146 Works

Dense seismic three-component nodal array at the Ramona Reservation

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High-Resolution imaging and monitoring of the subsurface structure and seismicity at a site along the San Jacinto fault zone using a dense seismic nodal array. The site is located about 6 km northwest of the town of Anza, California. The type of nodal sensor employed is the Fairfield Zland 3-component 5 Hz geophones (records ground velocity continuously at 500 sps). The array consists of 97 sensors, with 65 located along a linear across-fault profile and...

Permasense

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Ambient vibration data from seismic stations on the summit and ridge of one of the tallest freestanding mountains in the Swiss Alps – the Matterhorn – as from a nearby local reference seismic station

Data from: The truncated bell: an enigmatic but pervasive elevational diversity pattern in Middle American ants

John T. Longino & Michael G. Branstetter
Studies on elevation gradients in Panama and Costa Rica have shown that leaf-litter ants exhibit a mid-elevation peak in diversity. This diversity pattern has been observed in other groups and regions, but uncertainty remains as to just how pervasive it is and what might explain it. Here we examine the robustness of the mid-elevation peak in ant diversity across the entire Middle American corridor, from Veracruz, Mexico, to Costa Rica. We sampled 56 sites distributed...

Data from: Habitat disturbance selects against both small and large species across varying climates

Heloise Gibb, Nathan J. Sanders, Robert R. Dunn, Xavier Arnan, Heraldo L. Vasconcellos, David A. Donoso, Alan N. Andersen, Rogerio R. Silva, Tom R. Bishop, Crisanto Gomez, Blair F. Grossman, Kalsum M. Yusah, Sarah H. Luke, Renata Pacheco, Jessica Pearce-Duvet, Javier Retana, Melanie Tista, Catherine L. Parr & H. L. Vasconcelos
Global extinction drivers, including habitat disturbance and climate change, are thought to affect larger species more than smaller species. However, it is unclear if such drivers interact to affect assemblage body size distributions. We asked how these two key global change drivers differentially affect the interspecific size distributions of ants, one of the most abundant and ubiquitous animal groups on earth. We also asked whether there is evidence of synergistic interactions and whether effects are...

Data from: Morphological and molecular evolution and their consequences for conservation and taxonomy in the Le Conte's Thrasher (Toxostoma lecontei)

Hernán Vázquez-Miranda, Josie A. Griffin, Jay M. Sheppard, Jordan M. Herman, Octavio Rojas-Soto & Robert M. Zink
We evaluated geographic variation and subspecific taxonomy in the Le Conte's Thrasher (Toxostoma lecontei) by analyzing DNA sequences from 16 nuclear loci, one mitochondrial DNA locus, and four study skin characters, and compared these data sets with previously published data on plumage coloration and different mtDNA genes. Morphological support for the southernmost taxon, T. l. arenicola, is relatively weak: multivariate analyses of morphometrics or back coloration do not provide diagnostic support, although one color character...

Data from: The effect of nitrogen availability and water conditions on competition between a facultative CAM plant and an invasive grass

Kailiang Yu, Paolo D'Odorico, David E. Carr, Ashden Personius & Scott L. Collins
Abstract Plants with crassulacean acid metabolism (CAM) are increasing their abundance in drylands worldwide. The drivers and mechanisms underlying the increased dominance of CAM plants and CAM expression (i.e., nocturnal carboxylation) in facultative CAM plants, however, remain poorly understood. We investigated how nutrient and water availability affected competition between Mesembryanthemum crystallinum (a model facultative CAM species) and the invasive C3 grass Bromus mollis that co-occur in California's coastal grasslands. Specifically we investigated the extent to...

Contrasting effects of host tree isolation on population connectedness in two tropical epiphytic bromeliads

Autumn Amici, Nalini Nadkarni, Emily DiBlasi & Jon Seger
Premise of the study Conversion of primary forests to pastures is a major cause of habitat fragmentation in the tropics. Fragmentation is expected to impede gene flow for many plant species that are restricted to remaining forest fragments. Epiphytes may be especially vulnerable to this effect of forest fragmentation because they depend on host trees. However, trees that remain in pastures may enhance connectivity across the landscape for epiphyte species that can thrive on such...

Data from: Small-mammal isotope ecology tracks climate and vegetation gradients across western North America

Tara M. Smiley, Jennifer M. Cotton, Catherine Badgley & Thure E. Cerling
Stable carbon, nitrogen, hydrogen and oxygen isotopes have been used to infer aspects of species ecology and environment in both modern ecosystems and the fossil record. Compared to large mammals, stable isotopic studies of small-mammal ecology are limited; however, high species and ecological diversity within small mammals presents several advantages for quantifying resource use and organism–environment interactions using stable isotopes over various spatial and temporal scales. We analyzed the isotopic composition of hair from two...

Data from: Morphometric analysis of graphoglyptid trace fossils in two dimensions: implications for behavioral evolution in the deep sea

James Lehane & A. A. Ekdale
Graphoglyptids are deep-marine trace fossils, often found preserved as casts in positive relief on the base of turbidites. Previous analyses of the behavioral evolution of graphoglyptids suggested they were slowly diversifying, becoming optimized, and getting smaller over time until the Late Cretaceous, when a sudden increase in diversification occurred. This current study quantifies the morphology of approximately 400 different graphoglyptid specimens, ranging in age from the Cambrian to the present, in order to evaluate the...

Data from: The Oxytricha trifallax macronuclear genome: a complex eukaryotic genome with 16,000 tiny chromosomes

Estienne C. Swart, John R. Bracht, Vincent Magrini, Patrick Minx, Xiao Chen, Yi Zhou, Jaspreet S. Khurana, Aaron D. Goldman, Mariusz Nowacki, Klaas Schotanus, Seolkyoung Jung, Robert S. Fulton, Amy Ly, Sean McGrath, Kevin Haub, Jessica L. Wiggins, Donna Storton, John C. Matese, Lance Parsons, Wei-Jen Chang, Michael S. Bowen, Nicholas A. Stover, Thomas A. Jones, Sean R. Eddy, Thomas G. Doak … & Laura F. Landweber
The macronuclear genome of the ciliate Oxytricha trifallax displays an extreme and unique eukaryotic genome architecture with extensive genomic variation. During sexual genome development, the expressed, somatic macronuclear genome is whittled down to the genic portion of a small fraction (~5%) of its precursor “silent” germline micronuclear genome by a process of “unscrambling” and fragmentation. The tiny macronuclear “nanochromosomes” typically encode single, protein-coding genes (a small portion, 10%, encode 2–8 genes), have minimal noncoding regions,...

Data from: Tracking of host defenses and phylogeny during the radiation of Neotropical Inga-Feeding sawflies (Hymenoptera; Argidae)

María-José Endara, James A. Nicholls, Phyllis D. Coley, Dale L. Forrister, Gordon C. Younkin, Kyle G. Dexter, Catherine A. Kidner, R. Toby Pennington, Graham N. Stone & Thomas A. Kursar
Coevolutionary theory has long predicted that the arms race between plants and herbivores is a major driver of host selection and diversification. At a local scale, plant defenses contribute significantly to the structure of herbivore assemblages and the high alpha diversity of plants in tropical rain forests. However, the general importance of plant defenses in host associations and divergence at regional scales remains unclear. Here, we examine the role of plant defensive traits and phylogeny...

Data from: Mouse fitness measures reveal incomplete functional redundancy of Hox paralogous group 1 proteins

James S. Ruff, Raed B. Saffarini, Leda L. Ramoz, Linda C. Morrison, Shambralyn Baker, Sean M. Laverty, Petr Tvrdik, Mario R. Capecchi & Wayne K. Potts
Here we assess the fitness consequences of the replacement of the Hoxa1 coding region with its paralog Hoxb1 in mice (Mus musculus) residing in semi-natural enclosures. Previously, this Hoxa1B1 swap was reported as resulting in no discernible embryonic or physiological phenotype (i.e., functionally redundant), despite the 51% amino acid sequence differences between these two Hox proteins. Within heterozygous breeding cages no differences in litter size nor deviations from Mendelian genotypic expectations were observed in the...

Data from: Macroevolutionary patterns in overexpression of tyrosine: an anti-herbivore defense in a speciose tropical tree genus, Inga (Fabaceae)

Phyllis D. Coley, María‐José Endara, Gabrielle Ghabash, Catherine A. Kidner, James A. Nicholls, R. Toby Pennington, Anthony G. Mills, Abrianna J. Soule, Maristerra R. Lemes, Graham N. Stone & Thomas A. Kursar
Plant secondary metabolites are a key defence against herbivores, and their evolutionary origin is likely from primary metabolites. Yet for this to occur, an intermediate step of overexpression of primary metabolites would need to confer some advantage to the plant. Here, we examine the evolution of overexpression of the essential amino acid, L‐tyrosine and its role as a defence against herbivores. We examined overexpression of tyrosine in 97 species of Inga (Fabaceae), a genus of...

A local and global sensitivity analysis of a mathematical model of coagulation and platelet deposition under flow

Kathryn Link, Michael Stobb, Jorge Di Paola, Keith Neeves, Aaron Fogelson, Suzanne Sindi & Karin Leiderman
The hemostatic response involves blood coagulation and platelet aggregation to stop blood loss from an injured blood vessel. The complexity of these processes make it difficult to intuit the overall hemostatic response without quantitative methods. Mathematical models aim to address this challenge but are often accompanied by numerous parameters choices and thus need to be analyzed for sensitivity to such choices. Here we use local and global sensitivity analyses to study a model of coagulation...

Data from: Pulmonary anatomy in the Nile crocodile and the evolution of unidirectional airflow in Archosauria.

Emma R. Schachner, John R. Hutchinson, C. G. Farmer & CG Farmer
The lungs of birds have long been known to move air in only one direction during both inspiration and expiration through most of the tubular gas-exchanging bronchi (parabronchi). Recently a similar pattern of airflow has been observed in American alligators, a sister taxon to birds. The pattern of flow appears to be due to the arrangement of the primary and secondary bronchi, which, via their branching angles, generate inspiratory and expiratory aerodynamic valves. Both the...

The limits of convergence: the roles of phylogeny and dietary ecology in shaping non-avian amniote skulls

Keegan Melstrom, Kenneth Angielczyk, Kathleen Ritterbush & Randall Irmis
Cranial morphology is remarkably varied in living amniotes, ranging from short-faced mammals to the elongate snouts of crocodylians. This diversity of shapes is thought to correspond with feeding ecology, a relationship repeatedly demonstrated at smaller phylogenetic scales, but one that remains untested across amniote phylogeny. Using a combination of 2D geometric and linear morphometrics, we investigate the links between phylogenetic relationships, diet, and skull shape in an expansive dataset of extant amniotes with teeth: mammals,...

Data from: Vascular epiphytes show low physiological resistance and high recovery capacity to episodic, short-term drought in Monteverde, Costa Rica

Cameron Williams, Jessica Murray, Andrew Glunk, Todd Dawson, Nalini Nadkarni & Sybil Gotsch
Tropical montane cloud forests support abundant epiphytic vascular plant communities that serve important ecosystem functions, but their reliance on atmospheric inputs of water may make them susceptible to the drying effects of rising cloud bases and more frequent droughts. We conducted a common garden experiment to explore the combined effects of decreasing cloud influence—lower humidity, warmer temperature, brighter light—and meteorological drought (i.e., absence of rain) on the physiology and morphology of vascular epiphytes native to...

Individual differences determine the strength of ecological interactions

Jason I. Griffiths, Dylan Z. Childs, Ronald D. Bassar, Tim Coulson, David N Reznick & Mark Rees
Biotic interactions are central to both ecological and evolutionary dynamics. In the vast majority of empirical studies, the strength of intraspecific interactions is estimated by using simple mea- sures of population size. Biologists have long known that these are crude metrics, with experiments and theory suggesting that interactions between individuals should depend on traits, such as body size. Despite this, it has been difficult to estimate the impact of traits on competitive ability from ecological...

Data from: The arboreal ants of a Neotropical rainforest show high species density and comprise one third of the ant fauna

John Longino & Robert Colwell
In tropical rainforests, the ant community can be divided into ground and arboreal faunas. Here we report a thorough sampling of the arboreal ant fauna of La Selva Biological Station, a Neotropical rainforest site. Forty-five canopy fogging samples were centered around large trees. Individual samples harbored an average of 35 ant species, with up to 55 species in a single sample. The fogging samples yielded 163 observed species total, out of a statistically estimated 199...

Temperature‐associated decreases in demographic rates of Afrotropical bird species over 30 years

Montague H. C. Neate‐Clegg, Thomas R. Stanley, Çağan H. Şekercioğlu & William D. Newmark
Tropical mountains harbor globally significant levels of biodiversity and endemism. Climate change threatens many tropical montane species, yet little research has assessed the effects of climate change on the demographic rates of tropical species, particularly in the Afrotropics. Here, we report on the demographic rates of 21 Afrotropical bird species over 30 years in montane forests in Tanzania. We used mark-recapture analyses to model rates of population growth, recruitment, and apparent survival as functions of...

Biogeography and diversification of Old World buntings (Aves: Emberizidae): radiation in open habitats

Tianlong Cai, Guiyou Wu, Sun Lu, Yu Zhang, Zhaojie Peng, Yanqing Guo, Xinyue Liu, Tao Pan, Jiang Chang, Zhonglou Sun & Baowei Zhang
The Old World buntings (Aves: Emberizidae) mainly inhabit open habitats in Eurasia and Africa. It has long been debated whether the group originated in the New World or the Old World and whether their radiation is related to the expansion of open habitats and shifts in migratory behaviours. To answer these questions, we reconstructed their biogeographic histories and analysed their diversification patterns in terms of time, space and traits using a near-complete phylogeny. We found...

Hybridizations and fruit geography of Solanum jamesii

Bruce Pavlik & Lisbeth Louderback
Premise: Plant domestication can be detected when transport, use and manipulation of propagules impact reproductive functionality, especially in species with self-incompatible breeding systems. Methods: Evidence for human-caused founder effect in the Four Corners potato (Solanum jamesii Torr.) was examined by conducting 526 controlled matings between archaeological and non-archaeological populations from field-collected tubers grown in a greenhouse. Specimens from 24 major herbaria, along with collection records from >160 populations were examined to determine which produced fruits....

Diarrhea etiology prediction validation dataset - Bangladesh and Mali

Daniel Leung, Ben Brintz & Stephanie Garbern
Background: Diarrheal illness is a leading cause of antibiotic use for children in low- and middle-income countries. Determination of diarrhea etiology at the point-of-care without reliance on laboratory testing has the potential to reduce inappropriate antibiotic use. Methods: This prospective observational study aimed to develop and externally validate the accuracy of a mobile software application (“App”) for the prediction of viral-only etiology of acute diarrhea in children 0-59 months in Bangladesh and Mali. The App...

Adaptive introgression of the beta-globin cluster in two Andean waterfowl

Allie Graham & Kevin McCracken
Introgression of alleles has emerged as an important avenue for genetic adaptation in both plant and animal populations. In vertebrates, adaptation to hypoxic high-altitude environments involves the coordination of multiple molecular and cellular mechanisms, including selection on the Hypoxia-Inducible Factor (HIF) pathway and the blood-O2 transport protein hemoglobin (Hb). In two Andean duck species, a striking DNA sequence similarity reflecting identity by descent is present across the ~20 kb b-globin cluster including both embryonic (HBE)...

ENIGMA Pediatric msTBI diffusion MRI supplemental data

Emily Dennis
Objective: Our study addressed aims: (1) test the hypothesis that moderate-severe TBI in pediatric patients is associated with widespread white matter (WM) disruption; (2) test the hypothesis that age and sex impact WM organization after injury; and (3) examine associations between WM organization and neurobehavioral outcomes. Methods: Data from ten previously enrolled, existing cohorts recruited from local hospitals and clinics were shared with the ENIGMA (Enhancing NeuroImaging Genetics through Meta-Analysis) Pediatric msTBI working group. We...

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