55 Works

Data from: Small-scale intraspecific patterns of adaptive immunogenetic polymorphisms and neutral variation in Lake Superior lake trout

Shauna M. Baillie, Riley R. Hemstock, Andrew M. Muir, Charles C. Krueger & Paul Bentzen
Many fishes express high levels of intraspecific variability, often linked to resource partitioning. Several studies show that a species’ evolutionary trajectory of adaptive divergence can undergo reversals caused by changes in its environment. Such a reversal in neutral genetic and morphological variation among lake trout Salvelinus namaycush ecomorphs appears to be underway in Lake Superior. However, a water depth gradient in neutral genetic divergence was found to be associated with intraspecific diversity in the lake....

Data from: Harvesting biofuel grasslands has mixed effects on natural enemy communities and no effects on biocontrol services

Tania N. Kim, Aaron F. Fox, Bill D. Wills, Timothy D. Meehan, Douglas A. Landis & Claudio Gratton
1.Perennial bioenergy systems, such as switchgrass and restored prairies, are alternatives to commonly used annual monocultures such as maize. Perennial systems require lower chemical input, provide greater ecosystem services such as carbon storage, greenhouse gas mitigation, and support greater biodiversity of beneficial insects. However, biomass harvest will be necessary in managing these perennial systems for bioenergy production, and it is unclear how repeated harvesting might affect ecosystem services. 2.In this study, we examined how repeated...

Data from: Extensive gene tree discordance and hemiplasy shaped the genomes of North American columnar cacti

Dario Copetti, Alberto Burquez, Enriquena Bustamante, Joseph L. M. Charboneau, Kevin L. Childs, Luis E. Eguiarte, Seunghee Lee, Tiffany L. Liu, Michelle M. McMahon, Noah K. Whiteman, Rod A. Wing, Martin F. Wojciechowski & Michael J. Sanderson
Few clades of plants have proven as difficult to classify as cacti. One explanation may be an unusually high level of convergent and parallel evolution (homoplasy). To evaluate support for this phylogenetic hypothesis at the molecular level, we sequenced the genomes of four cacti in the especially problematic tribe Pachycereeae, which contains most of the large columnar cacti of Mexico and adjacent areas, including the iconic saguaro cactus (Carnegiea gigantea) of the Sonoran Desert. We...

Data from: Mutator genomes decay, despite sustained fitness gains, in a long-term experiment with bacteria

Alejandro Couce, Larissa Viraphong Caudwell, Christoph Feinauer, Thomas Hindré, Jean-Paul Feugeas, Martin Weigt, Richard E. Lenski, Dominique Schneider & Olivier Tenaillon
Understanding the extreme variation among bacterial genomes remains an unsolved challenge in evolutionary biology, despite long-standing debate about the relative importance of natural selection, mutation, and random drift. A potentially important confounding factor is the variation in mutation rates between lineages and over evolutionary history, which has been documented in several species. Mutation accumulation experiments have shown that hypermutability can erode genomes over short timescales. These results, however, were obtained under conditions of extremely weak...

Data from: Comparative water use by maize, perennial crops, restored prairie, and poplar trees in the US Midwest

S. K. Hamilton, M. Z. Hussain, A. K. Bhardwaj, B. Basso & G. P. Robertson
Water use by plant communities across years of varying water availability indicates how terrestrial water balances will respond to climate change and variability as well as to land cover change. Perennial biofuel crops, likely grown mainly on marginal lands of limited water availability, provide an example of a potentially extensive future land cover conversion. We measured growing-season evapotranspiration (ET) based on daily changes in soil profile water contents in five perennial systems—switchgrass, miscanthus, native grasses,...

Data from: Evolution of organismal stoichiometry in a long-term experiment with Escherichia coli

Caroline B. Turner, Brian D. Wade, Justin R. Meyer, Brooke A. Sommerfeld & Richard E. Lenski
Organismal stoichiometry refers to the relative proportion of chemical elements in the biomass of organisms, and it can have important effects on ecological interactions from population to ecosystem scales. Although stoichiometry has been studied extensively from an ecological perspective, much less is known about the rates and directions of evolutionary changes in elemental composition. We measured carbon, nitrogen and phosphorus content of 12 Escherichia coli populations that evolved under controlled carbon-limited, serial-transfer conditions for 50...

Data from: Core genes evolve rapidly in the long-term evolution experiment with Escherichia coli

Rohan Maddamsetti, Philip J. Hatcher, Anna G. Green, Barry L. Williams, Debora S. Marks & Richard E. Lenski
Bacteria can evolve rapidly under positive selection owing to their vast numbers, allowing their genes to diversify by adapting to different environments. We asked whether the same genes that evolve rapidly in the long-term evolution experiment with Escherichia coli (LTEE) have also diversified extensively in nature. To make this comparison, we identified ~2000 core genes shared among 60 E. coli strains. During the LTEE, core genes accumulated significantly more nonsynonymous mutations than flexible (i.e., noncore)...

Data from: Testing genotypic variation of an invasive plant species in response to soil disturbance and herbivory

Shannon L. J. Bayliss, Casey P. TerHorst & Jennifer A. Lau
Herbivores, competitors, and predators can inhibit biological invasions (“biotic resistance” sensu Elton 1959), while disturbance typically promotes biological invasions. Although biotic resistance and disturbance are often considered separately in the invasion literature, these two forces may be linked. One mechanism by which disturbance may facilitate biological invasions is by decreasing the effectiveness of biotic resistance. The effects of both disturbance and biotic resistance may vary across invading genotypes, and genetic variation in the invasive propagule...

Data from: Nitrogen fertilization challenges the climate benefit of cellulosic biofuels

Leilei Ruan, Ajay K. Bhardwaj, Stephen K. Hamilton & G. Philip Robertson
Cellulosic biofuels are intended to improve future energy and climate security. Nitrogen (N) fertilizer is commonly recommended to stimulate yields but can increase losses of the greenhouse gas nitrous oxide (N2O) and other forms of reactive N, including nitrate. We measured soil N2O emissions and nitrate leaching along a switchgrass (Panicum virgatum) high resolution N-fertilizer gradient for three years post-establishment. Results revealed an exponential increase in annual N2O emissions that each year became stronger (R...

Data from: Subgenome dominance in an interspecific hybrid, synthetic allopolyploid, and a 140-year-old naturally established neo-allopolyploid monkeyflower

Patrick P. Edger, Ronald D. Smith, Michael R. McKain, Arielle M. Cooley, Mario Vallejo-Marin, Yao-Wu Yuan, Adam J. Bewick, Lexiang Ji, Adrian E. Platts, Megan J. Bowman, Kevin Childs, Jacob D. Washburn, Robert Schmitz, Gregory D. Smith, J. Chris Pires & Joshua R. Puzey
Recent studies have shown that one of the parental subgenomes in ancient polyploids is generally more dominant - having both retained more genes and being more highly expressed - a phenomenon termed subgenome dominance. The genomic features that determine how quickly and which subgenome dominates within a newly formed polyploid remain poorly understood. To investigate the rate of subgenome dominance emergence, we examined gene expression, gene methylation, and transposable element (TE) methylation in a natural,...

Data from: Carbon debt of Conservation Reserve Program (CRP) grasslands converted to bioenergy production

Ilya Gelfand, Terenzio Zenone, Poonam Jasrotia, Jiquan Chen, Stephen K. Hamilton & G. Philip Robertson
Over 13 million ha of former cropland are enrolled in the US Conservation Reserve Program (CRP), providing well-recognized biodiversity, water quality, and carbon (C) sequestration benefits that could be lost on conversion back to agricultural production. Here we provide measurements of the greenhouse gas consequences of converting CRP land to continuous corn, corn–soybean, or perennial grass for biofuel production. No-till soybeans preceded the annual crops and created an initial carbon debt of 10.6 Mg CO2...

Data from: Dispersal and establishment limitation slows plant community recovery in post-agricultural longleaf pine savannas

Nash E. Turley, John L. Orrock, Joseph A. Ledvina & Lars A. Brudvig
Abandoned agricultural lands often have distinct plant communities from areas with no history of agriculture because plant species fail to recolonize. This may be due to dispersal limitation from a lack of seeds, or establishment limitation because of unsuitable environmental conditions. However, few experiments have directly tested how restoration activities may overcome these limitations. We studied longleaf pine savannas in South Carolina abandoned from agriculture >60 years ago that were immediately adjacent to remnant habitats...

Data from: Models for assessing local-scale co-abundance of animal species while accounting for differential detectability and varied responses to the environment

Jedediah F. Brodie, Olga E. Helmy, Jayasilan Mohd-Azlan, Alys Granados, Henry Bernard, Anthony J. Giordano & Elise Zipkin
We developed a new modeling framework to assess how the local abundance of one species influences the local abundance of a potential competitor while explicitly accounting for differential responses to environmental conditions. Our models also incorporate imperfect detection as well as abundance estimation error for both species. As a case study, we applied the model to four pairs of mammal species in Borneo, surveyed by extensive and spatially widespread camera trapping. We detected different responses...

Data from: Effects of beneficial mutations in pykF gene vary over time and across replicate populations in a long-term experiment with bacteria

Fen Peng, Scott Widmann, Andrea Wunsche, Kristina Duan, Katherine A Donovan, Renwick C. J. Dobson, Richard E. Lenski & Tim F. Cooper
The fitness effects of mutations can depend on the genetic backgrounds in which they occur and thereby influence future opportunities for evolving populations. In particular, mutations that fix in a population might change the selective benefit of subsequent mutations, giving rise to historical contingency. We examine these effects by focusing on mutations in a key metabolic gene, pykF, that arose independently early in the history of 12 Escherichia coli populations during a long-term evolution experiment....

Data from: Genome assembly and annotation of the medicinal plant Calotropis gigantea, a producer of anticancer and antimalarial cardenolides

Genevieve M. Hoopes, John P. Hamilton, Jeongwoon Kim, Dongyan Zhao, Krystle Wiegert-Rininger, Emily Crisovan & C. Robin Buell
Calotropis gigantea produces specialized secondary metabolites known as cardenolides which have anti-cancer and anti-malarial properties. Although transcriptomic studies have been conducted in other cardenolide-producing species, no nuclear genome assembly for an Asterid cardenolide-producing species has been reported to date. A high quality de novo assembly was generated for C. gigantea, representing 157,284,427 bp with an N50 scaffold size of 805,959 bp, for which quality assessments indicated a near complete representation of the genic space. Transcriptome...

Data from: Patterns of divergence across the geographic and genomic landscape of a butterfly hybrid zone associated with a climatic gradient

Sean F. Ryan, Michaël C. Fontaine, J. Mark Scriber, Michael E. Pfrender, Shawn T. O'Neil & Jessica J. Hellmann
Hybrid zones are a valuable tool for studying the process of speciation and for identifying the genomic regions undergoing divergence and the ecological (extrinsic) and non-ecological (intrinsic) factors involved. Here, we explored the genomic and geographic landscape of divergence in a hybrid zone between Papilio glaucus and Papilio canadensis. Using a genome scan of 28,417 ddRAD SNPs, we identified genomic regions under possible selection and examined their distribution in the context of previously identified candidate...

Data from: Evolution of drift robustness in small populations

Thomas LaBar & Christoph Adami
Most mutations are deleterious and cause a reduction in population fitness known as the mutational load. In small populations, weakened selection against slightly-deleterious mutations results in an additional fitness reduction. Many studies have established that populations can evolve a reduced mutational load by evolving mutational robustness, but it is uncertain whether small populations can evolve a reduced susceptibility to drift-related fitness declines. Here, using mathematical modeling and digital experimental evolution, we show that small populations...

Data from: Investigating the extent of parallelism in morphological and genomic divergence among lake trout ecotypes in Lake Superior

Alysse Perreault-Payette, Andrew M. Muir, Frederick Goetz, Charles Perrier, Eric Normandeau, Pascal Sirois & Louis Bernatchez
Understanding the emergence of species through the process of ecological speciation is a central question in evolutionary biology which also has implications for conservation and management. Lake Trout (Salvelinus namaycush) is renowned for the occurrence of different ecotypes linked to resource and habitat use throughout North America. We aimed to unravel the fine genetic structure of the four Lake Trout ecotypes in Lake Superior. A total of 486 individuals from four sites were genotyped at...

Data from: Novel fine-scale aerial mapping approach quantifies grassland weed cover dynamics and response to management

Carolyn M. Malmstrom, H. Scott Butterfield, Laura Planck, Christopher P. Long, Valerie T. Eviner & Christopher W. Long
Invasive weeds threaten the biodiversity and forage productivity of grasslands worldwide. However, management of these weeds is constrained by the practical difficulty of detecting small-scale infestations across large landscapes and by limits in understanding of landscape-scale invasion dynamics, including mechanisms that enable patches to expand, contract, or remain stable. While high-end hyperspectral remote sensing systems can effectively map vegetation cover, these systems are currently too costly and limited in availability for most land managers. We...

Data from: Initial nitrous oxide, carbon dioxide, and methane costs of converting conservation reserve program grassland to row crops under no-till vs. conventional tillage

Leilei Ruan & G. Philip Robertson
Around 4.4 million ha of land in USDA Conservation Reserve Program (CRP) contracts will expire between 2013 and 2018 and some will likely return to crop production. No-till (NT) management offers the potential to reduce the global warming costs of CO2 , CH4 , and N2 O emissions during CRP conversion, but to date there have been no CRP conversion tillage comparisons. In 2009, we converted portions of three 9-21 ha CRP fields in Michigan...

Data from: Temporal constraints on the potential role of fry odors as cues of past reproductive success for spawning lake trout

Tyler J. Buchinger, J. Ellen Marsden, Thomas R. Binder, Mar Huertas, Ugo Bussy, Ke Li, James A. Hanson, Charles C. Krueger, Weiming Li, Nicholas S. Johnson & James E. Hanson
Deciding where to reproduce is a major challenge for most animals. Many select habitats based upon cues of successful reproduction by conspecifics, such as the presence of offspring from past reproductive events. For example, some fishes select spawning habitat following odors released by juveniles whose rearing habitat overlaps with spawning habitat. However, juveniles may emigrate before adults begin to search for spawning habitat; hence, the efficacy of juvenile cues could be constrained by degradation or...

Data from: Fire does not strongly affect genetic diversity or structure of a common treefrog in the endangered Florida scrub

Jeanne M. Robertson, Sarah W. Fitzpatrick, Betsie B. Rothermel & Lauren M. Chan
Fire regimes influence natural populations of organisms in diverse ways, via direct effects on population dynamics as well as indirect effects on habitat and ecosystem processes. Although many amphibian species have evolved to persist in fire-dependent ecosystems, the effects of fire on the genetic diversity of amphibian populations remain relatively unexplored. We examined how different aspects of fire history relate to population genetic diversity and structure of an abundant anuran, Hyla femoralis, in a large,...

Data from: Neighbor effects on tree architecture: functional trade-offs balancing crown competitiveness with wind resistance

David W. MacFarlane & Brian Kane
1. The architecture of trees is the result of constrained, morphologically plastic growth—constrained by an underlying architectural model embedded in their genome, the structure of which can be significantly altered during growth to match the changing environmental conditions to which the tree is exposed. Here, we examined the hypothesis that crowding from neighbors should cause trees to optimize traits for light competition at the expense of wind resistance, with the reverse being true for trees...

Data from: Effects of grain size and niche breadth on species distribution modeling

Thomas Connor, Vanessa Hull, Andres Vina, Ashton Shortridge, Ying Tang, Jindong Zhang, Fang Wang & Jianguo Liu
Scale is a vital component to consider in ecological research, and spatial resolution or grain size is one of its key facets. Species distribution models (SDMs) are prime examples of ecological research in which grain size is an important component. Despite this, SDMs rarely explicitly examine the effects of varying the grain size of the predictors for species with different niche breadths. To investigate the effect of grain size and niche breadth on SDMs, we...

Data from: Hotspots of soil N2O emission enhanced through water absorption by plant residue

Alexandra N. Kravchenko, Ehsan R. Toosi, Andrey K. Guber, Nathaniel E. Ostrom, J. Yu, K. Azeem, Mark L. Rivers & G. Philip Robertson
N2O is a highly potent greenhouse gas and arable soils represent its major anthropogenic source. Field-scale assessments and predictions of soil N2O emission remain uncertain and imprecise due to the episodic and microscale nature of microbial N2O production, most of which occurs within very small discrete soil volumes. Such hotspots of N2O production are often associated with decomposing plant residue. Here we quantify physical and hydrological soil characteristics that lead to strikingly accelerated N2O emissions...

Registration Year

  • 2017

Resource Types

  • Dataset


  • Michigan State University
  • University of Florida
  • University of California, Davis
  • University of Minnesota
  • University of Wisconsin-Madison
  • United States Geological Survey
  • California State University, Northridge
  • University of Georgia
  • University of Cambridge
  • University of Vermont