34 Works

Data from: Using collision cones to assess biological deconfliction methods

Natalie L. Brace, Tyson L. Hedrick, Diane H. Theriault, Nathan W. Fuller, Zheng Wu, Margrit Betke, Julia K. Parrish, Daniel Grünbaum & Kristi A. Morgansen
Biological systems consistently outperform autonomous systems governed by engineered algorithms in their ability to reactively avoid collisions. To better understand this discrepancy, a collision avoidance algorithm was applied to frames of digitized video trajectory data from bats, swallows and fish (Myotis velifer, Petrochelidon pyrrhonota and Danio aequipinnatus). Information available from visual cues, specifically relative position and velocity, was provided to the algorithm which used this information to define collision cones that allowed the algorithm to...

Data from: Metapopulation dominance and genomic-island acquisition of Bradyrhizobium with superior catabolic capabilities

Amanda C. Hollowell, John U. Regus, David Turissini, Kelsey A. Gano-Cohen, Roxanne Bantay, Andrew Bernardo, Devora Moore, Jonathan Pham & Joel L. Sachs
Root nodule forming rhizobia exhibit a bipartite lifestyle, replicating in soil and also within plant cells where they fix nitrogen for legume hosts. Host control models posit that legume hosts act as a predominant selective force on rhizobia, but few studies have examined rhizobial fitness in natural populations. Here, we genotyped and phenotyped Bradyrhizobium isolates across >800km of the native Acmispon strigosus host range. We sequenced chromosomal genes expressed under free-living conditions and accessory symbiosis...

Data from: Female and male life tables for seven wild primate species

Anne M. Bronikowski, Marina Cords, Susan C. Alberts, Jeanne Altmann, Diane K. Brockman, Linda M. Fedigan, Anne Pusey, Tara Stoinski, Karen B. Strier & William F. Morris
We provide male and female census count data, age-specific survivorship, and female age-specific fertility estimates for populations of seven wild primates that have been continuously monitored for at least 29 years: sifaka (Propithecus verreauxi) in Madagascar; muriqui (Brachyteles hypoxanthus) in Brazil; capuchin (Cebus capucinus) in Costa Rica; baboon (Papio cynocephalus) and blue monkey (Cercopithecus mitis) in Kenya; chimpanzee (Pan troglodytes) in Tanzania; and gorilla (Gorilla beringei) in Rwanda. Using one-year age-class intervals, we computed point...

Data from: Host genotype and age shape the leaf and root microbiomes of a wild perennial plant

Maggie R. Wagner, Derek S. Lundberg, Tijana G. Del Rio, Susannah G. Tringe, Jeffery L. Dangl & Thomas Mitchell-Olds
Bacteria living on and in leaves and roots influence many aspects of plant health, so the extent of a plant’s genetic control over its microbiota is of great interest to crop breeders and evolutionary biologists. Laboratory-based studies, because they poorly simulate true environmental heterogeneity, may misestimate or totally miss the influence of certain host genes on the microbiome. Here we report a large-scale field experiment to disentangle the effects of genotype, environment, age and year...

Data from: Foraging at the edge of the world: low‐altitude, high‐speed maneuvering in barn swallows

Douglas R. Warrick, Tyson L. Hedrick, Andrew A. Biewener, Kristen E. Crandell & Bret W. Tobalske
While prior studies of swallow manoeuvering have focused on slow-speed flight and obstacle avoidance in still air, swallows survive by foraging at high speeds in windy environments. Recent advances in field-portable, high-speed video systems, coupled with precise anemometry, permit measures of high-speed aerial performance of birds in a natural state. We undertook the present study to test: (i) the manner in which barn swallows (Hirundo rustica) may exploit wind dynamics and ground effect while foraging...

Data from: Comparison of cerebral blood volume and plasma volume in untreated intracranial tumors

Soha Bazyar, Joana Ramalho, Cihat Eldeniz, Hongyu An, Yueh Lee & Yueh Z. Lee
Purpose: Plasma volume and blood volume are imaging-derived parameters that are often used to evaluation intracranial tumors. Physiologically, these parameters are directly related, but their two different methods of measurements, T1-dynamic contrast enhanced (DCE)- and T2-dynamic susceptibility contrast (DSC)-MR utilize different model assumptions and approaches. This poses the question of whether the interchangeable use of T1-DCE-MRI derived fractionated plasma volume (vp) and relative cerebral blood volume (rCBV) assessed using DSC-MRI, particularly in glioblastoma, is reliable,...

Data from: Local context drives infection of grasses by vector-borne generalist viruses

Elizabeth T. Borer, Eric W. Seabloom, Charles E. Mitchell & Alison G. Power
Host characteristics commonly determine infection risk, but infection can also be mediated by regional- or local-scale variation in the biotic and abiotic environment. Experiments can clarify the relative importance of these factors. We quantified drivers of infection by barley and cereal yellow dwarf viruses (B/CYDV), a group of generalist, vector-borne grass pathogens, at hierarchically nested spatial scales (105–1 m) by planting individuals of six common grass species into five Pacific Coast grassland sites spanning 7°...

Data from: Coral reef degradation is not correlated with local human population density

John F. Bruno
The global decline of reef-building corals is understood to be due to a combination of local and global stressors. However, many reef scientists assume that local factors predominate and that isolated reefs, far from human activities, are generally healthier and more resilient. Here we show that coral reef degradation is not correlated with human population density. This suggests that local factors such as fishing and pollution are having minimal effects or that their impacts are...

Data from: Three-dimensional simulation for fast forward flight of a calliope hummingbird

Jialei Song, Bret W. Tobalske, Donald R. Powers, Tyson L. Hedrick & Haoxiang Luo
We present a computational study of flapping-wing aerodynamics of a calliope hummingbird (Selasphorus calliope) during fast forward flight. Three-dimensional wing kinematics were incorporated into the model by extracting time-dependent wing position from high-speed videos of the bird flying in a wind tunnel at 8.3 m s−1. The advance ratio, i.e. the ratio between flight speed and average wingtip speed, is around one. An immersed-boundary method was used to simulate flow around the wings and bird...

Data from: Viral pathogen production in a wild grass host driven by host growth and soil nitrogen

Briana K. Whitaker, Megan A. Rúa & Charles E. Mitchell
Nutrient limitation is a basic ecological constraint that has received little attention in studies on virus production and disease dynamics. Nutrient availability could directly limit the production of viral nucleic acids and proteins, or alternatively limit host growth and thus indirectly limit metabolic pathways necessary for viral replication. In order to compare direct and indirect effects of nutrient limitation on virus production within hosts, we manipulated soil nitrogen (N) and phosphorus (P) availability in a...

Data from: Clinical factors associated with long-term complete remission versus poor response to chemotherapy in HIV-infected children and adolescents with Kaposi sarcoma receiving bleomycin and vincristine: a retrospective observational study

Nader Kim El-Mallawany, William Kamiyango, Jeremy S. Slone, Jimmy Villiera, Carrie L. Kovarik, Carrie M. Cox, Dirk P. Dittmer, Saeed Ahmed, Gordon E. Schutze, Michael E. Scheurer, Peter N. Kazembe & Parth S. Mehta
Kaposi sarcoma (KS) is the most common HIV-associated malignancy in children and adolescents in Africa. Pediatric KS is distinct from adult disease. We evaluated the clinical characteristics associated with long-term outcomes. We performed a retrospective observational analysis of 70 HIV-infected children and adolescents with KS less than 18 years of age diagnosed between 8/2010 and 6/2013 in Lilongwe, Malawi. Local first-line treatment included bleomycin and vincristine plus nevirapine-based highly active anti-retroviral therapy (HAART). Median age...

Data from: Chromosome-wide impacts on the expression of incompatibilities in hybrids of Tigriopus californicus

Christopher S. Willett, Thiago G. Lima, Lydia Hatfield & Inna Kovaleva
Chromosome rearrangements such as inversions have been recognized previously as contributing to reproductive isolation by maintaining alleles together that jointly contribute to deleterious genetic interactions and postzygotic reproductive isolation. In this study an impact of potential incompatibilities merely residing on the same chromosome is found in crosses of populations of the copepod Tigriopus californicus. When genetically divergent populations of this copepod are crossed, hybrids show reduced fitness and deviations from expected genotypic ratios can be...

Data from: The emergence of performance trade-offs during local adaptation: insights from experimental evolution

Lisa M. Bono, , David W. Pfennig, Christina L. Burch & Leno B. Smith
Environmental heterogeneity is considered a general explanation for phenotypic diversification, particularly when heterogeneity causes populations to diverge via local adaptation. Performance trade-offs, such as those stemming from antagonistic pleiotropy, are thought to contribute to the maintenance of diversity in this scenario. Specifically, alleles that promote adaptation in one environment are expected to promote maladaptation in alternative environments. Contrary to this expectation, however, alleles that underlie locally adaptive traits often fail to exhibit fitness costs in...

Data from: Context dependence in complex adaptive landscapes: frequency and trait-dependent selection surfaces within an adaptive radiation of Caribbean pupfishes

Christopher Herbert Martin
The adaptive landscape provides the foundational bridge between micro- and macroevolution. One well-known caveat to this perspective is that fitness surfaces depend on ecological context, including competitor frequency, traits measured, and resource abundance. However, this view is based largely on intraspecific studies. It is still unknown how context-dependence affects the larger features of peaks and valleys on the landscape which ultimately drive speciation and adaptive radiation. Here I explore this question using one of the...

Data from: The Mouse Universal Genotyping Array: from substrains to subspecies

Andrew P. Morgan, Chen-Ping Fu, Chia-Yu Kao, Catherine E. Welsh, John P. Didion, Liran Yadgary, Leeanna Hyacinth, Martin T. Ferris, Timothy A. Bell, Darla R. Miller, Paola Giusti-Rodriguez, Randal J. Nonneman, Kevin D. Cook, Jason K. Whitmire, Lisa E. Gralinski, Mark Keller, Alan D. Attie, Gary A. Churchill, Petko Petkov, Patrick F. Sullivan, Jennifer R. Brennan, Leonard McMillan & Fernando Pardo-Manuel De Villena
Genotyping microarrays are an important resource for genetic mapping, population genetics, and monitoring of the genetic integrity of laboratory stocks. We have developed the third generation of the Mouse Universal Genotyping Array (MUGA) series, GigaMUGA, a 143,259-probe Illumina Infinium II array for the house mouse (Mus musculus). The bulk of the content of GigaMUGA is optimized for genetic mapping in the Collaborative Cross and Diversity Outbred populations, and for substrain-level identification of laboratory mice. In...

Data from: A chemical-genomic screen of neglected antibiotics reveals illicit transport of kasugamycin and blasticidin S

Anthony L. Shiver, Hendrik Osadnik, George Kritikos, Bo Li, Nevan Krogan, Athanasios Typas & Carol A. Gross
Fighting antibiotic resistance requires a deeper understanding of the genetic factors that determine the antibiotic susceptibility of bacteria. Here we describe a chemical-genomic screen in Escherichia coli K-12 that was designed to discover new aspects of antibiotic resistance by focusing on a set of 26 antibiotics and other stresses with poorly characterized mode-of-action and determinants of resistance. We show that the screen identifies new resistance determinants for these antibiotics including a common signature from two...

Data from: Phenotypic shifts in urban areas in the tropical lizard Anolis cristatellus

Kristin M. Winchell, Robert Graham Reynolds, Sofia R. Prado-Irwin, Alberto R. Puente-Rolón & Liam J. Revell
Urbanization is an important dimension of global change, and urban areas impose significant natural selection on species within them. Although many species persist in urban areas, little research has investigated whether populations have adapted to urbanization. Even less work has considered tropical regions, which have recently experienced dramatic urban growth. In the present study we focused on the neotropical lizard, Anolis cristatellus. We tested whether lizard ecology and morphology differ between urban and natural areas...

Data from: Effects of reduced-impact selective logging on palm regeneration in Belize

Boris Arevalo, Jair Valladarez, Shahira Muschamp, Elma Kay, Alex Finkral, Anand Roopsind & Francis E. Putz
To assess the impacts of a low-intensity selective timber harvest on a palm community in Belize, we mapped logging infrastructure (i.e., roads, log landings, skid trails, and stumps) and measured palm regeneration 1 year after a timber harvest carried out using reduced-impact logging (RIL) practices. We sampled palms across a gradient of increasing harvest impact severity from areas not directly affected by logging, in felling gaps, on secondary and primary skid trails, and on log...

Data from: The cryptic origins of evolutionary novelty: 1,000-fold-faster trophic diversification rates without increased ecological opportunity or hybrid swarm

Christopher Herbert Martin
Ecological opportunity is frequently proposed as the sole ingredient for adaptive radiation into novel niches. An additional trigger may be genome-wide hybridization resulting from ‘hybrid swarm’. However, these hypotheses have been difficult to test due to the rarity of comparable control environments lacking adaptive radiations. Here I exploit such a pattern in microendemic radiations of Caribbean pupfishes. I show that a sympatric three-species radiation on San Salvador Island, Bahamas diversified 1,445 times faster than neighboring...

Data from: Diabolical survival in Death Valley: recent pupfish colonization, gene flow, and genetic assimilation in the smallest species range on earth

Christopher Martin, Jacob Crawford, Bruce Turner, Lee Simons, Jacob E. Crawford & Christopher H. Martin
One of the most endangered vertebrates, the Devils Hole pupfish Cyprinodon diabolis, survives in a nearly impossible environment: a narrow subterranean fissure in the hottest desert on earth, Death Valley. This species became a conservation icon after a landmark 1976 U.S. Supreme Court case affirming federal groundwater rights to its unique habitat. However, one outstanding question about this species remains unresolved: how long has diabolis persisted in this hellish environment? We used next-generation sequencing of...

Data from: The effect of temperature on Drosophila hybrid fitness

Charles J. J. Miller & Daniel R. Matute
Mechanisms of reproductive isolation inhibit gene flow between species and can be broadly sorted into two categories: prezygotic and postzygotic. While comparative studies suggest that prezygotic barriers tend to evolve first, postzygotic barriers are crucial for maintaining species boundaries and impeding gene flow that might otherwise cause incipient species to merge. Most, but not all, postzygotic barriers result from genetic incompatibilities between two or more loci from different species, and occur due to divergent evolution...

Data from: Male mate choice, male quality, and the potential for sexual selection on female traits under polygyny.

Courtney L. Fitzpatrick & Maria R. Servedio
Observations of male mate choice are increasingly common, even in species with traditional sex roles. In addition, female traits that bear the hallmarks of secondary sexual characters are increasingly reported. These concurrent empirical trends have led to the repeated inference that, even under polygyny, male mate choice is a mechanism of sexual selection on female traits. It is often either assumed or argued that in these cases females are competing for males of superior “quality”;...

Data from: The genetic architecture of novel trophic specialists: higher effect sizes are associated with exceptional oral jaw diversification in a pupfish adaptive radiation

Christopher H. Martin, Priscilla A. Erickson & Craig T. Miller
The genetic architecture of adaptation is fundamental to understanding the mechanisms and constraints governing diversification. However, most case studies focus on loss of complex traits or parallel speciation in similar environments. It is still unclear how the genetic architecture of these local adaptive processes compares to the architecture of evolutionary transitions contributing to morphological and ecological novelty. Here we identify quantitative trait loci (QTL) between two trophic specialists in an excellent case study for examining...

Data from: MycoDB, a global database of plant response to mycorrhizal fungi

V. Bala Chaudhary, Megan A. Rúa, Anita Antoninka, James D. Bever, Jeffery Cannon, Ashley Craig, Jessica Duchicela, Alicia Frame, Monique Gardes, Catherine Gehring, Michelle Ha, Miranda Hart, Jacob Hopkins, Baoming Ji, Nancy Collins Johnson, Wittaya Kaonongbua, Justine Karst, Roger T. Koide, Louis J. Lamit, James Meadow, Brook G. Milligan, John C. Moore, , Bridget Piculell, Blake Ramsby … & Jason D. Hoeksema
Plants form belowground associations with mycorrhizal fungi in one of the most common symbioses on Earth. However, few large-scale generalizations exist for the structure and function of mycorrhizal symbioses, as the nature of this relationship varies from mutualistic to parasitic and is largely context-dependent. We announce the public release of MycoDB, a database of 4,010 studies (from 438 unique publications) to aid in multi-factor meta-analyses elucidating the ecological and evolutionary context in which mycorrhizal fungi...

Data from: Color phenotypes are under similar genetic control in two distantly related species of Timema stick insect

Aaron Arthur Comeault, Clarissa Ferreira Carvalho, Stuart R. Dennis, Victor Soria-Carrasco, Patrik Nosil & Stuart Dennis
Ecology and genetics are both of general interest to evolutionary biologists as they can influence the phenotypic and genetic response to selection. The stick insects Timema podura and T. cristinae exhibit a green/melanistic body color polymorphism that is subject to different ecologically-based selective regimes in the two species. Here we describe aspects of the genetics of this color polymorphism in T. podura, and compare this to previous results in T. cristinae. We first show that...

Registration Year

  • 2016
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  • University of North Carolina
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  • Duke University
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  • University of California, Berkeley
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  • Indiana University Bloomington
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  • University of Mississippi
    2