7 Works

Data from: Multilocus phylogeographic assessment of the California Mountain Kingsnake (Lampropeltis zonata) suggests alternative patterns of diversification for the California Floristic Province

Edward A. Myers, Javier A. Rodríguez-Robles, Dale F. DeNardo, Richard E. Staub, Alyssa Stropoli, Sara Ruane & Frank T. Burbrink
Phylogeographic inference can determine the timing of population divergence, historical demographic processes, patterns of migration, and when extended to multiple species, the history of communities. Single locus analyses can mislead interpretations of the evolutionary history of taxa and comparative analyses. It is therefore important to revisit previous single-locus phylogeographic studies, particularly those that have been used to propose general patterns for regional biotas and the processes responsible for generating inferred patterns. Here we employ a...

Data from: Signatures of rapid evolution in urban and rural transcriptomes of white-footed mice (Peromyscus leucopus) in the New York metropolitan area

Stephen 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: Phylogeny and tempo of diversification in the superradiation of spiny-rayed fishes

Thomas J. Near, Alex Dornburg, Ron I. Eytan, Benjamin P. Keck, W. Leo Smith, Kristen L. Kuhn, Jon A. Moore, Samantha A. Price, Frank T. Burbrink, Matt Friedman & Peter C. Wainwright
Spiny-rayed fishes, or acanthomorphs, comprise nearly one-third of all living vertebrates. Despite their dominant role in aquatic ecosystems, the evolutionary history and tempo of acanthomorph diversification is poorly understood. We investigate the pattern of lineage diversification in acanthomorphs by using a well-resolved time-calibrated phylogeny inferred from a nuclear gene supermatrix that includes 520 acanthomorph species and 37 fossil age constraints. This phylogeny provides resolution for what has been classically referred to as the “bush at...

Data from: Characterization of human cortical gene expression in relation to glucose utilization.

Kirstin N. Sterner, Michael R. McGowen, Harry T. Chugani, Adi L. Tarca, Chet C. Sherwood, Patrick R. Hof, Christopher W. Kuzawa, Amy M. Boddy, Ryan L. Raaum, Amy Weckle, Leonard Lipovich, Lawrence I. Grossman, Monica Uddin, Morris Goodman & Derek E. Wildman
Objectives: Human brain development follows a unique pattern characterized by a prolonged period of postnatal growth and reorganization, and a postnatal peak in glucose utilization. The molecular processes underlying these developmental changes are poorly characterized. The objectives of this study were to determine developmental trajectories of gene expression and to examine the evolutionary history of genes differentially expressed as a function of age. Methods: We used microarrays to determine age-related patterns of mRNA expression in...

Data from: Recommendations for using msBayes to incorporate uncertainty in selecting an ABC model prior: a response to Oaks et al.

Michael James Hickerson, Graham N. Stone, Konrad Lohse, Terrence C. Demos, Xiaoou Xie, Cedric Landerer & Naoki Takebayashi
Prior specification is an essential component of parameter estimation and model comparison in Approximate Bayesian computation (ABC). Oaks et al. present a simulation-based power analysis of msBayes and conclude that msBayes has low power to detect genuinely random divergence times across taxa, and suggest the cause is Lindley's paradox. Although the predictions are similar, we show that their findings are more fundamentally explained by insufficient prior sampling that arises with poorly chosen wide priors that...

Data from: Conservation genetics of extremely isolated urban populations of the Northern Dusky Salamander (Desmognathus fuscus) in New York City

Jason Munshi-South, Yana Zak & Ellen Pehek
Urbanization is a major cause of amphibian decline. Stream-dwelling plethodontid salamanders are particularly susceptible to urbanization due to declining water quality and hydrological changes, but few studies have examined these taxa in cities. The northern dusky salamander (Desmognathus fuscus) was once common in the New York City metropolitan area, but has substantially declined throughout the region in recent decades. We used five tetranucleotide microsatellite loci to examine population differentiation, genetic variation, and bottlenecks among five...

Data from: A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes

R. Alexander Pyron, Frank T. Burbrink & John J. Wiens
Background: The extant squamates (>9400 known species of lizards and snakes) are one of the most diverse and conspicuous radiations of terrestrial vertebrates, but no studies have attempted to reconstruct a phylogeny for the group with large-scale taxon sampling. Such an estimate is invaluable for comparative evolutionary studies, and to clarify their taxonomy. Here, we present the first large-scale phylogenetic estimate for Squamata. Results: The estimated phylogeny contains 4161 species representing all currently recognized families...

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  • City University of New York
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