250 Works

Fundamentals of Quantum Materials Winter School and Workshop

Kristin Stenson
The Fundamentals of Quantum Materials Winter School and Workshop is an annual event unique to North America, dedicated specifically to the synthesis, characterization and electronic modeling of quantum materials. The FQM Winter School is aimed at providing fundamental training to our current and future generations of Quantum Materials scientists in synthesis and characterization techniques, bringing together senior and junior scientists to address topics at the forefront of current research into quantum materials, while also providing...

Data from: Fitness of Arabidopsis thaliana mutation accumulation lines whose spontaneous mutations are known

Charles B. Fenster, Matthew Thomas Rutter, Angela J. Roles, Jeffrey K. Conner, Ruth G. Shaw, Frank Holcomb Shaw, Korbinian Schneeberger, Stephan Ossowski & Detlef Weigel
Despite the fundamental importance of mutation to the evolutionary process, we have little knowledge of the direct consequences of specific spontaneous mutations to the fitness of the organism. Combining results of whole-genome sequencing with repeated field assays of survival and reproduction, we quantify the combined effects on fitness of spontaneous mutations identified in Arabidopsis thaliana. We demonstrate that the effects are beneficial, deleterious or neutral depending on the environmental context. Some lines, bearing mutations disrupting...

Data from: Influence of natural and novel organic carbon sources on denitrification in forest, degraded urban, and restored streams

Tamara A. Newcomer, Sujay S. Kaushal, Paul M. Mayer, Amy R. Shields, Elizabeth A. Canuel, Peter M. Groffman & Arthur J. Gold
Organic carbon is important in regulating ecosystem function, and its source and abundance may be altered by urbanization. We investigated shifts in organic carbon quantity and quality associated with urbanization and ecosystem restoration, and its potential effects on denitrification at the riparian–stream interface. Field measurements of streamwater chemistry, organic carbon characterization, and laboratory-based denitrification experiments were completed at two forested, two restored, and two unrestored urban streams at the Baltimore Long-Term Ecological Research site, Maryland,...

Data from: Localizing FST outliers on a QTL map reveals evidence for large genomic regions of reduced gene exchange during speciation-with-gene-flow

Sara Via, Gina Conte, Casey Mason-Foley & Kelly Mills
Populations that maintain phenotypic divergence in sympatry typically show a mosaic pattern of genomic divergence, requiring a corresponding mosaic of genomic isolation (reduced gene flow). However, mechanisms that could produce the genomic isolation required for divergence-with-gene-flow have barely been explored, apart from the traditional localized effects of selection and reduced recombination near centromeres or inversions. By localizing FST outliers from a genome scan of wild pea aphid host races on a Quantitative Trait Locus (QTL)...

Data from: Archaeopedological analysis of colluvial deposits in favourable and unfavourable areas: reconstruction of land use dynamics in SW Germany

Jessica Henkner, Jan Ahlrichs, Sean Downey, Markus Fuchs, Bruce James, Andrea Junge, Thomas Knopf, Thomas Scholten & Peter Kühn
Colluvial deposits, as the correlate sediments of human induced soil erosion, depict an excellent archive of land use and landscape history as representatives of human-environment interactions. This study establishes a chronostratigraphy of colluvial deposits and reconstructs past land use dynamics in the Swabian Jura, the Baar and the Black Forest in SW Germany. In the agriculturally favourable Baar area multiple main phases of colluvial deposition, and thus intensified land use, can be identified from the...

Data from: Fisher’s geometric model predicts the effects of random mutations when tested in the wild

Frank W. Stearns & Charles B. Fenster
Fisher's Geometric Model of Adaptation (FGM) has been the conceptual foundation for studies investigating the genetic basis of adaptation since the onset of the neo Darwinian synthesis. FGM describes adaptation as the movement of a genotype toward a fitness optimum due to beneficial mutations. To date, one prediction of FGM, the probability of improvement is related to the distance from the optimum, has only been tested in microorganisms under laboratory conditions. There is reason to...

Data from: Field measurements of genotype by environment interaction for fitness caused by spontaneous mutations in Arabidopsis thaliana

Angela J. Roles, Matthew Thomas Rutter, Ian Dworkin, Charles B. Fenster & Jeffrey K. Conner
As the ultimate source of genetic diversity, spontaneous mutation is critical to the evolutionary process. The fitness effects of spontaneous mutations are almost always studied under controlled laboratory conditions rather than under the evolutionarily relevant conditions of the field. Of particular interest is the conditionality of new mutations - i.e., is a new mutation harmful regardless of the environment in which it is found? In other words, what is the extent of genotype-environment interaction for...

Data from: Age specific survival rates of Steller sea lions at rookeries with divergent population trends in the Russian Far East

Alexey V. Altukhov, Russel D. Andrews, Donald G. Calkins, Thomas S. Gelatt, Eliezer D. Gurarie, Thomas R. Loughlin, Evgeny G. Mamaev, Victor S. Nikulin, Peter A. Permyakov, Sergey D. Ryazanov, Vladimir V. Vertyankin & Vladimir N. Burkanov
After a dramatic population decline, Steller sea lions have begun to recover throughout most of their range. However, Steller sea lions in the Western Aleutians and Commander Islands are continuing to decline. Comparing survival rates between regions with different population trends may provide insights into the factors driving the dynamics, but published data on vital rates have been extremely scarce, especially in regions where the populations are still declining. Fortunately, an unprecedented dataset of marked...

Data from: Globally, functional traits are weak predictors of juvenile tree growth, and we do not know why

C. E. Timothy Paine, Lucy Amissah, Harald Auge, Christopher Baraloto, Martin Baruffol, Nils Bourland, Helge Bruelheide, Kasso Daïnou, Roland C. De Gouvenain, Jean-Louis Doucet, Susan Doust, Paul V. A. Fine, Claire Fortunel, Josephine Haase, Karen D. Holl, Hervé Jactel, Xuefei Li, Kaoru Kitajima, Julia Koricheva, Cristina Martínez-Garza, Christian Messier, Alain Paquette, Christopher Philipson, Daniel Piotto, Lourens Poorter … & Andy Hector
1. Plant functional traits, in particular specific leaf area (SLA), wood density and seed mass, are often good predictors of individual tree growth rates within communities. Individuals and species with high SLA, low wood density and small seeds tend to have faster growth rates. 2. If community-level relationships between traits and growth have general predictive value, then similar relationships should also be observed in analyses that integrate across taxa, biogeographic regions and environments. Such global...

Bipartite network datasets for Permian host-plant--insect herbivory

Anshuman Swain, S. Augusta Maccracken, William Fagan & Conrad Labandeira
Plant–insect associations have been a significant component of terrestrial ecology for over 400 million years. Exploring these interactions in the fossil record, through novel perspectives, provides a window into understanding evolutionary and ecological forces that shaped these interactions. For the past several decades, researchers have documented, described and categorized fossil evidence of these interactions. Drawing on powerful tools from network science, we propose here a bipartite network representation of fossilized plants and their herbivore-induced leaf...

Invasive grass (Microstegium vimineum) indirectly benefits spider community by subsidizing available prey

Andrew Landsman, Karin Burghardt & Jacob Bowman
1. Invasive plant species cause a suite of direct, negative ecological impacts, but subsequent, indirect effects are more complex and difficult to detect. Where identified, indirect effects to other taxa can be wide-ranging and include ecological benefits in certain habitats or locations. 2. Here, we simultaneously examine the direct and indirect effects of a common, invasive grass species (Microstegium vimineum) on the invertebrate communities of understory deciduous forests in the eastern United States. To do...

Extraordinarily precise nematode sex ratios: adaptive responses to vanishingly rare mating opportunities

Justin Van Goor
Sex ratio theory predicts both mean sex ratio and variance under a range of population structures. Here, we compare two genera of phoretic nematodes (Parasitodiplogaster and Ficophagus spp.) associated with twelve fig-pollinating wasp species in Panama. The host wasps exhibit classic Local Mate Competition: only inseminated females disperse from natal figs, and their offspring form mating pools that consist of scores of the adult offspring contributed by one or a few foundress mothers. In contrast,...

13 Things To Say & 13 Things Not To Say To A Friend With Depression

Hanna Nettles, Curtis Smith, Emma Choplin, Caroline Vincent, Phoebe Rodda, Abigail Fleri & Natalie Charamut
Infographic for appropriate and helpful mental first aid talk.

Data from: A molecular phylogeny and revised higher-level classification for the leaf-mining moth family Gracillariidae and its implications for larval host-use evolution

Akito Y. Kawahara, David Plotkin, Issei Ohshima, Carlos Lopez-Vaamonde, Peter R. Houlihan, Jesse W. Breinholt, Atsushi Kawakita, Lei Xiao, Jerome C. Regier, Donald R. Davis, Tosio Kumata, Jay-Cheon Sohn, Jurate De Prins, Charles Mitter & JAE-CHEON SOHN
Gracillariidae are one of the most diverse families of internally feeding insects, and many species are economically important. Study of this family has been hampered by lack of a robust and comprehensive phylogeny. In the present paper, we sequenced up to 22 genes in 96 gracillariid species, representing all previously recognized subfamilies and genus groups, plus 20 outgroups representing other families and superfamilies. Following objective identification and removal of two rogue taxa, two datasets were...

Data from: Oscillatory signatures underlie growth regimes in Arabidopsis pollen tubes: computational methods to estimate tip location, periodicity and synchronization in growing cells

Daniel S.C. Damineli, Maria Teresa Portes & José A. Feijó
Oscillations in pollen tubes have been reported for many cellular processes, including growth, extracellular ion fluxes, and cytosolic ion concentrations. However, there is a shortage of quantitative methods to measure and characterize the different dynamic regimes observed. Herein, a suite of open-source computational methods and original algorithms were integrated into an automated analysis pipeline that we employed to characterize specific oscillatory signatures in pollen tubes of Arabidopsis thaliana (Col-0). Importantly, it enabled us to detect...

Data from: Centennial-scale reductions in nitrogen availability in temperate forests of the United States

K. K. McLauchlan, L. M. Gerhart, J. J. Battles, J. M. Craine, A. J. Elmore, P. E. Higuera, M. C. Mack, B. E. McNeil, D. M. Nelson, N. Pederson & S. S. Perakis
Forests cover 30% of the terrestrial Earth surface and are a major component of the global carbon (C) cycle. Humans have doubled the amount of global reactive nitrogen (N), increasing deposition of N onto forests worldwide. However, other global changes—especially climate change and elevated atmospheric carbon dioxide concentrations—are increasing demand for N, the element limiting primary productivity in temperate forests, which could be reducing N availability. To determine the long-term, integrated effects of global changes...

Data from: Phylotranscriptomics resolves ancient divergences in the Lepidoptera

Adam L. Bazinet, Kim T. Mitter, Donald R. Davis, Erik J. Van Nieukerken, Michael P. Cummings & Charles Mitter
Classic morphological studies of the oldest, so-called nonditrysian lineages of Lepidoptera yielded a well-resolved phylogeny, supported by the stepwise origin of the traits characterizing the clade Ditrysia, which contains over 98% of extant lepidopterans. Subsequent polymerase chain reaction (PCR)-based molecular studies have robustly supported many aspects of the morphological hypothesis and strongly contradicted others, while leaving some relationships unsettled. Here we bring the greatly expanded gene sampling of RNA-Seq to bear on nonditrysian phylogeny, especially...

Data from: Climate change, transgenic corn adoption and field-evolved resistance in corn earworm

P. Dilip Venugopal & Galen P. Dively
Increased temperature anomaly during the twenty-first century coincides with the proliferation of transgenic crops containing the bacterium Bacillus thuringiensis (Berliner) (Bt) to express insecticidal Cry proteins. Increasing temperatures profoundly affect insect life histories and agricultural pest management. However, the implications of climate change on Bt crop–pest interactions and insect resistance to Bt crops remains unexamined. We analysed the relationship of temperature anomaly and Bt adoption with field-evolved resistance to Cry1Ab Bt sweet corn in a...

Data from: Continental-scale patterns reveal potential for warming-induced shifts in cattle diet

Joseph M. Craine, Jay P. Angerer, Andrew Elmore & Noah Fierer
In North America, it has been shown that cattle in warmer, drier grasslands have lower quality diets than those cattle grazing cooler, wetter grasslands, which suggests warming will increase nutritional stress and reduce weight gain. Yet, little is known about how the plant species that comprise cattle diets change across these gradients and whether these shifts in dietary quality coincide with shifts in dietary composition, i.e. the relative abundance of different plant species consumed by...

Data from: Habitat features and long-distance dispersal modify the use of social information by a long-distance migratory bird

Clark S. Rushing, Michele R. Dudash & Peter P. Marra
1. The processes by which individuals select breeding sites have important consequences for individual tness as well as population- and community-dynamics. Although there is increasing evidence that many animal species use information acquired from conspecics to assess the suitability of potential breeding sites, little is known about how the use of this social information is modified by biotic and abiotic conditions. 2. We used an automated playback experiment to simulate two types of social information,...

Data from: Determination of the genetic architecture underlying short wavelength sensitivity in Lake Malawi cichlids

Sri Pratima Nandamuri, Brian E. Dalton & Karen L. Carleton
African cichlids are an exemplary system to study organismal diversity and rapid speciation. Species differ in external morphology including jaw shape and body coloration, but also differ in sensory systems including vision. All cichlids have 7 cone opsin genes with species differing broadly in which opsins are expressed. The differential opsin expression results in closely related species with substantial differences in spectral sensitivity of their photoreceptors. In this work, we take a first step in...

Data from: Diversification by host switching and dispersal shaped the diversity and distribution of avian malaria parasites in Amazonia

Alan Fecchio, Jeffrey Andrew Bell, Michael David Collins, Izeni Pires Farias, Christopher Harry Trisos, Joseph Andrew Tobias, Vasyl Volodymyr Tkach, Jason David Weckstein, Robert Eric Ricklefs & Henrique Batalha-Filho
Understanding how pathogens and parasites diversify through time and space is fundamental to predicting emerging infectious diseases. Here, we use biogeographic, coevolutionary and phylogenetic analyses to describe the origin, diversity, and distribution of avian malaria parasites in the most diverse avifauna on Earth. We first performed phylogenetic analyses using the mitochondrial cytochrome b (cyt b) gene to determine relationships among parasite lineages. Then, we estimated divergence times and reconstructed ancestral areas to uncover how landscape...

Data from: Biomass resilience of Neotropical secondary forests

Lourens Poorter, Frans Bongers, T. Mitchell Aide, Angélica M. Almeyda Zambrano, Patricia Balvanera, Justin M. Becknell, Vanessa Boukili, Pedro H. S. Brancalion, Eben N. Broadbent, Robin L. Chazdon, Dylan Craven, Jarcilene S. De Almeida-Cortez, George A. L. Cabral, Ben H. J. De Jong, Julie S. Denslow, Daisy H. Dent, Saara J. DeWalt, Juan M. Dupuy, Sandra M. Durán, Mario M. Espírito-Santo, María C. Fandino, Ricardo G. César, Jefferson S. Hall, José Luis Hernandez-Stefanoni, Catarina C. Jakovac … & Danaë M. A. Rozendaal
Land-use change occurs nowhere more rapidly than in the tropics, where the imbalance between deforestation and forest regrowth has large consequences for the global carbon cycle1. However, considerable uncertainty remains about the rate of biomass recovery in secondary forests, and how these rates are influenced by climate, landscape, and prior land use2, 3, 4. Here we analyse aboveground biomass recovery during secondary succession in 45 forest sites and about 1,500 forest plots covering the major...

Data from: Genetic inviability is a major driver of type-III survivorship in experimental families of a highly fecund marine bivalve

Louis V. Plough, Grace Shin & Dennis Hedgecock
The offspring of most highly fecund marine fish and shellfish suffer substantial mortality early in the life cycle, complicating prediction of recruitment and fisheries management. Early mortality has long been attributed to environmental factors and almost never to genetic sources. Previous work on a variety of marine bivalve species uncovered substantial genetic inviability among the offspring of inbred crosses, suggesting a large load of early-acting deleterious recessive mutations. However, genetic inviability of randomly bred offspring...

Data from: Recent admixture generates heterozygosity-fitness correlations during the range expansion of an invading species

Stephen R. Keller, Peter D. Fields, Andrea E. Berardi & Doug R. Taylor
Admixture, the mixing of historically isolated gene pools, can have immediate consequences for the genetic architecture of fitness traits. Admixture may be especially important for newly colonized populations, such as during range expansion and species invasions, by generating heterozygosity that can boost fitness through heterosis. Despite widespread evidence for admixture during species invasions, few studies have examined the demographic history leading to admixture, how admixture affects the heterozygosity and fitness of invasive genotypes, and whether...

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