41 Works

Data from: Genome reduction uncovers a large dispensable genome and adaptive role for copy number variation in asexually propagated Solanum tuberosum

Michael A. Hardigan, Emily Crisovan, John P. Hamilton, Jeongwoon Kim, Parker Laimbeer, Courtney P. Leisner, Norma C. Manrique-Carpintero, Linsey Newton, Gina M. Pham, Brieanne Vaillancourt, Xueming Yang, Zixian Zeng, David S. Douches, Jiming Jiang, Richard E. Veilleux & C. Robin Buell
Clonally reproducing plants have the potential to bear a significantly greater mutational load than sexually reproducing species. To investigate this possibility, we examined the breadth of genome-wide structural variation in a panel of monoploid/doubled monoploid clones generated from native populations of diploid potato (Solanum tuberosum), a highly heterozygous asexually propagated plant. As rare instances of purely homozygous clones, they provided an ideal set for determining the degree of structural variation tolerated by this species, and...

Data from: Socioecological predictors of immune defenses in wild spotted hyenas

Andrew S. Flies, Linda S. Mansfield, Emily J. Flies, Chris K. Grant & Kay E. Holekamp
Social rank can profoundly affect many aspects of mammalian reproduction and stress physiology, but little is known about how immune function is affected by rank and other socioecological factors in free-living animals. In this study, we examine the effects of sex, social rank and reproductive status on immune function in long-lived carnivores that are routinely exposed to a plethora of pathogens, yet rarely show signs of disease. Here, we show that two types of immune...

Data from: Incomplete loss of a conserved trait: function, latitudinal cline, and genetic constraints

Anne M. Royer, Colin Kremer, Kola George, Samuel G. Pérez, Douglas W. Schemske & Jeffrey K. Conner
Retention of nonfunctional traits over evolutionary time is puzzling, because the cost of trait production should drive loss. Indeed, several studies have found nonfunctional traits are rapidly eliminated by selection. However, theory suggests that complex genetic interactions and a lack of genetic variance can constrain evolution, including trait loss. In the mustard family Brassicaceae the conserved floral condition includes four long and two short stamens, but we show that short stamens in the highly self-pollinating...

Data from: Haplotype-phased synthetic long reads from short-read sequencing

James A. Stapleton, Jeongwoon Kim, John P. Hamilton, Ming Wu, Luiz C. Irber, Rohan Maddamsetti, Bryan Briney, Linsey Newton, Dennis R. Burton, C. Titus Brown, Christina Chan, C. Robin Buell & Timothy A. Whitehead
Next-generation DNA sequencing has revolutionized the study of biology. However, the short read lengths of the dominant instruments complicate assembly of complex genomes and haplotype phasing of mixtures of similar sequences. Here we demonstrate a method to reconstruct the sequences of individual nucleic acid molecules up to 11.6 kilobases in length from short (150-bp) reads. We show that our method can construct 99.97%-accurate synthetic reads from bacterial, plant, and animal genomic samples, full-length mRNA sequences...

Data from: Examining disease prevalence for species of conservation concern using non-invasive spatial capture-recapture techniques

Arthur B. Muneza, Daniel W. Linden, Robert A. Montgomery, Amy J. Dickman, Gary J. Roloff, David W. Macdonald & Julian T. Fennessy
1. Non-invasive techniques have long been used to estimate wildlife population abundance and density. However, recent technological breakthroughs have facilitated non-invasive estimation of the proportion of animal populations with certain diseases. Giraffes Giraffa camelopardalisare increasingly becoming recognized as a species of conservation concern with decreasing population trajectories across their range in Africa. 2. Diseases may be an important component impacting giraffe population declines, and the emerging ‘Giraffe Skin Disease’ (GSD), characterized by the appearance of...

Data from: Draft assembly of elite inbred line PH207 provides insights into genomic and transcriptome diversity in maize

Candice N. Hirsch, Cory D. Hirsch, Alex B. Brohammer, Megan J. Bowman, Ilya Soifer, Omer Barad, Doron Sehm-Tov, Kobi Baruch, Fei Lu, Alvaro G. Hernandez, Christopher J. Fields, Chris L. Wright, Klaus Koehler, Nathan M. Springer, Edward S. Buckler, C. Robin Buell, Natalia De Leon, Shawn M. Kaeppler, Kevin Childs & Mark A. Mikel
Intense artificial selection over the last 100 years has produced elite maize (Zea mays) inbred lines that combine to produce high-yielding hybrids. To further our understanding of how genome and transcriptome variation contribute to the production of high-yielding hybrids, we generated a draft genome assembly of the inbred line PH207 to complement and compare with the existing B73 reference sequence. B73 is a founder of the Stiff Stalk germplasm pool, while PH207 is a founder...

Data from: Phylogenomics from whole genome sequences using aTRAM

Julie M. Allen, Bret Boyd, Nam-Phuong Nguyen, Pranjal Vachaspati, Tandy Warnow, Daisie I. Huang, Patrick G. S. Grady, Kayce C. Bell, Quentin C.B. Cronk, Lawrence Mugisha, Barry R. Pittendrigh, M. Soledad Leonardi, David L. Reed & Kevin P. Johnson
Novel sequencing technologies are rapidly expanding the size of data sets that can be applied to phylogenetic studies. Currently the most commonly used phylogenomic approaches involve some form of genome reduction. While these approaches make assembling phylogenomic data sets more economical for organisms with large genomes, they reduce the genomic coverage and thereby the long-term utility of the data. Currently, for organisms with moderate to small genomes (<1000 Mbp) it is feasible to sequence the...

Data from: Cryptic individual scaling relationships and the evolution of morphological scaling

Austin P. Dreyer, Omid Saleh Ziabari, Eli Swanson, Akshita Chawla, W. Anthony Frankino, Alexander W. Shingleton & Eli M. Swanson
Morphological scaling relationships between organ and body size—also known as allometries—describe the shape of a species, and the evolution of such scaling relationships is central to the generation of morphological diversity. Despite extensive modeling and empirical tests, however, the modes of selection that generate changes in scaling remain largely unknown. Here, we mathematically model the evolution of the group-level scaling as an emergent property of individual-level variation in the developmental mechanisms that regulate trait and...

Data from: Adaptive divergence in flowering time among natural populations of Arabidopsis thaliana: estimates of selection and QTL mapping

Jon Ågren, Christopher G. Oakley, Sverre Lundemo & Douglas W. Schemske
To identify the ecological and genetic mechanisms of local adaptation requires estimating selection on traits, identifying their genetic basis, and evaluating whether divergence in adaptive traits is due to conditional neutrality or genetic tradeoffs. To this end, we conducted field experiments for three years using recombinant inbred lines derived from two ecotypes of Arabidopsis thaliana (Italy, Sweden), and at each parental site examined selection on flowering time and mapped QTL. There was strong selection for...

Data from: Experimental evidence does not support the Habitat Amount Hypothesis

Nick M. Haddad, Andrew Gonzalez, Lars A. Brudvig, Melissa A. Burt, Douglas J. Levey & Ellen I. Damschen
For a half century, habitat configuration – the arrangement of habitat patches within a landscape – has been central to theories of landscape ecology, population dynamics, and community assembly, in addition to conservation strategies. A recent hypothesis advanced by Fahrig (2013) would, if supported, greatly diminish the relevance of habitat configuration as a predictor of diversity. The Habitat Amount Hypothesis posits that the sample area effect overrides patch size and patch isolation effects of habitat...

Data from: Crop-associated virus infection in a native perennial grass: reduction in plant fitness and dynamic patterns of virus detection

Helen M. Alexander, Emily Bruns, Hayley Schebor & Carolyn M. Malmstrom
To understand the eco-evolutionary significance of plant viruses in nature, we must (i) quantify the effects of infection on plant fitness and (ii) recognize that native plants are increasingly exposed to crop-associated viruses. Studies of perennials are particularly needed: most of our knowledge of plant-virus interactions is from annuals, yet long-lived species dominate landscapes. Here we used aster models for life-history analysis and longitudinal measures of plant virus status to evaluate multi-year consequences of crop...

Data from: Adaptive divergence despite strong genetic drift: genomic analysis of the evolutionary mechanisms causing genetic differentiation in the island fox (Urocyon littoralis)

W. Chris Funk, Robert E. Lovich, Paul A. Hohenlohe, Courtney A. Hofman, Scott A. Morrison, T. Scott Sillett, Cameron K. Ghalambor, Jesús E. Maldonado, Torben C. Rick, Mitch D. Day, Nicholas R. Polato, Sarah W. Fizpatrick, Timothy J. Coonan, Kevin R. Crooks, Adam Dillon, David K. Garcelon, Julie L. King, Christina L. Boser, Nicholas Gould, William F. Andelt & Sarah W. Fitzpatrick
The evolutionary mechanisms generating the tremendous biodiversity of islands have long fascinated evolutionary biologists. Genetic drift and divergent selection are predicted to be strong on islands and both could drive population divergence and speciation. Alternatively, strong genetic drift may preclude adaptation. We conducted a genomic analysis to test the roles of genetic drift and divergent selection in causing genetic differentiation among populations of the island fox (Urocyon littoralis). This species consists of six subspecies, each...

Data from: Partitioning the effects of isolation by distance, environment, and physical barriers on genomic divergence between parapatric threespine stickleback

Jesse N. Weber, Gideon S. Bradburd, Yoel E. Stuart, William E. Stutz & Daniel I. Bolnick
Genetic divergence between populations is shaped by a combination of drift, migration, and selection, yielding patterns of isolation-by-distance (IBD) and isolation-by-environment (IBE). Unfortunately, IBD and IBE may be confounded when comparing divergence across habitat boundaries. For instance, parapatric lake and stream threespine stickleback (Gasterosteus aculeatus) may have diverged due to selection against migrants (IBE), or mere spatial separation (IBD). To quantitatively partition the strength of IBE and IBD, we used recently-developed population genetic software (BEDASSLE)...

Data from: Evolution of reproductive isolation in stickleback fish

Alycia C. R. Lackey & Janette Wenrick Boughman
To understand how new species form and what causes their collapse, we examined how reproductive isolation evolves during the speciation process, considering species pairs with little to extensive divergence, including a recently collapsed pair. We estimated many reproductive barriers in each of five sets of stickleback fish species pairs using our own data and decades of previous work. We found that the types of barriers important early in the speciation process differ from those important...

Data from: Ecological speciation of bacteriophage lambda in allopatry and sympatry

Justin R. Meyer, Devin T. Dobias, Sarah J. Medina, Lisa Servilio, Animesh Gupta & Richard E. Lenski
Understanding the conditions that allow speciation to occur is difficult because most research has focused on either long-lived organisms or asexual microorganisms. We propagated bacteriophage λ, a virus with rapid generations and frequent recombination, on two Escherichia coli host genotypes that expressed either the LamB or OmpF receptor. When supplied with either single host (allopatry), λ improved its binding to the available receptor while losing its ability to use the alternative. When evolving on both...

Data from: Immunoglobulin detection in wild birds: effectiveness of three secondary anti-avian IgY antibodies in direct ELISAs in 41 avian species

Carol A. Fassbinder-Orth, Travis E. Wilcoxen, Tiffany Tran, Raoul K. Boughton, Jeanne M. Fair, Erik K. Hofmeister, Jennifer L. Grindstaff & Jen C. Owen
1.Immunological reagents for wild, non-model species are limited or often non-existent for many species. 2. In this study, we compare the reactivity of a new anti-passerine IgY secondary antibody with existing secondary antibodies developed for use with birds. Samples from 41 species from the following six avian orders were analysed: Anseriformes (1 family, 1 species), Columbiformes (1 family, 2 species), Galliformes (1 family, 1 species), Passeriformes (16 families, 34 species), Piciformes (1 family, 2 species)...

Data from: Intra-organ growth coordination in Drosophila is mediated by systemic ecdysone signaling

Rewatee H. Gokhale, Takashi Hayashi, Christopher D. Mirque & Alexander W. Shingleton
Regulation of final organ size is a complex developmental process that involves the integration of systemic and organ-specific processes. Previously, we have shown that in developing Drosophila, perturbing the growth of one imaginal disc – the parts of a holometabolous larva that become the external adult organs – retards growth of other discs and delays development, resulting in tight inter-organ growth coordination and the generation of a correctly proportioned adult. Whether different parts of the...

Data from: The ‘heritability’ of domestication and its functional partitioning in the pig

Miguel Perez-Enciso, Gustavo De Los Campos, Nick Hudson, James Kijas & Antonio Reverter
We propose to estimate the proportion of variance explained by regression on genome-wide markers (or genomic heritability) when wild/domestic status is considered the phenotype of interest. This approach differs from the standard Fst in that it can accommodate genetic similarity between individuals in a general form. We apply this strategy to complete genome data from 47 wild and domestic pigs from Asia and Europe. When we partitioned the total genomic variance into components associated to...

Data from: Field measurements of genotype by environment interaction for fitness caused by spontaneous mutations in Arabidopsis thaliana

Angela J. Roles, Matthew Thomas Rutter, Ian Dworkin, Charles B. Fenster & Jeffrey K. Conner
As the ultimate source of genetic diversity, spontaneous mutation is critical to the evolutionary process. The fitness effects of spontaneous mutations are almost always studied under controlled laboratory conditions rather than under the evolutionarily relevant conditions of the field. Of particular interest is the conditionality of new mutations - i.e., is a new mutation harmful regardless of the environment in which it is found? In other words, what is the extent of genotype-environment interaction for...

Data from: Host coevolution alters the adaptive landscape of a virus

Alita R. Burmeister, Richard E. Lenski & Justin R. Meyer
The origin of new and complex structures and functions is fundamental for shaping the diversity of life. Such key innovations are rare because they require multiple interacting changes. We sought to understand how the adaptive landscape led to an innovation whereby bacteriophage λ evolved the new ability to exploit a receptor, OmpF, on Escherichia coli cells. Previous work showed that this ability evolved repeatedly, despite requiring four mutations in one virus gene. Here, we examine...

Data from: Increases in the mean and variability of thermal regimes result in differential phenotypic responses among genotypes during early ontogenetic stages of lake sturgeon (Acipenser fulvescens)

Kari J. Dammerman, Juan P. Steibel & Kim T. Scribner
Climate change is affecting thermal conditions worldwide. Understanding organismal responses associated with predicted changes are essential for predicting population persistence. Few studies have examined the effects of both increased mean and variance in temperature on organismal traits, particularly during early life stages. Using lake sturgeon (Acipenser fulvescens) from Black Lake, MI, we tested whether phenotypic variation differed among families reared in two constant (10 and 18°C) and two fluctuating temperature treatments (10-19°C) representing temperatures experienced...

Data from: Long-term nitrous oxide fluxes in annual and perennial agricultural and unmanaged ecosystems in the upper Midwest USA

Ilya Gelfand, Iurii Shcherbak, Neville Millar, Alexandra N. Kravchenko & G. Philip Robertson
Differences in soil nitrous oxide (N2O) fluxes among ecosystems are often difficult to evaluate and predict due to high spatial and temporal variabilities and few direct experimental comparisons. For 20 years, we measured N2O fluxes in 11 ecosystems in southwest Michigan USA: four annual grain crops (corn–soybean–wheat rotations) managed with conventional, no-till, reduced input, or biologically based/organic inputs; three perennial crops (alfalfa, poplar, and conifers); and four unmanaged ecosystems of different successional age including mature...

Data from: Different evolutionary paths to complexity for small and large populations of digital organisms

Thomas LaBar & Christoph Adami
A major aim of evolutionary biology is to explain the respective roles of adaptive versus non-adaptive changes in the evolution of complexity. While selection is certainly responsible for the spread and maintenance of complex phenotypes, this does not automatically imply that strong selection enhances the chance for the emergence of novel traits, that is, the origination of complexity. Population size is one parameter that alters the relative importance of adaptive and non-adaptive processes: as population...

Data from: Reduced snow cover increases wintertime nitrous oxide (N2O) emissions from an agricultural soil in the upper U.S. Midwest

Leilei Ruan & G. Philip Robertson
Throughout most of the northern hemisphere, snow cover decreased in almost every winter month from 1967 to 2012. Because snow is an effective insulator, snow cover loss has likely enhanced soil freezing and the frequency of soil freeze–thaw cycles, which can disrupt soil nitrogen dynamics including the production of nitrous oxide (N2O). We used replicated automated gas flux chambers deployed in an annual cropping system in the upper Midwest US for three winters (December–March, 2011–2013)...

Data from: Grazing effects on surface energy fluxes in a desert steppe on the Mongolian Plateau

Changliang Shao, Jiquan Chen, Linghao Li, Gang Dong, Juanjuan Han, Michael Abraha & Ranjeet John
Quantifying the surface energy fluxes of grazed and ungrazed steppes is essential to understand the roles of grasslands in local and global climate and in land use change. We used paired eddy-covariance towers to investigate the effects of grazing on energy balance (EB) components: net radiation (Rn), latent heat (LE), sensible heat (H), and soil heat (G) fluxes on adjacent grazed and ungrazed areas in a desert steppe of the Mongolian Plateau for a two-year...

Registration Year

  • 2016

Resource Types

  • Dataset


  • Michigan State University
  • University of Minnesota
  • University of Wisconsin-Madison
  • McMaster University
  • University of Maryland, College Park
  • The University of Texas at Austin
  • University of California, San Diego
  • Murray State University
  • University of Colorado Boulder
  • University of Nebraska - Lincoln