19 Works

Data from: Chironomus riparius (Diptera) genome sequencing reveals the impact of minisatellite transposable elements on population divergence

Ann-Marie Oppold, Hanno Schmidt, Marcel Rose, Sören Lukas Hellman, Florian Dolze, Fabian Ripp, Bettina Weich, Urs Schmidt-Ott, Erwin Schmidt, Robert Kofler, Thomas Hankeln & Markus Pfenninger
Active transposable elements (TEs) may result in divergent genomic insertion and abundance patterns among conspecific populations. Upon secondary contact, such divergent genetic backgrounds can theoretically give rise to classical Dobzhansky-Muller incompatibilities (DMI), thus contributing to the evolution of endogenous genetic barriers and eventually cause population divergence. We investigated differential TE abundance among conspecific populations of the non-biting midge Chironomus riparius and evaluated their potential role in causing endogenous genetic incompatibilities between these populations. We focussed...

Data from: Ecological network inference from long-term presence-absence data

Elizabeth L. Sander, J. Timothy Wootton & Stefano Allesina
Ecological communities are characterized by complex networks of trophic and nontrophic interactions, which shape the dy-namics of the community. Machine learning and correlational methods are increasingly popular for inferring networks from co-occurrence and time series data, particularly in microbial systems. In this study, we test the suitability of these methods for inferring ecological interactions by constructing networks using Dynamic Bayesian Networks, Lasso regression, and Pear-son’s correlation coefficient, then comparing the model networks to empirical trophic...

Data from: Ethnically Tibetan women in Nepal with low hemoglobin concentration have better reproductive outcomes

Jang Ik Cho, Buddha Basnyat, Choongwon Jeong, Anna Di Rienzo, Geoff Childs, Sienna Craig, Jiayang Sun, Cynthia Beall & Cynthia M. Beall
Abstract Background and objectives: Tibetans have distinctively low hemoglobin concentrations at high altitudes compared with visitors and Andean highlanders. This study hypothesized that natural selection favors an unelevated hemoglobin concentration among Tibetans. It considered nonheritable sociocultural factors affecting reproductive success and tested the hypotheses that a higher percent of oxygen saturation of hemoglobin (indicating less stress) or lower hemoglobin concentration (indicating dampened response) associated with higher lifetime reproductive success. Methodology: We sampled 1006 post-reproductive ethnically...

Data from: An early chondrichthyan and the evolutionary assembly of a shark body plan

Michael I. Coates, John A. Finarelli, Ivan J. Sansom, Plamen S. Andreev, Katharine E. Criswell, Kristen Tietjen, Mark L. Rivers & Patrick J. La Riviere
Although relationships among the major groups of living gnathostomes are well established, the relatedness of early jawed vertebrates to modern clades is intensely debated. Here, we provide a new description of Gladbachus, a Middle Devonian (Givetian ~385-million-year-old) stem chondrichthyan from Germany, and one of the very few early chondrichthyans in which substantial portions of the endoskeleton are preserved. Tomographic and histological techniques reveal new details of the gill skeleton, hyoid arch and jaws, neurocranium, cartilage,...

Data from: Hotspots of soil N2O emission enhanced through water absorption by plant residue

Alexandra N. Kravchenko, Ehsan R. Toosi, Andrey K. Guber, Nathaniel E. Ostrom, J. Yu, K. Azeem, Mark L. Rivers & G. Philip Robertson
N2O is a highly potent greenhouse gas and arable soils represent its major anthropogenic source. Field-scale assessments and predictions of soil N2O emission remain uncertain and imprecise due to the episodic and microscale nature of microbial N2O production, most of which occurs within very small discrete soil volumes. Such hotspots of N2O production are often associated with decomposing plant residue. Here we quantify physical and hydrological soil characteristics that lead to strikingly accelerated N2O emissions...

Data from: Reconstructing ecological niche evolution when niches are incompletely characterized

Erin E. Saupe, Narayani Barve, Hannah L. Owens, Jacob C. Cooper, Peter A. Hosner & A. Townsend Peterson
Evolutionary dynamics of abiotic ecological niches across phylogenetic history can shed light on large-scale biogeographic patterns, macroevolutionary rate shifts, and the relative ability of lineages to respond to global change. An unresolved question is how best to represent and reconstruct evolution of these complex traits at coarse spatial scales through time. Studies have approached this question by integrating phylogenetic comparative methods with niche estimates inferred from correlative and other models. However, methods for estimating niches...

Data from: Consequences of divergence and introgression for speciation in Andean cloud forest birds

Benjamin M. Winger
Divergence with gene flow is well documented and reveals the influence of ecological adaptation on speciation. Yet it remains intuitive that gene exchange inhibits speciation in many scenarios, particularly among ecologically similar populations. The influence of gene flow on the divergence of populations facing similar selection pressures has received less empirical attention than scenarios where differentiation is coupled with local environmental adaptation. I used a paired study design to test the influence of genomic divergence...

Data from: Mechanosensation is evolutionarily tuned to locomotor mechanics

Brett R. Aiello, Mark W. Westneat & Melina E. Hale
The biomechanics of animal limbs has evolved to meet the functional demands for movement associated with different behaviors and environments. Effective movement relies not only on limb mechanics but also on appropriate mechanosensory feedback. By comparing sensory ability and mechanics within a phylogenetic framework, we show that peripheral mechanosensation has evolved with limb biomechanics, evolutionarily tuning the neuromechanical system to its functional demands. We examined sensory physiology and mechanics of the pectoral fins, forelimb homologs,...

Data from: Feeding ecology is the primary driver of beak shape diversification in waterfowl

Aaron M. Olsen
The diversity of beak shapes among birds is often assumed to be largely the result of adaptations to different feeding behaviors and diets. However, this assumption has only been tested for a small subset of avian diversity, primarily within the order Passeriformes. Moreover, given the role of the beak in behaviors other than feeding and given that most previously identified beak-feeding associations concern beak size rather than shape, it remains unclear how much of beak...

Data from: The evolutionary origin of variation in song length and frequency in the avian family Cettiidae

Chentao Wei, Trevor D. Price, Jiayu Liu, Per Alström & Yanyun Zhang
Aspects of bird song have been shown to correlate with morphological and ecological features, including beak and body size, and habitat. Here we study evolution of song length and song frequency among 30 species belonging to the Cettiidae. Frequency is negatively correlated with body size, and song length increases with latitude. Although migration distance correlates with latitude, the association of song length with latitude is only present within the non-migratory species, implying the association is...

Data from: Nineteenth-century collapse of a benthic marine ecosystem on the open continental shelf

Adam Tomašových & Susan M. Kidwell
The soft-sediment seafloor of the open continental shelf is among the least-known biomes on Earth, despite its high diversity and importance to fisheries and biogeochemical cycling. Abundant dead shells of epifaunal suspension-feeding terebratulid brachiopods (Laqueus) and scallops on the now-muddy mainland continental shelf of southern California reveal the recent, previously unsuspected extirpation of an extensive offshore shell-gravel ecosystem, evidently driven by anthropogenic siltation. Living populations of attached epifauna, which formerly existed in a middle- and...

Data from: Inferring the geographic origin of a range expansion: latitudinal and longitudinal coordinates inferred from genomic data in an ABC framework with the program X-ORIGIN

Qixin He, Joyce R. Prado & Laura Lacey Knowles
Climatic or environmental change is not only driving distributional shifts in species today, but it has also caused distributions to expand and contract in the past. Inferences about the geographic locations of past populations, especially regions that served as refugia (i.e., source populations) and migratory routes are a challenging endeavor. Refugial areas may be evidenced from fossil records or regions of temporal stability inferred from ecological niche models. Genomic data offer an alternative and broadly...

Data from: Genome sequences reveal cryptic speciation in the human pathogen Histoplasma capsulatum

Victoria E. Sepúlveda, Roberto Márquez, David A. Turissini, Willam E. Goldman & Daniel R. Matute
Histoplasma capsulatum is a pathogenic fungus that causes life-threatening lung infections. About 500,000 people are exposed to H. capsulatum each year in the United States, and over 60% of the U.S. population has been exposed to the fungus at some point in their life. We performed genome-wide population genetics and phylogenetic analyses with 30 Histoplasma isolates representing four recognized areas where histoplasmosis is endemic and show that the Histoplasma genus is composed of at least...

Data from: Evolutionary history of Daphnia drives divergence in grazing selectivity and alters temporal community dynamics of producers

John S. Park & David M. Post
Consumers with different seasonal life histories encounter different communities of producers during specific seasonal phases. If consumers evolve to prefer the producers that they encounter, then consumers may reciprocally influence the temporal composition of producer communities. Here we study the keystone consumer Daphnia ambigua, whose seasonal life history has diverged due to intraspecific predator divergence across lakes of New England. We ask whether grazing preferences of Daphnia have diverged also, and test whether any grazing...

Data from: Independent evolution of baleen whale gigantism linked to Plio-Pleistocene ocean dynamics

Graham J. Slater, Jeremy A. Goldbogen & Nicholas D. Pyenson
Vertebrates have evolved to gigantic sizes repeatedly over the past 250 Myr, reaching their extreme in today's baleen whales (Mysticeti). Hypotheses for the evolution of exceptionally large size in mysticetes range from niche partitioning to predator avoidance, but there has been no quantitative examination of body size evolutionary dynamics in this clade and it remains unclear when, why or how gigantism evolved. By fitting phylogenetic macroevolutionary models to a dataset consisting of living and extinct...

Data from: A longitudinal cline characterizes the genetic structure of human populations in the Tibetan plateau

Choognwon Jeong, Benjamin M. Peter, Buddha Basnyat, Maniraj Neupane, Cynthia M. Beall, Geoff Childs, Sienna R. Craig, John Novembre, Anna Di Rienzo & Choongwon Jeong
Indigenous populations of the Tibetan plateau have attracted much attention for their good performance at extreme high altitude. Most genetic studies of Tibetan adaptations have used genetic variation data at the genome scale, while genetic inferences about their demography and population structure are largely based on uniparental markers. To provide genome-wide information on population structure, we analyzed new and published data of 338 individuals from indigenous populations across the plateau in conjunction with worldwide genetic...

Data from: Is male rhesus macaque facial coloration under intrasexual selection?

Megan Petersdorf, Constance Dubuc, Alexander V. Georgiev, Sandra Winters & James P. Higham
Exaggerated male traits can evolve under intra- or intersexual selection, but it remains less clear how often both mechanisms act together on trait evolution. While the males of many anthropoid primate species exhibit colorful signals that appear to be badges of status under intrasexual selection, the red facial coloration of male rhesus macaques (Macaca mulatta) appears to have evolved primarily under intersexual selection and female mate choice. Nonetheless, experiments show that red color is salient...

Data from: Fungal interactions reduce carbon use efficiency

Daniel S. Maynard, Thomas W. Crowther & Mark A. Bradford
The efficiency by which fungi decompose organic matter contributes to the amount of carbon that is retained in biomass vs. lost to the atmosphere as respiration. This carbon use efficiency (CUE) is affected by various abiotic conditions, including temperature and nutrient availability. Theoretically, the physiological costs of interspecific interactions should likewise alter CUE, yet the magnitude of these costs is untested. Here we conduct a microcosm experiment to quantify how interactions among wood-decay basidiomycete fungi...

Data from: The dynamics of Kelp Forests in the Northeast Pacific Ocean and the relationship with environmental drivers

Catherine A. Pfister, Helen D. Berry & Thomas Mumford
1.The dynamics of foundation species in ecosystems are key to the fate of many species. Kelp forests are foundation species in temperate ocean ecosystems and contribute to carbon storage, macronutrient dynamics, primary production, and biodiversity of myriad associated species. Downward trends in their abundance globally have been of concern. 2.We analyzed 26 years of aerial censuses (1989-2015) of 2 canopy kelp species in Washington State (USA) waters. We compared these modern censuses with censuses in...

Registration Year

  • 2017

Resource Types

  • Dataset


  • University of Chicago
  • University of Michigan-Ann Arbor
  • Washington University in St. Louis
  • Yale University
  • Case Western Reserve University
  • University of Oxford
  • Oxford University Clinical Research Unit
  • University of Kansas
  • Stanford University
  • Field Museum of Natural History