230 Works

Data from: Integrating fossils with molecular phylogenies improves inference of trait evolution

Graham James Slater, Luke J. Harmon & Michael E. Alfaro
Comparative biologists often attempt to draw inferences about tempo and mode in evolution by comparing the fit of evolutionary models to phylogenetic comparative data consisting of a molecular phylogeny with branch lengths and trait measurements from extant taxa. These kinds of approaches ignore historical evidence for evolutionary pattern and process contained in the fossil record. In this paper we show through simulation that incorporation of fossil information dramatically improves our ability to distinguish among models...

Data from: Ecological opportunity and sexual selection together predict adaptive radiation

Catherine E. Wagner, Luke J. Harmon & Ole Seehausen
A fundamental challenge to our understanding of biodiversity is to explain why some groups of species undergo adaptive radiations, diversifying extensively into many and varied species, while others do not. Both extrinsic environmental factors (e.g. resource availability, climate) and intrinsic lineage-specific traits (e.g. behavioural or morphological traits, genetic architecture) influence diversification, but few studies have addressed how such factors interact. Radiations of cichlid fish in the African great lakes provide some of the most dramatic...

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: 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: 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: Inbreeding depression in pronghorn (Antilocapra americana) fawns

Stacey J. Dunn, Erin Clancey, Lisette P. Waits & John A. Byers
Although inbreeding depression affects survival, fitness and population viability, the extent of inbreeding depression in wild populations remains unclear. We examined inbreeding depression in the small, isolated National Bison Range (NBR), MT, pronghorn (Antilocapra americana) population following a bottleneck. We have studied the NBR pronghorn extensively since 1981, and we have detailed birth, survival and mate choice data. We genotyped all animals in the population between 1999-2010 at 19 microsatellite loci, assigned paternities to all...

Data from: Multiple continental radiations and correlates of diversification in Lupinus (Leguminosae): testing for key innovation with incomplete taxon sampling

Christopher S. Drummond, Ruth J. Eastwood, Silvia T. S. Miotto & Colin E. Hughes
Replicate radiations provide powerful comparative systems to address questions about the interplay between opportunity and innovation in driving episodes of diversification and the factors limiting their subsequent progression. However, such systems have been rarely documented at intercontinental scales. Here, we evaluate the hypothesis of multiple radiations in the genus Lupinus (Leguminosae), which exhibits some of the highest known rates of net diversification in plants. Given that incomplete taxon sampling, background extinction, and lineage-specific variation in...

Data from: Oligocene niche shift, Miocene diversification - cold tolerance and accelerated speciation rates in the St. John's Worts (Hypericum, Hypericaceae)

Nicolai M. Nürk, Simon Uribe-Convers, Berit Gehrke, David C. Tank & Frank R. Blattner
Background: Our aim is to understand the evolution of species-rich plant groups that shifted from tropical into cold/temperate biomes. It is well known that climate affects evolutionary processes, such as how fast species diversify, species range shifts, and species distributions. Many plant lineages may have gone extinct in the Northern Hemisphere due to Late Eocene climate cooling, while some tropical lineages may have adapted to temperate conditions and radiated; the hyper-diverse and geographically widespread genus...

Data from: Evaluating the interaction of faecal pellet deposition rates and DNA degradation rates to optimize sampling design for DNA-based mark-recapture analysis of Sonoran pronghorn

Susannah P. Woodruff, Timothy R. Johnson & Lisette P. Waits
Knowledge of population demographics is important for species management but can be challenging in low-density, wide-ranging species. Population monitoring of the endangered Sonoran pronghorn (Antilocapra americana sonoriensis) is critical for assessing the success of recovery efforts, and noninvasive DNA sampling (NDS) could be more cost-effective and less intrusive than traditional methods. We evaluated faecal pellet deposition rates and faecal DNA degradation rates to maximize sampling efficiency for DNA-based mark–recapture analyses. Deposition data were collected at...

Data from: Genetic structure across broad spatial and temporal scales: Rocky Mountain tailed frogs (Ascaphus montanus; Anura: Ascaphidae) in the inland temperate rainforest

Genevieve Metzger, Anahi Espindola, Lisette P. Waits & Jack Sullivan
Contemporary and historical processes interact to structure genetic variation, however discerning between these can be difficult. Here, we analyze range-wide variation at 13 microsatellite loci in 2098 Rocky Mountain tailed frogs, Ascaphus montanus, collected from 117 streams across the species distribution in the Inland Northwest (INW) and interpret that variation in light of historical phylogeography, contemporary landscape genetics, and the reconstructed paleodistribution of the species. Further, we project species distribution models (SDMs) to predict future...

Data from: The population genomics of rapid adaptation: disentangling signatures of selection and demography in white sands lizards

Stefan Laurent, Susanne P. Pfeifer, Matthew Settles, Samuel S. Hunter, Kayla M. Hardwick, Louise Ormond, Vitor C. Sousa, Jeffrey D. Jensen, Erica Bree Rosenblum & Matthew L. Settles
Understanding the process of adaptation during rapid environmental change remains one of the central focal points of evolutionary biology. The recently formed White Sands system of southern New Mexico offers an outstanding example of rapid adaptation, with a variety of species having rapidly evolved blanched forms on the dunes that contrast with their close relatives in the surrounding dark soil habitat. In this study, we focus on two of the White Sands lizard species, Sceloporus...

Data from: Host-adapted aphid populations differ in their migratory patterns and capacity to colonize crops

Sanford D. Eigenbrode, Thomas S. Davis, Jennifer R. Adams, Lisette P. Waits, David Hawthorne & Damon S. Husebye
Although phytophagous insects can vary genetically in host use and exhibit long-range movements, the combined implications of these phenomena for pest management have received limited attention. To address this, we surveyed the genetic diversity of pea aphid Acyrthosiphon pisum using twelve microsatellite loci and assessed host association patterns and annual movement from a putative source region (Columbia River Basin) to the Palouse region of northern Idaho and western Washington, where the aphid is a pest...

Data from: How much of the world is woody?

Richard G. FitzJohn, Matt W. Pennell, Amy E. Zanne, Peter F. Stevens, David C. Tank, William K. Cornwell & Matthew W. Pennell
1.The question posed by the title of this paper is a basic one, and it is surprising that the answer is not known. Recently assembled trait datasets provide an opportunity to address this, but scaling these datasets to the global scale is challenging because of sampling bias. Although we currently know the growth form of tens of thousands of species, these data are not a random sample of global diversity; some clades are exhaustively characterised,...

Data from: Shifts in diversification rates linked to biogeographic movement into new areas: an example of a recent radiation in the Andes

Simon Uribe-Convers & David C. Tank
PREMISE OF THE STUDY: Clade-specific bursts in diversification are often associated with the evolution of key innovations. However, in groups with no obvious morphological innovations, observed upticks in diversification rates have also been attributed to the colonization of a new geographic environment. In this study, we explore the systematics, diversification dynamics, and historical biogeography of the plant clade Rhinantheae in the Orobanchaceae, with a special focus on the Andean clade of the genus Bartsia. METHODS:...

Data from: Environmentally dependent host-pathogen and vector-pathogen interactions in the barley yellow dwarf virus pathosystem

Thomas Seth Davis, Nilsa A. Bosque-Perez, Nathaniel E. Foote, Troy Magney & Sanford D. Eigenbrode
1. Understanding environmentally dependent variation in interspecific interactions is needed for evaluating how agroecosystems respond to abiotic stressors, including climate change. Both biotic and abiotic conditions shape crop responses to stress events, but interactions between environmental conditions and insect borne plant pathogens remain poorly understood. 2. We tested the hypothesis that drought stress, as applied by experimental water deprivation, drives conditional outcomes in host–pathogen and host–vector interactions using a cereal–aphid–virus association and greenhouse experiments. 3....

Data from: Infection of the fittest: devil facial tumour disease has greatest effect on individuals with highest reproductive output

Konstans Wells, Rodrigo K. Hamede, Douglas H. Kerlin, Andrew Storfer, Paul A. Hohenlohe, Menna E. Jones & Hamish I. McCallum
Emerging infectious diseases rarely affect all members of a population equally and determining how individuals’ susceptibility to infection is related to other components of their fitness is critical to understanding disease impacts at a population level and for predicting evolutionary trajectories. We introduce a novel state-space model framework to investigate survival and fecundity of Tasmanian devils (Sarcophilus harrisii) affected by a transmissible cancer, devil facial tumour disease. We show that those devils that become host...

Data from: Fire-regime variability impacts forest carbon dynamics for centuries to millennia

Tara W. Hudiburg, Philip E. Higuera & Jeffrey A. Hicke
Wildfire is a dominant disturbance agent in forest ecosystems, shaping important biogeochemical processes including net carbon (C) balance. Long-term monitoring and chronosequence studies highlight a resilience of biogeochemical properties to large, stand-replacing, high-severity fire events. In contrast, the consequences of repeated fires or temporal variability in a fire regime (e.g., the characteristic timing or severity of fire) are largely unknown, yet theory suggests that such variability could strongly influence forest C trajectories (i.e., future states...

Data from: Keeping pace with the Red Queen: identifying the genetic basis of susceptibility to infectious disease

Ailene MacPherson, Sarah P. Otto & Scott L. Nuismer
Genome-wide association studies are widely used to identify "disease genes" conferring resistance/susceptibility to infectious diseases. Using a combination of mathematical models and simulations we demonstrate that genetic interactions between hosts and parasites (GxG interactions) can drastically affect the results of these association scans and hamper our ability to detect genetic variation in susceptibility. When hosts and parasites coevolve, these GxG interactions often make Genome-wide association studies unrepeatable over time or across host populations. Reanalyzing previously...

Data from: Comparative landscape genetics of two frugivorous bats in a biological corridor undergoing agricultural intensification

Katherine A. Cleary, Lisette P. Waits & Bryan Finegan
Agricultural intensification in tropical landscapes poses a new threat to the ability of biological corridors to maintain functional connectivity for native species. We use a landscape genetics approach to evaluate impacts of expanding pineapple plantations on two widespread and abundant frugivorous bats in a biological corridor in Costa Rica. We hypothesize that the larger, more mobile Artibeus jamaicensis will be less impacted by pineapple than the smaller Carollia castanea. In 2012 and 2013, we sampled...

Data from: Phylogenomic analyses reveal a deep history of hybridization and polyploidy in the Neotropical genus Lachemilla (Rosaceae)

Diego F. Morales-Briones, Aaron Liston & David C. Tank
Hybridization, incomplete lineage sorting, and phylogenetic error produce similar incongruence patterns, representing a great challenge for phylogenetic reconstruction. Here, we use sequence capture data and multiple species tree and species network approaches to resolve the backbone phylogeny of the Neotropical genus Lachemilla, while distinguishing among sources of incongruence. We used 396 nuclear loci and nearly complete plastome sequences from 27 species to clarify the relationships among the major groups of Lachemilla, and explored multiple sources...

Data from: Spatiotemporal heterogeneity in prey abundance and vulnerability shapes the foraging tactics of an omnivore

Nathaniel D. Rayl, Guillaume Bastille-Rousseau, John F. Organ, Matthew A. Mumma, Shane P. Mahoney, Colleen E. Soulliere, Keith P. Lewis, Robert D. Otto, Dennis L. Murray, Lisette P. Waits & Todd K. Fuller
1. Prey abundance and prey vulnerability vary across space and time, but we know little about how they mediate predator-prey interactions and predator foraging tactics. To evaluate the interplay between prey abundance, prey vulnerability, and predator space use, we examined patterns of black bear (Ursus americanus) predation of caribou (Rangifer tarandus) neonates in Newfoundland, Canada using data from 317 collared individuals (9 bears, 34 adult female caribou, 274 caribou calves). 2. During the caribou calving...

Data from: Tracing the rise of malignant cell lines: distribution, epidemiology and evolutionary interactions of two transmissible cancers in Tasmanian devils

Samantha James, Geordie Jennings, Young Mi Kwon, Maximilian Stammnitz, Alexandra Fraik, Andrew Storfer, Sebastien Comte, David Pemberton, Samantha Fox, Bill Brown, Ruth Pye, Gregory Woods, Bruce Lyons, Paul Hohenlohe, Hamish McCallum, Hannah V. Siddle, Frederic Thomas, Beata Ujvari, Elizabeth P. Murchison, Menna Jones & Rodrigo Hamede
Emerging infectious diseases are rising globally and understanding host-pathogen interactions during the initial stages of disease emergence is essential for assessing potential evolutionary dynamics and designing novel management strategies. Tasmanian devils (Sarcophilus harrisii) are endangered due to a transmissible cancer – devil facial tumour disease (DFTD) – that since its emergence in the 1990’s, has affected most populations throughout Tasmania. Recent studies suggest that devils are adapting to the DFTD epidemic and that disease-induced extinction...

Data from: Fire-regime complacency and sensitivity to centennial- through millennial-scale climate change in Rocky Mountain subalpine forests, Colorado, U.S.A.

Philip E. Higuera, Christy E. Briles & Cathy Whitlock
1. Key uncertainties in anticipating future fire regimes are their sensitivity to climate change, and the degree to which climate will impact fire regimes directly, through increasing the probability of fire, versus indirectly, through changes in vegetation and landscape flammability. 2. We studied the sensitivity of subalpine forest fire regimes (i.e., fire frequency, fire severity) to previously documented climate variability over the past 6000 years, utilizing pollen and macroscopic charcoal from high-resolution lake-sediment records in...

Data from: Chloroplast primers for clade-wide phylogenetic studies of Thalictrum (Ranunculaceae)

Diego Fernando Morales-Briones, Tatiana Arias, Verónica Di Stilio & David C. Tank
Premise Chloroplast primers were developed for phylogenetic and comparative studies in Thalictrum (Ranunculaceae). Methods and Results We assembled and annotated the complete plastome sequence of T. thalictroides by combining multiple whole genome sequencing libraries. Using transcriptome‐sequencing libraries, we also assembled a partial plastome of the related species T. hernandezii. From the newly assembled plastomes and one previously sequenced plastome, we designed and validated 28 primer pairs to target variable portions of the chloroplast genome in...

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