43 Works

Data from: Molecular phylogenetics of Kosteletzkya (Malvaceae, Hibisceae) reveals multiple independent and successive polyploid speciation events

Kurt M. Neubig, , W. Mark Whitten, Stuart F. McDaniel & Orland J. Blanchard
Kosteletzkya s.s. is a genus of 17 species (excluding the endemic species of Madagascar), found in the New World, continental Africa, Madagascar, and Southeast Asia. Recent chromosome counts revealed diploid, tetraploid, and hexaploid species. To estimate the history of the genus, we sequenced nuclear and plastid loci for nearly all Kosteletzkya spp., in the majority of cases, with multiple accessions per species. The African species form a paraphyletic grade relative to a New World clade....

Data from: Abiotic stress does not magnify the deleterious effects of spontaneous mutations

Jacob R. Andrew, Melody M. Dossey, Veniel O. Garza, Michelle Keller-Pearson, Charles F. Baer & Joanna Joyner-Matos
Although the effects of deleterious alleles often are predicted to be greater in stressful environments, there is no theoretical basis for this prediction and the empirical evidence is mixed. Here we characterized the effects of three types of abiotic stress (thermal, oxidative and hyperosmotic) on two sets of nematode (Caenorhabditis elegans) mutation accumulation (MA) lines that differ by threefold in fitness. We compared the survival and egg-to-adult viability between environments (benign and stressful) and between...

Data from: Anatomy, systematics, paleoenvironment, growth, and age of the sauropod dinosaur Sonorasaurus thompsoni from the Cretaceous of Arizona, USA

Michael D. D'Emic, Brady Z. Foreman & Nathan A. Jud
Sauropod dinosaurs are rare in the Cretaceous North American fossil record in general and are absent from that record for most of the Late Cretaceous. Sonorasaurus thompsoni from the Turney Ranch Formation of the Bisbee Group of Arizona, USA, potentially represents one of the youngest sauropods before their ca. 30-million-year-long hiatus from the record. The anatomy of Sonorasaurus has only been briefly described, its taxonomic validity has been questioned, several hypotheses have been proposed regarding...

Data from: Identifying differentially expressed genes under heat stress and developing molecular markers in orchardgrass (Dactylis glomerata L.) through transcriptome analysis

Lin K. Huang, Hai D. Yan, J. Wang, T. Frazier, X. X. Zhao, X. Q. Zhang, X. Huang, D. F. Yan, W. J. Zang, X. Ma, Y. Peng, Y. H. Yan, W. Liu & G. Yin
Orchardgrass (Dactylis glomerata L.) is a long-lived, cool-season forage grass that is commonly used for hay production. Despite its economic importance, orchardgrass genome remains relatively unexplored. In this study, we used Illumina RNA sequencing to identify gene-associated molecular markers, including simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs), as well as heat stress-induced differentially expressed genes (DEGs) in two orchardgrass genotypes, ‘Baoxing’ (heat resistant) and ‘01998’ (heat susceptible). Approximately 163 million high-quality trimmed reads...

Data from: Synthesis of phylogeny and taxonomy into a comprehensive tree of life

Cody E. Hinchliff, Stephen A. Smith, James F. Allman, J. Gordon Burleigh, Ruchi Chaudhary, Lyndon M. Coghill, Keith A. Crandall, Jiabin Deng, Bryan T. Drew, Romina Gazis, Karl Gude, David S. Hibbett, Laura A. Katz, , Emily Jane McTavish, Peter E. Midford, Christopher L. Owen, Richard H. Ree, Jonathan A. Rees, Douglas E. Soltis, Tiffani Williams & Karen Ann Cranston
Reconstructing the phylogenetic relationships that unite all lineages (the tree of life) is a grand challenge. The paucity of homologous character data across disparately related lineages currently renders direct phylogenetic inference untenable. To reconstruct a comprehensive tree of life, we therefore synthesized published phylogenies, together with taxonomic classifications for taxa never incorporated into a phylogeny. We present a draft tree containing 2.3 million tips—the Open Tree of Life. Realization of this tree required the assembly...

Data from: A quantitative framework for investigating risk of deadly collisions between marine wildlife and boats

Julien Martin, Quentin Sabatier, Timothy A. Gowan, Christophe Giraud, Eliezer Gurarie, Charles Scott Calleson, Joel G. Ortega-Ortiz, Charles J. Deutsch, Athena Rycyk & Stacie M. Koslovsky
Speed regulations of watercraft in protected areas are designed to reduce lethal collisions with wildlife but can have economic consequences. We present a quantitative framework for investigating the risk of deadly collisions between boats and wildlife. We apply encounter rate theory to demonstrate how marine mammal-boat encounter rate can be used to predict the expected number of deaths associated with management scenarios. We illustrate our approach with management scenarios for two endangered species: the Florida...

Data from: Convergence of soil nitrogen isotopes across global climate gradients

Joseph M. Craine, Andrew J. Elmore, Lixin Wang, Laurent Augusto, W. Troy Baisden, E. N. J. Brookshire, Michael D. Cramer, Niles J. Hasselquist, Erik A. Hobbie, Ansgar Kahmen, Keisuke Koba, J. Marty Kranabetter, Michelle C. Mack, Erika Marin-Spiotta, Jordan R. Mayor, Kendra K. McLauchlan, Anders Michelsen, Gabriela B. Nardoto, Rafael S. Oliveira, Steven S. Perakis, Pablo L. Peri, Carlos A. Quesada, Andreas Richter, Louis A. Schipper, Bryan A. Stevenson … & Bernd Zeller
Quantifying global patterns of terrestrial nitrogen (N) cycling is central to predicting future patterns of primary productivity, carbon sequestration, nutrient fluxes to aquatic systems, and climate forcing. With limited direct measures of soil N cycling at the global scale, syntheses of the 15N:14N ratio of soil organic matter across climate gradients provide key insights into understanding global patterns of N cycling. In synthesizing data from over 6000 soil samples, we show strong global relationships among...

Data from: Genetic structure, admixture, and invasion success in a Holarctic defoliator, the gypsy moth (Lymantria dispar, Lepidoptera: Erebidae)

Yunke Wu, John J. Molongoski, Deborah F. Winograd, Steven M. Bogdanowicz, Artemis S. Louyakis, David R. Lance, Victor C. Mastro & Richard G. Harrison
Characterizing the current population structure of potentially invasive species provides a critical context for identifying source populations and for understanding why invasions are successful. Non-native populations inevitably lose genetic diversity during initial colonization events, but subsequent admixture among independently introduced lineages may increase both genetic variation and adaptive potential. Here we characterize the population structure of the gypsy moth (Lymantria dispar Linnaeus), one of the world's most destructive forest pests. Native to Eurasia and recently...

Data from: Climate mediates the effects of disturbance on ant assemblage structure

Heloise Gibb, Nathan J. Sanders, Robert R. Dunn, Simon Watson, Manoli Photakis, Silvia Abril, Alan N. Andersen, Elena Angulo, Inge Armbrecht, Xavier Arnan, Fabricio B. Baccaro, Tom R. Bishop, Raphael Boulay, Cristina Castracani, Israel Del Toro, Thibaut Delsinne, Mireia Diaz, David A. Donoso, Martha L. Enríquez, Tom M. Fayle, Donald H. Feener, Matthew C. Fitzpatrick, Crisanto Gómez, Donato A. Grasso, Sarah Groc … & C. Gomez
Many studies have focused on the impacts of climate change on biological assemblages, yet little is known about how climate interacts with other major anthropogenic influences on biodiversity, such as habitat disturbance. Using a unique global database of 1128 local ant assemblages, we examined whether climate mediates the effects of habitat disturbance on assemblage structure at a global scale. Species richness and evenness were associated positively with temperature, and negatively with disturbance. However, the interaction...

Data from: Exploring origins, invasion history and genetic diversity of Imperata cylindrica (L.) P. Beauv. (Cogongrass) in the United States using genotyping by sequencing

A. Millie Burrell, Alan E. Pepper, George Hodnett, John A. Goolsby, William A. Overholt, Alexis E. Racelis, Rodrigo Diaz & Patricia E. Klein
Imperata cylindrica (Cogongrass, Speargrass) is a diploid C4 grass that is a noxious weed in 73 countries and constitutes a significant threat to global biodiversity and sustainable agriculture. We used a cost-effective genotyping-by-sequencing (GBS) approach to identify the reproductive system, genetic diversity and geographic origins of invasions in the south-eastern United States. In this work, we demonstrated the advantage of employing the closely related, fully sequenced crop species Sorghum bicolor (L.) Moench as a proxy...

Data from: Phylogeny of the island archipelago frog genus Sanguirana: another endemic Philippine radiation that diversified 'Out-of-Palawan'

Rafe M. Brown, Yong-Chao Su, Brenna Barger, Cameron D. Siler, Marites B. Sanguila, Arvin C. Diesmos & David C. Blackburn
Recent higher-level frog phylogenetic analyses have included a few members of the endemic Philippine frog genus Sanguirana. Although the monophyly of the group has never been disputed, the recent phylogenetically-supported inclusion of the Palawan Wood Frog (Sanguirana sanguinea) in this clade was highly unexpected. In addition, species boundaries and relationships remain unclear and new species continue to be discovered. We estimate the phylogeny for this endemic Philippine genus using two mitochondrial gene regions and six...

Data from: Differential responses of marine communities to natural and anthropogenic changes

Michal Kowalewski, Jacelyn M. Wittmer, Troy A. Dexter, Alessandro Amorosi & Daniele Scarponi
Responses of ecosystems to environmental changes vary greatly across habitats, organisms, and observational scales. The Quaternary fossil record of the Po Basin demonstrates that marine communities of Northern Adriatic reemerged unchanged following the most recent glaciation, which lasted ~100,000 years. The Late Pleistocene and Holocene interglacial ecosystems were both dominated by the same species, species turnover rates approximated predictions of resampling models of a homogenous system, and comparable bathymetric gradients in species composition, sample-level diversity,...

Data from: Orchid phylogenomics and multiple drivers of their extraordinary diversification

Thomas J. Givnish, Daniel Spalink, Mercedes Ames, Stephanie P. Lyon, Steven J. Hunter, Alejandro Zuluaga, William J. D. Iles, Mark A. Clements, Mary T. K. Arroyo, James Leebens-Mack, Lorena Endara, Ricardo Kriebel, Kurt M. Neubig, W. Mark Whitten, Norris H. Williams & Kenneth M. Cameron
Orchids are the most diverse family of angiosperms, with over 25 000 species, more than mammals, birds and reptiles combined. Tests of hypotheses to account for such diversity have been stymied by the lack of a fully resolved broad-scale phylogeny. Here, we provide such a phylogeny, based on 75 chloroplast genes for 39 species representing all orchid subfamilies and 16 of 17 tribes, time-calibrated against 17 angiosperm fossils. A supermatrix analysis places an additional 144...

Data from: Rapid diversification associated with ecological specialization in Neotropical Adelpha butterflies

Emily R. Ebel, Jeffrey M. DaCosta, Michael D. Sorenson, Ryan I. Hill, Adriana D. Briscoe, Keith R. Willmott & Sean P. Mullen
Rapid diversification is often associated with morphological or ecological adaptations that allow organisms to radiate into novel niches. Neotropical Adelpha butterflies, which comprise over 200 species and subspecies, are characterized by extraordinary breadth in host plant use and wing colour patterns compared to their closest relatives. To examine the relationship between phenotypic and species diversification, we reconstructed the phylogenetic history of Adelpha and its temperate sister genus Limenitis using genomewide restriction-site-associated DNA (RAD) sequencing. Despite...

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: Utilizing next-generation sequencing to resolve the backbone of the Core Goodeniaceae and inform future taxonomic and floral form studies

Andrew G. Gardner, Emily B. Sessa, Pryce Michener, Eden Johnson, Kelly A. Shepherd, Dianella G. Howarth & Rachel S. Jabaily
Though considerable progress has been made in inferring phylogenetic relationships of many plant lineages, deep unresolved nodes remain a common problem that can impact downstream efforts, including taxonomic decision-making and character reconstruction. The Core Goodeniaceae is a group affected by this issue: data from the plastid regions trnL-trnF and matK have been insufficient to generate adequate support at key nodes along the backbone of the phylogeny. We performed genome skimming for 24 taxa representing major...

Data from: Affinity for natal environments by dispersers impacts reproduction and explains geographic structure of a highly mobile bird

Robert J. Fletcher, Ellen P. Robertson, Rebecca C. Wilcox, Brian E. Reichert, Wiley M. Kitchens & James D. Austin
Understanding dispersal and habitat selection behaviours is central to many problems in ecology, evolution and conservation. One factor often hypothesized to influence habitat selection by dispersers is the natal environment experienced by juveniles. Nonetheless, evidence for the effect of natal environment on dispersing, wild vertebrates remains limited. Using 18 years of nesting and mark–resight data across an entire North American geographical range of an endangered bird, the snail kite (Rostrhamus sociabilis), we tested for natal...

Data from: Evolution and biogeography of the endemic Roucela complex (Campanulaceae: Campanula) in the eastern Mediterranean

Andrew A. Crowl, Clayton J. Visger, Guilhem Mansion, Ralf Hand, Hsin-Hui Wu, Georgia Kamari, Dimitrios Phitos & Nico Cellinese
At the intersection of geological activity, climatic fluctuations, and human pressure, the Mediterranean Basin – a hotspot of biodiversity – provides an ideal setting for studying endemism, evolution, and biogeography. Here, we focus on the Roucela complex (Campanula subgenus Roucela), a group of 13 bellflower species found primarily in the eastern Mediterranean Basin. Plastid and low-copy nuclear markers were employed to reconstruct evolutionary relationships and estimate divergence times within the Roucela complex using both concatenation...

Registration Year

  • 2015

Resource Types

  • Dataset


  • University of Florida
  • University of Kansas
  • Field Museum of Natural History
  • University of Alberta
  • Utah State University
  • Princeton University
  • University of Michigan-Ann Arbor
  • Duke University
  • University of Wyoming
  • University of California, Berkeley