39 Works

Data from: Consequences of whole-genome triplication as revealed by comparative genomic analyses of the wild radish Raphanus raphanistrum and three other Brassicaceae species

Gaurav D. Moghe, David E. Hufnagel, Haibao Tang, Yongli Xiao, Ian Dworkin, Christopher D. Town, Jeffrey K. Conner & Shin-Han Shiu
Polyploidization events are frequent among flowering plants, and the duplicate genes produced via such events contribute significantly to plant evolution. We sequenced the genome of wild radish (Raphanus raphanistrum), a Brassicaceae species that experienced a whole-genome triplication event prior to diverging from Brassica rapa. Despite substantial gene gains in these two species compared with Arabidopsis thaliana and Arabidopsis lyrata, ∼70% of the orthologous groups experienced gene losses in R. raphanistrum and B. rapa, with most...

Data from: Social network analysis of mating patterns in American black bears (Ursus americanus)

Jennifer A. Moore, Ran Xu, Kenneth Frank, Hope Draheim & Kim T. Scribner
Nonrandom mating can structure populations and has important implications for population-level processes. Investigating how and why mating deviates from random is important for understanding evolutionary processes as well as informing conservation and management. Prior to the implementation of parentage analyses, understanding mating patterns in solitary, elusive species like bears was virtually impossible. Here, we capitalize on a long-term genetic data set collected from black bears (Ursus americanus) (N = 2422) in the Northern Lower Peninsula...

Data from: The challenge of accurately documenting bee species richness in agroecosystems: bee diversity in eastern apple orchards

Laura A. Russo, Mia Park, Jason Gibbs, Bryan Danforth & Laura Russo
Bees are important pollinators of agricultural crops, and bee diversity has been shown to be closely associated with pollination, a valuable ecosystem service. Higher functional diversity and species richness of bees have been shown to lead to higher crop yield. Bees simultaneously represent a mega-diverse taxon that is extremely challenging to sample thoroughly and an important group to understand because of pollination services. We sampled bees visiting apple blossoms in 28 orchards over 6 years....

Data from: A comparison of methods to measure fitness in Escherichia coli

Michael J. Wiser & Richard E. Lenski
In order to characterize the dynamics of adaptation, it is important to be able to quantify how a population’s mean fitness changes over time. Such measurements are especially important in experimental studies of evolution using microbes. The Long-Term Evolution Experiment (LTEE) with Escherichia coli provides one such system in which mean fitness has been measured by competing derived and ancestral populations. The traditional method used to measure fitness in the LTEE and many similar experiments,...

Data from: Mixed-ancestry and admixture in Kaua’i’s feral chickens: invasion of domestic genes into ancient Red Junglefowl reservoirs?

Eben Gering, Martin Johnsson, Pamela Willis, Thomas Getty & Dominic Wright
A major goal of invasion genetics is to determine how establishment histories shape non-native organisms' genotypes and phenotypes. While domesticated species commonly escape cultivation to invade feral habitats, few studies have examined how this process shapes feral gene pools and traits. We collected genomic and phenotypic data from feral chickens (Gallus gallus) on the Hawaiian island of Kauai to (i) ascertain their origins and (ii) measure standing variation in feral genomes, morphology and behaviour. Mitochondrial...

Data from: Synthesis of phylogeny and taxonomy into a comprehensive tree of life

Cody E. Hinchliff, Stephen A. Smith, James F. Allman, J. Gordon Burleigh, Ruchi Chaudhary, Lyndon M. Coghill, Keith A. Crandall, Jiabin Deng, Bryan T. Drew, Romina Gazis, Karl Gude, David S. Hibbett, Laura A. Katz, , Emily Jane McTavish, Peter E. Midford, Christopher L. Owen, Richard H. Ree, Jonathan A. Rees, Douglas E. Soltis, Tiffani Williams & Karen Ann Cranston
Reconstructing the phylogenetic relationships that unite all lineages (the tree of life) is a grand challenge. The paucity of homologous character data across disparately related lineages currently renders direct phylogenetic inference untenable. To reconstruct a comprehensive tree of life, we therefore synthesized published phylogenies, together with taxonomic classifications for taxa never incorporated into a phylogeny. We present a draft tree containing 2.3 million tips—the Open Tree of Life. Realization of this tree required the assembly...

Data from: Bouncing Back: plant-associated soil microbes respond rapidly to prairie establishment

Randall D. Jackson, Anna J. Herzberger & David S. Duncan
It is well established that soil microbial communities change in response to altered land use and land cover, but less is known about the timing of these changes. Understanding temporal patterns in recovering microbial communities is an important part of improving how we assess and manage reconstructed ecosystems. We assessed patterns of community-level microbial diversity and abundance in corn and prairie plots 2 to 4 years after establishment in agricultural fields, using phospholipid fatty acid...

Data from: Oil palm plantations fail to support mammal diversity

Sam Yue, Jedediah F. Brodie, Elise F. Zipkin & Henry Bernard
Agricultural expansion is the largest threat to global biodiversity. In particular, the rapid spread of tree plantations is a primary driver of deforestation in hyperdiverse tropical regions. Plantations tend to support considerably lower biodiversity than native forest, but it remains unclear whether plantation traits affect their ability to sustain native wildlife populations, particularly for threatened taxa. If animal diversity varies across plantations with different characteristics, these traits could be manipulated to make plantations more “wildlife...

Data from: Evolutionary stasis despite selection on a heritable trait in an invasive zooplankton

Andrea L.J. Miehls, Scott D. Peacor, Lindsey Valliant, Andrew G. McAdam & A. L. J. Miehls
Invasive species are one of the greatest threats to ecosystems and there is evidence that evolution plays an important role in the success or failure of invasions. Yet, few studies have measured natural selection and evolutionary responses to selection in invasive species, particularly invasive animals. We quantified the strength of natural selection on the defensive morphology (distal spine) of an invasive zooplankton, Bythotrephes longimanus, in Lake Michigan across multiple months during three growing seasons. We...

Data from: Synonymous genetic variation in natural isolates of Escherichia coli does not predict where synonymous substitutions occur in a long-term experiment

Rohan Maddamsetti, Philip J. Hatcher, Stéphane Cruveiller, Claudine Médigue, Jeffrey E. Barrick & Richard E. Lenski
Synonymous genetic differences vary by more than 20-fold among genes in natural isolates of Escherichia coli. One hypothesis to explain this heterogeneity is that genes with high levels of synonymous variation mutate at higher rates than genes with low synonymous variation. If so, then one would expect to observe similar mutational patterns in evolution experiments. In fact, however, the pattern of synonymous substitutions in a long-term evolution experiment with E. coli does not support this...

Data from: Adaptation, clonal interference, and frequency-dependent interactions in a long-term evolution experiment with Escherichia coli

Rohan Maddamsetti, Jeff E. Barrick, Richard E. Lenski & Jeffrey E. Barrick
Twelve replicate populations of Escherichia coli have been evolving in the laboratory for >25 years and 60,000 generations. We analyzed bacteria from whole-population samples frozen every 500 generations through 20,000 generations for one well-studied population, called Ara−1. By tracking 42 known mutations in these samples, we reconstructed the history of this population’s genotypic evolution over this period. The evolutionary dynamics of Ara−1 show strong evidence of selective sweeps as well as clonal interference between competing...

Data from: Spatial analysis of anthropogenic landscape disturbance and Buruli ulcer disease in Benin

Lindsay P. Campbell, Andrew O. Finley, Mark Eric Benbow, Jenni Gronseth, Pamela Small, Roch Christian Johnson, Ghislain E. Sopoh, Richard M. Merritt, Heather Williamson & Jiaguo Qi
Background: Land use and land cover (LULC) change is one anthropogenic disturbance linked to infectious disease emergence. Current research has focused largely on wildlife and vector-borne zoonotic diseases, neglecting to investigate landscape disturbance and environmental bacterial infections. One example is Buruli ulcer (BU) disease, a necrotizing skin disease caused by the environmental pathogen Mycobacterium ulcerans (MU). Empirical and anecdotal observations have linked BU incidence to landscape disturbance, but potential relationships have not been quantified as...

Data from: Gene flow from an adaptively divergent source causes rescue through genetic and demographic factors in two wild populations of Trinidadian guppies

Sarah W. Fitzpatrick, Jill C. Gerberich, Lisa M. Angeloni, Larissa L. Bailey, Emily Dale Broder, Julian Torres-Dowdall, Corey A. Handelsman, Andrés López-Sepulcre, David N. Reznick, Cameron K. Ghalambor & W. Chris Funk
Genetic rescue, an increase in population growth owing to the infusion of new alleles, can aid the persistence of small populations, but its use as a management tool is limited by a lack of empirical data geared towards predicting effects of gene flow on local adaptation and demography. Experimental translocations provide an ideal opportunity to monitor the demographic consequences of gene flow. In this study we take advantage of two experimental introductions of Trinidadian guppies...

Data from: Contemporary evolution during invasion: evidence for differentiation, natural selection, and local adaptation

Robert I. Colautti & Jennifer A. Lau
Biological invasions are ‘natural’ experiments that can improve our understanding of contemporary evolution. We evaluate evidence for population differentiation, natural selection and adaptive evolution of invading plants and animals at two nested spatial scales: (i) among introduced populations (ii) between native and introduced genotypes. Evolution during invasion is frequently inferred, but rarely confirmed as adaptive. In common garden studies, quantitative trait differentiation is only marginally lower (~3.5%) among introduced relative to native populations, despite genetic...

Data from: Diversity and population structure of northern switchgrass as revealed through exome capture sequencing

Joseph Evans, Emily Crisovan, Kerrie Barry, Chris Daum, Jerry Jenkins, Govindarajan Kunde-Ramamoorthy, Aruna Nandety, Chew Yee Ngan, Brieanne Vaillancourt, Chia-Lin Wei, Jeremy Schmutz, Shawn M. Kaeppler, Michael D. Casler, Carol Robin Buell & Chia-Lin Wei
Switchgrass (Panicum virgatum L.) is a polyploid, perennial grass species that is native to North America, and is being developed as a future biofuels feedstock crop. Switchgrass is present primarily in two ecotypes: a northern upland ecotype composed of tetraploid and octoploid accessions, and a southern lowland ecotype composed of primarily tetraploid accessions. We employed high-coverage exome capture sequencing (~2.4 Tb) to genotype 537 individuals from 45 upland and 21 lowland populations. From these data,...

Data from: Tradeoffs between maize silage yield and nitrate leaching in a Mediterranean nitrate-vulnerable zone under current and projected climate scenarios

Bruno Basso, Pietro Giola, Benjamin Dumont, Massimiliano De Antoni Migliorati, Davide Cammarano, Giovanni Pruneddu, Francesco Giunta & Massimiliano De Antoni Migliorati
Future climatic changes may have profound impacts on cropping systems and affect the agronomic and environmental sustainability of current N management practices. The objectives of this work were to i) evaluate the ability of the SALUS crop model to reproduce experimental crop yield and soil nitrate dynamics results under different N fertilizer treatments in a farmer’s field, ii) use the SALUS model to estimate the impacts of different N fertilizer treatments on NO3- leaching under...

Data from: Modeling and quantifying frequency-dependent fitness in microbial populations with cross-feeding interactions

Noah Ribeck & Richard E. Lenski
Coexistence of two or more populations by frequency-dependent selection is common in nature, and it often arises even in well-mixed experiments with microbes. If ecology is to be incorporated into models of population genetics, then it is important to represent accurately the functional form of frequency-dependent interactions. However, measuring this functional form is problematic for traditional fitness assays, which assume a constant fitness difference between competitors over the course of an assay. Here, we present...

Data from: The importance of terrestrial subsidies in stream food webs varies along a stream size gradient

Sarah M. Collins, Tyler J. Kohler, Steven A. Thomas, William W. Fetzer & Alexander S. Flecker
Cross system subsidies of energy and materials can be a substantial fraction of food web fluxes in ecosystems, especially when autochthonous production is strongly limited by light or nutrients. We explored whether assimilation of terrestrial energy varied in specific consumer taxa collected from streams of different sizes and resource availabilities. Since headwater streams are often unproductive, we expected that inputs from surrounding terrestrial systems (i.e. leaf litter, terrestrial invertebrates) would be a more important food...

Data from: How diverse detrital environments influence nutrient stoichiometry between males and females of the co-occurring container mosquitoes Aedes albopictus, Ae. aegypti, and Culex quinquefasciatus

Donald A. Yee, Michael G. Kaufman & Nnaemeka F. Ezeakacha
Allocation patterns of carbon and nitrogen in animals are influenced by food quality and quantity, as well as by inherent metabolic and physiological constraints within organisms. Whole body stoichiometry also may vary between the sexes who differ in development rates and reproductive allocation patterns. In aquatic containers, such as tree holes and tires, detrital inputs, which vary in amounts of carbon and nitrogen, form the basis of the mosquito-dominated food web. Differences in development times...

Data from: Replaying evolution to test the cause of extinction of one ecotype in an experimentally evolved population

Caroline B. Turner, Zachary D. Blount & Richard E. Lenski
In a long-term evolution experiment with Escherichia coli, bacteria in one of twelve populations evolved the ability to consume citrate, a previously unexploited resource in a glucose-limited medium. This innovation led to the frequency-dependent coexistence of citrate-consuming (Cit+) and non-consuming (Cit–) ecotypes, with Cit−bacteria persisting on the exogenously supplied glucose as well as other carbon molecules released by the Cit+ bacteria. After more than 10,000 generations of coexistence, however, the Cit−lineage went extinct; cells with...

Data from: Can impacts of climate change and agricultural adaptation strategies be accurately quantified if crop models are annually re-initialized?

Bruno Basso, David W. Hyndman, Anthony D. Kendall, Peter R. Grace & G. Philip Robertson
Estimates of climate change impacts on global food production are generally based on statistical or process-based models. Process-based models can provide robust predictions of agricultural yield responses to changing climate and management. However, applications of these models often suffer from bias due to the common practice of re-initializing soil conditions to the same state for each year of the forecast period. If simulations neglect to include year-to-year changes in initial soil conditions and water content...

Data from: Nitrous oxide emissions during establishment of eight alternative cellulosic bioenergy cropping systems in the North Central United States

Lawrence G. Oates, David S. Duncan, Ilya Gelfand, Neville Millar, G. Philip Robertson & Randall D. Jackson
Greenhouse gas (GHG) emissions from soils are a key sustainability metric of cropping systems. During crop establishment, disruptive land-use change is known to be a critical, but under reported period, for determining GHG emissions. We measured soil N2O emissions and potential environmental drivers of these fluxes from a three-year establishment-phase bioenergy cropping systems experiment replicated in southcentral Wisconsin (ARL) and southwestern Michigan (KBS). Cropping systems treatments were annual monocultures (continuous corn, corn–soybean–canola rotation), perennial monocultures...

Data from: Genome-wide errant targeting by Hairy

Kurtulus Kok, Ahmet Ay, Li M. Li & David N. Arnosti
Metazoan transcriptional repressors regulate chromatin through diverse histone modifications. Contributions of individual factors to the chromatin landscape in development is difficult to establish, as global surveys reflect multiple changes in regulators. Therefore, we studied the conserved Hairy/Enhancer of Split family repressor Hairy, analyzing histone marks and gene expression in Drosophila embryos. This long-range repressor mediates histone acetylation and methylation in large blocks, with highly context-specific effects on target genes. Most strikingly, Hairy exhibits biochemical activity...

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: Effects of land use on lake nutrients: the importance of scale, hydrologic connectivity, and region

Patricia A. Soranno, Kendra Spence Cheruvelil, Tyler Wagner, Katherine E. Webster & Mary Tate Bremigan
Catchment land uses, particularly agriculture and urban uses, have long been recognized as major drivers of nutrient concentrations in surface waters. However, few simple models have been developed that relate the amount of catchment land use to downstream freshwater nutrients. Nor are existing models applicable to large numbers of freshwaters across broad spatial extents such as regions or continents. This research aims to increase model performance by exploring three factors that affect the relationship between...

Registration Year

  • 2015

Resource Types

  • Dataset


  • Michigan State University
  • University of Wisconsin-Madison
  • University of Kansas
  • University of Minnesota
  • Texas A&M University
  • University of Tennessee at Knoxville
  • Queensland University of Technology
  • Cornell University
  • Grand Valley State University
  • California State University, Northridge