56 Works

Altered Gut Microbiome Profile in Patients with Pulmonary Arterial Hypertension

Seungbum Kim
Pulmonary arterial hypertension (PAH) is considered a disease of the pulmonary vasculature. Limited progress has been made in preventing or arresting progression of PAH despite extensive efforts. Our previous studies indicated that PAH could be considered a systemic disease since its pathology involves interplay of multiple organs. This, coupled with increasing implication of the gut and its microbiome in chronic diseases, led us to hypothesize that PAH patients exhibit a distinct gut microbiome that contributes...

Optimizing Coastal Restoration with the Stress Gradient Hypothesis

Hallie S Fischman, Sinead M Crotty & Christine Angelini
Restoration efforts have been escalating worldwide in response to widespread habitat degradation. However, coastal restoration attempts notoriously vary in their ability to establish resilient, high-functioning ecosystems. Conventional restoration attempts disperse transplants in competition-minimizing arrays, yet recent studies suggest that clumping transplants to maximize facilitative interactions may improve restoration success. Here, we modify the Stress Gradient Hypothesis to generate predictions about where each restoration design will perform best across environmental stress gradients. We then test this...

Data from: Preserved collagen reveals species identity in archaeological marine turtle bones from Caribbean and Florida sites

Michael Buckley, Virginia L. Harvey, Michelle J. LeFebvre, Susan D. DeFrance, Casper Toftgaard & Andrew C. Kitchener
Advancements in molecular science are continually improving our understanding of marine turtle biology and evolution. However, there are still considerable gaps in our understanding, such as past marine turtle distributions, which can benefit from advanced zooarchaeological analyses. Here we apply collagen fingerprinting to 130 archaeological marine turtle bone samples up to 2500 years old from the Caribbean and Florida’s Gulf Coast for faunal identification, finding the vast majority of samples (88%) to contain preserved collagen...

Data from: Interaction among ploidy, breeding system, and lineage diversification

Rosana Zenil-Ferguson, J. Gordon Burleigh, William A. Freyman, Boris Igic, Itay Mayrose & Emma E. Goldberg
If particular traits consistently affect rates of speciation and extinction, broad macroevolutionary patterns can be interpreted as consequences of selection at high levels of the biological hierarchy. Identifying traits associated with diversification rates is difficult because of the wide variety of characters under consideration and the statistical challenges of testing for associations from comparative phylogenetic data. Ploidy (diploid vs. polyploid states) and breeding system (self-incompatible vs. self-compatible states) are both thought to be drivers of...

Data from: A new ancient lineage of frog (Anura: Nyctibatrachidae: Astrobatrachinae subfam. nov.) endemic to the Western Ghats of Peninsular India

Seenapuram Palaniswamy Vijayakumar, Robert Alexander Pyron, K. P. Dinesh, Varun R. Torsekar, Achyuthan N. Srikanthan, Priyanka Swamy, Edward L. Stanley, David C. Blackburn & Kartik Shanker
The Western Ghats (WG) is an escarpment on the west coast of Peninsular India, housing one of the richest assemblages of frogs in the world, with three endemic families. Here, we report the discovery of a new ancient lineage from a high-elevation massif in the Wayanad Plateau of the southern WG. Phylogenetic analysis reveals that the lineage belongs to Natatanura and clusters with Nyctibatrachidae, a family endemic to the WG/Sri Lanka biodiversity hotspot. Based on...

Data from: Snail herbivory affects seedling establishment in a temperate forest in the Ozark region

Anna J. Liang, Claudia Stein, Eleanor Pearson, Jonathan A. Myers, Raelene M. Crandall & Scott A. Mangan
1. Species-specific herbivores are hypothesized to maintain plant diversity by preventing the dominance of any one plant species. However, a large proportion of herbivores have wide host ranges, and these generalists could have similar effects on plant community composition if they exhibit differences in their host preference. Here, we coupled lab and field experiments to test whether a common forest-understory snail (Neohelix alleni), a generalist herbivore, has the potential to influence forest composition through differential...

Data from: Natural selection and repeated patterns of molecular evolution following allopatric divergence

Yibo Dong, Shichao Chen, Shifeng Cheng, Wenbin Zhou, Qing Ma, Zhiduan Chen, Cheng-Xin Fu, Xin Liu, Yun-Peng Zhao, Pamela S. Soltis, Gane Ka-Shu Wong, Douglas E. Soltis & Jenny Xiang
Background: Geographic speciation is a major force in generating biodiversity. However, how genomes diverge over time after geographic isolation has halted gene flow has remained unclear. We examine genome-wide divergence of putatively single-copy orthologous genes (POGs) from transcriptomes in 20 allopatric species/variety pairs from diverse angiosperm clades. Sixteen of these pairs reflect the well-known eastern Asia – eastern North America floristic disjunction; these species have been isolated for different lengths of time, from the Miocene...

Data from: Patterns of nitrogen-fixing tree abundance in forests across Asia and America

Duncan N. L. Menge, Ryan A. Chisholm, Stuart J. Davies, Kamariah Abu Salim, David Allen, Mauricio Alvarez, Norm Bourg, Warren Y. Brockelman, Sarayudh Bunyavejchewin, Nathalie Butt, Min Cao, Wirong Chanthorn, Wei-Chun Chao, Keith Clay, Richard Condit, Susan Cordell, João Batista Da Silva, H. S. Dattaraja, Ana Cristina Segalin De Andrade, Alexandre A. Oliveira, Jan Den Ouden, Michael Drescher, Christine Fletcher, Christian P. Giardina, C. V. Savitri Gunatilleke … & Tak Fung
Symbiotic nitrogen (N)‐fixing trees can provide large quantities of new N to ecosystems, but only if they are sufficiently abundant. The overall abundance and latitudinal abundance distributions of N‐fixing trees are well characterised in the Americas, but less well outside the Americas. Here, we characterised the abundance of N‐fixing trees in a network of forest plots spanning five continents, ~5,000 tree species and ~4 million trees. The majority of the plots (86%) were in America...

Data from: Cardiac and skeletal muscle effects in the randomized HOPE-Duchenne trial

Michael Taylor, John Jefferies, Barry Byrne, Joao Lima, Bharath Ambale-Venkatesh, Mohammad R. Ostovaneh, Raj Makkar, Bryan Goldstein, Rachel Ruckdeschel Smith, James Fudge, Konstantinos Malliaras, Brian Fedor, Jeff Rudy, Janice M. Pogoda, Linda Marbán, Deborah D. Ascheim, Eduardo Marbán & Ronald G. Victor
Objective: To assess the feasibility, safety, and efficacy of intracoronary allogeneic cardiosphere-derived cells (CAP-1002) in patients with Duchenne muscular dystrophy (DMD). Methods: The Halt Cardiomyopathy Progression (HOPE)-Duchenne trial is a phase I/II, randomized, controlled, open-label trial (NCT02485938). Patients with DMD >12 years old, with substantial myocardial fibrosis, were randomized (1:1) to usual care (control) or global intracoronary infusion of CAP-1002 (75 million cells). Participants were enrolled at 3 US medical centers between January and August...

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: 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...

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...

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: 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...

Data from: Heterochronic shifts and conserved embryonic shape underlie crocodylian craniofacial disparity and convergence

Zachary S. Morris, Kent A. Vliet, Arkhat Abzhanov & Stephanie E. Pierce
The distinctive anatomy of the crocodylian skull is intimately linked with dietary ecology, resulting in repeated convergence on blunt- and slender-snouted ecomorphs. These evolutionary shifts depend upon modifications of the developmental processes which direct growth and morphogenesis. Here we examine the evolution of cranial ontogenetic trajectories to shed light on the mechanisms underlying convergent snout evolution. We use geometric morphometrics to quantify skeletogenesis in an evolutionary context and reconstruct ancestral patterns of ontogenetic allometry to...

Data from: Intersexual 'arms race' and the evolution of the sphragis in Pteronymia butterflies

Ana Paula S. Carvalho, Luísa L. Mota & Akito Y. Kawahara
Sexual reproduction is often associated with intra- and intersexual conflict, especially in species where females mate multiple times. A strategy that has evolved in males to ensure offspring paternity is the ability to produce a complex, external mating plug called a sphragis. The sphragis has been found in 273 butterfly species; however, little is known about the sphragides of the butterflies in the nymphalid genus Pteronymia. In this study, we describe the sphragides of all...

Data from: Density-dependent fitness, not dispersal movements, drives temporal variation in spatial genetic structure in dark-eyed juncos (Junco hyemalis)

Eric B. Liebgold, Nicole M. Gerlach & Ellen D. Ketterson
Some studies have found that dispersal rates and distances increase with density, indicating that density-dependent dispersal likely affects spatial genetic structure. In an 11-year mark-recapture study on a passerine, the dark-eyed junco, we tested whether density affected dispersal distance and/or fine-scale spatial genetic structure. Contrary to expectations, we found no effect of pre-dispersal density on dispersal distance or the proportion of locally-produced juveniles returning to the population from which they hatched. However, even though density...

The microbial associates of precipitation over four seasons, at three locations in the United States

Ken Aho, C.F. Weber, J. T. Werth, A. L. H. Bayless-Edwards, R. Joyce, B. C. Christner, K. Failor, B. A. Vinatzer, D. G. Schmale III & C. E. Morris
These data were used in a paper accepted in Ecological Monographs on 17 September 2019, entitled "Spatiotemporal patterns of microbial composition and diversity in precipitation", hereafter Aho et al. (in press). Microbes in the atmosphere have broad ecological impacts, including the potential to trigger precipitation through species and strains that act as ice nucleation particles. To characterize spatiotemporal trends of microbial assemblages in precipitation we sequenced 16S (bacterial) and 18S (fungal) rRNA gene amplicon libraries...

Data from: The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor

Lei Gao, Itay Gonda, Honghe Sun, Qiyue Ma, Kan Bao, Denise M. Tieman, Elizabeth A. Burzynski-Chang, Tara L. Fish, Kaitlin A. Stromberg, Gavin L. Sacks, Theodore W. Thannhauser, Majid R. Foolad, Maria Jose Diez, Joaquin Canizares, Yimin Xu, Esther Van Der Knaap, Sanwen Huang, Harry J. Klee, James J. Giovannoni & Zhangjun Fei
Modern tomatoes have narrow genetic diversity limiting their improvement potential. We present a tomato pan-genome constructed using genome sequences of 725 phylogenetically and geographically representative accessions, revealing 4,873 genes absent from the reference genome. Presence/absence variation analyses reveal substantial gene loss and intense negative selection of genes and promoters during tomato domestication and improvement. Lost or negatively selected genes are enriched for important traits, especially disease resistance. We identify a rare allele in TomLoxC promoter...

Data from: The pursuit strategy of predatory bluefish

Matthew McHenry, Jacob Johansen, Alberto Soto, Brian Free, Derek Paley & James Liao
A predator's ability to capture prey depends critically on how it coordinates its approach in response to a prey's motion. Flying insects, bats, and raptors are capable of capturing prey with a strategy known as parallel navigation, which allows a predator to move directly toward the anticipated point of interception. It is unclear if predators using other modes of locomotion are capable of employing this strategy when pursuing evasive prey. Using kinematic measurements and mathematical...

Data from: Prey colour biases in jumping spiders (Habronattus brunneus) differ across populations

Erin C. Powell, Collette Cook, Jeffrey Coco, Michelle Brock, Lauren A. Holian & Lisa A. Taylor
Predators often avoid aposematic prey as a result of aversions to particular prey signals (e.g., bright colours and noxious odours). These aversions may be flexible, that is, they can be reinforced or extinguished with experience. As such, we might expect populations to differ in their biases against certain prey characteristics (e.g., colour or pattern) depending on the prey available in the community. Here, we tested whether the jumping spider, Habronattus brunneus(Salticidae), exhibits colour biases against...

Data from: Repetitive desiccation events weaken a salt marsh mutualism

Marlous Derksen-Hooijberg, Christine Angelini, Jasper R. H. Hoogveld, Leon P. M. Lamers, Annieke Borst, Alfons Smolders, Sarah Fay Harpenslager, Laura L. Govers & Tjisse Van Der Heide
Salt marshes suffered large‐scale degradation in recent decades. Extreme events such as hot and dry spells contributed significantly to this, and are predicted to increase not only in intensity, but also in frequency under future climate scenarios. Such repetitive extreme events may generate cumulative effects on ecosystem resilience. It is therefore important to elucidate how marsh vegetation responds to repetitive stress, and whether changes in key species interactions can modulate vegetation resilience. In this study,...

Data from: Virulence-driven trade-offs in disease transmission: a meta-analysis

Miguel A. Acevedo, Forrest P. Dillemuth, Andrew J. Flick, Matthew J. Faldyn & Bret D. Elderd
The virulence--transmission trade-off hypothesis proposed more than 30 years ago is the cornerstone in the study of host-parasite co-evolution. This hypothesis rests on the premise that virulence is an unavoidable and increasing cost because the parasite uses host resources to replicate. This cost associated with replication ultimately results in a deceleration in transmission rate because increasing within-host replication increases host mortality. Empirical tests of predictions of the hypothesis have found mixed support, which cast doubt...

Data from: Detrital traits affect substitutability of a range-expanding foundation species across latitude

Rachel S. Smith, Todd Z. Osborne, Ilka C. Feller & James E. Byers
Climate-driven range shifts of foundation species could alter ecosystem processes and community composition by providing different resources than resident foundation species. Along the US Atlantic coast, the northward expanding foundation species, black mangrove, Avicennia germinans, is replacing the dominant salt marsh foundation species, marsh cordgrass, Spartina alterniflora. These species have distinct detrital attributes that ostensibly provide different resources to epifauna. We experimentally examined how detritus of these species affects decomposition and community composition in different...

Data from: Optimizing Coastal Restoration with the Stress Gradient Hypothesis

Hallie Fischman, Sinead M. Crotty & Christine Angelini
Restoration efforts have been escalating worldwide in response to widespread habitat degradation. However, coastal restoration attempts notoriously vary in their ability to establish resilient, high-functioning ecosystems. Conventional restoration attempts disperse transplants in competition-minimizing arrays, yet recent studies suggest that clumping transplants to maximize facilitative, intraspecific interactions improves restoration success. Here, we modify the Stress Gradient Hypothesis to generate predictions about where each restoration design will perform best across environmental stress gradients. We then test the...

Registration Year

  • 2019

Resource Types

  • Dataset
  • Text


  • University of Florida
  • University of Georgia
  • Florida Museum of Natural History
  • Chinese Academy of Sciences
  • University of Minnesota
  • United States Department of Agriculture
  • Washington University in St. Louis
  • University of Kansas
  • Virginia Tech
  • Icesi University