76 Works

Data from: Testing support for the northern and southern dispersal routes out of Africa: an analysis of Levantine and southern Arabian populations

Deven N. Vyas, Ali Al-Meeri & Connie J. Mulligan
Objectives: The Northern Dispersal Route (NDR) and Southern Dispersal Route (SDR) are hypothesized to have been used by modern humans in the dispersal out of Africa. The NDR follows the Nile into Northeast Africa and crosses the Red Sea into the Levant. The SDR emerges from the Horn of Africa and crosses the Bab el-Mandeb into southern Arabia. In this study, we analyze genetic data from populations living along the NDR and SDR to test...

Data from: Patterns of divergence across the geographic and genomic landscape of a butterfly hybrid zone associated with a climatic gradient

Sean F. Ryan, Michaël C. Fontaine, J. Mark Scriber, Michael E. Pfrender, Shawn T. O'Neil & Jessica J. Hellmann
Hybrid zones are a valuable tool for studying the process of speciation and for identifying the genomic regions undergoing divergence and the ecological (extrinsic) and non-ecological (intrinsic) factors involved. Here, we explored the genomic and geographic landscape of divergence in a hybrid zone between Papilio glaucus and Papilio canadensis. Using a genome scan of 28,417 ddRAD SNPs, we identified genomic regions under possible selection and examined their distribution in the context of previously identified candidate...

Data from: Experimental evolution with Caenorhabditis nematodes

Henrique Teotónio, Suzanne Estes, Patrick C. Phillips & Charles F. Baer
The hermaphroditic nematode Caenorhabditis elegans has been one of the primary model systems in biology since the 1970s, but only within the last two decades has this nematode also become a useful model for experimental evolution. Here, we outline the goals and major foci of experimental evolution with C. elegans and related species, such as C. briggsae and C. remanei, by discussing the principles of experimental design, and highlighting the strengths and limitations of Caenorhabditis...

Data from: Non-random patterns of invasion and extinction reduce phylogenetic diversity in island bird assemblages

Benjamin Baiser, Dennis Valle, Zoe Zelazny & J. Gordon Burleigh
Anthropogenically driven changes in bird communities on oceanic islands exemplify the biotic upheaval experienced by island floras and faunas. While the influence of invasions and extinctions on species richness and beta-diversity of island bird assemblages have been explored, little is known about the impact of these invasions and extinctions on phylogenetic diversity. Here we quantify phylogenetic diversity of island bird assemblages resulting from extinctions alone, invasions alone, and the combination of extinctions and invasions in...

Data from: Effects of a non-native grass invasion decline over time

S. Luke Flory, Jonathan Bauer, Richard P. Phillips & Keith Clay
Most research on dynamics and impacts of plant invasions has evaluated patterns and effects over brief time periods (i.e. <4 years). As such, little is known about the persistence of invasions and their long-term impacts on native species. To experimentally evaluate longer-term effects of invasions, we established field plots with native tree and herbaceous species and then invaded half of the plots with the most widespread invasive grass in the eastern United States (Microstegium vimineum)....

Data from: Novel host plant leads to the loss of sexual dimorphism in a sexually-selected male weapon

Pablo Allen, Christine W. Miller & Pablo E. Allen
In this time of massive global change, species are now frequently interacting with novel players. Greater insight into the impact of these novel interactions on traits linked to fitness is essential, because effects on these traits can hinder population existence or promote rapid adaptation. Sexually-selected weapons and ornaments frequently influence fitness and often have heightened condition-dependence in response to nutrition. Condition-dependence in response to different ecological conditions, a form of developmental plasticity, may be responsible...

Data from: Compensatory mutations improve general permissiveness to antibiotic resistance plasmids

Wesley Loftie-Eaton, Kelsie Bashford, Hannah Quinn, Kieran Dong, Jack Millstein, Samuel Hunter, Maureen K. Thomason, Houra Merrikh, Jose M. Ponciano & Eva M. Top
Horizontal gene transfer mediated by broad-host-range plasmids is an important mechanism of antibiotic resistance spread. While not all bacteria maintain plasmids equally well, plasmid persistence can improve over time, yet no general evolutionary mechanisms have emerged. Our goal was to identify these mechanisms, and to assess if adaptation to one plasmid affects the permissiveness to others. We experimentally evolved Pseudomonas sp. H2 containing multi-drug resistance plasmid RP4, determined plasmid persistence and cost using a joint...

Data from: Nitrogen-fixing tree abundance in higher-latitude North America is not constrained by diversity

Duncan N. L. Menge, Sarah A. Batterman, Wenying Liao, Benton N. Taylor, Jeremy W. Lichstein & Gregorio Ángeles-Pérez
The rarity of nitrogen (N)-fixing trees in frequently N-limited higher-latitude (here, > 35°) forests is a central biogeochemical paradox. One hypothesis for their rarity is that evolutionary constraints limit N-fixing tree diversity, preventing N-fixing species from filling available niches in higher-latitude forests. Here, we test this hypothesis using data from the USA and Mexico. N-fixing trees comprise only a slightly smaller fraction of taxa at higher vs. lower latitudes (8% vs. 11% of genera), despite...

Data from: Application of genomic estimation methods of inbreeding and population structure in an Arabian horse herd

Mohammed A. Al Abri, Uta Koenig Von Borstel, Veronique Strecker & Samantha A. Brooks
Horse breeders rely heavily on pedigrees for identification of ancestry in breeding stock. Inaccurate pedigrees may erroneously assign individuals to false lineages or breed memberships resulting in wrong estimates of inbreeding and coancestry. Moreover, discrepancies in pedigree records can lead breeders seeking to limit inbreeding into making misguided breeding decisions. Genome-wide SNPs provide a quantitative tool to aid in the resolution of lineage assignments and the calculation of genomic measures of relatedness. The aim of...

Data from: Surrogate taxa and fossils as reliable proxies of spatial biodiversity patterns in marine benthic communities

Carrie L. Tyler & Michał Kowalewski
Rigorous documentation of spatial heterogeneity (β-diversity) in present-day and preindustrial ecosystems is required to assess how marine communities respond to environmental and anthropogenic drivers. However, the overwhelming majority of contemporary and palaeontological assessments have centred on single higher taxa. To evaluate the validity of single taxa as community surrogates and palaeontological proxies, we compared macrobenthic communities and sympatric death assemblages at 52 localities in Onslow Bay (NC, USA). Compositional heterogeneity did not differ significantly across...

Data from: Multiple stressors and the potential for synergistic loss of New England salt marshes

Sinead M. Crotty, Christine Angelini & Mark D. Bertness
Climate change and other anthropogenic stressors are converging on coastal ecosystems worldwide. Understanding how these stressors interact to affect ecosystem structure and function has immediate implications for coastal planning, however few studies quantify stressor interactions. We examined past and potential future interactions between two leading stressors on New England salt marshes: sea-level rise and marsh crab (Sesarma reticulatum) grazing driven low marsh die-off. Geospatial analyses reveal that crab-driven die-off has led to an order of...

Data from: Priority effects can persist across floral generations in nectar microbial metacommunities

Hirokazu Toju, Rachel L. Vannette, Marie-Pierre L. Gauthier, Manpreet K. Dhami & Tadashi Fukami
The order of species arrival can influence how species interact with one another and, consequently, which species may coexist in local communities. This phenomenon, called priority effects, has been observed in various types of communities, but it remains unclear whether priority effects persist over the long term spanning multiple generations of local communities in metacommunities. Focusing on bacteria and yeasts that colonize floral nectar of the sticky monkey flower, Mimulus aurantiacus, via hummingbirds and other...

Data from: Reconstructing ecological niche evolution when niches are incompletely characterized

Erin E. Saupe, Narayani Barve, Hannah L. Owens, Jacob C. Cooper, Peter A. Hosner, A. Townsend Peterson, Jacob C Cooper, Erin E Saupe, Peter A Hosner, Hannah L Owens & A Townsend Peterson
Evolutionary dynamics of abiotic ecological niches across phylogenetic history can shed light on large-scale biogeographic patterns, macroevolutionary rate shifts, and the relative ability of lineages to respond to global change. An unresolved question is how best to represent and reconstruct evolution of these complex traits at coarse spatial scales through time. Studies have approached this question by integrating phylogenetic comparative methods with niche estimates inferred from correlative and other models. However, methods for estimating niches...

Data from: Effects of grain size and niche breadth on species distribution modeling

Thomas Connor, Vanessa Hull, Andres Vina, Ashton Shortridge, Ying Tang, Jindong Zhang, Fang Wang & Jianguo Liu
Scale is a vital component to consider in ecological research, and spatial resolution or grain size is one of its key facets. Species distribution models (SDMs) are prime examples of ecological research in which grain size is an important component. Despite this, SDMs rarely explicitly examine the effects of varying the grain size of the predictors for species with different niche breadths. To investigate the effect of grain size and niche breadth on SDMs, we...

Data from: Biological factors contributing to bark and ambrosia beetle species diversification

Jostein Gohli, Lawrence R. Kirkendall, Sarah M. Smith, Anthony I. Cognato, Jiri Hulcr & Bjarte H. Jordal
The study of species diversification can identify the processes that shape patterns of species richness across the tree of life. Here we perform comparative analyses of species diversification using a large dataset of bark beetles. Three examined covariates – permanent inbreeding (sibling mating), fungus farming, and major host type – represent a range of factors that may be important for speciation. We studied the association of these covariates with species diversification while controlling for evolutionary...

Data from: Oxidative stress-mediated NFκB phosphorylation upregulates p62/SQSTM1 and promotes retinal pigmented epithelial cell survival through increased autophagy

Chunjuan Song, Sayak K. Mitter, Xiaoping Qi, Eleni Beli, Haripriya V. Rao, Jindong Ding, Colin S. Ip, Hongmei Gu, D. Akin, William A. Dunn, Catherine Bowes Rickman, Alfred S. Lewin, Maria B. Grant, Michael E. Boulton & Debra Akin
p62 is a scaffolding adaptor implicated in the clearance of protein aggregates by autophagy. Reactive oxygen species (ROS) can either stimulate or inhibit NFκB-mediated gene expression influencing cellular fate. We studied the effect of hydrogen peroxide (H2O2)-mediated oxidative stress and NFκB signaling on p62 expression in the retinal pigment epithelium (RPE) and investigated its role in regulation of autophagy and RPE survival against oxidative damage. Cultured human RPE cell line ARPE-19 and primary human adult...

Data from: Climatic variation modulates the indirect effects of large herbivores on small-mammal habitat use

Ryan A. Long, Alois Wambua, Jacob R. Goheen, Todd M. Palmer & Robert M. Pringle
Large mammalian herbivores (LMH) strongly shape the composition and architecture of plant communities. A growing literature shows that negative direct effects of LMH on vegetation frequently propagate to suppress the abundance of smaller consumers. Indirect effects of LMH on the behaviour of these consumers, however, have received comparatively little attention despite their potential ecological significance. We sought to understand (i) how LMH indirectly shape small-mammal habitat use by altering the density and distribution of understorey...

Data from: Unmanned aerial systems measure structural habitat features for wildlife across multiple scales

Peter J. Olsoy, Lisa A. Shipley, Janet L. Rachlow, Jennifer S. Forbey, Nancy F. Glenn, Matthew A. Burgess & Daniel H. Thornton
1.Assessing habitat quality is a primary goal of ecologists. However, evaluating habitat features that relate strongly to habitat quality at fine-scale resolutions across broad-scale extents is challenging. Unmanned aerial systems (UAS) provide an avenue for bridging the gap between relatively high spatial resolution, low spatial extent field-based habitat quality measurements and lower spatial resolution, higher spatial extent satellite-based remote sensing. Our goal in this study was to evaluate the potential for UAS structure from motion...

Data from: Microsatellite mutation rate in Atlantic sturgeon (Acipenser oxyrinchus)

Hanna Panagiotopoulou, James D. Austin, Katarzyna Zalewska, Magdalena Gonciarz, Kinga Czarnogórska, Jan Gawor, Piotr Weglenski & Danijela Popovic
Understanding mutation rates can greatly extend the utility of population and conservation genetic analyses. Herein we present an estimate of genome-wide microsatellite mutation rate in Atlantic sturgeon (Acipenser oxyrinchus) based on parent-offspring transmission patterns. We screened 307 individuals for parentage and mutation-rate analysis applying 43 variable markers. Out of 13,228 allele transfers, 11 mutations were detected, producing a mutation rate of 8.3x10-4 per locus per generation (95%CI: 1.48x10-3, 4.15x10-4). Single-step mutations predominated and there were...

Data from: Foraging impacts of Asian megafauna on tropical rainforest structure and biodiversity

John Terborgh, Lisa C. Davenport, Lisa Ong & Ahimsa Campos-Arceiz
Megaherbivores are known to influence the structure, composition, and diversity of vegetation. In Central Africa, forest elephants act as ecological filters by breaking tree saplings and stripping them of foliage. Much less is known about impacts of megafauna on Southeast Asian rain forests. Here, we ask whether herbivory by Asian megafauna has impacts analogous to those of African forest elephants. To answer this, we studied forest (1) structure, (2) composition, (3) diversity, and (4) tree...

Data from: Evaluation and comparison of classical interatomic potentials through a user-friendly interactive web-interface

Kamal Choudhary, Faical Yannick P. Congo, Tao Liang, Chandler Becker, Richard G. Hennig & Francesca Tavazza
Classical empirical potentials/force-fields (FF) provide atomistic insights into material phenomena through molecular dynamics and Monte Carlo simulations. Despite their wide applicability, a systematic evaluation of materials properties using such potentials and, especially, an easy-to-use user-interface for their comparison is still lacking. To address this deficiency, we computed energetics and elastic properties of variety of materials such as metals and ceramics using a wide range of empirical potentials and compared them to density functional theory (DFT)...

Data from: Benthic communities under anthropogenic pressure show resilience across the Quaternary

Julieta C. Martinelli, Luis P. Soto, Jorge González & Marcelo M. Rivadeneira
The Southeast Pacific is characterized by rich upwelling systems that have sustained and been impacted by human groups for at least 12 ka. Recent fishing and aquaculture practices have put a strain on productive coastal ecosystems from Tongoy Bay, in north-central Chile. We use a temporal baseline to determine whether potential changes to community structure and composition over time are due to anthropogenic factors, natural climatic variations or both. We compiled a database (n =...

Data from: Response of pumas (Puma concolor) to migration of their primary prey in Patagonia

Lyn C. Branch, Maria L. Gelin, Matthew J. Gould, Daniel H. Thornton & Andrés J. Novaro
Large-scale ungulate migrations result in changes in prey availability for top predators and, as a consequence, can alter predator behavior. Migration may include entire populations of prey species, but often prey populations exhibit partial migration with some individuals remaining resident and others migrating. Interactions of migratory prey and predators have been documented in North America and some other parts of the world, but are poorly studied in South America. We examined the response of pumas...

Data from: Logging and indigenous hunting impacts on persistence of large Neotropical animals

Anand Roopsind, T. Trevor Caughlin, Hemchandranauth Sambhu, Jose M.V. Fragoso, Francis E. Putz., Francis E. Putz & Jose M. V. Fragoso
Areas allocated for industrial logging and community-owned forests account for over 50% of all remaining tropical forests. Landscape-scale conservation strategies that include these forests are expected to have substantial benefits for biodiversity, especially for large mammals and birds that require extensive habitat but that are susceptible to extirpation due to synergies between logging and hunting. In addition, their responses to logging alone are poorly understood due to their cryptic behavior and low densities. In this...

Data from: Aquatic microfauna alter larval food resources and affect development and biomass of West Nile and Saint Louis encephalitis vector Culex nigripalpus (Diptera: Culicidae)

Dagne Duguma, Michael G. Kaufman & Arthur B. Simas Domingos
Ciliate protists and rotifers are ubiquitous in aquatic habitats and can comprise a significant portion of the microbial food resources available to larval mosquitoes, often showing substantial declines in abundance in the presence of mosquito larvae. This top-down regulation of protists is reported to be strong for mosquitoes inhabiting small aquatic containers such as pitcher plants or tree holes, but the nature of these interactions with larval mosquitoes developing in other aquatic habitats is poorly...

Registration Year

  • 2017

Resource Types

  • Dataset


  • University of Florida
  • The University of Texas at Austin
  • Princeton University
  • University of California, Berkeley
  • Florida Museum of Natural History
  • Michigan State University
  • Helmholtz Centre for Environmental Research
  • Sun Yat-sen University
  • University of Washington
  • Stanford University