26 Works

Data from: Identification of sex-specific molecular markers using restriction site associated DNA sequencing (RAD-seq)

Tony Gamble & David Zarkower
A major barrier to evolutionary studies of sex determination and sex chromosomes has been a lack of information on the types of sex-determining mechanisms that occur among different species. This is particularly problematic in groups where most species lack visually heteromorphic sex chromosomes, such as fish, amphibians and reptiles, because cytogenetic analyses will fail to identify the sex chromosomes in these species. We describe the use of restriction site associated DNA (RAD) sequencing, or RAD-seq,...

Data from: Epiphytes improve host plant water use by microenvironment modification

Daniel E. Stanton, Jackelyn Huallpa Chávez, Luis Villegas, Francisco Villasante, Juan Armesto, Lars O. Hedin & Henry Horn
1. Epiphytes have the potential to modify the canopy environments in which they grow. Accurately evaluating the impact of epiphytes can be challenging, since plants without epiphytes may also otherwise differ from host plants, and experimental removal is impractical and difficult to replicate in many forests. 2. We studied the impacts of epiphytes (primarily fruticose lichens and Tillandsia spp.) on host plants (Eulychnia saint-pieana and Caesalpinia spinosa) in two fog ecosystems in Chile (Pan de...

Data from: Population-level consequences of risky dispersal

Allison K. Shaw, Matti Jalasvuori & Hanna Kokko
Achieving sufficient connectivity between populations is essential for persistence, but costs of dispersal may select against individual traits or behaviours that, if present, would improve connectivity. Existing dispersal models tend to ignore the multitude of risks to individuals: while many assess the effect of mortality costs, there is also a risk of failing to find new habitat, especially when the entire inhabitable area remains both small and fragmented. There are few known rules governing whether...

Data from: Indirect effects drive evolutionary responses to global change

Jennifer A. Lau, Ruth G. Shaw, Peter B. Reich & Peter Tiffin
Anthropogenic environmental changes pose significant threats to plant and animal populations. These changes also may affect the evolution of natural populations either directly or indirectly by altering the outcome of species interactions that are important drivers of evolution. This latter indirect pathway may be especially important for evolutionary responses to elevated atmospheric CO2 concentrations (eCO2), which appear to have minimal direct effects on plant evolution but have large effects on interspecific interactions, such as competition....

Data from: Are leaf functional traits “invariant” with plant size, and what is “invariance” anyway?

Charles A. Price, Ian J. Wright, David D. Ackerly, Ülo Niinemets, Peter B. Reich & Erik J. Veneklaas
Studies of size-related plant traits have established a suite of mathematical functions describing whole plant investment and allocation. In parallel, studies of plant “economic spectra” have measured the scaling and variance composition of traits related to the major dimensions of both structure and function. Here we explore the intersection of these two broad areas by exploring the notion that many leaf economic traits are invariant with species differences in adult plant size. Invariant traits are...

Data from: Bayesian hierarchical models for spatially misaligned data in R

Andrew O. Finley, Sudipto Banerjee & Bruce D. Cook
Spatial misalignment occurs when at least one of multiple outcome variables is missing at an observed location. For spatial data, prediction of these missing observations should be informed by within location association among outcomes and by proximate locations where measurements were recorded. This study details and illustrates a Bayesian regression framework for modelling spatially misaligned multivariate data. Particular attention is paid to developing valid probability models capable of estimating parameter posterior distributions and propagating uncertainty...

Data from: The nutritionally responsive transcriptome of the polyphenic beetle Onthophagus taurus and the importance of sexual dimorphism and body region

Teiya Kijimoto, Emilie C. Snell-Rood, Melissa H. Pespeni, Guilherme Rocha, Karen Kafadar & Armin P. Moczek
Developmental responses to nutritional variation represent one of the ecologically most important classes of adaptive plasticity. However, knowledge of genome-wide patterns of nutrition-responsive gene expression is limited. Here, we studied genome-wide transcriptional responses to nutritional variation and their dependency on trait and sex in the beetle Onthophagus taurus. We find that averaged across the transcriptome, nutrition contributes less to overall variation in gene expression than do sex or body region, but that for a modest...

Data from: Pulsing hydrology determines top-down control of basal resources in a tropical river-floodplain ecosystem

Kirk O. Winemiller, Jose V. Montoya, Daniel L. Roelke, James B. Cotner, Craig A. Layman, Luzmila Sanchez & Maria M. Castillo
Variable hydrology of rivers strongly affects biophysical factors that influence primary production and population densities, thereby affecting the relative influence of bottom-up and top-down processes in trophic networks. Many tropical floodplain rivers have sustained seasonal flood pulses driven by precipitation patterns of the Intertropical Convergence Zone. These changes in flow alter concentrations of dissolved nutrients, aquatic primary productivity, and per-unit-area densities of aquatic organisms. Therefore, one would predict that the strength of top-down effects of...

Data from: Courting disaster: how diversification rate affects fitness under risk

William C. Ratcliff, Peter Hawthorne & Eric Libby
Life is full of risk. To deal with this uncertainty, many organisms have evolved bet-hedging strategies that spread risk through phenotypic diversification. These rates of diversification can vary by orders of magnitude in different species. Here we examine how key characteristics of risk and organismal ecology affect the fitness consequences of variation in diversification rate. We find that rapid diversification is strongly favored when the risk faced has a wide spatial extent, with a single...

Data from: Multiple stressors and the cause of amphibian abnormalities

Mari K. Reeves, Margaret Perdue, Marcel Holyoak, Birgit Hagedorn, Daniel Rinella, Daniel Bogan, LeeAnn Munk, William Battaglin, Christine L. Dolph & Kimberly A. Trust
The repeated occurrence of abnormal amphibians in nature points to ecological imbalance, yet identifying causes of these abnormalities has proved complex. Multiple studies have linked amphibian abnormalities to chemically contaminated areas, but inference about causal mechanisms is lacking. Here we use a high incidence of abnormalities in Alaskan wood frogs to strengthen inference about the mechanism for these abnormalities. We suggest that limb abnormalities are caused by a combination of multiple stressors. Specifically, toxicants lead...

Data from: Roaming Romeos: male crickets evolving in silence show increased locomotor behaviours

Susan L. Balenger & Marlene Zuk
Loss of sexual signals should be strongly selected against when these signals are necessary for mate attraction or acquisition. Male Teleogryllus oceanicus field crickets produce a long-distance calling song to attract females. Separate genetic mutations recently evolved on the Hawaiian Islands of Kauai and Oahu, rendering approximately 90% and 50% of males, respectively, incapable of calling. We examined whether males from three populations, each with a distinct prevalence of this silent ‘flatwing’ phenotype, show behavioural...

Data from: Coordination of fictive motor activity in the larval zebrafish is generated by non-segmental mechanisms

Timothy D. Wiggin, Jack H. Peck & Mark A. Masino
The cellular and network basis for most vertebrate locomotor central pattern generators (CPGs) is incompletely characterized, but organizational models based on known CPG architectures have been proposed. Segmental models propose that each spinal segment contains a circuit that controls local coordination and sends longer projections to coordinate activity between segments. Unsegmented/continuous models propose that patterned motor output is driven by gradients of neurons and synapses that do not have segmental boundaries. We tested these ideas...

Data from: Assessment of dysmyelination with RAFFn MRI: application to murine MPS I

David Satzer, Christina DiBartolomeo, Michael M. Ritchie, Christine Storino, Timo Liimatainen, Hanne Hakkarainen, Djaudat Idiyatullin, Silvia Mangia, Shalom Michaeli, Ann M. Parr & Walter C. Low
Type I mucopolysaccharidosis (MPS I) is an autosomal recessive lysosomal storage disorder with neurological features. Humans and laboratory animals with MPS I exhibit various white matter abnormalities involving the corpus callosum and other regions. In this study, we first validated a novel MRI technique, entitled Relaxation Along a Fictitious Field in the rotating frame of rank n (RAFFn), as a measure of myelination and dysmyelination in mice. We then examined differences between MPS I mice...

Data from: Replicated evolutionary divergence in the cuticular hydrocarbon profile of male crickets associated with the loss of song in the Hawaiian archipelago

Leigh W. Simmons, Melissa L. Thomas, Brian Gray & Marlene Zuk
Female choice based on male secondary sexual traits is well documented, although the extent to which this selection can drive an evolutionary divergence in male traits among populations is less clear. Male field crickets Teleogryllus oceanicus attract females using a calling song and once contacted switch to courtship song to persuade them to mate. These crickets also secrete onto their cuticle a cocktail of long-chained fatty acids or cuticular hydrocarbons (CHCs). Females choose among potential...

Data from: Mate finding, Allee effects, and selection for sex-biased dispersal

Allison K. Shaw & Hanna Kokko
Although dispersal requires context-dependent decision-making in three distinct stages (emigration, transit, immigration), these decisions are commonly ignored in simple models of dispersal. For sexually reproducing organisms, mate availability is an important factor in dispersal decisions. Difficulty finding mates can lead to an Allee effect where population growth decreases at low densities. Surprisingly, theoretical studies on mate finding and on sex-biased dispersal produce opposing predictions: in the former one sex is predicted to move less if...

Data from: Distinguishing the effects of selection from demographic history in the genetic variation of two sister passerines based on mitochondrial-nuclear comparison

Chih-Ming Hung & Robert M. Zink
Determining the mechanisms responsible for the distribution of genetic diversity in natural populations has occupied a central role in molecular evolution. Our study was motivated by the unprecedented observation that a widespread Eurasian flycatcher, Ficedula albicilla, exhibited no variation at the mitochondrial DNA (mtDNA) ND2 gene in 75 individuals sampled over a 5000-km distance. In contrast, its sister species, F. parva, had low but considerably higher levels of mtDNA variation. We assessed whether natural selection...

Data from: A framework phylogeny of the American oak clade based on sequenced RAD data

Andrew L. Hipp, Deren A. R. Eaton, Jeannine Cavender-Bares, Elisabeth Fitzek, Rick Nipper & Paul S. Manos
Previous phylogenetic studies in oaks (Quercus, Fagaceae) have failed to resolve the backbone topology of the genus with strong support. Here, we utilize next-generation sequencing of restriction-site associated DNA (RAD-Seq) to resolve a framework phylogeny of a predominantly American clade of oaks whose crown age is estimated at 23–33 million years old. Using a recently developed analytical pipeline for RAD-Seq phylogenetics, we created a concatenated matrix of 1.40 E06 aligned nucleotides, constituting 27,727 sequence clusters....

Data from: Detection and decay rates of prey and prey symbionts in the gut of a predator through metagenomics

Debora P. Paula, Benjamin Linard, David A. Andow, Edison R. Sujii, Carmen S. S. Pires & Alfried P. Vogler
DNA methods are useful to identify ingested prey items from the gut of predators, but reliable detection is hampered by low amounts of degraded DNA. PCR-based methods can retrieve minute amounts of starting material but suffer from amplification biases and cross-reactions with the predator and related species genomes. Here, we use PCR-free direct shotgun sequencing of total DNA isolated from the gut of the harlequin ladybird Harmonia axyridis at five time points after feeding on...

Data from: The global distribution of diet breadth in insect herbivores

Matthew L. Forister, Vojtech Novotny, Anna K. Panorska, Leontine Baje, Yves Basset, Philip T. Butterill, Lukas Cizek, Phyllis D. Coley, Francesca Dem, Ivone R. Diniz, Pavel Drozd, Mark Fox, Andrea E. Glassmire, Rebecca Hazen, Jan Hrcek, Joshua P. Jahner, Ondrej Kaman, Tomasz J. Kozubowski, Thomas Kursar, Owen T. Lewis, John Lill, Robert J. Marquis, Scott E. Miller, Helena C. Morais, Masashi Murakami … & Lee A. Dyer
Understanding variation in resource specialization is important for progress on issues that include coevolution, community assembly, ecosystem processes, and the latitudinal gradient of species richness. Herbivorous insects are useful models for studying resource specialization, and the interaction between plants and herbivorous insects is one of the most common and consequential ecological associations on the planet. However, uncertainty persists regarding fundamental features of herbivore diet breadth, including its relationship to latitude and plant species richness. Here...

Data from: Complementarity of statistical treatments to reconstruct worldwide routes of invasion: the case of the Asian ladybird Harmonia axyridis

Eric Lombaert, Thomas Guillemaud, Jonathan Lundgren, Robert Koch, Benoît Facon, Audrey Grez, Antoon Loomans, Thibaut Malausa, Oldrich Nedved, Emma Rhule, Arnstein Staverlokk, Tove Steenberg & Arnaud Estoup
Inferences about introduction histories of invasive species remain challenging because of the stochastic demographic processes involved. Approximate Bayesian computation (ABC) can help to overcome these problems, but such method requires a prior understanding of population structure over the study area, necessitating the use of alternative methods and an intense sampling design. In this study, we made inferences about the worldwide invasion history of the ladybird Harmonia axyridis by various population genetics statistical methods, using a...

Data from: New insights into New World biogeography: an integrated view from the phylogeny of blackbirds, cardinals, sparrows, tanagers, warblers, and allies

F. Keith Barker, Kevin J. Burns, John Klicka, Scott M. Lanyon & Irby J. Lovette
Understanding the biogeographic origins and temporal sequencing of groups within a region or of lineages within an ecosystem can yield important insights into evolutionary dynamics and ecological processes. Fifty years ago, Ernst Mayr generated comprehensive—if limited—inferences about the origins of the New World avifaunas, including the importance of pre-Isthmian dispersal between North and South America. Since then, methodological advances have improved our ability to address many of the same questions, but the phylogenies upon which...

Data from: Rapid evolution of reproductive isolation between incipient outcrossing and selfing Clarkia species

Ryan Dawkins Briscoe Runquist, Eric Chu, Justin L. Iverson, Jason C. Kopp & David A. Moeller
A major goal of speciation research is to understand the processes involved in the earliest stages of the evolution of reproductive isolation. One important challenge has been to identify systems where lineages have very recently diverged and opportunities for hybridization are present. We conducted a comprehensive examination of the components of reproductive isolation across the life cycle of two subspecies of Clarkia xantiana, which diverged recently (ca. 65,000 bp). One subspecies is primarily outcrossing, but...

Data from: Speciation and introgression between Mimulus nasutus and Mimulus guttatus

Yaniv Brandvain, Amanda M. Kenney, Lex Flagel, Graham Coop & Andrea L. Sweigart
Mimulus guttatus and M. nasutus are an evolutionary and ecological model sister species pair differentiated by ecology, mating system, and partial reproductive isolation. Despite extensive research on this system, the history of divergence and differentiation in this sister pair is unclear. We present and analyze a population genomic data set which shows that M. nasutus budded from a central Californian M. guttatus population within the last 200 to 500 thousand years. In this time, the...

Data from: A hidden Markov model to identify and adjust for selection bias: an example involving mixed migration strategies

John R. Fieberg & Paul B. Conn
An important assumption in observational studies is that sampled individuals are representative of some larger study population. Yet, this assumption is often unrealistic. Notable examples include online public-opinion polls, publication biases associated with statistically significant results, and in ecology, telemetry studies with significant habitat-induced probabilities of missed locations. This problem can be overcome by modeling selection probabilities simultaneously with other predictor–response relationships or by weighting observations by inverse selection probabilities. We illustrate the problem and...

Data from: Anthropogenic changes in sodium affect neural and muscle development in butterflies

Emilie C. Snell-Rood, Anne Espeset, Christopher J. Boser, William A. White & Rhea Smykalski
The development of organisms is changing drastically because of anthropogenic changes in once-limited nutrients. Although the importance of changing macronutrients, such as nitrogen and phosphorus, is well-established, it is less clear how anthropogenic changes in micronutrients will affect organismal development, potentially changing dynamics of selection. We use butterflies as a study system to test whether changes in sodium availability due to road salt runoff have significant effects on the development of sodium-limited traits, such as...

Registration Year

  • 2014

Resource Types

  • Dataset


  • University of Minnesota
  • Australian National University
  • University of South Bohemia in České Budějovice
  • Western Sydney University
  • University of Western Australia
  • Michigan State University
  • University of Eastern Finland
  • Princeton University
  • Field Museum of Natural History
  • Duke University