36 Works

Data from: Powerful methods for detecting introgressed regions from population genomic data

Benjamin K. Rosenzweig, James B. Pease, Nora J. Besansky & Matthew H. Hahn
Understanding the types and functions of genes that are able to cross species boundaries—and those that are not—is an important step in understanding the forces maintaining species as largely independent lineages across the remainder of the genome. With large next-generation sequencing data sets we are now able to ask whether introgression has occurred across the genome, and multiple methods have been proposed to detect the signature of such events. Here, we introduce a new summary...

Data from: Does older adults' cognitive function disrupt the malleability of their attitudes toward outgroup members?: an fMRI investigation

Anne C. Krendl & Elizabeth A. Kensinger
In the current study we examine how individual differences in older adults’ global cognitive function impacts the extent to which their attitudes toward stigmatized individuals are malleable. Because prior research has elucidated the neural processes that are involved in evaluating stigmatized individuals who are responsible or not responsible for their condition, a cognitive neuroscience approach may be well-suited to answer this question. In the current study, 36 older and 17 young adults underwent functional magnetic...

Data from: Effect of acute stressor on reproductive behavior differs between urban and rural birds

Mikus Abolins-Abols, Sydney F. Hope & Ellen D. Ketterson
The life-history trade-off between self-maintenance and reproduction posits that investment in one function decreases investment in the other. Manipulating the costs and benefits of functions involved in a trade-off may alter this interaction. Here we ask whether investment in self-maintenance during a stress response alters territorial behavior in wild Dark-eyed Juncos and whether rural and urban birds, which are known to differ in the magnitude of the stress response (greater in rural), also differ in...

Data from: Molecular mechanisms of postmating prezygotic reproductive isolation uncovered by transcriptome analysis

James B. Pease, Rafael F. Guerrero, Natasha Sherman, Matthew Hahn, Leonie C. Moyle, Matthew W. Hahn & Natasha A. Sherman
Little is known about the physiological responses and genetic mutations associated with reproductive isolation between species, especially for postmating prezygotic isolating barriers. Here, we examine changes in gene expression that accompany the expression of ‘unilateral incompatibility’ (UI)—a postmating prezygotic barrier in which fertilization is prevented by gamete rejection in the reproductive tract [in this case of pollen tubes (male gametophytes)] in one direction of a species cross, but is successful in the reciprocal crossing direction....

Data from: Herbivory enhances the diversity of primary producers in pond ecosystems

Mathew A. Leibold, Spencer R. Hall, Val H. Smith & David A. Lytle
Diversity of primary producer is often surprisingly high, despite few limiting factors such as nutrients and light to facilitate species coexistence. In theory, the presence of herbivores could increase the diversity of primary producers, resolving this “paradox of the plankton”. Little experimental evidence supports this natural enemies hypothesis, but previous tests suffer from several deficiencies. Previous experiments often did not allow for multigeneration effects; utilized low diversity assemblages of herbivores; and limited opportunities for new...

Data from: Comparative developmental transcriptomics reveals rewiring of a highly conserved gene regulatory network during a major life history switch in the sea urchin genus Heliocidaris

Jennifer W. Israel, Megan L. Martik, Maria Byrne, Elizabeth C. Raff, Rudolf A. Raff, David R. McClay & Gregory A. Wray
The ecologically significant shift in developmental strategy from planktotrophic (feeding) to lecithotrophic (nonfeeding) development in the sea urchin genus Heliocidaris is one of the most comprehensively studied life history transitions in any animal. Although the evolution of lecithotrophy involved substantial changes to larval development and morphology, it is not known to what extent changes in gene expression underlie the developmental differences between species, nor do we understand how these changes evolved within the context of...

Data from: Genome-wide patterns of regulatory divergence revealed by introgression lines

Rafael F. Guerrero, Amanda L. Posto, Leonie Clare Moyle & Matthew W. Hahn
Understanding the genetic basis for changes in transcriptional regulation is an important aspect of understanding phenotypic evolution. Using interspecific introgression lines, we infer the mechanisms of divergence in genome-wide patterns of gene expression between the nightshades Solanum pennellii and S. lycopersicum (domesticated tomato). We find that cis- and trans-regulatory changes have had qualitatively similar contributions to divergence in this clade, unlike results from other systems. Additionally, expression data from four tissues (shoot apex, ripe fruit,...

Data from: Coevolutionary interactions with parasites constrain the spread of self-fertilization into outcrossing host populations

Samuel Preston Slowinski, Levi T. Morran, , Eric R. Cui, Amrita Bhattacharya, Curtis M. Lively, Patrick C. Phillips & Raymond C. Parrish
Given the cost of sex, outcrossing populations should be susceptible to invasion and replacement by self-fertilization or parthenogenesis. However, biparental sex is common in nature, suggesting that cross-fertilization has substantial short-term benefits. The Red Queen hypothesis (RQH) suggests that coevolution with parasites can generate persistent selection favoring both recombination and outcrossing in host populations. We tested the prediction that coevolving parasites can constrain the spread of self-fertilization relative to outcrossing. We introduced wild-type Caenorhabditis elegans...

Data from: Reticulate evolutionary history and extensive introgression in mosquito species revealed by phylogenetic network analysis

Dingqiao Wen, Yun Yu, Matthew W. Hahn & Luay Nakhleh
The role of hybridization and subsequent introgression has been demonstrated in an increasing number of species. Recently, Fontaine et al. (Science, 347, 2015, 1258524) conducted a phylogenomic analysis of six members of the Anopheles gambiae species complex. Their analysis revealed a reticulate evolutionary history and pointed to extensive introgression on all four autosomal arms. The study further highlighted the complex evolutionary signals that the co-occurrence of incomplete lineage sorting (ILS) and introgression can give rise...

Data from: Joint effects of habitat, zooplankton, host stage structure and diversity on amphibian chytrid

Jessica L. Hite, Jaime Bosch, Saioa Fernández-Beaskoetxea, Daniel Medina & Spencer R. Hall
Why does the severity of parasite infection differ dramatically across habitats? This question remains challenging to answer because multiple correlated pathways drive disease. Here, we examined habitat–disease links through direct effects on parasites and indirect effects on parasite predators (zooplankton), host diversity and key life stages of hosts. We used a case study of amphibian hosts and the chytrid fungus, Batrachochytrium dendrobatidis, in a set of permanent and ephemeral alpine ponds. A field experiment showed...

Data from: Neofunctionalization of embryonic head patterning genes facilitates the positioning of novel traits on the dorsal head of adult beetles

Eduardo E. Zattara, Hannah A. Busey, David M. Linz, Yoshinori Tomoyasu & Armin P. Moczek
The origin and integration of novel traits are fundamental processes during the developmental evolution of complex organisms. Yet how novel traits integrate into pre-existing contexts remains poorly understood. Beetle horns represent a spectacular evolutionary novelty integrated within the context of the adult dorsal head, a highly conserved trait complex present since the origin of insects. We investigated whether otd1/2 and six3, members of a highly conserved gene network that instructs the formation of the anterior...

Data from: Remarkable life history polymorphism may be evolving under divergent selection in the silverleaf sunflower

Brook T. Moyers & Loren H. Rieseberg
Substantial intraspecific variation in life history is rare and potentially a signal of incipient ecological speciation, if variation is driven by geographically heterogenous natural selection. We present the first report of extensive life history polymorphism in Helianthus argophyllus, the silverleaf sunflower, and examine evidence for its evolution by divergent selection. In 18 populations sampled from across the species range and grown in a common garden, most quantitative traits covaried such that individuals could be assigned...

Data from: The missing link in grassland restoration: arbuscular mycorrhizal fungi inoculation increases plant diversity and accelerates succession

Liz Koziol & James D. Bever
Because soil microbial communities are often altered by anthropogenic disturbance, successful plant community restoration may require the restoration of beneficial soil microbes, such as arbuscular mycorrhizal (AM) fungi. Recent evidence suggests that later successional grassland species are more strongly affected by AM fungi relative to early successional plants and that late successional plants consistently benefit from some AM fungi but not other AM fungal species. Many of these late successional species are also often missing...

Data from: Weak coordination between leaf structure and function among closely related tomato species

Christopher D. Muir, Miquel À. Conesa, Emilio J. Roldán, Arántzazu Molins & Jeroni Galmés
Theory predicts that natural selection should favor coordination between leaf physiology, biochemistry and anatomical structure along a functional trait spectrum from fast, resource-acquisitive syndromes to slow, resource-conservative syndromes. However, the coordination hypothesis has rarely been tested at a phylogenetic scale most relevant for understanding rapid adaptation in the recent past or for the prediction of evolutionary trajectories in response to climate change. We used a common garden to examine genetically based coordination between leaf traits...

Data from: A stochastic neuronal model predicts random search behaviors at multiple spatial scales in C. elegans

William M. Roberts, Steven B. Augustine, Kristy J. Lawton, Theodore H. Lindsay, Tod R. Thiele, Eduardo J. Izquierdo, Serge Faumont, Rebecca A. Lindsay, Matthew Cale Britton, Navin Pokala, Cornelia I. Bargmann & Shawn R. Lockery
Random search is a behavioral strategy used by organisms from bacteria to humans to locate food that is randomly distributed and undetectable at a distance. We investigated this behavior in the nematode Caenorhabditis elegans, an organism with a small, well-described nervous system. Here we formulate a mathematical model of random search abstracted from the C. elegans connectome and fit to a large-scale kinematic analysis of C. elegans behavior at submicron resolution. The model predicts behavioral...

Data from: Phylogenomics reveals three sources of adaptive variation during a rapid radiation

James B. Pease, David C. Haak, Matthew W. Hahn & Leonie C. Moyle
Speciation events often occur in rapid bursts of diversification, but the ecological and genetic factors that promote these radiations are still much debated. Using whole transcriptomes from all 13 species in the ecologically and reproductively diverse wild tomato clade (Solanum sect. Lycopersicon), we infer the species phylogeny and patterns of genetic diversity in this group. Despite widespread phylogenetic discordance due to the sorting of ancestral variation, we date the origin of this radiation to approximately...

Data from: Modulation of the cutaneous silent period in the upper-limb with whole-body instability

Nathaniel R. Eckert, Brach Poston, Zachary A. Riley & Nathanial R. Eckert
The silent period induced by cutaneous electrical stimulation of the digits has been shown to be task-dependent, at least in the grasping muscles of the hand. However, it is unknown if the cutaneous silent period is adaptable throughout muscles of the entire upper limb, in particular when the task requirements are substantially altered. The purpose of the present study was to examine the characteristics of the cutaneous silent period in several upper limb muscles when...

Data from: Nematode-bacteria nutualism: selection within the mutualism supersedes selection outside of the mutualism

Levi T. Morran, McKenna J. Penley, Victoria S. Byrd, Andrew J. Meyer, Timothy S. O'Sullivan, Farrah Bashey-Visser, Heidi Goodrich-Blair, Curtis M. Lively & Farrah Bashey
The coevolution of interacting species can lead to codependent mutualists. Little is known about the effect of selection on partners within verses apart from the association. Here, we determined the effect of selection on bacteria (Xenorhabdus nematophila) both within and apart from its mutualistic partner (a nematode, Steinernema carpocapsae). In nature, the two species cooperatively infect and kill arthropods. We passaged the bacteria either together with (M+), or isolated from (M−), nematodes under two different...

Data from: Community functional trait composition at the continental scale: the effects of non-ecological processes

A. Michelle Lawing, Jussi T. Eronen, Jessica L. Blois, Catherine H. Graham & P. David Polly
Ecological communities and their response to environmental gradients are increasingly being described by measures of trait composition at the community level – the trait-based approach. Whether ecological or non-ecological processes influence trait composition between communities has been debated. Understanding the processes that influence trait composition is important for reconstructing paleoenvironmental conditions from fossil deposits and for understanding changes in community functionality through time. Here, we assess the influence of ecological and non-ecological processes on the...

Data from: Habitat, predators, and hosts regulate disease in Daphnia through direct and indirect pathways

Alexander T. Strauss, Marta S. Shocket, David J. Civitello, Jessica L. Hite, Rachel M. Penczykowski, Meghan A. Duffy, Carla E. Cáceres & Spencer R. Hall
Community ecology can link habitat to disease via interactions among habitat, focal hosts, other hosts, their parasites, and predators. However, complicated food web interactions (i.e., trophic interactions among predators, and their impacts on host density and diversity) often obscure the important pathways regulating disease. Here, we disentangle community drivers in a case study of planktonic disease, using a two-step approach. In step one, we tested univariate field patterns linking community interactions to two disease metrics....

Data from: Aging alters interspecific competition between two sympatric insect-parasitic nematode species

Farrah Bashey-Visser, Tara Sarin, Curtis M. Lively & Farrah Bashey
Interspecific competition can vary depending on the stage, age, or physiological state of the competitors. Competitive ability often increases with age or size; alternatively, senescence can lead to a loss of viability and reduced competitive success. Differences between species in their age-specific competitive abilities can promote coexistence in the face of substantial niche overlap. We examined two sympatric species of nematodes (genus Steinernema) to determine whether their competitive relationship changes as a function of age....

Data from: Factors essential for L,D-transpeptidase-mediated peptidoglycan cross-linking and β-lactam resistance in Escherichia coli

Christiane Bouchier, Jean-Emmanuel Hugonnet, Michel Arthur, Dominique Mengin-Lecreulx, Yves Brun, Michael Van Nieuwenhze, Louis B Rice, Alejandro Monton, Tanneke Den Blaauwen, Etienne Carbonnelle, Carole Veckerlé & Kuyek Tu
The target of β-lactam antibiotics is the D,D-transpeptidase activity of penicillin-binding proteins (PBPs) for synthesis of 4→3 cross-links in the peptidoglycan of bacterial cell walls. Unusual 3→3 cross-links formed by L,D-transpeptidases were first detected in Escherichia coli more than four decades ago, however no phenotype has previously been associated with their synthesis. Here we show that production of the L,D-transpeptidase YcbB in combination with elevated synthesis of the (p)ppGpp alarmone by RelA lead to full...

Data from: Viral pathogen production in a wild grass host driven by host growth and soil nitrogen

Briana K. Whitaker, Megan A. Rúa & Charles E. Mitchell
Nutrient limitation is a basic ecological constraint that has received little attention in studies on virus production and disease dynamics. Nutrient availability could directly limit the production of viral nucleic acids and proteins, or alternatively limit host growth and thus indirectly limit metabolic pathways necessary for viral replication. In order to compare direct and indirect effects of nutrient limitation on virus production within hosts, we manipulated soil nitrogen (N) and phosphorus (P) availability in a...

Data from: Aggressive behaviours track transitions in seasonal phenotypes of female Siberian hamsters

Nikki M. Rendon, Andrea C. Amez, Melissa R. Proffitt, Elizabeth R. Bauserman & Gregory E. Demas
Seasonally breeding animals exhibit profound physiological and behavioural responses to changes in ambient day length (photoperiod), including changes in reproductive function and territorial aggression. Species where aggression persists when gonads are regressed and circulating levels of gonadal hormones are low, such as Siberian hamsters (Phodopus sungorus) and song sparrows (Melospiza melodia), challenge the well-established framework that gonadal hormones are important mediators of aggression. A solution to this apparent paradox is that a season-specific increase in...

Data from: How phylogeny and foraging ecology drive the level of chemosensory exploration in lizards and snakes

Simon Baeckens, Raoul Van Damme, & W. E. Cooper
The chemical senses are crucial for squamates (lizards and snakes). The extent to which squamates utilize their chemosensory system, however, varies greatly among taxa and species’ foraging strategies, and played an influential role in squamate evolution. In lizards, Scleroglossa evolved a state where species use chemical cues to search for food (active-foragers), while Iguania retained the use of vision to hunt prey (ambush-foragers). However, such strict dichotomy is flawed since shifts in foraging modes have...

Registration Year

  • 2016

Resource Types

  • Dataset


  • Indiana University Bloomington
  • University of British Columbia
  • University of Kansas
  • Indiana University
  • University of Oregon
  • Virginia Tech
  • University of Michigan-Ann Arbor
  • University of North Carolina
  • University of Wisconsin-Madison
  • University of Mississippi