28 Works

Data from: Bayesian estimation of the global biogeographical history of the Solanaceae

Julia Dupin, Nicholas J. Matzke, Tiina Särkinen, Sandra Knapp, Richard G. Olmstead, Lynn Bohs & Stacey D. Smith
Aim: The tomato family Solanaceae is distributed on all major continents except Antarctica and has its centre of diversity in South America. Its worldwide distribution suggests multiple long-distance dispersals within and between the New and Old Worlds. Here, we apply maximum likelihood (ML) methods and newly developed biogeographical stochastic mapping (BSM) to infer the ancestral range of the family and to estimate the frequency of dispersal and vicariance events resulting in its present-day distribution. Location:...

Data from: The evolutionary relationships and age of Homo naledi: an assessment using dated Bayesian phylogenetic methods

Mana Dembo, Davorka Radovčić, Heather M. Garvin, Myra F. Laird, Lauren Schroeder, Jill E. Scott, Juliet Brophy, Rebecca R. Ackermann, Charles M. Musiba, Darryl J. De Ruiter, Arne Ø. Mooers, Mark Collard & Chares M. Musiba
Homo naledi is a recently discovered species of fossil hominin from South Africa. A considerable amount is already known about H. naledi but some important questions remain unanswered. Here we report a study that addressed two of them: “Where does H. naledi fit in the hominin evolutionary tree?” and “How old is it?” We used a large supermatrix of craniodental characters for both early and late hominin species and Bayesian phylogenetic techniques to carry out...

Data from: Treating cattle with antibiotics affects greenhouse gas emissions, and microbiota in dung and dung beetles

Tobin J. Hammer, Noah Fierer, Bess Hardwick, Asko Simojoki, Eleanor Slade, Juhani Taponen, Heidi Viljanen & Tomas Roslin
Antibiotics are routinely used to improve livestock health and growth. However, this practice may have unintended environmental impacts mediated by interactions among the wide range of micro- and macroorganisms found in agroecosystems. For example, antibiotics may alter microbial emissions of greenhouse gases by affecting livestock gut microbiota. Furthermore, antibiotics may affect the microbiota of non-target animals that rely on dung, such as dung beetles, and the ecosystem services they provide. To examine these interactions, we...

Data from: Effects of sea ice cover on satellite-detected primary production in the Arctic Ocean

Mati Kahru, Zhongping Lee, Brian Greg Mitchell & Cynthia D. Nevison
The influence of decreasing Arctic sea ice on net primary production (NPP) in the Arctic Ocean has been considered in multiple publications but is not well constrained owing to the potentially large errors in satellite algorithms. In particular, the Arctic Ocean is rich in coloured dissolved organic matter (CDOM) that interferes in the detection of chlorophyll a concentration of the standard algorithm, which is the primary input to NPP models. We used the quasi-analytic algorithm...

Data from: Phenotypic differentiation is associated with divergent sexual selection among closely related barn swallow populations

Matthew R. Wilkins, Hakan Karaardıç, Yoni Vortman, Thomas L. Parchman, Tomáš Albrecht, Adéla Petrželková, Leyla Özkan, Peter L. Pap, Joanna K. Hubbard, Amanda K. Hund & Rebecca J. Safran
Sexual selection plays a key role in the diversification of numerous animal clades and may accelerate trait divergence during speciation. However, much of our understanding of this process comes from phylogenetic comparative studies, which rely on surrogate measures such as dimorphism that may not represent selection in wild populations. In this study, we assess sexual selection pressures for multiple male visual signals across four barn swallow (Hirundo rustica) populations. Our sample encompassed 2400 linear km...

Data from: Herbivory mediates the long-term shifts in the relative importance of microsite and propagule limitation

Anu Eskelinen, Patrick Saccone, Marko J. Spasojevic & Risto Virtanen
Microsite and propagule limitation are predicted to jointly influence plant community assembly and diversity, with shifts in their relative contributions under different ecological conditions. Mammalian herbivory can also exhibit strong impact on community assembly and diversity. However, to date few studies have considered how herbivory might interact with propagule and microsite limitation and how herbivory might alter their relative importance. Even fewer studies have examined how these processes manifest over time to influence community assembly....

Data from: Lambda interferon restructures the nasal microbiome and increases susceptibility to Staphylococcus aureus superinfection

Paul J. Planet, Dane Parker, Taylor S. Cohen, Hannah Smith, Justinne D. Leon, Chanelle Ryan, Tobin J. Hammer, Noah Fierer, Emily I. Chen & Alice S. Prince
Much of the morbidity and mortality associated with influenza virus respiratory infection is due to bacterial coinfection with pathogens that colonize the upper respiratory tract such as methicillin-resistant Staphylococcus aureus (MRSA) and Streptococcus pneumoniae. A major component of the immune response to influenza virus is the production of type I and III interferons. Here we show that the immune response to infection with influenza virus causes an increase and restructuring of the upper respiratory microbiota...

Data from: A comparative assessment of SNP and microsatellite markers for assigning parentage in a socially monogamous bird

Sara Kaiser, Scott A. Taylor, Nancy Chen, Scott Sillett, Eliana R. Bondra, Michael Webster, Sara A. Kaiser & T. Scott Sillett
Single-nucleotide polymorphisms (SNPs) are preferred over microsatellite markers in many evolutionary studies, but have only recently been applied to studies of parentage. Evaluations of SNPs and microsatellites for assigning parentage have mostly focused on special cases that require a relatively large number of heterozygous loci, such as species with low genetic diversity or with complex social structures. We developed 120 SNP markers from a transcriptome assembled using RNA-sequencing of a songbird with the most common...

Data from: Commensal associations and benthic habitats shape macroevolution of the bivalve clade Galeommatoidea

Jingchun Li, Diarmaid Ó Foighil & Ellen E. Strong
The great diversity of marine life has been shaped by the interplay between abiotic and biotic factors. Among different biotic interactions, symbiosis is an important yet less studied phenomenon. Here, we tested how symbiotic associations affected marine diversification, using the bivalve superfamily Galeommatoidea as a study system. This superfamily contains large numbers of obligate commensal as well as free-living species and is therefore amenable to comparative approaches. We constructed a global molecular phylogeny of Galeommatoidea...

Data from: Evaluating shell variation across different populations of a freshwater snail

Daniela Vergara, Jesualdo A. Fuentes, Kayla S. Stoy & Curtis M. Lively
The freshwater snail Potamopyrgus antipodarum has become a model system for studying invasion ecology, host–parasite coevolution, the maintenance of sexual reproduction and ecotoxicology. One understudied aspect of this snail is the variation in morphology within and among populations, which could provide insights into ecological differences across its native range. In this study of 17 New Zealand lake populations of P. antipodarum we used linear measurements and geometric morphometrics to compare several aspects of shell size...

Data from: Plumage genes and little else distinguish the genomes of hybridizing warblers

David P. L. Toews, Scott A. Taylor, Rachel Vallender, Alan Brelsford, Bronwyn G. Butcher, Philipp W. Messer & Irby J. Lovette
When related taxa hybridize extensively, their genomes may become increasingly homogenized over time. This mixing via hybridization creates conservation challenges when it reduces genetic or phenotypic diversity and when it endangers previously distinct species via genetic swamping [ 1 ]. However, hybridization also facilitates admixture mapping of traits that distinguish each species and the associated genes that maintain distinctiveness despite ongoing gene flow [ 2 ]. We address these dual aspects of hybridization in the...

Data from: Continental-scale patterns reveal potential for warming-induced shifts in cattle diet

Joseph M. Craine, Jay P. Angerer, Andrew Elmore & Noah Fierer
In North America, it has been shown that cattle in warmer, drier grasslands have lower quality diets than those cattle grazing cooler, wetter grasslands, which suggests warming will increase nutritional stress and reduce weight gain. Yet, little is known about how the plant species that comprise cattle diets change across these gradients and whether these shifts in dietary quality coincide with shifts in dietary composition, i.e. the relative abundance of different plant species consumed by...

Data from: Partitioning the effects of isolation by distance, environment, and physical barriers on genomic divergence between parapatric threespine stickleback

Jesse N. Weber, Gideon S. Bradburd, Yoel E. Stuart, William E. Stutz & Daniel I. Bolnick
Genetic divergence between populations is shaped by a combination of drift, migration, and selection, yielding patterns of isolation-by-distance (IBD) and isolation-by-environment (IBE). Unfortunately, IBD and IBE may be confounded when comparing divergence across habitat boundaries. For instance, parapatric lake and stream threespine stickleback (Gasterosteus aculeatus) may have diverged due to selection against migrants (IBE), or mere spatial separation (IBD). To quantitatively partition the strength of IBE and IBD, we used recently-developed population genetic software (BEDASSLE)...

Data from: Sound settlement: noise surpasses land cover in explaining breeding habitat selection of secondary cavity-nesting birds

Nathan J. Kleist, Robert P. Guralnick, Alexander Cruz & Clinton D. Francis
Birds breeding in heterogeneous landscapes select nest sites by cueing in on a variety of factors from landscape features and social information to the presence of natural enemies. We focus on determining the relative impact of anthropogenic noise on nest site occupancy, compared to amount of forest cover, which is known to strongly influence the selection process. We examine chronic, industrial noise from natural gas wells directly measured at the nest box as well as...

Data from: Diversification of R2R3-MYB transcription factors in the tomato family Solanaceae

Daniel J. Gates, Susan R. Strickler, Lukas A. Mueller, Bradley J. S. C. Olson & Stacey D. Smith
MYB transcription factors play an important role in regulating key plant developmental processes involving defense, cell shape, pigmentation, and root formation. Within this gene family, sequences containing an R2R3 MYB domain are the most abundant type and exhibit a wide diversity of functions. In this study, we identify 559 R2R3 MYB genes using whole genome data from four species of Solanaceae and reconstruct their evolutionary relationships. We compare the Solanaceae R2R3 MYBs to the well-characterized...

Data from: Stress response, gut microbial diversity, and sexual signals correlate with social interactions

Iris I. Levin, David M. Zonana, Bailey K. Fosdick, Se Jin Song, Rob Knight & Rebecca J. Safran
Theory predicts that social interactions are dynamically linked to phenotype. Yet because social interactions are difficult to quantify, little is known about the precise details on how interactivity is linked to phenotype. Here, we deployed proximity loggers on North American barn swallows (Hirundo rustica erythrogaster) to examine intercorrelations among social interactions, morphology and features of the phenotype that are sensitive to the social context: stress-induced corticosterone (CORT) and gut microbial diversity. We analysed relationships at...

Data from: The same picture through different lenses: quantifying the effects of two preservation pathways on Green River Formation insects

Evan P. Anderson & Dena M. Smith
Insects in the fossil record are generally preserved in lacustrine shales or in amber. For those in lacustrine shales, preservation is usually via keroginization or mineralization. Given the extended period of microbial decay required to generate ions for mineralization, there is a predicted inherent bias toward lower preservation quality for this pathway by most taphonomic indices compared with keroginization. This study tests this hypothesis by comparing multiple measures of preservation quality between sites with similar...

Data from: Edaphic properties enable facilitative and competitive interactions resulting in fairy circle formation

Michael D. Cramer, Nichole N. Barger & Walter R. Tschinkel
Millions of generally regularly spaced, roughly circular barren patches called fairy circles occur in a narrow band ca. 100 km inland of the south-west African coast. These generally have conspicuously taller peripheral grasses in a shorter grass matrix. The origins of these fairy circles are controversial, but one possibility is that they are self-organizing emergent vegetation patterns that are the consequence of interplay between positive (facilitative) and negative (competitive) interactions between grasses. We hypothesized that...

Data from: Landscape genetic approaches to guide native plant restoration in the Mojave Desert

Daniel F. Shryock, Caroline A. Havrilla, Lesley A. DeFalco, Todd C. Esque, Nathan A. Custer & Troy E. Wood
Restoring dryland ecosystems is a global challenge due to synergistic drivers of disturbance coupled with unpredictable environmental conditions. Dryland plant species have evolved complex life-history strategies to cope with fluctuating resources and climatic extremes. Although rarely quantified, local adaptation is likely widespread among these species and potentially influences restoration outcomes. The common practice of reintroducing propagules to restore dryland ecosystems, often across large spatial scales, compels evaluation of adaptive divergence within these species. Such evaluations...

Data from: Parasite infection alters nitrogen cycling at the ecosystem scale

John Mischler, Pieter T. J. Johnson, Valerie J. McKenzie & Alan R. Townsend
Despite growing evidence that parasites often alter nutrient flows through their hosts and can comprise a substantial amount of biomass in many systems, whether endemic parasites influence ecosystem nutrient cycling, and which nutrient pathways may be important, remains conjectural. A framework to evaluate how endemic parasites alter nutrient cycling across varied ecosystems requires an understanding of: (1) parasite effects on host nutrient excretion, (2) ecosystem nutrient limitation, (3) effects of parasite abundance, host density, host...

Data from: Host and parasite thermal acclimation responses depend on the stage of infection

Karie A. Altman, Sara H. Paull, Pieter T. J. Johnson, Michelle N. Golembieski, Jeffrey P. Stephens, Bryan E. LaFonte & Thomas R. Raffel
1. Global climate change is expected to alter patterns of temperature variability, which could influence species interactions including parasitism. Species interactions can be difficult to predict in variable-temperature environments because of thermal acclimation responses, i.e. physiological changes that allow organisms to adjust to a new temperature following a temperature shift. 2. The goal of this study was to determine how thermal acclimation influences host resistance to infection and to test for parasite acclimation responses, which...

Data from: Non-equilibrium dynamics and floral trait interactions shape extant angiosperm diversity

Brian C. O'Meara, Stacey D. Smith, W. Scott Armbruster, Lawrence D. Harder, Christopher R. Hardy, Lena C. Hileman, Larry Hufford, Amy Litt, Susana Magallon, Stephen A. Smith, Peter F. Stevens, Charles B. Fenster & Pamela K. Diggle
Why are some traits and trait combinations exceptionally common across the tree of life, whereas others are vanishingly rare? The distribution of trait diversity across a clade at any time depends on the ancestral state of the clade, the rate at which new phenotypes evolve, the differences in speciation and extinction rates across lineages, and whether an equilibrium has been reached. Here we examine the role of transition rates, differential diversification (speciation minus extinction), and...

Data from: Genome-wide SNP discovery in the annual herb, Lasthenia fremontii (Asteraceae): genetic resources for the conservation and restoration of a California vernal pool endemic

Lorena Torres-Martínez & Nancy C. Emery
California vernal pool (VP) ecosystems support a diverse community of endemic plants that are threatened by multiple anthropogenic pressures, generating a need for molecular tools to quantify the extent and distribution of genetic variation in native populations. Here, we used RADseq to discover single nucleotide polymorphisms (SNPs) for a widespread VP endemic plant species, Lasthenia fremontii. We discovered nuclear-based SNPs using a RAD-tag library of 12 individuals from different VP complexes using SbfI, a restriction...

Data from: Genome-wide differentiation in closely related populations: the roles of selection and geographic isolation

Rebecca J. Safran, Elizabeth S. C. Scordato, Matthew R. Wilkins, Joanna K. Hubbard, Brittany R. Jenkins, Tomas Albrecht, Samuel M. Flaxman, Hakan Karaardic, Yoni Vortman, Arnon Lotem, Patrik Nosil, Péter Pap, Sheng-Feng Shen, Shih-Fan Chan, Thomas L. Parchman, Nolan C. Kane, S.-F. Chan & T.L. Parchman
Population divergence in geographic isolation is due to a combination of factors. Natural and sexual selection may be important in shaping patterns of population differentiation, a pattern referred to as ‘isolation by adaptation’ (IBA). IBA can be complementary to the well-known pattern of ‘isolation by distance’ (IBD), in which the divergence of closely related populations (via any evolutionary process) is associated with geographic isolation. The barn swallow Hirundo rustica complex comprises six closely related subspecies,...

Data from: \"Willing to pay?\" Tax compliance in Britain and Italy: an experimental analysis

Nan Zhang, Giulia Andrighetto, Stefania Ottone, Ferruccio Ponzano & Sven Steinmo
As shown by the recent crisis, tax evasion poses a significant problem for countries such as Greece, Spain and Italy. While these societies certainly possess weaker fiscal institutions as compared to other EU members, might broader cultural differences between northern and southern Europe also help to explain citizens’ (un)willingness to pay their taxes? To address this question, we conduct laboratory experiments in the UK and Italy, two countries which straddle this North-South divide. Our design...

Registration Year

  • 2016
    28

Resource Types

  • Dataset
    28

Affiliations

  • University of Colorado Boulder
    28
  • University of Nebraska - Lincoln
    3
  • Tel Aviv University
    3
  • University of California, San Diego
    2
  • University of Nevada Reno
    2
  • Charles University
    2
  • University of Cape Town
    2
  • University of Maryland, College Park
    2
  • Cornell University
    2
  • Michigan State University
    2