex allocation. Here we test the hypothesis that sex allocation evolved towards a more female-biased function in populations of...

Data from: Revisiting the Iberian honey bee (Apis mellifera iberiensis) contact zone: maternal and genome-wide nuclear variation provide support for secondary contact from historical refugia

M. Alice Pinto, Julio C. Chávez-Galarza, Dora Henriques, J. Spencer Johnston, Miguel Carneiro, José Rufino & John C. Patton
Dissecting diversity patterns of organisms endemic to Iberia has been truly challenging for a variety of taxa, and the Iberian honey bee is no exception. Surveys of genetic variation in the Iberian honey bee are among the most extensive for any honey bee subspecies. From these, differential and complex patterns of diversity have emerged, which have yet to be fully resolved. Here, we used a genome-wide data set of 309 neutrally tested single nucleotide polymorphisms...

Data from: Environmental gradients and the evolution of successional habitat specialization: a test case with 14 Neotropical forest sites

Susan G. Letcher, Jesse R. Lasky, Robin L. Chazdon, Natalia Norden, S. Joseph Wright, Jorge A. Meave, Eduardo A. Pérez-García, Rodrigo Muñoz, Eunice Romero-Pérez, Ana Andrade, José Luis Andrade, Patricia Balvanera, Justin M. Becknell, Tony V. Bentos, Radika Bhaskar, Frans Bongers, Vanessa Boukili, Pedro H. S. Brancalion, Ricardo G. César, Deborah A. Clark, David B. Clark, Dylan Craven, Alexander DeFrancesco, Juan M. Dupuy, Bryan Finegan … & G. Bruce Williamson
1. Successional gradients are ubiquitous in nature, yet few studies have systematically examined the evolutionary origins of taxa that specialize at different successional stages. Here we quantify successional habitat specialization in Neotropical forest trees and evaluate its evolutionary lability along a precipitation gradient. Theoretically, successional habitat specialization should be more evolutionarily conserved in wet forests than in dry forests due to more extreme microenvironmental differentiation between early and late successional stages in wet forest. 2....

Data from: Intraspecific variation among social insect colonies: persistent regional and colony-level differences in fire ant foraging behavior

Alison A. Bockoven, Shawn M. Wilder & Micky D. Eubanks
Individuals vary within a species in many ecologically important ways, but the causes and consequences of such variation are often poorly understood. Foraging behavior is among the most profitable and risky activities in which organisms engage and is expected to be under strong selection. Among social insects there is evidence that within-colony variation in traits such as foraging behavior can increase colony fitness, but variation between colonies and the potential consequences of such variation are...

Data from: Metabolic rate is canalized in the face of variable life history and nutritional environment

Rebecca M. Clark, Anthony J. Zera & Spencer T. Behmer
Despite its central importance in organismal physiology, we have poor understanding of how metabolic rate is influenced by two key factors – food nutritional content and an organism's physiological characteristics. We examined how variation in nutrients and physiological aspects of life history affect standard metabolic rate in Gryllus firmus cricket morphs that differ dramatically in flight capability and early-age fecundity. Newly moulted female morphs were fed one of 13 diets that differed in concentrations of...

Data from: Inclusive fitness and differential productivity across the life course determine intergenerational transfers in a small-scale human society

Paul L. Hooper, Michael Gurven, Jeffrey Winking & Hillard S. Kaplan
Transfers of resources between generations are an essential element in current models of human life-history evolution accounting for prolonged development, extended lifespan and menopause. Integrating these models with Hamilton's theory of inclusive fitness, we predict that the interaction of biological kinship with the age-schedule of resource production should be a key driver of intergenerational transfers. In the empirical case of Tsimane’ forager–horticulturalists in Bolivian Amazonia, we provide a detailed characterization of net transfers of food...

Data from: The effects of food limitation on life history tradeoffs in pregnant male Gulf pipefish

Kimberly A. Paczolt & Adam G. Jones
Syngnathid fishes (pipefishes, seahorses and seadragons) are characterized by a unique mode of paternal care in which embryos develop on or in the male’s body, often within a structure known as a brood pouch. Evidence suggests that this pouch plays a role in mediating postcopulatory sexual selection and that males have some control over the events occurring within the pouch during the pregnancy. These observations lead to the prediction that males should invest differently in...

Data from: Challenging the inbreeding hypothesis in a eusocial mammal: population genetics of the naked mole-rat, Heterocephalus glaber.

Colleen M. Ingram, Nicholas J. Troendle, Clare A. Gill, Stanton Braude & Rodney L. Honeycutt
The role of genetic relatedness in the evolution of eusociality has been the topic of much debate, especially when contrasting eusocial insects with vertebrates displaying reproductive altruism. The naked mole-rat, Heterocephalus glaber, was the first described eusocial mammal. Although this discovery was based on an ecological constraints model of eusocial evolution, early genetic studies reported high levels of relatedness in naked mole-rats, providing a compelling argument that low dispersal rates and consanguineous mating (inbreeding as...

Data from: Description of a soft-bodied invertebrate with microcomputed tomography and revision of the genus Chtonobdella (Hirudinea: Haemadipsidae)

Michael Tessler, Amalie Barrio, Elizabeth Borda, Rebecca Rood-Goldman, Morgan Hill & Mark E. Siddall
Two-jawed (duognathous) terrestrial leeches in the Haemadipsidae are major pests across their wide geographic range, represented by numerous endemic species in Australia and across many islands in the Indian and Pacific Oceans. However, haemadipsid taxonomy, based largely on externally visible characters, remains in conflict with phylogenetic relationships. We capitalize on the power of microcomputed tomography (μCT), allowing for the first description of an extant soft-bodied species – Chtonobdella tanae sp. n. – using this technology....

Data from: Naturally occurring variation in tadpole morphology and performance linked to predator regime

James B. Johnson, Daniel Saenz, Cory K. Adams & Toby J. Hibbitts
Divergent natural selection drives a considerable amount of the phenotypic and genetic variation observed in natural populations. For example, variation in the predator community can generate conflicting selection on behavioral, life-history, morphological, and performance traits. Differences in predator regime can subsequently increase phenotypic and genetic variations in the population and result in the evolution of reproductive barriers (ecological speciation) or phenotypic plasticity. We evaluated morphology and swimming performance in field collected Bronze Frog larvae (Lithobates...

Data from: Spatial averaging and disturbance lead to high productivity in aquatic metacommunities

Evangelia Smeti, Daniel L. Roelke & Sofie Spatharis
Dispersal in heterogeneous ecosystems, such as coastal metacommunities, is a major driver of diversity and productivity. According to theory, both species richness and spatial averaging shape a unimodal relationship of productivity with dispersal. We experimentally tested the hypothesis that disturbances acting on local patches would buffer the loss of productivity at high dispersal by preventing synchronized species oscillations. To simulate these disturbances, our experimental assemblages involved species that self-organized in isolation under three inflow pulsing...

Data from: Synthesis of phylogeny and taxonomy into a comprehensive tree of life

Cody E. Hinchliff, Stephen A. Smith, James F. Allman, J. Gordon Burleigh, Ruchi Chaudhary, Lyndon M. Coghill, Keith A. Crandall, Jiabin Deng, Bryan T. Drew, Romina Gazis, Karl Gude, David S. Hibbett, Laura A. Katz, , Emily Jane McTavish, Peter E. Midford, Christopher L. Owen, Richard H. Ree, Jonathan A. Rees, Douglas E. Soltis, Tiffani Williams & Karen Ann Cranston
Reconstructing the phylogenetic relationships that unite all lineages (the tree of life) is a grand challenge. The paucity of homologous character data across disparately related lineages currently renders direct phylogenetic inference untenable. To reconstruct a comprehensive tree of life, we therefore synthesized published phylogenies, together with taxonomic classifications for taxa never incorporated into a phylogeny. We present a draft tree containing 2.3 million tips—the Open Tree of Life. Realization of this tree required the assembly...

Data from: Open-ocean fish reveal an omnidirectional solution to camouflage in polarized environments

Parrish C. Brady, Alexander A. Gilerson, George W. Kattawar, James M. Sullivan, Michael S. Twardowski, Heidi M. Dierssen, Meng Gao, Kort Travis, Robert I. Etheredge, Alberto Tonizzo, Amir Ibrahim, Carlos Carrizo, Yalong Gu, Brandon J. Russell, Kathryn Mislinski, Shulei Zhao & Molly E. Cummings
Despite appearing featureless to our eyes, the open ocean is a highly variable environment for polarization-sensitive viewers. Dynamic visual backgrounds coupled with predator encounters from all possible directions make this habitat one of the most challenging for camouflage. We tested open-ocean crypsis in nature by collecting more than 1500 videopolarimetry measurements from live fish from distinct habitats under a variety of viewing conditions. Open-ocean fish species exhibited camouflage that was superior to that of both...

Data from: Genome-wide analysis of alternative splicing landscapes modulated during plant-virus interactions in Brachypodium distachyon

Kranthi K. Mandadi & Karen-Beth G. Scholthof
In eukaryotes, alternative splicing (AS) promotes transcriptome and proteome diversity. The extent of genome-wide AS changes occurring during a plant-microbe interaction is largely unknown. Here, using high-throughput, paired-end RNA sequencing, we generated an isoform-level spliceome map of Brachypodium distachyon infected with Panicum mosaic virus and its satellite virus. Overall, we detected ∼44,443 transcripts in B. distachyon, ∼30% more than those annotated in the reference genome. Expression of ∼28,900 transcripts was ≥2 fragments per kilobase of...

Data from: Exploring origins, invasion history and genetic diversity of Imperata cylindrica (L.) P. Beauv. (Cogongrass) in the United States using genotyping by sequencing

A. Millie Burrell, Alan E. Pepper, George Hodnett, John A. Goolsby, William A. Overholt, Alexis E. Racelis, Rodrigo Diaz & Patricia E. Klein
Imperata cylindrica (Cogongrass, Speargrass) is a diploid C4 grass that is a noxious weed in 73 countries and constitutes a significant threat to global biodiversity and sustainable agriculture. We used a cost-effective genotyping-by-sequencing (GBS) approach to identify the reproductive system, genetic diversity and geographic origins of invasions in the south-eastern United States. In this work, we demonstrated the advantage of employing the closely related, fully sequenced crop species Sorghum bicolor (L.) Moench as a proxy...

Registration Year

  • 2015

Resource Types

  • Dataset


  • Texas A&M University
  • National Autonomous University of Mexico
  • University of Connecticut
  • University of Florida
  • University of Missouri
  • American Museum of Natural History
  • University of Kansas
  • City University of New York
  • Estación Biológica de Doñana
  • Museo de Historia Natural Noel Kempff Mercado