Data from: The effects of model choice and mitigating bias on the ribosomal tree of lifeErica Lasek-Nesselquist & Johann Peter Gogarten
Deep-level relationships within Bacteria, Archaea, and Eukarya as well as the relationships of these three domains to each other require resolution. The ribosomal machinery, universal to all cellular life, represents a protein repertoire resistant to horizontal gene transfer, which provides a largely congruent signal necessary for reconstructing a tree suitable as a backbone for life’s reticulate history. Here, we generate a ribosomal tree of life from a robust taxonomic sampling of Bacteria, Archaea, and Eukarya...
Data from: Contrasting the ecological and taxonomic consequences of extinctionMax Christie, Steven M. Holland & Andrew M. Bush
Extinction in the fossil record is most often measured by the percentage of taxa (species, genera, families, etc.) that go extinct in a certain time interval. This is a measure of taxonomic loss, but previous work has indicated that taxonomic loss may be decoupled from the ecological effects of an extinction. To understand the role extinction plays in ecological change, extinction should also be measured in terms of loss of functional diversity. This study tests...
Data from: Advancing population ecology with integral projection models: a practical guideCory Merow, Johan P. Dalgren, C. Jessica E. Metcalf, Dylan Z. Childs, M. E. K. Evans, Eelke Jongejans, Sydne Record, Mark Rees, Roberto Salguero-Gómez, Sean M. McMahon, Margaret E.K. Evans & Johan P. Dahlgren
Integral Projection Models (IPMs) use information on how an individual's state influences its vital rates - survival, growth and reproduction - to make population projections. IPMs are constructed from regression models predicting vital rates from state variables (e.g., size or age) and covariates (e.g., environment). By combining regressions of vital rates, an IPM provides mechanistic insight into emergent ecological patterns such as population dynamics, species geographic distributions, or life history strategies. Here, we review important...
Data from: Historical changes in northeastern US bee pollinators related to shared ecological traitsIgnasi Bartomeus, John S. Ascher, Jason Gibbs, Bryan N. Danforth, David L. Wagner, Shannon M. Hedtke & Rachael Winfree
Pollinators such as bees are essential to the functioning of terrestrial ecosystems. However, despite concerns about a global pollinator crisis, long-term data on the status of bee species are limited. We present a long-term study of relative rates of change for an entire regional bee fauna in the northeastern United States, based on >30,000 museum records representing 438 species. Over a 140-y period, aggregate native species richness weakly decreased, but richness declines were significant only...
Data from: Rarefaction and extrapolation with Hill numbers: a framework for sampling and estimation in species diversity studiesAnne Chao, Nicholas J. Gotelli, T. C. Hsieh, Elizabeth L. Sander, K. H. Ma, Robert K. Colwell & Aaron M. Ellison
Quantifying and assessing changes in biological diversity are central aspects of many ecological studies, yet accurate methods of estimating biological diversity from sampling data have been elusive. Hill numbers, or the effective number of species, are increasingly used to characterize the taxonomic, phylogenetic, or functional diversity of an assemblage. However, empirical estimates of Hill numbers, including species richness, tend to be an increasing function of sampling effort and, thus, tend to increase with sample completeness....
Data from: Signatures of rapid evolution in urban and rural transcriptomes of white-footed mice (Peromyscus leucopus) in the New York metropolitan areaStephen E. Harris, Jason Munshi-South, Craig Obergfell, Rachel O'Neill & Rachel O’Neill
Urbanization is a major cause of ecological degradation around the world, and human settlement in large cities is accelerating. New York City (NYC) is one of the oldest and most urbanized cities in North America, but still maintains 20% vegetation cover and substantial populations of some native wildlife. The white-footed mouse, Peromyscus leucopus, is a common resident of NYC’s forest fragments and an emerging model system for examining the evolutionary consequences of urbanization. In this...
Data from: Evolution mediates the effects of apex predation on aquatic food websMark C. Urban
Ecological and evolutionary mechanisms are increasingly thought to shape local community dynamics. Here, I evaluate if the local adaptation of a meso-predator to an apex predator alters local food webs. The marbled salamander (Ambystoma opacum) is an apex predator that consumes both the spotted salamander (Ambystoma maculatum) and shared zooplankton prey. Common garden experiments reveal that spotted salamander populations which co-occur with marbled salamanders forage more intensely than those that face other predator species. These...
Data from: Strong selection barriers explain microgeographic adaptation in wild salamander populationsJonathan L. Richardson & Mark C. Urban
Microgeographic adaptation occurs when populations evolve divergent fitness advantages across the spatial scales at which focal organisms regularly disperse. Although an increasing number of studies find evidence for microgeographic adaptation, the underlying causes often remain unknown. Adaptive divergence requires some combination of limited gene flow and strong divergent natural selection among populations. In this study, we estimated the relative influence of selection, gene flow and the spatial arrangement of populations in shaping patterns of adaptive...
University of Connecticut8
City University of New York1
University of Queensland1
University of Georgia1
National Tsing Hua University1
University of Vermont1
Radboud University Nijmegen1
Max Planck Institute for Demographic Research1
Smithsonian Environmental Research Center1