1,073 Works

Data from: Phylogenomics clarifies repeated evolutionary origins of inbreeding and fungus farming in bark beetles (Curculionidae, Scolytinae)

Andrew Johnson, McKenna, Bjarte H. Jordal, Anthony I. Cognato, Sarah M. Smith, Alan R. Lemmon, Emily L. Moriarty Lemmon & Jiri Hulcr
Bark and ambrosia beetles (Curculionidae, Scolytinae) display a conspicuous diversity of unusual genetic and ecological attributes and behaviors. Reconstructing the evolution of Scolytinae, particularly the large and ecologically significant tribe Cryphalini (pygmy borers), has long been problematic. These challenges have not adequately been addressed using morphological characters, and previous research has used only DNA sequence data from small numbers of genes. Through a combination of anchored hybrid enrichment, low-coverage draft genomes, and transcriptomes, we addressed...

Data from: Character evolution and missing (morphological) data across Asteridae

Gregory W. Stull, Melanie Schori, Douglas E. Soltis & Pamela S. Soltis
Premise of the study: Our current understanding of flowering plant phylogeny provides an excellent framework for exploring various aspects of character evolution through comparative analyses. However, attempts to synthesize this phylogenetic framework with extensive morphological datasets have been surprisingly rare. Here, we explore character evolution in Asteridae (asterids), a major angiosperm clade, using an extensive morphological data set and a well-resolved phylogeny. Methods: We scored 15 phenotypic characters (spanning chemistry, vegetative anatomy, and floral, fruit,...

Data from: Multiple stages of tree seedling recruitment are altered in tropical forests degraded by selective logging

Rajeev Pillay, Fangyuan Hua, Bette A. Loiselle, Henry Bernard & Robert J. Fletcher
Tropical forest degradation is a global environmental issue. In degraded forests, seedling recruitment of canopy trees is vital for forest regeneration and recovery. We investigated how selective logging, a pervasive driver of tropical forest degradation, impacts canopy tree seedling recruitment, focusing on an endemic dipterocarp Dryobalanops lanceolata in Sabah, Borneo. During a mast-fruiting event in intensively logged and nearby unlogged forest, we examined four stages of the seedling recruitment process: seed production, seed predation, and...

Data from: Genomic differentiation during speciation-with-gene-flow: comparing geographic and host-related variation in divergent life history adaptation in Rhagoletis pomonella

Meredith M. Doellman, Gregory J. Ragland, Glen R. Hood, Peter J. Meyers, Scott P. Egan, Thomas H.Q. Powell, Peter Lazorchak, Mary M. Glover, Cheyenne Tait, Hannes Schuler, Daniel A. Hahn, Stewart H. Berlocher, James J. Smith, Patrik Nosil, Jeffrey L. Feder, Daniel Hahn, Stewart Berlocher, Peter Meyers, Scott Egan, Jeffrey Feder, Glen Hood, Thomas Powell & Gregory Ragland
A major goal of evolutionary biology is to understand how variation within populations gets partitioned into differences between reproductively isolated species. Here, we examine the degree to which diapause life history timing, a critical adaptation promoting population divergence, explains geographic and host-related genetic variation in ancestral hawthorn and recently derived apple-infesting races of Rhagoletis pomonella. Our strategy involved combining experiments on two different aspects of diapause (initial diapause intensity and adult eclosion time) with a...

Data from: Origin and macroevolution of micro-moths on sunken Hawaiian islands

Chris A. Johns, Emmanuel F.A. Toussaint, Jesse W. Breinholt, Akito Y. Kawahara & Emmanuel F. A. Toussaint
The origins and evolution of Hawaiian biodiversity are a matter of controversy, and the mechanisms of lineage diversification for many organisms on this remote archipelago remain unclear. Here we focus on the poorly-known endemic leaf-mining moth genus Philodoria (Lepidoptera, Gracillariidae), whose species feed on a diversity of Hawaiian plant lineages, many of which are critically endangered. We use anchored hybrid enrichment to assemble the first phylogenomic dataset (507 loci) for any Hawaiian animal taxon. To...

Data from: Application of CRISPR/Cas9 to Tragopogon (Asteraceae), an evolutionary model for the study of polyploidy

Shengchen Shan, Evgeny V. Mavrodiev, Riqing Li, Zhengzhi Zhang, Bernard A. Hauser, Pamela S. Soltis, Douglas E. Soltis & Bing Yang
Tragopogon (Asteraceae) is an excellent natural system for studies of recent polyploidy. Development of an efficient CRISPR/Cas9-based genome editing platform in Tragopogon will facilitate novel studies of the genetic consequences of polyploidy. Here, we report our initial results of developing CRISPR/Cas9 in Tragopogon. We have established a feasible tissue culture and transformation protocol for Tragopogon. Through protoplast transient assays, use of the TragCRISPR system (i.e. the CRISPR/Cas9 system adapted for Tragopogon) was capable of introducing...

Data from: Concussion Biomarkers Assessed in Collegiate Student-Athletes (BASICS) I: normative study

Breton Michael Asken, Russell M. Bauer, Steven Trent DeKosky, Zachary Morgan Houck, Charles C. Moreno, Michael S. Jaffee, Arthur G. Weber & James R. Clugston
Objective: To describe variability in concussion biomarker concentrations collected from serum in a sample of healthy collegiate athletes, as well as report reliability metrics in a subsample of female athletes. Methods: Observational cohort study - Aβ42, total tau, S100B, UCH-L1, GFAP, MAP2, and CNPase serum concentrations were measured in 415 (61% male, 40% white, age 19.0±1.2 years) non-concussed collegiate athletes without recent exposure to head impacts. Standardized normative distributions are reported for each biomarker. We...

Data from: Stratigraphic signatures of mass extinctions: ecological and sedimentary determinants

Rafał Nawrot, Daniele Scarponi, Michele Azzarone, Troy A. Dexter, Kristopher M. Kusnerik, Jacalyn M. Wittmer, Alessandro Amorosi & Michal Kowalewski
Stratigraphic patterns of last occurrences of fossil taxa (LOs) potentially fingerprint mass extinctions and delineate rates and geometries of those events. Although empirical studies of mass extinctions recognize that random sampling causes LOs to occur earlier than the time of extinction (Signor–Lipps effect), sequence-stratigraphic controls on the position of LOs are rarely considered. By tracing stratigraphic ranges of extant mollusc species preserved in the Holocene succession of the Po coastal plain (Italy), we demonstrated that,...

Data from: A universal probe set for targeted sequencing of 353 nuclear genes from any flowering plant designed using k-medoids clustering

Matthew G. Johnson, Lisa Pokorny, Steven Dodsworth, Laura R. Botigue, Robyn S. Cowan, Alison Devault, Wolf L. Eiserhardt, Niroshini Epitawalage, Félix Forest, Jan T. Kim, James Leebens-Mack, Ilia J. Leitch, Olivier Maurin, Doug Soltis, Pamela S. Soltis, Gane Ka-Shu Wong, William J. Baker & Norman Wickett
Sequencing of target-enriched libraries is an efficient and cost-effective method for obtaining DNA sequence data from hundreds of nuclear loci for phylogeny reconstruction. Much of the cost of developing targeted sequencing approaches is associated with the generation of preliminary data needed for the identification of orthologous loci for probe design. In plants, identifying orthologous loci has proven difficult due to a large number of whole-genome duplication events, especially in the angiosperms (flowering plants). We used...

Data from: Effects of taxon sampling and tree reconstruction methods on phylodiversity metrics

Johanna Jantzen, W. Mark Whitten, Kurt Neubig, Lucas Majure, Douglas Soltis & Pam Soltis
1. The amount and patterns of phylodiversity in a community are often used to draw inferences about the local and historical factors affecting community assembly and can be used to prioritize communities and locations for conservation. Because measures of phylodiversity are based on the topology and branch lengths of phylogenetic trees, which are affected by the number and diversity of taxa in the tree, these analyses may be sensitive to changes in taxon sampling and...

Data from: Genomics overrules mitochondrial DNA, siding with morphology on a controversial case of species delimitation

Carmen R. Del Pedraza-Marrón, Raimundo Silva, Jonathan Deeds, Steven M. Van Belleghem, Alicia Mastretta-Yanes, Omar Domínguez-Domínguez, Rafael A. Rivero-Vega, Loretta Lutackas, Debra Murie, Daryl Parkyn, Lewis H. Bullock, Kristin Foss, Humberto Ortiz-Zuazaga, Juan Narváez-Barandica, Arturo Acero, Grazielle Gomes & Ricardo Betancur-R.
Species delimitation is a major quest in biology and is essential for adequate management of the organismal diversity. A challenging example comprises the fish species of red snappers in the Western Atlantic. Red snappers have been traditionally recognized as two separate species based on morphology: Lutjanus campechanus (northern red snapper) and L. purpureus (southern red snappers). Recent genetic studies using mitochondrial markers, however, failed to delineate these nominal species, leading to the current lumping of...

Populations of a widespread invader and co-occurring native species vary in phenotypic plasticity

Drew Hiatt & Luke Flory
Phenotypic plasticity can promote plant invasions and enhance impacts on native species but little is known about variation in plasticity among invader populations compared to native species. Variation in plasticity among invader populations could inform more precise predictions of invader spread and impacts across heterogeneous resource environments. We used a common garden experiment with sun and shade treatments to test for variation in plasticity among 12 populations of an invasive grass, and to determine if...

Data from: Allocation of invasive plant management expenditures for conservation: lessons from Florida, USA

Drew Hiatt, Kristina Serbesoff-King, Deah Lieurance, Doria R. Gordon & S. Luke Flory
Although the ecological impacts of biological invasions are well studied, comprehensive analyses of spending on invasive species management are lacking. Such analyses could inform both effective resource allocation and management planning. We evaluated long-term invasive plant management expenditures and their potential geographic, economic, and ecological drivers for freshwater and terrestrial conservation areas in Florida, USA. Average expenditures for managing invaders were approximately US$45M annually, with over 90% of funding provided by the state. Our model...

Data from: The biotic interactions hypothesis partially explains bird species turnover along a lowland Neotropical precipitation gradient

Juan Pablo Gomez, Jose Miguel Ponciano, Gustavo Londoño & Scott Robinson
Aim: We evaluated the influence of climate in determining bird communities along precipitation gradients. We argue that mechanisms responsible for community turnover along precipitation gradients are similar to mechanisms operating along temperature and latitudinal gradients. We test the hypothesis that environmental conditions affect community composition in dry forests, whereas biotic interactions affect community composition in wet forests. Location: Low-elevation forests along a precipitation gradient in Colombia where precipitation ranges from 700 – 4000 mm annually...

Phylogeny and biogeography of some Cretaceous spatangoid echinoids with special emphasis on taxa from the Western Interior Seaway

Bruce Lieberman & Steven Byrum
Members of the echinoid order Spatangoida, a highly diverse and abundant marine invertebrate clade, were important denizens of the Cretaceous Western Interior Seaway (WIS), an epicontinental seaway that divided North America in two during an interval of greenhouse conditions between roughly 100 and 65 million years ago. A phylogenetic analysis of spatangoids was conducted using a character matrix of 32 characters from 21 species. Species that occur in the WIS were considered comprehensively, and species...

Habitat complexity dampens selection on prey activity level

Carl Keiser, Spencer Ingley, Benjamin Toscano, Inon Scharf & Jonathan Pruitt
Conspecific prey individuals often exhibit persistent differences in behavior (i.e., animal personality) and consequently vary in their susceptibility to predation. How this form of selection varies across environmental contexts is essential to predicting ecological and evolutionary dynamics, yet remains currently unresolved. Here, we use three separate predator–prey systems (sea star–snail, wolf spider–cricket, and jumping spider–cricket) to independently examine how habitat structural complexity influences the selection that predators impose on prey behavioral types. Prior to conducting...

Local extinction risk under climate change in a neotropical asymmetrically dispersed epiphyte

Miguel Acevedo, Lydia Beaudrot, Elvia Melendez-Ackerman & Raymond Tremblay
1. The long-term fate of populations experiencing disequilibrium conditions with their environment will ultimately depend on how local colonization and extinction dynamics respond to abiotic conditions (e.g. temperature and rainfall), dispersal limitation and biotic interactions (e.g. competition, facilitation, or interactions with natural enemies). Understanding how these factors influence distributional dynamics under climate change is a major knowledge gap, particularly for small ranged and dispersal-limited plant species, which are at higher risk of extinction. Epiphytes are...

Patch size and vegetation structure drive changes to mixed-species flock diversity and composition across a gradient of fragment sizes in the Western Andes of Colombia

Harrison Jones & Scott Robinson
This data set represents a series of 502 mixed-species bird flock compositions, and derived taxonomic, functional, and phylogenetic diversity indices, that were gathered along a gradient of forest fragment sizes (range = 10-173 ha) in the Colombian Western Andes. We sampled mixed-species flocks using transect surveys along 14 transects in 8 fragments and a continuous forest reference site in the same landscape and at the same elevation (~1900-2200 m.a.s.l.). We also used buffer analysis to...

Spatial point pattern analysis of traces (SPPAT): an approach for visualizing and quantifying site-selectivity patterns of drilling predators

Alexis Rojas, Gregory Dietl, Michal Kowalewski, Roger W. Portell, Austin Hendy & Jason Blackburn
Site-selectivity analysis in drilling predation may provide useful behavioral information of a predator interacting with its prey. However, traditional approaches exclude some spatial information (i.e., oversimplified trace position) and are dependent on the scale of analysis (e.g., arbitrary grid system used to divide the prey skeleton into sectors). Here we introduce the spatial point pattern analysis of traces (SPPAT), an approach for visualizing and quantifying the distribution of traces on shelled invertebrate prey, which includes...

Data from: The evolutionary origins of the cat attractant nepetalactone in catnip

Benjamin R. Lichman, Grant T. Godden, John P. Hamilton, Lira Palmer, Mohamed O. Kamileen, Dongyan Zhao, Brieanne Vaillancourt, Joshua Wood, Miao Sun, Taliesin J. Kinser, Laura K. Henry, Carlos Rodriguez Lopez, Natalia Dudareva, Douglas E. Soltis, Pamela S. Soltis, C. Robin Buell & Sarah E. O’Connor
The evolutionary origins of the cat attractant nepetalactone in catnip

Critical PO2 as a diagnostic biomarker for the effects of low-oxygen modified and controlled atmospheres on phytosanitary irradiation treatments in the Cabbage Looper Trichoplusia ni (Hübner)

Chao Chen, Catriona Condon, Leigh Boardman, Robert Meagher, Laura Jeffers, Andrea Beam, Woodward Bailey & Daniel Hahn
BACKGROUND: Phytosanitary irradiation is a sustainable alternative to chemical fumigants for disinfesting fresh commodities from insect pests. However, irradiating insects in modified atmospheres with very low oxygen (<1 kPa O2) has repeatedly been shown to increase radioprotective response. Thus, there is a concern that modified atmosphere packaging could reduce the efficacy of phytosanitary irradiation. One hurdle slowing the widespread application of phytosanitary irradiation is a lack of knowledge about how moderate levels of hypoxia relevant...

Influences of patch-burn grazing on headwater prairie streams and subsequent recovery

Jessica Fulgoni, Matt Whiles, Walter Dodds, Danelle Larson, Karen Jackson & Bartosz Grudzinski
1. Patch-burn grazing (PBG) can promote terrestrial heterogeneity and biodiversity, but can temporarily increase stream nutrients, ecosystem metabolism, and alter macroinvertebrate assemblages. The impacts of grazing on stream channel morphology and post-PBG recovery patterns are unclear. 2. We assessed the influence of grazing in PBG managed grassland streams in Missouri, USA, and subsequent recovery when grazing ceased for two years. We hypothesized that grazing would degrade water quality, stream biotic integrity, and channel morphology, but...

Data from: Increasing synergistic effects of habitat destruction and hunting on mammals over three decades in the Gran Chaco

Alfredo Romero-Muñoz, Ana Benítez-López, Damaris Zurell, Matthias Baumann, Micaela Camino, Julieta Decarre, Hugo Del Castillo, Anthony Giordano, Bibiana Gómez-Valencia, Christian Levers, Andrew Noss, Veronica Quiroga, Jeffrey Thompson, Ricardo Torres, Marianela Velilla, Andrea Weiler & Tobias Kuemmerle
Habitat destruction and overexploitation are the main threats to biodiversity and where they co-occur, their combined impact is often larger than their individual one. Yet, detailed knowledge of the spatial footprints of these threats is lacking, including where they overlap and how they change over time. These knowledge gaps are real barriers for effective conservation planning. Here, we develop a novel approach to reconstruct the individual and combined footprints of both threats over time. We...

Bat community response to intensification of biomass production for bioenergy across the southeastern United States

Holly Ober, Gavin Jones, Isabel Gottlieb, Shelly Johnson, Lora Smith, Berry Brosi & Robert Fletcher
Human demand for food, fiber, and space is accelerating the rate of change of land cover and land use. Much of the world now consists of a matrix of natural forests, managed forests, agricultural cropland, and urbanized plots. Expansion of domestic energy production efforts in the United States is one driver predicted to influence future land-use and land management practices across large spatial scales. Favorable growing conditions make the southeastern United States an ideal location...

Data from: Clonal integration enhances performance of an invasive grass

Chris Wilson, James Estrada & Stephen Flory
While many clonal plants are highly successful invaders, not all clonal plants share resources, often making the contribution of clonal integration (i.e., the translocation of resources among ramets) to invasion unclear. To determine if photosynthate translocation augments performance of emerging daughter ramets for a globally invasive grass (Imperata cylindrica), we combined a 13CO2 pulse-chase experiment with a greenhouse experiment manipulating light levels and rhizome attachment. Model simulations were also used to determine if clonal integration...

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  • University of Florida
  • Chinese Academy of Medical Sciences & Peking Union Medical College
  • Shanghai Jiao Tong University
  • Chinese Academy of Agricultural Sciences
  • Sichuan University
  • Chinese Academy of Sciences
  • Ministry of Agriculture and Rural Affairs
  • Zhejiang University
  • Nantong University
  • Fudan University