39 Works

Data from: Multi-scaled drivers of ecosystem state: quantifying the importance of the regional spatial scale

Kendra S. Cheruvelil, Patricia A. Soranno, Katherine E. Webster & Mary T. Bremigan
The regional spatial scale is a vital linkage for the informed extrapolation of results from local to continental scales to address broad-scale environmental problems. Among-region variation in ecosystem state is commonly accounted for by using a regionalization framework, such as an ecoregion classification. Rarely have alternative regionalization frameworks been tested for variables measuring ecosystem state, nor have the underlying relationships with the variables that are used to define them been assessed. In this study, we...

Data from: Comparative transcriptome atlases reveal altered gene expression modules between two Cleomaceae C3 and C4 plant species

Canan Külahoglu, Manuel Sommer, Janina Maß, Simon Schliesky, Barbara Berckmans, Elsa Gongora-Castillo, C. Robin Buell, Rüdiger Simon, Lieven De Veylder, Andrea Bräutigam, Andreas P. M. Weber, Alisandra K. Denton & Thomas J. Wrobel
C4 photosynthesis outperforms the ancestral C3 state in a wide range of natural and agro-ecosystems by affording higher water-use and nitrogen-use efficiencies. It therefore represents a prime target for engineering novel, high-yielding crops by introducing the trait into C3 backgrounds. However, the genetic architecture of C4 photosynthesis remains largely unknown. To define the divergence in gene expression modules between C3 and C4 photosynthesis during leaf ontogeny, we generated comprehensive transcriptome atlases of two Cleomaceae species,...

Data from: Flowering time QTL in natural populations of Arabidopsis thaliana and implications for their adaptive value

Emily L. Dittmar, Christopher G. Oakley, Jon Ågren & Douglas W. Schemske
The genetic basis of phenotypic traits is of great interest to evolutionary biologists, but their contribution to adaptation in nature is often unknown. To determine the genetic architecture of flowering time in ecologically relevant conditions, we used a recombinant inbred line population created from two locally adapted populations of Arabidopsis thaliana from Sweden and Italy. Using these RILs, we identified flowering time QTL in growth chambers that mimicked the natural temperature and photoperiod variation across...

Data from: Gene amplification of 5-enol-pyruvylshikimate-3-phosphate synthase in glyphosate-resistant Kochia scoparia

Andrew T. Wiersma, Todd A. Gaines, Christopher Preston, John P. Hamilton, Darci Giacomini, C. Robin Buell, Jan E. Leach & Philip Westra
The widely used herbicide glyphosate inhibits the shikimate pathway enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS). Globally, the intensive use of glyphosate for weed control has selected for glyphosate resistance in 31 weed species. Populations of suspected glyphosate-resistant Kochia scoparia were collected from fields located in the US central Great Plains. Glyphosate dose response verified glyphosate resistance in nine populations. The mechanism of resistance to glyphosate was investigated using targeted sequencing, quantitative PCR, immunoblotting, and whole transcriptome de...

Data from: The potential influence of morphology on the evolutionary divergence of an acoustic signal.

William R. Pitchers, Chris P. Klingenberg, Tom Tregenza, John Hunt & Ian Dworkin
The evolution of acoustic behaviour and that of the morphological traits mediating its production are often coupled. Lack of variation in the underlying morphology of signalling traits has the potential to constrain signal evolution. This relationship is particularly likely in field crickets, where males produce acoustic advertisement signals to attract females by stridulating with specialized structures on their forewings. In this study, we characterize the size and geometric shape of the forewings of males from...

Data from: Gape-limited predators as agents of selection on the defensive morphology of an invasive invertebrate

Andrea L. J. Miehls, Scott D. Peacor & Andrew G. McAdam
Invasive species have widespread and pronounced effects on ecosystems and adaptive evolution of invaders is often considered responsible for their success. Despite the potential importance of adaptation to invasion, we still have limited knowledge of the agents of natural selection on invasive species. Bythotrephes longimanus, a cladoceran zooplankton, invaded multiple Canadian Shield lakes over the past several decades. Bythotrephes have a conspicuous caudal process (tail spine) that provides a morphological defense against fish predation. We...

Data from: Large chromosomal rearrangements during a long-term evolution experiment with Escherichia coli

Colin Raeside, Joël Gaffé, Daniel E. Deatherage, Olivier Tenaillon, Adam M. Briska, Ryan N. Ptashkin, Stéphane Cruveiller, Claudine Médigue, Richard E. Lenski, Jeffrey E. Barrick & Dominique Schneider
Large-scale rearrangements may be important in evolution because they can alter chromosome organization and gene expression in ways not possible through point mutations. In a long-term evolution experiment, twelve Escherichia coli populations have been propagated in a glucose-limited environment for over 25 years. We used whole-genome mapping (optical mapping) combined with genome sequencing and PCR analysis to identify the large-scale chromosomal rearrangements in clones from each population after 40,000 generations. A total of 110 rearrangement...

Data from: Transcriptome analysis indicates considerable divergence in alternative splicing between duplicated genes in Arabidopsis thaliana

David C. Tack, William R. Pitchers & Keith L. Adams
Gene and genome duplication events have created a large number of new genes in plants that can diverge by evolving new expression profiles and functions (neofunctionalization) or dividing extant ones (subfunctionalization). Alternative splicing (AS) generates multiple types of mRNA from a single type of pre-mRNA by differential intron splicing. It can result in new protein isoforms or down-regulation of gene expression by transcript decay. Using RNA-seq we investigated the degree to which alternative splicing patterns...

Data from: Height and clonality traits determine plant community responses to fertilization

Timothy L. Dickson, Gary G. Mittelbach, Heather L. Reynolds & Katherine L. Gross
Fertilization via agricultural inputs and nutrient deposition is one of the major threats to global terrestrial plant richness, yet we still do not fully understand the mechanisms by which fertilization decreases plant richness. Tall clonal species have recently been proposed to cause declines in plant species richness by increasing in abundance in response to fertilization and competing strongly with other species. We tested this hypothesis in a fertilization experiment in a low productivity grassland by...

Data from: Insights into the maize pan-genome and pan-transcriptome

Candice N. Hirsch, Jillian M. Foerster, James M. Johnson, Rajandeep S. Sekhon, German Muttoni, Brieanne Vaillancourt, Francisco Peñagaricano, Erika Lindquist, Mary Ann Pedraza, Kerrie Barry, Natalia De Leon, Shawn M. Kaeppler & C. Robin Buell
Genomes at the species level are dynamic, with genes present in every individual (core) and genes in a subset of individuals (dispensable) that collectively constitute the pan-genome. Using transcriptome sequencing of seedling RNA from 503 maize (Zea mays) inbred lines to characterize the maize pan-genome, we identified 8681 representative transcript assemblies (RTAs) with 16.4% expressed in all lines and 82.7% expressed in subsets of the lines. Interestingly, with linkage disequilibrium mapping, 76.7% of the RTAs...

Data from: Generation of transcript assemblies and identification of single nucleotide polymorphisms from seven lowland and upland cultivars of switchgrass

Kevin L. Childs, Aruna Nandety, Candice N. Hirsch, Elsa Góngora-Castillo, Jeremy Schmutz, Shawn M. Kaeppler, Michael D. Casler & C. Robin Buell
Switchgrass (Panicum virgatum) is a North American perennial prairie species that has been used as a rangeland and forage crop and has recently been targeted as a potential biofuel feedstock species. Switchgrass, which occurs as tetraploid and octoploid forms, is classified into lowland or upland ecotypes that differ in growth phenotypes and adaptation to distinct habitats. Using RNA-sequencing reads derived from crown, young shoot and leaf tissues, we generated sequence data from seven switchgrass cultivars,...

Data from: The evolutionary origin of somatic cells under the dirty work hypothesis

Heather J. Goldsby, David B. Knoester, Charles Ofria & Benjamin Kerr
Reproductive division of labor is a hallmark of multicellular organisms. However, the evolutionary pressures that give rise to delineated germ and somatic cells remain unclear. Here we propose a hypothesis that the mutagenic consequences associated with performing metabolic work favor such differentiation. We present evidence in support of this hypothesis gathered using a computational form of experimental evolution. Our digital organisms begin each experiment as undifferentiated multicellular individuals, and can evolve computational functions that improve...

Data from: Coevolution drives the emergence of complex traits and promotes evolvability

Luis Zaman, Justin R. Meyer, Suhas Devangam, David M. Bryson, Richard E. Lenski & Charles Ofria
The evolution of complex organismal traits is obvious as a historical fact, but the underlying causes—including the role of natural selection—are contested. Gould argued that a random walk from a necessarily simple beginning would produce the appearance of increasing complexity over time. Others contend that selection, including coevolutionary arms races, can systematically push organisms toward more complex traits. Methodological challenges have largely precluded experimental tests of these hypotheses. Using the Avida platform for digital evolution,...

Data from: Long-term nitrogen addition causes the evolution of less cooperative mutualists

Dylan Jones Weese, Katy D. Heath, Bryn T. M. Dentinger & Jennifer Ann Lau
Human activities have altered the global nitrogen (N) cycle, and as a result, elevated N inputs are causing profound ecological changes in diverse ecosystems. The evolutionary consequences of this global change have been largely ignored even though elevated N inputs are predicted to cause mutualism breakdown and the evolution of decreased cooperation between resource mutualists. Using a long-term (22 year) N addition experiment, we find that elevated N inputs have altered the legume-rhizobium mutualism (where...

Data from: Coordination of wing and whole body development at developmental milestones ensures robustness against environmental and physiological perturbations

Marisa M. Oliveira, Alexander W. Shingleton & Christen K. Mirth
Development produces correctly patterned tissues under a wide range of conditions that alter the rate of development in the whole body. We propose two hypotheses through which tissue patterning could be coordinated with whole body development to generate this robustness. Our first hypothesis states that tissue patterning is tightly coordinated with whole body development over time. The second hypothesis is that tissue patterning aligns at developmental milestones. To distinguish between our two hypotheses, we developed...

Data from: QTL mapping of freezing tolerance: links to fitness and adaptive trade-offs

Christopher G. Oakley, Jon Ågren, Rachel A. Atchison & Douglas W. Schemske
Local adaptation, defined as higher fitness of local vs. non-local genotypes, is commonly identified in reciprocal transplant experiments. Reciprocally adapted populations display fitness trade-offs across environments, but little is known about the traits and genes underlying fitness trade-offs in reciprocally adapted populations. We investigated the genetic basis and adaptive significance of freezing tolerance using locally adapted populations of Arabidopsis thaliana from Italy and Sweden. Previous reciprocal transplant studies of these populations indicated that sub-freezing temperature...

Data from: Coexistence of evolving bacteria stabilized by a shared Black Queen function

James Jeffrey Morris, Spiridon E. Papoulis & Richard E. Lenski
The Black Queen Hypothesis (BQH) was originally proposed to explain the dependence of some marine bacteria on helper organisms for protection from hydrogen peroxide (HOOH). The BQH predicts that selection for the evolutionary loss of leaky functions from individuals can produce commensal or mutualistic interactions. We demonstrated the leakiness of HOOH detoxification by complementing a HOOH-sensitive Escherichia coli mutant with a plasmid-encoded HOOH-detoxifying enzyme, KatG, and then evolving populations founded by this strain in two...

Data from: Genetic architecture of a hormonal response to gene knockdown in honey bees

Kate E. Ihle, Olav Rueppell, Ying Wang, M. Kim Fondrk, , Gro V. Amdam & Zachary Y. Huang
Variation in endocrine signaling is proposed to underlie the evolution and regulation of social life histories, but the genetic architecture of endocrine signaling is still poorly understood. An excellent example of a hormonally influenced set of social traits is found in the honey bee (Apis mellifera): a dynamic and mutually suppressive relationship between juvenile hormone (JH) and the yolk precursor protein vitellogenin (Vg) regulates behavioral maturation and foraging of workers. Several other traits cosegregate with...

Data from: Shifts of tundra bacterial and archaeal communities along a permafrost thaw gradient in Alaska

Jie Deng, Yunfu Gu, Jin Zhang, Kai Xue, Yujia Qin, Mengting Yuan, Huaqun Yin, Zhili He, Liyou Wu, Edward Schuur, James Tiedje, Jizhong Zhou, James M. Tiedje & Edward A. G. Schuur
Understanding the response of permafrost microbial communities to climate warming is crucial for evaluating ecosystem feedbacks to global change. This study investigated soil bacterial and archaeal communities by Illumina MiSeq sequencing of 16S rRNA gene amplicons across a permafrost thaw gradient at different depths in Alaska with thaw progression for over three decades. Over 4.6 million passing 16S rRNA gene sequences were obtained from a total of 97 samples, corresponding to 61 known classes and...

Data from: Perturbing the cellular cevels of steroid receptor coactivator-2 impairs murine endometrial function

Maria M. Szwarc, Ramakrishna Kommagani, Jae-Wook Jeong, San-Pin Wu, Sophia Y. Tsai, Ming-Jer Tsai, Bert W. O'Malley, Francesco J. DeMayo & John P. Lydon
As pleiotropic coregulators, members of the p160/steroid receptor coactivator (SRC) family control a broad spectrum of transcriptional responses that underpin a diverse array of physiological and pathophysiological processes. Because of their potent coregulator properties, strict controls on SRC expression levels are required to maintain normal tissue functionality. Accordingly, an unwarranted increase in the cellular levels of SRC members has been causally linked to the initiation and/or progression of a number of clinical disorders. Although knockout...

Data from: Causes and consequences of genetic background effects illuminated by integrative genomic analysis

Christopher H. Chandler, Sudarshan Chari, David Tack & Ian Dworkin
The phenotypic consequences of individual mutations are modulated by the wild-type genetic background in which they occur. Although such background dependence is widely observed, we do not know whether general patterns across species and traits exist, nor about the mechanisms underlying it. We also lack knowledge on how mutations interact with genetic background to influence gene expression, and how this in turn mediates mutant phenotypes. Furthermore, how genetic background influences patterns of epistasis remains unclear....

Data from: Nutritional control of body size through FoxO-Ultraspiracle mediated ecdysone biosynthesis

Takashi Koyama, Marisa A. Rodrigues, Alekos Athanasiadis, Alexander W. Shingleton & Christen K. Mirth
Despite their fundamental importance for body size regulation, the mechanisms that stop growth are poorly understood. In Drosophila melanogaster, growth ceases in response to a peak of the molting hormone ecdysone that coincides with a nutrition-dependent checkpoint, critical weight. Previous studies indicate that insulin/insulin-like growth factor signaling (IIS)/Target of Rapamycin (TOR) signaling in the prothoracic glands (PGs) regulates ecdysone biosynthesis and critical weight. Here we elucidate a mechanism through which this occurs. We show that...

Data from: Aboveground herbivory by red milkweed beetles facilitates above- and below-ground conspecific insects and reduces fruit production in common milkweed

Alexis C. Erwin, Tobias Züst, Jared G. Ali & Anurag A. Agrawal
1. Initial herbivory and induced plant responses can influence subsequent above- and belowground herbivore attack. When two life stages of the same herbivore damage different plant parts sequentially, there is strong potential for plants to respond with induced plant defense against the later attacker. Alternatively, the earlier attacker could manipulate the host plant to facilitate the later-feeding life stage. 2. We studied herbivory by foliage-feeding adults and root-feeding larvae of the red milkweed beetle (Tetraopes...

Data from: Epistasis and allele specificity in the emergence of a stable polymorphism in Escherichia coli

Jessica Plucain, Thomas Hindré, Mickaël Le Gac, Olivier Tenaillon, Stéphane Cruveiller, Claudine Médigue, Nicholas Leiby, William R. Harcombe, Christopher J. Marx, Richard E. Lenski & Dominique Schneider
Ecological opportunities promote population divergence into coexisting lineages. However, the genetic mechanisms that enable new lineages to exploit these opportunities are poorly understood except in cases of single mutations. We examined how two Escherichia coli lineages diverged from their common ancestor at the outset of a long-term coexistence. By sequencing genomes and reconstructing the genetic history of one lineage, we showed that three mutations together were sufficient to produce the frequency-dependent fitness effects that allowed...

Data from: Trade-offs drive resource specialization and the gradual establishment of ecotypes

Bjørn Østman, Randall Lin & Christoph Adami
Background: Speciation is driven by many different factors. Among those are trade-offs between different ways an organism utilizes resources, and these trade-offs can constrain the manner in which selection can optimize traits. Limited migration among allopatric populations and species interactions can also drive speciation, but here we ask if trade-offs alone are sufficient to drive speciation in the absence of other factors. Results: We present a model to study the effects of trade-offs on specialization...

Registration Year

  • 2014
    39

Resource Types

  • Dataset
    39

Affiliations

  • Michigan State University
    39
  • University of Wisconsin-Madison
    5
  • California State University, Northridge
    2
  • University of Minnesota
    2
  • Great Lakes Bioenergy Research Center
    2
  • University of Oklahoma
    2
  • Lawrence Berkeley National Laboratory
    2
  • Indiana University Bloomington
    2
  • Inserm
    2
  • University of Florida
    2