19 Works

Data from: Early bursts of body size and shape evolution are rare in comparative data

Luke J. Harmon, Jonathan B. Losos, T. Jonathan Davies, Rosemary G. Gillespie, John L. Gittleman, W. Bryan Jennings, Kenneth H. Kozak, Mark A. McPeek, Franck Moreno-Roark, Thomas J. Near, Andy Purvis, Robert E. Ricklefs, Dolph Schluter, , Ole Seehausen, Brian L. Sidlauskas, Omar Torres-Carvajal, Jason T. Weir & Arne Ø. Mooers
George Gaylord Simpson famously postulated that much of life's diversity originated as adaptive radiations—more or less simultaneous divergences of numerous lines from a single ancestral adaptive type. However, identifying adaptive radiations has proven difficult due to a lack of broad-scale comparative datasets. Here, we use phylogenetic comparative data on body size and shape in a diversity of animal clades to test a key model of adaptive radiation, in which initially rapid morphological evolution is followed...

Data from: Divergence in an obligate mutualism is not explained by divergent climatic factors

William Godsoe, Eva Strand, Christopher Irwin Smith, Jeremy B. Yoder, Todd C. Esque & Olle Pellmyr
Adaptation to divergent environments creates and maintains biological diversity, but we know little about the importance of different agents of ecological divergence. Coevolution in obligate mutualisms has been hypothesized to drive divergence, but this contention has rarely been tested against alternative ecological explanations. Here, we use a well-established example of coevolution in an obligate pollination mutualism, Yucca brevifolia and its two pollinating yucca moths, to test the hypothesis that divergence in this system is the...

Data from: Evaluating DNA degradation rates in faecal pellets of the endangered pygmy rabbit

Stephanie M. DeMay, Penny A. Becker, Chad A. Eidson, Janet L. Rachlow, Timothy R. Johnson & Lisette P. Waits
Noninvasive genetic sampling of faecal pellets can be a valuable method for monitoring rare and cryptic wildlife populations, like the pygmy rabbit (Brachylagus idahoensis). To investigate this method’s efficiency for pygmy rabbit monitoring, we evaluated the effect of sample age on DNA degradation in faecal pellets under summer field conditions. We placed 275 samples from known individuals in natural field conditions for 1 to 60 days and assessed DNA quality by amplifying a 294 base...

Data from: Thermal adaptation and acclimation of ectotherms from differing aquatic climates

Shawn R. Narum, Nathan R. Campbell, Kevin A. Meyer, Michael R. Miller & Ronald W. Hardy
To elucidate the mechanisms of thermal adaptation and acclimation in ectothermic aquatic organisms from differing climates, we used a common-garden experiment for thermal stress to investigate the heat shock response of redband trout (Oncorhynchus mykiss gairdneri) from desert and montane populations. Evidence for adaptation was observed as expression of heat shock genes in fish from the desert population was more similar to control (unstressed) fish and significantly different (P ≤ 0.05) from those from the...

Data from: Enhanced understanding of predator–prey relationships using molecular methods to identify predator species, individual and sex

Matthew A. Mumma, Colleen E. Soulliere, Shane P. Mahoney & Lisette P. Waits
Predator species identification is an important step in understanding predator-prey interactions, but predator identifications using kill site observations are often unreliable. We used molecular tools to analyse predator saliva, scat and hair from caribou calf kills in Newfoundland, Canada to identify the predator species, individual and sex. We sampled DNA from 32 carcasses using cotton swabs to collect predator saliva. We used fragment length analysis and sequencing of mitochondrial DNA to distinguish between coyote, black...

Data from: A long PCR based approach for DNA enrichment prior to next-generation sequencing for systematic studies

Simon Uribe-Convers, Justin R. Duke, Michael J. Moore & David C. Tank
Premise of the study: We present an alternative approach for molecular systematic studies that combines long PCR and next-generation sequencing (NGS). Our approach can be used to generate templates from any DNA source for NGS. Here we test our approach by amplifying complete chloroplast genomes and we present a set of 58 potentially universal primers for angiosperms to do so. Additionally, this approach is likely to be particularly useful for nuclear regions. Methods and Results:...

Data from: Variation in setal micromechanics and performance of two gecko

Travis J. Hagey, Jonathan B. Puthoff, Madisen Holbrook, Luke J. Harmon, Autumn Kellar & Kellar Autumn
Biomechanical models of the gecko adhesive system typically focus on setal mechanics from a single gecko species, Gekko gecko. In this study, we compared the predictions from three mathematical models with experimental observations considering an additional gecko species Phelsuma grandis, to quantify interspecific variation in setal micromechanics. We also considered the accuracy of our three focal models: the frictional adhesion model, work of detachment model, and the effective modulus model. Lastly, we report a novel...

Data from: Three keys to the radiation of angiosperms into freezing environments

Amy E. Zanne, David C. Tank, William K. Cornwell, Jonathan M. Eastman, Stephen A. Smith, Richard G. FitzJohn, Daniel J. McGlinn, Brian C. O'Meara, Angela T. Moles, Peter B. Reich, Dana L. Royer, Douglas E. Soltis, Peter F. Stevens, Mark Westoby, Ian J. Wright, Lonnie Aarssen, Robert I. Bertin, Andre Calaminus, Rafaël Govaerts, Frank Hemmings, Michelle R. Leishman, Jacek Oleksyn, Pamela S. Soltis, Nathan G. Swenson, Laura Warman … & Alejandro Ordonez
Early flowering plants are thought to have been woody species restricted to warm habitats1, 2, 3. This lineage has since radiated into almost every climate, with manifold growth forms4. As angiosperms spread and climate changed, they evolved mechanisms to cope with episodic freezing. To explore the evolution of traits underpinning the ability to persist in freezing conditions, we assembled a large species-level database of growth habit (woody or herbaceous; 49,064 species), as well as leaf...

Data from: Effects of gene flow on phenotype matching between two varieties of Joshua tree (Yucca brevifolia; Agavaceae) and their pollinators

Jeremy B. Yoder, Christopher I. Smith, Daniel J. Rowley, Ramona Flatz, William Godsoe, Christopher Drummond & Olle Pellmyr
In animal-pollinated plants, local adaptation to pollinator behaviour or morphology can restrict gene flow among plant populations; but gene flow may also prevent divergent adaptation. Here, we examine possible effects of gene flow on plant-pollinator trait matching in two varieties of Joshua tree (Agavaceae: Yucca brevifolia). The two varieties differ in strikingly in floral morphology, which matches differences in the morphology of their pollinators. However, this co-divergence is not present at a smaller scale: within...

Data from: Host resistance, population structure and the long-term persistence of bubonic plague: contributions of a modelling approach in the Malagasy focus

Fanny Gascuel, Marc Choisy, Jean-Marc Duplantier, Florence Débarre & Carine Brouat
Although bubonic plague is an endemic zoonosis in many countries around the world, the factors responsible for the persistence of this highly virulent disease remain poorly known. Classically, the endemic persistence of plague is suspected to be due to the coexistence of plague resistant and plague susceptible rodents in natural foci, and/or to a metapopulation structure of reservoirs. Here, we test separately the effect of each of these factors on the long-term persistence of plague....

Data from: Model selection as a tool for phylogeographic inference: an example from the willow Salix melanopsis

Bryan C. Carstens, Reid S. Brennan, Vivien Chua, Caroline V. Duffie, Michael G. Harvey, Rachel A. Koch, Caleb D. McMahan, Bradley J. Nelson, Catherine E. Newman, Jordan D. Satler, Glenn Seeholzer, Karine Posbic, David C. Tank & Jack Sullivan
Phylogeographic inference has typically relied on analyses of data from one or a few genes to provide estimates of demography and population histories. While much has been learned from these studies, all phylogeographic analysis is conditioned on the data, and thus, inferences derived from data that represent a small sample of the genome are unavoidably tenuous. Here, we demonstrate one approach for moving beyond classic phylogeographic research. We use sequence capture probes and Illumina sequencing...

Data from: Genetic regulatory network motifs constrain adaptation through curvature in the landscape of mutational (co)variance

Tyler D. Hether & Paul A. Hohenlohe
Systems biology is accumulating a wealth of understanding about the structure of genetic regulatory networks, leading to a more complete picture of the complex genotype-phenotype relationship. However, models of multivariate phenotypic evolution based on quantitative genetics have largely not incorporated a network-based view of genetic variation. Here we model a set of two-node, two-phenotype genetic network motifs, covering a full range of regulatory interactions. We find that network interactions result in different patterns of mutational...

Data from: Rates of speciation and morphological evolution are correlated across the largest vertebrate radiation

Daniel L. Rabosky, Francesco Santini, Jonathan Eastman, Stephen A. Smtih, Brian Sidlauskas, Jonathan Chang & Michael E. Alfaro
Several evolutionary theories predict that rates of morphological change should be positively associated with the rate at which new species arise. For example, the theory of punctuated equilibrium proposes that phenotypic change typically occurs in rapid bursts associated with speciation events. However, recent phylogenetic studies have found little evidence linking these processes in nature. Here we demonstrate that rates of species diversification are highly correlated with the rate of body size evolution across the 30,000+...

Data from: Genomic patterns of introgression in rainbow and westslope cutthroat trout illuminated by overlapping paired-end RAD sequencing

Paul A. Hohenlohe, Mitch D. Day, Stephen J. Amish, Michael R. Miller, Nicholas Kamps-Hughes, Matthew C. Boyer, Clint C. Muhlfeld, Fred W. Allendorf, Eric A. Johnson, Gordon Luikart & Nick Kamps-Hughes
Rapid and inexpensive methods for genomewide single nucleotide polymorphism (SNP) discovery and genotyping are urgently needed for population management and conservation. In hybridized populations, genomic techniques that can identify and genotype thousands of species-diagnostic markers would allow precise estimates of population- and individual-level admixture as well as identification of ‘super invasive’ alleles, which show elevated rates of introgression above the genomewide background (likely due to natural selection). Techniques like restriction-site-associated DNA (RAD) sequencing can discover...

Data from: A method for estimating population sex ratio for sage-grouse using noninvasive genetic samples

Jeremy A. Baumgardt, Caren S. Goldberg, Kerry P. Reese, Jack W. Connelly, David D. Musil, Edward O. Garton & Lisette P. Waits
Population sex ratio is an important metric for wildlife management and conservation, but estimates can be difficult to obtain, particularly for sexually monomorphic species or for species that differ in detection probability between the sexes. Noninvasive genetic sampling (NGS) using polymerase chain reaction (PCR) has become a common method for identifying sex from sources such as hair, feathers, or feces, and is a potential source for estimating sex ratio. If, however, PCR success is sex-biased,...

Data from: Quantifying the effects of migration and mutation on adaptation and demography in spatially heterogeneous environments

Florence Débarre, Ophélie Ronce & Sylvain Gandon
How do mutation and gene flow influence population persistence, niche expansion, and local adaptation in spatially heterogeneous environments? In this article, we analyse a demographic and evolutionary model of adaptation to an environment containing two habitats in equal frequencies, and we bridge the gap between different theoretical frameworks. Qualitatively, our model yields four qualitative types of outcomes: (i) global extinction of the population (ii) adaptation to one habitat only, but also adaptation to both habitats...

Data from: Do habitat shifts drive the diversity in teleost fishes? An example from the pufferfishes (Tetraodontidae)

Francesco Santini, Mai T. T. Nguyen, Laurie Sorenson, Thomas B. Waltzek, Jessica W. Lynch Alfaro, Jonathan M. Eastman & Michael E. Alfaro
Habitat shifts are implicated as the cause of many vertebrate radiations, yet relatively few empirical studies quantify patterns of diversification following colonization of new habitats in fishes. The pufferfishes (family Tetraodontidae) occur in several habitats, including coral reefs and freshwater, which are thought to provide ecological opportunity for adaptive radiation, and thus provide a unique system for testing the hypothesis that shifts to new habitats alter diversification rates. To test this hypothesis we sequenced eight...

Data from: Factors influencing detection of eDNA from a stream-dwelling amphibian

David S. Pilliod, Caren S. Goldberg, Robert S. Arkle & Lisette P. Waits
Environmental DNA (eDNA) methods for detecting and estimating abundance of aquatic species are emerging rapidly, but little is known about how processes such as secretion rate, environmental degradation, and time since colonization or extirpation from a given site affect eDNA measurements. Using stream-dwelling salamanders and quantitative PCR (qPCR) analysis, we conducted three experiments to assess eDNA: (1) production rate, (2) persistence time under different temperature and light conditions, and (3) detectability and concentration through time...

Data from: Consequences of climate change for biotic disturbances in North American forests

Aaron S. Weed, Matthew P. Ayres, Jeffrey Hicke & Jeffrey A. Hicke
About one third of North America is forested. These forests are of incalculable value to human society in terms of harvested resources and ecosystem services and are sensitive to disturbance regimes. Epidemics of forest insects and diseases are the dominant sources of disturbance to North American forests. Here we review current understanding of climatic effects on the abundance of forest insects and diseases in North America, and of the ecological and socioeconomic impacts of biotic...

Registration Year

  • 2013

Resource Types

  • Dataset


  • University of Idaho
  • University of British Columbia
  • University of Minnesota
  • University of Michigan-Ann Arbor
  • University of Oregon
  • University of Florida
  • United States Geological Survey
  • University of Missouri–St. Louis
  • Idaho Department of Fish and Game
  • University of California Los Angeles