128 Works

Data from: Phylogenomic analysis of transcriptome data elucidates co-occurrence of a paleopolyploid event and the origin of bimodal karyotypes in Agavoideae (Asparagaceae)

Michael R. McKain, Norman Wickett, Yeting Zhang, Saravanaraj Ayyampalayam, W. Richard McCombie, Mark W. Chase, J. Chris Pires, Claude W. DePamphilis, Jim Leebens-Mack & Claude W. De Pamphilis
PREMISE OF THE STUDY: The stability of the bimodal karyotype found in Agave and closely related species has long interested botanists. The origin of the bimodal karyotype has been attributed to allopolyploidy, but this hypothesis has not been tested. Next Generation transcriptome sequence data were used to test whether a paleopolyploid event occurred on the same branch of the Agavoideae phylogenetic tree as the origin of the Yucca-Agave bimodal karyotype. METHODS: Illumina RNAseq data were...

Data from: Functional attributes of savannah soils: contrasting effects of tree canopies and herbivores on bulk density, nutrients and moisture dynamics

Ricardo M. Holdo & Michelle C. Mack
1. Savannahs are highly heterogeneous tree-grass mixtures, and the structural variation imposed by a discontinuous canopy cover results in spatial variation in soil properties such as plant-available nutrients, temperature and soil moisture. Many savannahs are also dominated by large vertebrate herbivores, which impose a different suite of effects on soil properties related to consumption, excretion and physical disturbance. 2. In nutrient-poor, water-limited systems, variation in soil resource availability may play a fundamental role in structuring...

Data from: Effects of removing woody cover on long‐term population dynamics of a rare annual plant (Agalinis auriculata): a study comparing remnant prairie and oldfield habitats

Helen M. Alexander, Cathy D. Collins, Aaron W. Reed, W. Dean Kettle, Daniel A. Collis, Lucy D. Christiana & Vaughn B. Salisbury
1. Worldwide, grasslands are becoming shrublands/forests. In North America, eastern red cedar (Juniperus virginiana) often colonizes prairies. Habitat management can focus on woody removal, but we often lack long-term data on whether removal leads to population recovery of herbaceous plants without seeding. 2. We undertook a long-term study (17 years) of numbers of the rare annual plant Agalinis auriculata in a gridwork of 100 m2 plots in adjacent prairie and oldfield sites in Kansas, USA....

Data from: Independent evolution of ancestral and novel defenses in a genus of toxic plants (Erysimum, Brassicaceae)

Tobias Züst, Susan Strickler, Adrian Powell, Makenzie Mabry, Hong An, Mahdieh Mirzaei, Thomas York, Cynthia Holland, Pavan Kumar, Matthias Erb, Georg Petschenka, José-María Gomez, Francisco Perfectti, Caroline Mueller, Chris Pires, Lukas Mueller & Georg Jander
Phytochemical diversity is thought to result from coevolutionary cycles as specialization in herbivores imposes diversifying selection on plant chemical defenses. Plants in the speciose genus Erysimum (Brassicaceae) produce both ancestral glucosinolates and evolutionarily novel cardenolides as defenses. Here we test macroevolutionary hypotheses on co-expression, co-regulation, and diversification of these potentially redundant defenses across this genus. We sequenced and assembled the genome of E. cheiranthoides and foliar transcriptomes of 47 additional Erysimum species to construct a...

Intraspecific genetic variation underlying postmating reproductive barriers between species in the wild tomato clade (Solanum sect. Lycopersicon)

Cathleen Jewell, Simo Zhang, Matthew Gibson, Alejandro Tovar-Mendez, Bruce McClure & Leonie Moyle
A goal of speciation genetics is to understand how the genetic components underlying interspecific reproductive barriers originate within species. Unilateral incompatibility (UI) is a postmating prezygotic barrier in which pollen rejection in the female reproductive tract (style) occurs in only one direction of an interspecific cross. Natural variation in the strength of UI has been observed among populations within species in the wild tomato clade. In some cases, molecular loci underlying self-incompatibility (SI) are associated...

Data from: The evolution of morphological diversity in continental assemblages of Passerine birds

Knud Andreas Jønsson, Jean Philippe Lessard, Robert E. Ricklefs & Jean-Philippe Lessard
Understanding geographic variation in the species richness and lineage composition of regional biotas is a long standing goal in ecology. Why do some evolutionary lineages proliferate while others do not, and how do new colonists fit into an established fauna? Here, we analyse the morphological structure of assemblages of passerine birds in four biogeographic regions to examine the relative influence of colonization history and niche-based processes on regional communities of passerine birds. Using morphological traits...

RAMP data subset, January 1 through May 31, 2019

Jonathan Wheeler, Kenning Arlitsch, Minh Pham, Nikolaus Parulian, Patrick OBrien & Jeff Mixter
The data are a subset of data from RAMP, the Repository Analytics and Metrics Portal (http://ramp.montana.edu/), consisting of data from 35 (out of 50) participating institutional repositories (IR) from the period of January 1 through May 31, 2019. This subset represents data analyzed for a pending publication. For a description of the data collection, processing, and output methods, please see the "methods" section below. The 'RAMP Primer,' a Jupyter Notebook consisting of Python code for...

Data from: Do artificial nectar feeders affect bat–plant interactions in an Ecuadorian cloud forest?

Rossana Maguiña & Nathan Muchhala
Plant–pollinator interactions are critical to ecosystems. However, when artificial nectar feeders are available in an area, they could draw pollinators away from plants. We tested the effects of artificial nectar feeders in an Ecuadorian cloud forest on four aspects of bat–plant interactions: (1) bat relative abundance; (2) bat pollen loads; (3) flower visitation rates, and (4) breeding success of a bat-pollinated species (Burmeistera glabrata). We divided the study site into areas close to (~30 m)...

Data from: Top predators and habitat complexity alter an intraguild predation module in pond communities

Thomas L. Anderson & Raymond D. Semlitsch
Predator diversity and habitat complexity frequently influence species interactions at lower trophic levels, yet their joint investigation has been performed infrequently despite the demonstrated importance of each individual factor. We investigated how different top predators and varying habitat complexity influence the function of an intraguild predation module consisting of two larval salamanders, intraguild predator Ambystoma annulatum and intraguild prey A. maculatum. We manipulated predator food webs and habitat complexity in outdoor mesocosms. Top predators significantly...

Data from: Homing of invasive Burmese pythons in South Florida: evidence for map and compass senses in snakes

Shannon E. Pittman, Kristen M. Hart, Michael S. Cherkiss, Ray W. Snow, Ikuko Fujisaki, Brian J. Smith, Frank J. Mazzotti & Michael E. Dorcas
Navigational ability is a critical component of an animal's spatial ecology and may influence the invasive potential of species. Burmese pythons (Python molurus bivittatus) are apex predators invasive to South Florida. We tracked the movements of 12 adult Burmese pythons in Everglades National Park, six of which were translocated 21–36 km from their capture locations. Translocated snakes oriented movement homeward relative to the capture location, and five of six snakes returned to within 5 km...

Data from: How much of the world is woody?

Richard G. FitzJohn, Matt W. Pennell, Amy E. Zanne, Peter F. Stevens, David C. Tank, William K. Cornwell & Matthew W. Pennell
1.The question posed by the title of this paper is a basic one, and it is surprising that the answer is not known. Recently assembled trait datasets provide an opportunity to address this, but scaling these datasets to the global scale is challenging because of sampling bias. Although we currently know the growth form of tens of thousands of species, these data are not a random sample of global diversity; some clades are exhaustively characterised,...

Data from: Joint histology in Alligator mississippiensis challenges the identification of synovial joints in fossil archosaurs and inferences of cranial kinesis

Alida M. Bailleul & Casey M. Holliday
Archosaurs, like all vertebrates, have different types of joints that allow or restrict cranial kinesis, such as synovial joints and fibrous joints. In general, synovial joints are more kinetic than fibrous joints, because the former possess a fluid-filled cavity and articular cartilage that facilitate movement. Even though there is a considerable lack of data on the microstructure and the structure–function relationships in the joints of extant archosaurs, many functional inferences of cranial kinesis in fossil...

Data from: Phylogeographic analyses of American black bears (Ursus americanus) suggest four glacial refugia and complex patterns of post-glacial admixture

Emily E. Puckett, Paul D. Etter, Eric A. Johnson & Lori S. Eggert
Studies of species with continental distributions continue to identify intraspecific lineages despite continuous habitat. Lineages may form due to isolation by distance, adaptation, divergence across barriers, or genetic drift following range expansion. We investigated lineage diversification and admixture within American black bears (Ursus americanus) across their range using 22 k single nucleotide polymorphisms and mitochondrial DNA sequences. We identified three subcontinental nuclear clusters which we further divided into nine geographic regions: Alaskan (Alaska-East), eastern (Central...

Data from: How shrub encroachment under climate change could threaten pollination services for alpine wildflowers: a case study using the alpine skypilot, Polemonium viscosum

Jessica A. Kettenbach, Nicole Miller-Struttmann, Zoë Moffett & Candace Galen
Under climate change, shrubs encroaching into high altitude plant communities disrupt ecosystem processes. Yet effects of encroachment on pollination mutualisms are poorly understood. Here, we probe potential fitness impacts of interference from encroaching Salix (willows) on pollination quality of the alpine skypilot, Polemonium viscosum. Overlap in flowering time of Salix and Polemonium is a precondition for interference and was surveyed in four extant and 25 historic contact zones. Pollinator sharing was ascertained from observations of...

Data from: Day/night upper thermal limits differ within Ectatomma ruidum ant colonies

Annika S. Nelson, Trey Scott, Maciej Barczyk, Terrence P. McGlynn, Arian Avalos, Elizabeth Clifton, Amlan Das, Andreia Figueiredo, Laura L. Figueroa, Mark Janowiecki, Sarah Pahlke, Jignasha D. Rana & Sean O'Donnell
In the tropics, daily temperature fluctuations can pose physiological challenges for ectothermic organisms, and upper thermal limits may affect foraging activity over the course of the day. Variation in upper thermal limits can occur among and within species, and for social insects such as ants, within colonies. Within colonies, upper thermal limits may differ among individuals or change for an individual throughout the day. Daytime foragers of the Neotropical ant Ectatomma ruidum have higher critical...

Data from: Retrotransposon proliferation coincident with the evolution of dioecy in asparagus

Alex Harkess, Francesco Mercati, Loredana Abbate, Michael McKain, J. Chris Pires, Tea Sala, Francesco Sunseri, Agostino Falavigna & Jim Leebens-Mack
Current phylogenetic sampling reveals that dioecy and an XY sex chromosome pair evolved once or possibly twice in the genus Asparagus. Although there appear to be some lineage-specific polyploidization events, the base chromosome number of 2n=2x=20 is relatively conserved across the Asparagus genus. Regardless, dioecious species tend to have larger genomes than hermaphroditic species. Here we test whether this genome size expansion in dioecious species is related to a polyploidization and subsequent chromosome fusion or...

RNA-sequencing of endometrial explants

Sandra Recuero, José María Sánchez, Sandra Bagés-Arnal, Michael McDonald, Susanta K. Behura, Thomas E. Spencer, Marc Yeste, Pat Lonergan & Beatriz Fernandez-Fuertes
Seminal plasma (SP) has been shown to modulate the female reproductive environment in mammalian species in which the ejaculate comes into direct contact with the endometrium, such as mice, pigs and horses. In contrast, cattle ejaculate in the vagina, and it is questionable whether the fluid portion reaches the uterus. A recent study from our group reported that mating to intact, but not vasectomised, bulls modifies the endometrium transcriptome. However, it is not clear whether...

Desulfovibrio vulgaris Hildenborough Genetic Constructs

Judy Wall, Grant Zane, Thomas Juba, Jennifer Kuehl, Jayashree Ray, Swapnil Chhabra, Valentine Trotter, Maxim Shatsky, Kara De Leon, Kimberly Keller, Kelly Bender, Gareth Butland, Adam Arkin & Adam Deutschbauer
The dissimilatory sulfate-reducing Deltaproteobacterium, Desulfovibrio vulgaris Hildenborough (ATCC 29579), was chosen by the LBNL-led research collaboration ENIGMA to explore tools and protocols for bringing this anaerobe to model status. Here we describe a collection of genetic constructs generated by ENIGMA, which are available to the research community.

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...

Adaptation without specialization early in a host shift: fecundity data

Rafael Rodriguez, Thomas Wood, Frank Stearns, Robert Snyder, Kelley Tilmon, Michael Cast, Randy Hunt & Reginald Cocroft
Students of speciation debate the role of performance trade-offs across different environments early in speciation. We tested for early performance trade-offs with a host shift experiment using a member of the Enchenopa binotata species complex of treehoppers (Hemiptera: Membracidae). In this clade of plant-feeding insects, different species live on different host plants and exhibit strong behavioral and physiological host specialization. After five generations, the experimental host shifts resulted either in no adaptation or in adaptation...

Data from: The genome sequence and insights into the immunogenetics of the bananaquit (Passeriformes: Coereba flaveola)

Jennifer Antonides, Robert Ricklefs & J.A. DeWoody
Avian genomics, especially of non-model species, is in its infancy relative to mammalian genomics. Here, we describe the sequencing, assembly, and annotation of a new avian genome, that of the bananaquit Coereba flaveola (Passeriformes: Thraupidae). We produced ∼30-fold coverage of the genome with an assembly size of ca. 1.2 Gb, including approximately 16,500 annotated genes. Passerine birds, such as the bananaquit, are commonly infected by avian malarial parasites (Haemosporida), which presumably drive adaptive evolution of...

Data from: Does hunting or hiking affect wildlife communities in protected areas?

Roland Kays, Arielle W. Parsons, Megan C. Baker, Ellizabeth L. Kalies, Tavis Forrester, Robert Costello, Christopher T. Rota, Joshua J. Millspaugh & William J. McShea
Managed public wild areas have dual mandates to protect biodiversity and provide recreational opportunities for people. These goals could be at odds if recreation, ranging from hiking to legal hunting, disrupts wildlife enough to alter their space use or community structure. We evaluated the effect of managed hunting and recreation on 12 terrestrial wildlife species by employing a large citizen science camera trapping survey at 1947 sites stratified across different levels of human activities in...

Data from: Influence of preexisting preference for color on sampling and tracking behavior in bumble bees

Gyanpriya Maharaj, Patricia Panzica, Marisa Yoder, Aimee S. Dunlap & Patricia Horack
Animals reduce uncertainty in their lifetime by using information to guide decision making. Information available can be inherited from the past or gathered from the present. Therefore, animals must balance inherited biases with new information that may be in conflict with those potential biases. In our study, we set up color pairings such that an arbitrarily chosen focal color, human-orange, would result in an inherent bias in comparison to three other colors tested resulting in...

Data from: Taxonomic composition and body-mass distribution in the terminal Pleistocene mammalian fauna from the Marmes site, southeastern Washington state, U.S.A.

R. Lee Lyman
Mean adult body mass of mammal taxa is a fundamental ecological variable. Variability in the distributions of body masses of a mammal fauna suggest variability in habitat structure. Mammal remains from the Marmes archaeological site in southeastern Washington State date between 13,200 and 10,400 b.p., during the Pleistocene–Holocene transition (PHT). Known environmental history prompts the expectations that the Marmes PHT mammal remains should represent greater species richness and a larger array of body-mass sizes than...

Data from: Taphonomy of the Ediacaran fossil Pteridinium simplex preserved three-dimensionally in mass flow deposits, Nama Group, Namibia

Michael Meyer, David Elliott, James Schiffbauer, Patricia Vickers-Rich, Michael Hall, Karl Hoffman, Gabi Schneider, Shuhai Xiao, James D. Schiffbauer & Mike Meyer
Ediacara-type fossils are found in a diverse array of preservational styles, implying that multiple taphonomic mechanisms might have been responsible for their preservational expression. For many Ediacara fossils, the “death mask” model has been invoked as the primary taphonomic pathway. The key to this preservational regime is the replication or sealing of sediments around the degrading organisms by microbially induced precipitation of authigenic pyrite, leading toward fossil preservation along bedding planes. Nama-style preservation, on the...

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