54 Works

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: 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: 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: 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: 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: 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: 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...

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...

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...

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: 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...

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: 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: 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: Habitat urbanization and stress response are primary predictors of personality variation in Northern cardinals (Cardinalis cardinalis)

Ping Huang, Colette St. Mary & Rebecca Kimball
Behavioral traits that vary consistently among individuals across different contexts are often termed as personality traits. The correlated suite formed by those traits, called a ‘behavioral syndrome’, can provide a more comprehensive way to view animal behavior. Both extrinsic and intrinsic ‘states’ (defined as strategically relevant individual features affecting the cost-and-benefit trade-offs of behavioral actions) have the potential to shape among-individual variation in personality traits, as well as behavioral syndromes. Here, we used Northern cardinals...

Phylogeography and population genetics of pine butterflies: sky islands increase genetic divergence

Dale Halbritter, Caroline Storer, Akito Kawahara & Jaret Daniels
The sky islands of southeastern Arizona (AZ) mark a major transition zone between tropical and temperate biota and are considered a neglected biodiversity hotspot. Dispersal ability and host plant specificity are thought to impact the history and diversity of insect populations across the sky islands. We aimed to investigate the population structure and phylogeography of two pine-feeding pierid butterflies, the pine white (Neophasia menapia) and the Mexican pine white (N. terlooii), restricted to these "islands"...

Unoccupied aerial system enabled functional modeling of maize (Zea mays L.) height reveals dynamic expression of loci associated to temporal growth

Steven Anderson, Seth Murray, Yuanyuan Chen, Lonesome Malambo, Anjin Chang, Sorin Popescu, Dale Cope & Jinha Jung
Unoccupied aerial systems (UAS) were used to phenotype growth trajectories of inbred maize populations under field conditions. Three recombinant inbred line populations were surveyed on a weekly basis collecting RGB images across two irrigation regimens (irrigated and non-irrigated/rain fed). Plant height, estimated by the 95th percentile (P95) height from UAS generated 3D point clouds, exceeded 70% correlation to manual ground truth measurements and 51% of experimental variance was explained by genetics. The Weibull sigmoidal function...

Data from: Environmental and spatial effects on coastal stream fishes in the Atlantic rainforest

Cristina Gonçalves, Robert Holt, Mary Christman & Lilian Casatti
Contemporary and historical factors influence assemblage structure. The environmental and spatial influences acting on fish organization of rainforest coastal streams in the Atlantic rainforest of Brazil were examined. Fish (and functional traits such as morphology, diet, velocity preference, body size), environmental variables (pH, water conductivity, dissolved oxygen, temperature, stream width, flow, depth, substrate) and altitude were measured from 59 stream reaches. Asymmetric eigenvector maps were used to model the spatial structure considering direction of fish...

Extreme variation in testes size in an insect is linked to recent mating activity

Ginny Greenway, Lauren Cirino, Daniela Wilner, Ummat Somjee, Maria-Eleni Anagnostou, Russell Hepple & Christine Miller
Ample sperm production is essential for successful male reproduction in many species. The amount of sperm a male can produce is typically constrained by the size of his testes, which can be energetically expensive to grow and maintain. Whilst the economics of ejaculate allocation has been the focus of much theoretical and empirical literature, relatively little attention has been paid to individual adult variation and plasticity at the source of sperm production, the testes themselves....

Relationships among wood-boring beetles, fungal endophytes and saprotrophs, and the decomposition of forest biomass.

James Skelton, Michelle Jusino, Paige Carlson, Katherine Smith, Mark Banik, Daniel Linder, Jonathan Palmer & Jiri Hulcr
A prevailing paradigm in forest ecology is that wood-boring beetles facilitate wood decay and carbon cycling, but empirical tests have yielded mixed results. We experimentally determined the effects of wood borers on fungal community assembly and wood decay within pine trunks in the southeastern United States. Pine trunks were made either beetle-accessible or inaccessible. Fungal communities were compared using culturing and high-throughput meta-barcode sequencing of DNA and RNA. Prior to beetle infestation, living pines had...

Data from: Using functional and phylogenetic diversity to infer avian community assembly along elevational gradients

Flavia A. Montaño-Centellas, Christy McCain & Bette Loiselle
Aim We present the first global analysis of elevational gradients in functional and phylogenetic diversity of birds and test for signals of deterministic processes (i.e., environmental filtering and limiting similarity) in community assembly. Further, we examine for latitudinal effects in the strength of these processes. Location Forty-six elevational gradients across the globe. Time period Current (between 1924 and 2016) Major taxa Birds. Methods We systematically selected, compiled and analyzed published data on bird diversity along...

Data from: A high-density exome capture genotype-by-sequencing panel for forestry breeding in Pinus radiata

Emily J Telfer, Natalie J Graham, Yongjun Li, Jaroslav Klapste, , Leandro G Neves, Heidi Dungey & Phillip Wilcox
Development of genome-wide resources for application in genomic selection or genome-wide association studies, in the absences of full reference genomes, present a challenge to the forestry industry, where longer breeding cycles could benefit from the accelerated selection possible through marker-based breeding value predictions. In particular, large conifer megagenomes require a strategy to reduce complexity, whilst ensuring genome-wide coverage is achieved. Using a transcriptome-based reference template, we have successfully developed a high density exome capture genotype-by-sequencing...

Sex‐differences in disease avoidance behavior vary across modes of pathogen exposure

Carl N. Keiser, Volker H.W. Rudolf, Matthew C. Luksik & Julia B. Saltz
Sex‐differences in disease susceptibility are widespread, and these disparities are often compounded in cases where sexual dimorphism increases exposure risk to parasites for one sex more than the other. Studies rarely link sex‐differences in disease susceptibility to sex‐differences in infection avoidance behavior. Yet, understanding the intersection of hosts’ susceptibility to infection and infection avoidance behavior is essential to predicting infection risk variation. Here, we use the fruit fly Drosophila melanogaster and a generalist entomopathogenic fungus,...

Data from: A chromosomal-scale genome assembly of Tectona grandis reveals the importance of tandem gene duplication and enables discovery of genes in natural product biosynthetic pathways

Dongyan Zhao, John P. Hamilton, Wajid Waheed Bhat, Sean R. Johnson, Grant T. Godden, Taliesin J. Kinser, Benoît Boachon, Natalia Dudareva, Douglas E. Soltis, Pamela S. Soltis, Bjoern Hamberger & C. Robin Buell
Background: Teak, a member of the Lamiaceae family, produces one of the most expensive hardwoods in the world. High demand coupled with deforestation have caused a decrease in natural teak forests, and future supplies will be reliant on teak plantations. Hence, selection of teak tree varieties for clonal propagation with superior growth performance is of great importance, and access to high-quality genetic and genomic resources can accelerate the selection process by identifying genes underlying desired...

Data from: Overexpression of an antioxidant enzyme improves male mating performance after stress in a lek-mating fruit fly

Nicholas M. Teets, Vanessa S. Vias, Bailey Pierce, Marc F. Schetelig, Alfred M. Handler & Daniel A. Hahn
In many species, courtship displays are reliable signals of male quality, and current hypotheses suggest that mitochondrial function is a key mechanism underlying these condition-dependent traits. Environmental stressors generate reactive oxygen species (ROS) that impair mitochondrial function, and thus antioxidant pathways that remove ROS are likely critical for preserving complex sexual behaviors. Here, we test the hypothesis that enhanced antioxidant activity in mitochondria preserves mating performance following oxidative stress. Using a transgenic approach, we directly...

Registration Year

  • 2019

Resource Types

  • Dataset


  • 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