4 Works

Data from: Dissecting molecular evolution in the highly diverse plant clade Caryophyllales using transcriptome sequencing

Ya Yang, Michael J. Moore, Samuel F. Brockington, Douglas E. Soltis, Gane Ka-Shu Wong, Eric J. Carpenter, Yong Zhang, Li Chen, Zhixiang Yan, Yinlong Xie, Rowan F. Sage, Sarah Covshoff, Julian M. Hibberd, Matthew N. Nelson & Stephen A. Smith
Many phylogenomic studies based on transcriptomes have been limited to “single-copy” genes due to methodological challenges in homology and orthology inferences. Only a relatively small number of studies have explored analyses beyond reconstructing species relationships. We sampled 69 transcriptomes in the hyperdiverse plant clade Caryophyllales and 27 outgroups from annotated genomes across eudicots. Using a combined similarity- and phylogenetic tree-based approach, we recovered 10,960 homolog groups, where each was represented by at least eight ingroup...

Data from: Relationships between spatial metrics and plant diversity in constructed freshwater wetlands

Erika C. Brandt, John E. Petersen, Jake J. Grossman, George A. Allen & David H. Benzing
The diversity of plant species and their distribution in space are both thought to have important effects on the function of wetland ecosystems. However, knowledge of the relationships between plant species and spatial diversity remains incomplete. In this study, we investigated relationships between spatial pattern and plant species diversity over a five year period following the initial restoration of experimental wetland ecosystems. In 2003, six identical and hydrologically-isolated 0.18 ha wetland “cells” were constructed in...

Data from: Electricity and water conservation on college and university campuses in response to national competitions among dormitories: quantifying relationships between behavior, conservation strategies and psychological metrics

John E. Petersen, Cynthia M. Frantz, , Tess M. Yanisch, Evan Tincknell & Noel Myers
“Campus Conservation Nationals” (CCN) is a recurring, nation-wide electricity and water-use reduction competition among dormitories on college campuses. We conducted a two year empirical study of the competition’s effects on resource consumption and the relationship between conservation, use of web technology and various psychological measures. Significant reductions in electricity and water use occurred during the two CCN competitions examined (n = 105,000 and 197,000 participating dorm residents respectively). In 2010, overall reductions during the competition...

Data from: Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants

Stephen A. Smith, Ya Yang, Joseph W. Brown & Michael J. Moore
Background: The use of transcriptomic and genomic datasets for phylogenetic reconstruction has become increasingly common as researchers attempt to resolve recalcitrant nodes with increasing amounts of data. The large size and complexity of these datasets introduce significant phylogenetic noise and conflict into subsequent analyses. The sources of conflict may include hybridization, incomplete lineage sorting, or horizontal gene transfer, and may vary across the phylogeny. For phylogenetic analysis, this noise and conflict has been accommodated in...

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  • Oberlin College
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  • University of Michigan-Ann Arbor
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  • University of Cambridge
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  • University of Minnesota
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  • New York University
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  • University of Florida
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  • Beijing Genomics Institute
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  • University of Western Australia
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