29 Works

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: Social networks predict gut microbiome composition in wild baboons

Jenny Tung, Luis B. Barriero, Michael B. Burns, J. C. Grenier, Josh Lynch, L. E. Grieneisen, J. Altmann, S. C. Alberts, R. Blekhman, E. A. Archie, Laura E Grieneisen, Elizabeth A Archie, Susan C Alberts, Jeanne Altmann, Luis B Barreiro, Jean-Christophe Grenier, Michael B Burns & Ran Blekhman
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: 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: 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: 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: Into the light: diurnality has evolved multiple times in geckos

Tony Gamble, Eli Greenbaum, Todd R. Jackman & Aaron M. Bauer
Geckos are the only major lizard group consisting mostly of nocturnal species. Nocturnality is presumed to have evolved early in gecko evolution and geckos possess numerous adaptations to functioning in low light and at low temperatures. However, not all gecko species are nocturnal and most diurnal geckos have their own distinct adaptations to living in warmer, sunlit environments. We reconstructed the evolution of gecko activity patterns using a newly generated time-calibrated phylogeny. Our results provide...

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: 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: Incorporating animal spatial memory in step selection functions

Luiz Gustavo R. Oliveira-Santos, James D. Forester, Ubiratan Piovezan, Walfrido M. Tomas & Fernando A. S. Fernandez
Memory is among the most important and neglected forces that shapes animal movement patterns. Research on the movement-memory interface is crucial to understand how animals use spatial learning to navigate across space because memory-biased navigation is directly linked to animals’ space use and home range behaviour; however, because memory cannot be measured directly, it is difficult to account for. Here, we incorporated spatial memory into Step Selection Functions (SSF) to understand how resource selection and...

Data from: Trade-offs in juvenile growth potential vs. shade tolerance among subtropical rainforest trees on soils of contrasting fertility

Kerrie M. Sendall, Christopher H. Lusk & Peter B. Reich
Plant adaptation to gradients of light availability involves a well-studied functional trade-off, as does adaptation to gradients of nutrient availability. However, little is known about how these two major trade-offs interact, and thus, it remains unclear whether and how the nature of the growth–shade tolerance trade-off differs on soils of contrasting fertility. We asked whether juvenile growth–shade tolerance trade-offs differed in slope and elevation between tree assemblages on nutrient-rich basalt and nutrient-poor rhyolite soils in...

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

Adam Ralph Zeilinger, Dawn M. Olson, David A. Andow & Adam R. Zeilinger
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: Raccoon contact networks predict seasonal susceptibility to rabies outbreaks and limitations of vaccination

Jennifer J. H. Reynolds, Ben T. Hirsch, Stanley D. Gehrt & Meggan E. Craft
1. Infectious disease transmission often depends on the contact structure of host populations. Although it is often challenging to capture the contact structure in wild animals, new technology has enabled biologists to obtain detailed temporal information on wildlife social contacts. In this study, we investigated the effects of raccoon contact patterns on rabies spread using network modelling. 2. Raccoons (Procyon lotor) play an important role in the maintenance of rabies in the United States. It...

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: 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: Host associations and beta diversity of fungal endophyte communities in New Guinea rainforest trees

John B. Vincent, George D. Weiblen, Georgiana May, G. May, G. D. Weiblen & J. B. Vincent
Processes shaping the distribution of foliar fungal endophyte species remain poorly understood. Despite increasing evidence that these cryptic fungal symbionts of plants mediate interactions with pathogens and herbivores, there remain basic questions regarding the extent to which dispersal limitation and host specificity might shape fungal endophyte community composition in rainforests. To assess the relative importance of spatial pattern and host specificity, we isolated fungi from a sample of mapped trees in lowland Papua New Guinea....

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: 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: 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: 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: 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: 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...

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: Tempo and mode of flower color evolution

Stacey D. Smith & Emma E. Goldberg
Premise of the study: Flower color is one of the best-studied floral traits in terms of its genetic basis and ecological significance, yet few studies have examined the processes that shape its evolution across deep timescales. Advances in comparative methods along with larger phylogenies for floral radiations offer new opportunities for investigating the macroevolution of flower color. Methods: We examined the tempo and mode of flower color evolution in four clades (Antirrhineae, Iochrominae, Loeselieae, Quamoclit)...

Data from: Cattle sex-specific recombination and genetic control from a large pedigree analysis

Li Ma, Jeffrey R. O'Connell, Paul M. Vanraden, Botong Shen, Abinash Padhi, Chuanyu Sun, Derek M. Bickhart, John B. Cole, Daniel J. Null, George E. Liu, Yang Da & George R. Wiggans
Meiotic recombination is an essential biological process that generates genetic diversity and ensures proper segregation of chromosomes during meiosis. From a large USDA dairy cattle pedigree with over half million genotyped animals, we extracted 186,927 three-generation families, identified over 8.5 million maternal and paternal recombination events, and constructed sex-specific recombination maps for 59,309 autosomal SNPs. The recombination map spans for 25.5 Morgans in males and 23.2 Morgans in females, for a total studied region of...

Registration Year

  • 2015

Resource Types

  • Dataset


  • University of Minnesota
  • Smithsonian Tropical Research Institute
  • University of California System
  • Western Sydney University
  • Duke University
  • Aarhus University
  • Macquarie University
  • National Autonomous University of Mexico
  • University of Wisconsin–Madison
  • University of British Columbia
  • Joint Genome Institute
  • Michigan State University
  • University of Massachusetts Amherst
  • VU Amsterdam
  • Rice University