37 Works

Data from: Phylogeny and biogeography of the American live oaks (Quercus subsection Virentes): a genomic and population genetics approach

Jeannine Cavender-Bares, Antonio González-Rodríguez, Deren A. R. Eaton, Andrew A. L. Hipp, Anne Beulke & Paul S. Manos
The nature and timing of evolution of niche differentiation among closely related species remains an important question in ecology and evolution. The American live oak clade, Virentes, which spans the unglaciated temperate and tropical regions of North America and Mesoamerica, provides an instructive system in which to examine speciation and niche evolution. We generated a fossil-calibrated phylogeny of Virentes using RADseq data to estimate divergence times and used nuclear microsatellites, chloroplast sequences and an intron...

Data from: Whole genome resequencing reveals extensive natural variation in the model green alga Chlamydomonas reinhardtii

Jonathan M. Flowers, Khaled M. Hazzouri, Gina M. Pham, Ulises Rosas, Tayebeh Bahmani, Basel Khraiwesh, David R. Nelson, Kenan Jijakli, Rasha Abdrabu, Elizabeth H. Harris, Paul A. Lefebvre, Erik F. Y. Hom, Kourosh Salehi-Ashtiani & Michael D. Purugganan
We performed whole-genome resequencing of 12 field isolates and eight commonly studied laboratory strains of the model organism Chlamydomonas reinhardtii to characterize genomic diversity and provide a resource for studies of natural variation. Our data support previous observations that Chlamydomonas is among the most diverse eukaryotic species. Nucleotide diversity is ∼3% and is geographically structured in North America with some evidence of admixture among sampling locales. Examination of predicted loss-of-function mutations in field isolates indicates...

Data from: Trace DNA from insect skins: a comparison of five extraction protocols and direct PCR on chironomid pupal exuviae

Petra Kranzfelder, Torbjørn Ekrem & Elisabeth Stur
Insect skins (exuviae) are of extracellular origin and shed during moulting. The skins do not contain cells or DNA themselves, but epithelial cells and other cell-based structures might accidentally attach as they are shed. This source of trace DNA can be sufficient for PCR amplification and sequencing of target genes and aid in species identification through DNA barcoding or association of unknown life stages. Species identification is essential for biomonitoring programs, as species vary in...

Data from: Elevating perceived predation risk modifies the relationship between parental effort and song complexity in the song sparrow (Melospiza melodia)

Melissa L. Grunst, John T. Rotenberry & Andrea S. Grunst
Adult-directed predation risk elevates costs of parental care, and may modify relationships between sexually selected ornaments and parental effort by accentuating the tradeoff between survival and parental investment. We assessed multiple hypotheses regarding the relationship between maternal effort, paternal effort, and the sexually selected trait of male song complexity in the song sparrow Melospiza melodia. Further, we explored whether experimentally elevating perceived adult-directed predation risk near nests affected these relationships. We quantified two dimensions of...

Data from: Solidago altissima differs with respect to ploidy frequency and clinal variation across the prairie-forest biome border in Minnesota

Julie R. Etterson, Rachel H. Toczydlowski, Katharine J. Winkler, Jessica A. Kirschbaum & Tim S. McAulay
PREMISE OF THE STUDY: Although our awareness of ploidy diversity has expanded with the application of flow cytometry, we still know little about the extent to which cytotypes within mixed-ploidy populations are genetically differentiated across environmental gradients. METHODS: To address this issue, we reared 14 populations of Solidago altissima spanning the prairie–forest ecotone in Minnesota in a common garden with a watering treatment. We assessed ploidy frequencies and measured survival, flowering phenology, and plant architectural...

Data from: Parallelism in adaptive radiations of experimental Escherichia coli populations

Gerda Saxer & Michael Travisano
Adaptive radiations are major contributors to species diversity. While the underlying mechanisms of adaptive radiations, specialization and trade-offs, are relatively well understood, the tempo and repeatability of adaptive radiations remain elusive. Ecological specialization can occur through the expansion into novel niches or through partitioning of an existing niche. To test how the mode of resource specialization affects the tempo and repeatability of adaptive radiations, we selected replicate bacterial populations in environments that promoted the evolution...

Data from: Environmentally induced changes in correlated responses to selection reveal variable pleiotropy across a complex genetic network

Kristin L. Sikkink, Rose M. Reynolds, William A. Cresko & Patrick C. Phillips
Selection in novel environments can lead to a coordinated evolutionary response across a suite of characters. Environmental conditions can also potentially induce changes in the genetic architecture of complex traits, which in turn could alter the pattern of the multivariate response to selection. We describe a factorial selection experiment using the nematode Caenorhabditis remanei in which two different stress-related phenotypes (heat and oxidative stress resistance) were selected under three different environmental conditions. The pattern of...

Data from: Life history as a constraint on plasticity: developmental timing is correlated with phenotypic variation in birds

Emilie C. Snell-Rood, Eli M. Swanson & Rebecca L. Young
Understanding why organisms vary in developmental plasticity has implications for predicting population responses to changing environments and the maintenance of intraspecific variation. The epiphenotype hypothesis posits that the timing of development can constrain plasticity—the earlier alternate phenotypes begin to develop, the greater the difference that can result amongst the final traits. This research extends this idea by considering how life history timing shapes the opportunity for the environment to influence trait development. We test the...

Data from: The susceptibility of Echinacea angustifolia to a specialist aphid: eco-evolutionary perspective on genotypic variation and demographic consequences

Ruth G. Shaw, Stuart Wagenius & Charles J. Geyer
1. Plants and their herbivores may influence each other's fitness and, hence, genetic dynamics, as well as their demography. Conversely, variation in fitness-related traits may influence the occurrence or intensity of the interaction. Disentangling the fitness consequences of an interaction in nature from the influence of fitness variation on it is challenging, but important to clarifying the ecological and evolutionary dynamics of plants with their herbivores. 2. As part of a larger effort to elucidate...

Data from: Snapshot Serengeti, high-frequency annotated camera trap images of 40 mammalian species in an African savanna

Alexandra B. Swanson, Margaret Kosmala, Chris J. Lintott, Robert J. Simpson, Arfon Smith & Craig Packer
Camera traps can be used to address large-scale questions in community ecology by providing systematic data on an array of wide-ranging species. We deployed 225 camera traps across 1,125 km2 in Serengeti National Park, Tanzania, to evaluate spatial and temporal inter-species dynamics. The cameras have operated continuously since 2010 and had accumulated 99,241 camera-trap days and produced 1.2 million sets of pictures by 2013. Members of the general public classified the images via the citizen-science...

Data from: Model inadequacy and mistaken inferences of trait-dependent speciation

Daniel Rabosky, Emma E. Goldberg & Daniel L. Rabosky
Species richness varies widely across the tree of life, and there is great interest in identifying ecological, geographic, and other factors that affect rates of species proliferation. Recent methods for explicitly modeling the relationships among character states, speciation rates, and extinction rates on phylogenetic trees- BiSSE, QuaSSE, GeoSSE, and related models - have been widely used to test hypotheses about character state-dependent diversification rates. Here, we document the disconcerting ease with which neutral traits are...

Data from: Bayesian estimates of male and female African lion mortality for future use in population management

Julia A. Barthold, Andrew J. Loveridge, David W. Macdonald, Craig Packer & Fernando Colchero
The global population size of African lions is plummeting, and many small fragmented populations face local extinction. Extinction risks are amplified through the common practice of trophy hunting for males, which makes setting sustainable hunting quotas a vital task. Various demographic models evaluate consequences of hunting on lion population growth. However, none of the models use unbiased estimates of male age-specific mortality because such estimates do not exist. Until now, estimating mortality from resighting records...

Data from: Species richness, but not phylogenetic diversity, influences community biomass production and temporal stability in a re-examination of 16 grassland biodiversity studies

Patrick Venail, Kevin Gross, Todd H. Oakley, Anita Narwani, Eric Allan, Pedro Flombaum, Forest Isbell, Jasmin Joshi, Peter B. Reich, David Tilman, Jasper Van Ruijven & Bradley J. Cardinale
1.Hundreds of experiments have now manipulated species richness of various groups of organisms and examined how this aspect of biological diversity influences ecosystem functioning. Ecologists have recently expanded this field to look at whether phylogenetic diversity among species, often quantified as the sum of branch lengths on a molecular phylogeny leading to all species in a community, also predicts ecological function. Some have hypothesized that phylogenetic divergence should be a superior predictor of ecological function...

Data from: Optimizing techniques to capture and extract environmental DNA for detection and quantification of fish

Jessica J. Eichmiller, Loren M. Miller & Peter W. Sorensen
Few studies have examined capture and extraction methods for environmental DNA (eDNA) to identify techniques optimal for detection and quantification. In this study, precipitation, centrifugation and filtration eDNA capture methods and six commercially available DNA extraction kits were evaluated for their ability to detect and quantify common carp (Cyprinus carpio) mitochondrial DNA using quantitative PCR in a series of laboratory experiments. Filtration methods yielded the most carp eDNA, and a glass fibre (GF) filter performed...

Data from: Competitive release and outbreaks of non-target pests associated with transgenic Bt cotton

Adam Ralph Zeilinger, Dawn M. Olson & David A. Andow
The adoption of transgenic Bt cotton has, in some cases, led to environmental and economic benefits through reduced insecticide use. However, the distribution of these benefits and associated risks among cotton growers and cotton-growing regions, has been uneven due in part to outbreaks of non-target or secondary pests, thereby requiring the continued use of synthetic insecticides. In the southeastern United States, Bt cotton adoption has resulted in increased abundance of and damage from stink bug...

Data from: Social networks predict gut microbiome composition in wild baboons

Jenny Tung, Luis B. Barriero, Michael B. Burns, J. C. Grenier, Josh Lynch, Laura E Grieneisen, Jeanne Altmann, Susan C Alberts, Ran Blekhman, Elizabeth A Archie & Jean-Christophe Grenier
Social relationships have profound effects on health in humans and other primates, but the mechanisms that explain this relationship are not well understood. Using shotgun metagenomic data from wild baboons, we found that social group membership and social network relationships predicted both the taxonomic structure of the gut microbiome and the structure of genes encoded by gut microbial species. Rates of interaction directly explained variation in the gut microbiome, even after controlling for diet, kinship,...

Data from: Global effects of soil and climate on leaf photosynthetic traits and rates

Vincent Maire, Ian J. Wright, I. Colin Prentice, Niels H. Batjes, Radika Bhaskar, Peter M. Van Bodegom, Will K. Cornwell, David Ellsworth, Ülo Niinemets, Alejandro Ordoñez, Peter B. Reich & Louis S. Santiago
Aim: The influence of soil properties on photosynthetic traits in higher plants is poorly quantified in comparison with that of climate. We address this situation by quantifying the unique and joint contributions to global leaf-trait variation from soils and climate. Location: Terrestrial ecosystems world-wide. Methods: Using a trait dataset comprising 1509 species from 288 sites, with climate and soil data derived from global datasets, we quantified the effects of 20 soil and 26 climate variables...

Data from: The evolutionary legacy of size-selective harvesting extends from genes to populations

Silva Uusi-Heikkilä, Andrew R. Whiteley, Anna Kuparinen, Shuichi Matsumura, Paul A. Venturelli, Christian Wolter, Jon Slate, Craig R. Primmer, Thomas Meinelt, Shaun S. Killen, David Bierbach, Giovanni Polverino, Arne Ludwig & Robert Arlinghaus
Size-selective harvesting is assumed to alter life histories of exploited fish populations, thereby negatively affecting population productivity, recovery, and yield. However, demonstrating that fisheries-induced phenotypic changes in the wild are at least partly genetically determined has proved notoriously difficult. Moreover, the population-level consequences of fisheries-induced evolution are still being controversially discussed. Using an experimental approach, we found that five generations of size-selective harvesting altered the life histories and behavior, but not the metabolic rate, of...

Data from: Dioecy does not consistently accelerate or slow lineage diversification across multiple genera of angiosperms

Niv Sabath, Emma E. Goldberg, Lior Glick, Moshe Einhorn, Tia-Lynn Ashman, Ray Ming, Sarah P. Otto, Jana Vamosi, Itay Mayrose & Jana C. Vamosi
Dioecy, the sexual system in which male and female organs are found in separate individuals, allows greater specialization for sex-specific functions and can be advantageous under various ecological and environmental conditions. However, dioecy is rare among flowering plants. Previous studies identified contradictory trends regarding the relative diversification rates of dioecious lineages vs their nondioecious counterparts, depending on the methods and data used. We gathered detailed species-level data for dozens of genera that contain both dioecious...

Data from: Evolution of novel wood decay mechanisms in Agaricales revealed by the genome sequences of Fistulina hepatica and Cylindrobasidium torrendii

Dimitrios Floudas, Benjamin W. Held, Robert Riley, Laszlo G. Nagy, Gage Koehler, Anthony S. Ransdell, Hina Younus, Julianna Chow, Jennifer Chiniquy, Anna Lipzen, Andrew Tritt, Hui Sun, Sajeet Haridas, Kurt LaButti, Robin A. Ohm, Ursula Kues, Robert A. Blanchette, Igor V. Grigoriev, Robert E. Minto & David S. Hibbett
Wood decay mechanisms in Agaricomycotina have been traditionally separated in two categories termed white and brown rot. Recently the accuracy of such a dichotomy has been questioned. Here, we present the genome sequences of the white rot fungus Cylindrobasidium torrendii and the brown rot fungus Fistulina hepatica both members of Agaricales, combining comparative genomics and wood decay experiments. Cylindrobasidium torrendii is closely related to the white-rot root pathogen Armillaria mellea, while F. hepatica is related...

Data from: The impact of Quaternary climate oscillations on divergence times and historical population sizes in Thylamys opossums from the Andes

Thomas C. Giarla & Sharon A. Jansa
Climate oscillations during the Quaternary altered the distributions of terrestrial animals at a global scale. In mountainous regions, temperature fluctuations may have led to shifts in range size and population size as species tracked their shifting habitats upslope or downslope. This creates the potential for both allopatric speciation and population size fluctuations, as species are either constrained to smaller patches of habitat at higher elevations or able to expand into broader areas at higher latitudes....

Data from: A daily global mesoscale ocean eddy dataset from satellite altimetry

James H. Faghmous, Ivy Frenger, Yuanshun Yao, Robert Warmka, Aron Lindell & Vipin Kumar
Mesoscale ocean eddies are ubiquitous coherent rotating structures of water with radial scales on the order of 100 kilometers. Eddies play a key role in the transport and mixing of momentum and tracers across the World Ocean. We present a global daily mesoscale ocean eddy dataset that contains ~45 million mesoscale features and 3.3 million eddy trajectories that persist at least two days as identified in the AVISO dataset over a period of 1993–2014. This...

Data from: Shared genomic regions between derivatives of a large segregating population of maize identified using bulked segregant analysis sequencing and traditional linkage analysis

Nicholas J. Haase, Timothy Beissinger, Candice N. Hirsch, Brieanne Vaillancourt, Shweta Deshpande, Kerrie Barry, C. Robin Buell, Shawn M. Kaeppler & Natalia De Leon
Delayed transition from the vegetative stage to the reproductive stage of development and increased plant height have been shown to increase biomass productivity in grasses. The goal of this project was to detect quantitative trait loci using extremes from a large synthetic population, as well as a related recombinant inbred line mapping population for these two traits. Ten thousand individuals from a B73 × Mo17 noninbred population intermated for 14 generations (IBM Syn14) were grown...

Data from: Relationships between spatial metrics and plant diversity in constructed freshwater wetlands

Erika C. Brandt, John E. Petersen, Jake J. Grossman, George A. Allen & David H. Benzing
The diversity of plant species and their distribution in space are both thought to have important effects on the function of wetland ecosystems. However, knowledge of the relationships between plant species and spatial diversity remains incomplete. In this study, we investigated relationships between spatial pattern and plant species diversity over a five year period following the initial restoration of experimental wetland ecosystems. In 2003, six identical and hydrologically-isolated 0.18 ha wetland “cells” were constructed in...

Data from: Pervasive and strong effects of plants on soil chemistry: a meta-analysis of individual plant ‘Zinke’ effects

Bonnie G. Waring, Leonor Álvarez-Cansino, Kathryn E. Barry, Kristen K. Becklund, Sarah Dale, Maria G. Gei, Adrienne B. Keller, Omar R. Lopez, Lars Markesteijn, Scott Mangan, Charlotte E. Riggs, Maria Elizabeth Rodríguez-Ronderos, R. Max Segnitz, Stefan A. Schnitzer & Jennifer S. Powers
Plant species leave a chemical signature in the soils below them, generating fine-scale spatial variation that drives ecological processes. Since the publication of a seminal paper on plant-mediated soil heterogeneity by Paul Zinke in 1962, a robust literature has developed examining effects of individual plants on their local environments (individual plant effects). Here, we synthesize this work using meta-analysis to show that plant effects are strong and pervasive across ecosystems on six continents. Overall, soil...

Registration Year

  • 2015
    37

Resource Types

  • Dataset
    37

Affiliations

  • University of Minnesota
    37
  • Smithsonian Tropical Research Institute
    4
  • University of California System
    3
  • Duke University
    3
  • University of Michigan-Ann Arbor
    2
  • Aarhus University
    2
  • United States Department of Agriculture
    2
  • Macquarie University
    2
  • University of Wisconsin-Madison
    2
  • Western Sydney University
    2