88 Works

Data from: Synergistic effects of fire and elephants on arboreal animals in an African savannah

Robert M. Pringle, Duncan M. Kimuyu, Ryan L. Sensenig, Todd M. Palmer, Corinna Riginos, Kari E. Veblen & Truman P. Young
1. Disturbance is a crucial determinant of animal abundance, distribution and community structure in many ecosystems, but the ways in which multiple disturbance types interact remain poorly understood. The effects of multiple-disturbance interactions can be additive, subadditive or super-additive (synergistic). Synergistic effects in particular can accelerate ecological change; thus, characterizing such synergies, the conditions under which they arise, and how long they persist has been identified as a major goal of ecology. 2. We factorially...

Data from: Genome-wide signature of local adaptation linked to variable CpG methylation in oak populations

Alexander Platt, Paul F. Gugger, Victoria L. Sork & Matteo Pellegrini
It has long been known that adaptive evolution can occur through genetic mutations in DNA sequence, but it is unclear whether adaptive evolution can occur through analogous epigenetic mechanisms, such as through DNA methylation. If epigenetic variation contributes directly to evolution, species under threat of disease, invasive competition, climate change or other stresses would have greater stores of variation from which to draw. We looked for evidence of natural selection acting on variably methylated DNA...

Data from: Early postembryonic to mature ontogeny of the oryctocephalid trilobite Duodingia duodingensis from the lower Cambrian (Series 2) of southern China

Jin-Bo Hou, Nigel C. Hughes, Tian Lan, Jie Yang & Xi-Guang Zhang
Many well-preserved, articulated exoskeletons recovered from the early Cambrian (Stage 3) Mingxinsi Formation in Weng'an, Guizhou Province, southern China, permit reconstruction of the early postembryonic to mature (i.e. protaspid to holaspid) ontogeny of the small oryctocephalid trilobite Duodingia duodingensis Chow. It is likely that the type material is a latest stage meraspis, and the species had nine thoracic segments in the holaspid phase rather than the eight suggested previously. The earliest holaspis is relatively small...

Data from: The scale-of-choice effect and how estimates of assortative mating in the wild can be biased due to heterogeneous samples

Emilio Rolan-Alvarez, Antonio Carvajal-Rodriguez, Alicia De Coo, Beatriz Cortés, Daniel Estévez-Barcia, Mar Ferreira, Rubén González & Adriana D. Briscoe
The mode in which sexual organisms choose mates is a key evolutionary process, as it can have a profound impact on fitness and speciation. One way to study mate choice in the wild is by measuring trait correlation between mates. Positive assortative mating is inferred when individuals of a mating pair display traits that are more similar than those expected under random mating while negative assortative mating is the opposite. A recent review of 1134...

Data from: Reduced crossover interference and increased ZMM-independent recombination in the absence of Tel1/ATM

Carol M. Anderson, Ashwini Oke, Phoebe Yam, Tangna Zhuge & Jennifer C. Fung
Meiotic recombination involves the repair of double-strand break (DSB) precursors as crossovers (COs) or noncrossovers (NCOs). The proper number and distribution of COs is critical for successful chromosome segregation and formation of viable gametes. In budding yeast the majority of COs occurs through a pathway dependent on the ZMM proteins (Zip2-Zip3-Zip4-Spo16, Msh4-Msh5, Mer3), which form foci at CO-committed sites. Here we show that the DNA-damage-response kinase Tel1/ATM limits ZMM-independent recombination. By whole-genome mapping of recombination...

Data from: Negligible nuclear introgression despite complete mitochondrial capture between two species of chipmunks

Jeffrey M. Good, Dan Vanderpool, Sara Maria Keeble, Ke Bi & Sara Keeble
The idea that species boundaries can be semipermeable to gene flow is now widely accepted but the evolutionary importance of introgressive hybridization remains unclear. Here we examine the genomic contribution of gene flow between two hybridizing chipmunk species, Tamias ruficaudus and Tamias amoenus. Previous studies have shown that ancient hybridization has resulted in complete fixation of introgressed T. ruficaudus mitochondrial DNA (mtDNA) in some populations of T. amoenus, but the extent of nuclear introgression is...

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: Indirect effects of global change accumulate to alter plant diversity but not ecosystem function in alpine tundra

Emily Farrer, Isabel Ashton, Marko Spasojevic, Shiyang Fu, David Gonzalez, Katharine Suding, Emily C. Farrer, David J. X. Gonzalez, Katharine N. Suding & Marko J. Spasojevic
1. Environmental change can affect species directly by altering their physical environment and indirectly by altering the abundance of interacting species. A key challenge at the interface of community ecology and conservation biology is to predict how direct and indirect effects combine to influence response in a changing environment. In particular, little is known about how direct and indirect effects on biodiversity develop over time or their potential to influence ecosystem function. 2. We studied...

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: Detecting recent selective sweeps while controlling for mutation rate and background selection

Christian D. Huber, Michael DeGiorgio, Ines Hellmann & Rasmus Nielsen
A composite likelihood ratio test implemented in the program SweepFinder is a commonly used method for scanning a genome for recent selective sweeps. SweepFinder uses information on the spatial pattern (along the chromosome) of the site frequency spectrum (SFS) around the selected locus. To avoid confounding effects of background selection and variation in the mutation process along the genome, the method is typically applied only to sites that are variable within species. However, the power...

Data from: Social network structure in wintering golden-crowned sparrows is not correlated with kinship

Nina N. Arnberg, Bruce E. Lyon, Daizaburo Shizuka & Alexis S. Chaine
Stable social organization in a wide variety of organisms has been linked to kinship, which can minimize conflict due to the indirect fitness benefits from cooperating with relatives. In birds, kin selection has been mostly studied in the context of reproduction or in species that are social year round. Many birds however are migratory, and the role of kinship in the winter societies of these species is virtually unexplored. In a previous study, we discovered...

Data from: High-arctic butterflies become smaller with rising temperatures

Joseph Bowden, Anne Eskildsen, Rikke R. Hansen, Kent Olsen, Carolyn M. Kurle, Toke Høye & Joseph J. Bowden
The response of body size to increasing temperature constitutes a universal response to climate change that could strongly affect terrestrial ectotherms, but the magnitude and direction of such responses remain unknown in most species. The metabolic cost of increased temperature could reduce body size but long growing seasons could also increase body size as was recently shown in an Arctic spider species. Here, we present the longest known time series on body size variation in...

Data from: Targeted capture and resequencing of 1040 genes reveal environmentally driven functional variation in gray wolves

Rena M. Schweizer, Jacqueline Robinson, Ryan Harrigan, Pedro Silva, Marco Galaverni, Marco Musiani, Richard E. Green, John Novembre & Robert K. Wayne
In an era of ever-increasing amounts of whole genome sequence data for individuals and populations, the utility of traditional single nucleotide polymorphisms (SNPs) array-based genome scans is uncertain. We previously performed a SNP array-based genome scan to identify candidate genes under selection in six distinct gray wolf (Canis lupus) ecotypes. Using this information, we designed a targeted capture array for 1040 genes, including all exons and flanking regions, as well as 5000 1 kb non-genic...

Data from: Climate and habitat interacts to shape the thermal reaction norms of breeding phenology across lizard populations

Alexis Rutschmann, Donald B. Miles, Jean-François Le Galliard, Murielle Richard, Sylvain Moulhérat, Barry Sinervo & Jean Clobert
1. Substantial plastic variation in phenology in response to environmental heterogeneity through time in the same population has been uncovered in many species. However, our understanding of differences in reaction norms of phenology among populations from a given species remains limited. 2. Since the plasticity of phenological traits is often influenced by local thermal conditions, we expect local temperature to generate variation in the reaction norms between populations. 3. Here, we explored temporal variation in...

Data from: Bulk genotyping of biopsies can create spurious evidence for heterogeneity in mutation content

Rumen Kostadinov, Carlo Maley, Mary Kuhner, Carlo C. Maley & Mary K. Kuhner
When multiple samples are taken from the neoplastic tissues of a single patient, it is natural to compare their mutation content. This is often done by bulk genotyping of whole biopsies, but the chance that a mutation will be detected in bulk genotyping depends on its local frequency in the sample. When the underlying mutation count per cell is equal, homogenous biopsies will have more high-frequency mutations, and thus more detectable mutations, than heterogeneous ones....

Data from: Seascape drivers of Macrocystis pyrifera population genetic structure in the northeast Pacific

Mattias L. Johansson, Filipe Alberto, Daniel C. Reed, Peter T. Raimondi, Nelson C. Coelho, Mary A. Young, Patrick T. Drake, Christopher A. Edwards, Kyle Cavanaugh, Jorge Assis, Lydia B. Ladah, Tom W. Bell, James A. Coyer, David A. Siegel & Ester A. Serrão
At small spatial and temporal scales, genetic differentiation is largely controlled by constraints on gene flow, while genetic diversity across a species' distribution is shaped on longer temporal and spatial scales. We assess the hypothesis that oceanographic transport and other seascape features explain different scales of genetic structure of giant kelp, Macrocystis pyrifera. We followed a hierarchical approach to perform a microsatellite-based analysis of genetic differentiation in Macrocystis across its distribution in the northeast Pacific....

Data from: Towards automated annotation of benthic survey images: variability of human experts and operational modes of automation

Oscar Beijbom, Peter J. Edmunds, Chris Roelfsema, Jennifer Smith, David I. Kline, Benjamin Neal, Matthew J. Dunlap, Vincent Moriarty, Tung-Yung Fan, Chih-Jui Tan, Stephen Chan, Tali Treibitz, Anthony Gamst, B. Greg Mitchell, David Kriegman & Benjamin P. Neal
Global climate change and other anthropogenic stressors have heightened the need to rapidly characterize ecological changes in marine benthic communities across large scales. Digital photography enables rapid collection of survey images to meet this need, but the subsequent image annotation is typically a time consuming, manual task. We investigated the feasibility of using automated point-annotation to expedite cover estimation of the 17 dominant benthic categories from survey-images captured at four Pacific coral reefs. Inter- and...

Data from: Molecular evidence for hybridization in Colias (Lepidoptera: Pieridae): are Colias hybrids really hybrids?

Heather E. Dwyer, Marie Jasieniuk, Miki Okada & Arthur M. Shapiro
Gene flow and hybridization among species dramatically affect our understanding of the species as a biological unit, species relationships, and species adaptations. In North American Colias eurytheme and Colias eriphyle, there has been historical debate over the extent of hybridization occurring and the identity of phenotypically intermediate individuals as genetic hybrids. This study assesses the population structure of these two species to measure the extent of hybridization and the genetic identity of phenotypic intermediates as...

Data from: Body reserves influence allocation to immune responses in capital breeding female northern elephant seals

Hannah E. Peck, Daniel P. Costa & Daniel E. Crocker
Mounting an immune response requires substantial energy. Ecological immunology theory predicts allocation trade-offs between reproductive effort and immune responses under conditions of energy limitation. Little is known about the impact of capital breeding strategies on energy allocation to immune function in mammals. Northern elephant seals (NES) forage in the marine environment, breed in dense terrestrial colonies and exhibit high rates of energy expenditure for lactation while fasting. Body reserves strongly influence reproductive effort and lactation...

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: The transcriptomic and evolutionary signature of social interactions regulating honey bee caste development

Svjetlana Vojvodic, Brian R. Johnson, Brock A. Harpur, Clement F. Kent, Amro Zayed, Kirk E. Anderson & Timothy A. Linksvayer
The caste fate of developing female honey bee larvae is strictly socially regulated by adult nurse workers. As a result of this social regulation, nurse-expressed genes as well as larval-expressed genes may affect caste expression and evolution. We used a novel transcriptomic approach to identify genes with putative direct and indirect effects on honey bee caste development, and we subsequently studied the relative rates of molecular evolution at these caste-associated genes. We experimentally induced the...

Data from: Conservation implications of ameliorating survival of little brown bats with White-Nose Syndrome

Brooke Maslo, Mick Valent, John F. Gumbs & Winifred F. Frick
Management of wildlife populations impacted by novel threats is often challenged by a lack of data on temporal changes in demographic response. Populations may suffer rapid declines from the introduction of new stressors, but how demography changes over time is critical to determining long-term outcomes for populations. White-nose syndrome (WNS), an infectious disease of hibernating bats, has caused massive and rapid population declines in several hibernating species of bats in North America since the disease...

Data from: Forest disturbance accelerates thermophilization of understory plant communities

Jens T. Stevens, Hugh D. Safford, Susan Harrison & Andrew M. Latimer
1. Climate change is likely to shift plant communities towards species from warmer regions, a process termed “thermophilization.” In forests, canopy disturbances such as fire may hasten this process by increasing temperature and moisture stress in the understory, yet little is known about the mechanisms that might drive such shifts, or the consequences of these processes for plant diversity. 2. We sampled understory vegetation across a gradient of disturbance severity from a large-scale natural experiment...

Data from: Climate mediates the effects of disturbance on ant assemblage structure

Heloise Gibb, Nathan J. Sanders, Robert R. Dunn, Simon Watson, Manoli Photakis, Silvia Abril, Alan N. Andersen, Elena Angulo, Inge Armbrecht, Xavier Arnan, Fabricio B. Baccaro, Tom R. Bishop, Raphael Boulay, Cristina Castracani, Israel Del Toro, Thibaut Delsinne, Mireia Diaz, David A. Donoso, Martha L. Enríquez, Tom M. Fayle, Donald H. Feener, Matthew C. Fitzpatrick, Crisanto Gómez, Donato A. Grasso, Sarah Groc … & T. C. Munyai
Many studies have focused on the impacts of climate change on biological assemblages, yet little is known about how climate interacts with other major anthropogenic influences on biodiversity, such as habitat disturbance. Using a unique global database of 1128 local ant assemblages, we examined whether climate mediates the effects of habitat disturbance on assemblage structure at a global scale. Species richness and evenness were associated positively with temperature, and negatively with disturbance. However, the interaction...

Data from: Posterior predictive checks of coalescent models: P2C2M, an R package

Michael Gruenstaeudl, Noah M. Reid, Gregory L. Wheeler & Bryan C. Carstens
Bayesian inference operates under the assumption that the empirical data are a good statistical fit to the analytical model, but this assumption can be challenging to evaluate. Here, we introduce a novel r package that utilizes posterior predictive simulation to evaluate the fit of the multispecies coalescent model used to estimate species trees. We conduct a simulation study to evaluate the consistency of different summary statistics in comparing posterior and posterior predictive distributions, the use...

Registration Year

  • 2015

Resource Types

  • Dataset


  • University of California System
  • Stanford University
  • Duke University
  • University of Minnesota
  • Southwest Fisheries Science Center
  • French National Centre for Scientific Research
  • Utah State University
  • Princeton University
  • University of Michigan-Ann Arbor
  • Swiss Federal Institute of Aquatic Science and Technology