Data and scripts from: Phylogenomic analysis points to a South American origin of Manihot and illuminates the primary gene pool of cassavaMarcelo F. Simon, J. Moises Mendoza F., Márcio Lacerda Lopes Martins, Sergei V. Drovetski, Natalia A. S. Przelomska, Hope Loiselle, Taciana B. Cavalcanti, Peter W. Inglis, Natalie G. Mueller, Robin G. Allaby, Fábio De Oliveira Freitas & Logan Kistler
The genus Manihot, with around 120 known species, is native to a wide range of habitats and regions in the tropical and subtropical Americas. Its high species richness and recent diversification only ~6Mya have significantly complicated previous phylogenetic analyses. Several basic elements of Manihot evolutionary history therefore remain unresolved. Here, we conduct a comprehensive phylogenomic analysis of Manihot, focusing on exhaustive sampling of South American taxa. We find that two recently described species from northeast...
Accelerations cause brain tissue to move, and this data summarizes MRI-based observations of 3D brain movement during an in vivo impact (brain-skull displacement and brain tissue deformation). The data is a group average, or atlas, of indivudial data from two groups of study participants: neck extension (n=10) and neck rotation (n=9).
Objective: The primary objective of this study was to evaluate the correlation of large mitochondrial DNA deletions in skin samples of people with HIV with measure of neuropathy and prior exposure to therapy. We hypothesized that deletions would be associated with the presence of neuropathy. As secondary objectives we determined the correlation of deletion burden with demographic data and neuropathy measures. Methods: In this retrospective cohort study we measured the accumulation of large mtDNA deletions...
Microbes must adapt to the presence of other species, but it can be difficult to recreate the natural context for these interactions in the laboratory. We describe a method for inferring the existence of symbiotic adaptations by experimentally evolving microbes that would normally interact in an artificial environment without access to other species. By looking for changes in the fitness effects microbes adapted to isolation have on their partners, we can infer the existence of...
Objective: Perform a longitudinal analysis of clinical features associated with Neurofibromatosis Type 1 (NF1) based on demographic and clinical characteristics, and to apply a machine learning strategy to determine feasibility of developing exploratory predictive models of optic pathway glioma (OPG) and attention-deficit/hyperactivity disorder (ADHD) in a pediatric NF1 cohort. Methods: Using NF1 as a model system, we perform retrospective data analyses utilizing a manually-curated NF1 clinical registry and electronic health record (EHR) information, and develop...
Data from two dimensional electronic spectroscopy showing that photosynthesis tunes quantum-mechanical mixing of electronic and vibrational states to steer exciton energy transferJacob Higgins, Lawson Lloyd, Sara Sohail, Marco Allodi, John Otto, Rafael Saer, Ryan Wood, Sara Massey, Po-Chieh Ting, Robert Blankenship & Gregory Engel
Raw data from an ultrafast two dimensional electronic spectrometer investigating a series of mutants from the Fenna-Matthews Olson photosynthetic complex from Chlorobaculum tepidum is included here. This data was analyzed and reduced using the enclosed matlab scripts to show that this complex responds to changing oxidation conditions by breaking a resonance between a gap between electronic states and an attendant vibration within the bacteriochlorophyll molecules. Breaking this resonance steers energy differently through the complex and...
Data from: Niche shifts after island colonization spurred adaptive diversification and speciation in a cosmopolitan bird cladeOriol Lapiedra, Ferran Sayol, Joan Garcia-Porta & Daniel Sol
Islands have long been recognized as key contributors to biodiversity because islands facilitate geographic isolation and ecological divergence from mainland ancestors. However, island colonization has traditionally been considered an evolutionary dead-end process, and its consequences for continental biodiversity remain understudied. Here, we studied the evolutionary radiation of Columbiformes (i.e. pigeons and doves) to examine if ecological niche shifts on islands shaped biological diversification and community composition on continents. We show that the colonization of islands...
Abstract The evolution of key innovations—unique features that enable a lineage to interact with the environment in a novel way—may drive broad patterns of adaptive diversity. However, traditional tests of the key innovation hypothesis, those which attempt to identify the evolutionary effect of a purported key innovation by comparing patterns of diversity between lineages with and without the key trait, have been challenged on both conceptual and statistical grounds. Here, we explore alternative, untested hypotheses...
Data from: Equivalent learning, but unequal participation: male bumble bees learn comparably to females, but participate in cognitive assessments at lower ratesMatthew Austin, Tian Manning, Kamau MuseMorris & Aimee Dunlap
Sex-specific cognitive abilities are well documented. These can occur when sexes engage in different ecological contexts. Less known is whether different ecological contexts can also drive sex-specific participation rates in behavioral tests. Here, we explore this question in bumble bees, a group of eusocial insects where worker females and males exhibit stark socioecological differences. Among myriad colony maintenance tasks, workers forage for themselves and developing brood, while males forage only for themselves while mate-searching. Following...
Phenotype and QTL mapping data from: Genetic trade-offs underlie divergent life history strategies for local adaptation in white cloverKenneth Olsen
Local adaptation is common in plants, yet characterization of its underlying genetic basis is rare in herbaceous perennials. Moreover, while many plant species exhibit intraspecific chemical defense polymorphisms, their importance for local adaptation remains poorly understood. We examined the genetic architecture of local adaptation in a perennial, obligately-outcrossing herbaceous legume, white clover (Trifolium repens). This widespread species displays a well-studied chemical defense polymorphism for cyanogenesis (HCN release following tissue damage) and has evolved climate-associated cyanogenesis...
Studies have demonstrated that hurricanes can drive selection in Neotropical anoles. In a recent study it was shown that post-hurricane survivors showed increased toepad areas, and surprisingly, shorter femurs. One potential explanation for the reduction in femur length is that increased drag on individuals with longer femurs causes them to be blown off their perch. Consequently, lizards with shorter femora might survive better in hurricanes. To gain insight into the form-function relationships of drag-reduction in...
Habitat structure mediates vulnerability to climate change through its effects on thermoregulatory behaviorLauren Neel, Michael Logan, Daniel Nicholson, Christina Miller, Albert Chung, Inbar Maayan, Zach Degon, Madeline DuBois, John David Curlis, Q Taylor, Kaitlin Keegan, Owen McMillan, Jonathan Losos & Christian Cox
Tropical ectotherms are thought to be especially vulnerable to climate change because they are thermal specialists, having evolved in aseasonal thermal environments. However, even within the tropics, habitat structure can influence opportunities for behavioral thermoregulation. Open (and edge) habitats likely promote more effective thermoregulation due to the high spatial heterogeneity of the thermal landscape, while forests are thermally homogenous and may constrain opportunities for behavioral buffering of environmental temperatures. Nevertheless, the ways in which behavior...
This dataset (Andean_AGB.xlsx) has the data employed in the paper entitled Old-growth Andean forests as globally important carbon sinks and future carbon refuges. The data was compiled as the results of the work of several research teams spread out across the Andean region. The information available here has data about aboveground carbon stocks and dynamics and the main explanatory variables, such as climate and symbiotic root associations.
Wild Dictyostelium discoideum social amoebae show plastic responses to the presence of nonrelatives during multicellular developmentSuegene Noh, Lauren Christopher, Joan Strassmann & David Queller
When multiple strains of microbes form social groups, such as the multicellular fruiting bodies of Dictyostelium discoideum, conflict can arise regarding cell fate. Both fixed and plastic differences among strains can contribute to cell fate, and plastic responses may be particularly important if social environments frequently change. We used RNA-sequencing and photographic time series analysis to detect possible conflict-induced plastic differences between wild D. discoideum aggregates formed by single strains compared to mixed pairs of...
Washington University in St. Louis21
Emory University School of Medicine1
Columbus State University1
University of Antwerp1
Consortium for Sustainable Development of the Andean Ecoregion1
University of Michigan-Ann Arbor1
New Mexico Museum of Natural History and Science1
University of Queensland1