163 Works

Vegetation Change in the Natural Reserve of Orange County

Katherine Suding, Sara Jo Dickens & Samuel Bedgood
This data set describes vegetation change in 109 areas in the Nature Reserve of Orange County. The authors of this data were mainly interested in the success of artichoke thistle (Cynara cardunculus) control, but it could be approached in many different ways. Surveyors identified and recorded more than 375 plant species from the years 1998, 2008, and 2013.

Terminus data for: Multi-decadal retreat of Greenland’s marine-terminating glaciers

Ian M. Howat & Alex Eddy
Many marine-terminating glaciers draining the Greenland ice sheet have retreated over the past decade, yet the extent and magnitude of retreat relative to past variability is unknown. We measure changes in front positions of 210 marine-terminating glaciers using Landsat imagery spanning nearly four decades and compare decadal-scale rates of change with earlier observations. We find that 90% of the observed glaciers retreated between 2000 and 2010, approaching 100% in the northwest, with rapid retreat observed...

Bending and Looping of long DNA by Polycomb repressive complex 2 revealed by AFM imaging in liquid

Patrick Heenan, Anne Gooding, Xueyin Wang, Thomas Perkins & Thomas Cech
Polycomb repressive complex 2 (PRC2) is a histone methyltransferase that methylates histone H3 at Lysine 27. PRC2 is critical for epigenetic gene silencing, cellular differentiation, and the formation of facultative heterochromatin. It can also promote or inhibit oncogenesis. Despite this importance, the molecular mechanisms by which PRC2 compacts chromatin are relatively understudied. Here, we visualized the binding of PRC2 to naked DNA in liquid at the single-molecule level using atomic force microscopy. Analysis of the...

Data used for 2002-2019 spotted knapweed research

Timothy Seastedt
Data documentation required for submission of manscript, "Decadal response of the wicked weed of the West, spotted knapweed, Centaurea stoebe, to multiple biological control agents.

Exploring dynamical phase transitions with a Cavity-QED platform

Juan Andres Muniz Silva, Diego Barberena, Robert J. Lewis-Swan, Dylan J. Young, Julia R. K. Cline, Ana Maria Rey & James K. Thompson
Atom-light interactions in optical cavities provide a platform for investigating many-body quantum physics in controlled environments. In particular, they have been proposed for the realization of collective quantum spin models with tunable long-range interactions. Besides the investigation of the rich steady-state phases that can arise due to the interplay between atom-light interactions and dissipation from the cavity, one opportunity offered by these systems is the study of out-of-equilibrium dynamical phases of matter precluded from existence...

Data from: The ecology and evolution of seed predation by Darwin's finches on Tribulus cistoides on the Galápagos Islands

Sofía Carvajal-Endara, Andrew P. Hendry, Nancy C. Emery, Corey P. Neu, Diego Carmona, Kiyoko M. Gotanda, T. Jonathan Davies, Jaime A. Chaves & Marc T. J Johnson
Predator-prey interactions play a key role in the evolution of species traits through antagonistic coevolutionary arms-races. The evolution of beak morphology in the Darwin’s finches in response to competition for seed resources is a classic example of evolution by natural selection. The seeds of Tribulus cistoides are an important food source for the largest ground finch species (Geospiza fortis, G. magnirostris, and G. conirostris) in dry months, and the hard spiny morphology of the fruits...

Data from: Food and habitat provisions jointly determine competitive and facilitative interactions among distantly related herbivores

Duofeng Pan, Xincheng Li, Kejia De, Ling Wang, Deli Wang, Qinfeng Guo, Chao Gao, Zhiwei Zhong, Zhu Hui, Zhongbao Shen & Timothy Seastedt
1. Interactions between distantly related herbivores exert powerful influences on ecosystems, but most studies to date have only considered unidirectional effects. Few have simultaneously examined the mutual effects that vertebrate herbivores and insect herbivores have on one another. 2. We conducted a set of manipulative experiments to evaluate the potential competition and facilitation between two pairs of distantly related herbivore taxa: an insect caterpillar (Gynaephora alpherakii) and two large vertebrate herbivores, yak (Bos grunniens) and...

Fruit syndromes in Viburnum: correlated evolution of color, nutritional content, and morphology in bird-dispersed fleshy fruits

Miranda Sinnott-Armstrong, Chong Lee, Wendy Clement & Michael Donoghue
Premise A key question in plant dispersal via animal vectors is where and why fruit colors vary between species and how color relates to other fruit traits. To better understand the factors shaping the evolution of fruit color diversity, we tested for the existence of syndromes of traits (color, morphology, and nutrition) in the fruits of Viburnum. We placed these results in a larger phylogenetic context and reconstructed ancestral states to assess how Viburnum fruit...

Do different rates of gene flow underlie variation in phenotypic and phenological clines in a montane grasshopper community?

Sean Schoville, Rachel Slatyer, César Nufio & Lauren Buckley
Species responses to environmental change are likely to depend on existing genetic and phenotypic variation, as well as evolutionary potential. A key challenge is to determine whether gene flow might facilitate or impede genomic divergence among populations responding to environmental change, and if emergent phenotypic variation is limited by gene flow rates. A general expectation is that patterns of genetic differentiation in a set of co-distributed species reflect differences in dispersal ability. In less-dispersive species,...

Gene copy number is associated with phytochemistry in Cannabis sativa

Daniela Vergara
Gene copy number variation is known to be important in nearly every species where it has been examined. Alterations in gene copy number may provide a fast way of acquiring diversity, allowing rapid adaptation under strong selective pressures, and may also be a key component of standing genetic variation within species. Cannabis sativa plants produce a distinguishing set of secondary metabolites, the cannabinoids, many of which have medicinal utility. Two major cannabinoids -THCA and CBDA...

Migratory divides coincide with reproductive barriers across replicated avian hybrid zones above the Tibetan Plateau

Elizabeth Scordato, Chris C. R. Smith, Georgy A. Semenov, Yu Liu, Matthew R. Wilkins, Wei Liang, Alexander Rubtsov, Gomboobaatar Sundev, Kazuo Koyama, Sheela P. Turbek, Michael B. Wunder, Craig A. Stricker & Rebecca Safran
Migratory divides are proposed to be catalysts for speciation across a diversity of taxa. However, it is difficult to test the relative contributions of migratory behavior vs. other divergent traits to reproductive isolation. Comparing hybrid zones with and without migratory divides offers a rare opportunity to directly examine the contribution of divergent migratory behavior to reproductive barriers. We show that across replicate sampling transects of two pairs of barn swallow (Hirundo rustica) subspecies, strong reproductive...

Arctic shrub colonization lagged peak postglacial warmth: Molecular evidence in lake sediment from Arctic Canada

Sarah Crump, Gifford Miller, Matthew Power, Julio Sepúlveda, Nadia Dildar, Megan Coghlan & Michael Bunce
Arctic shrubification is an observable consequence of climate change, already resulting in ecological shifts and global-scale climate feedbacks including changes in land surface albedo and enhanced evapotranspiration. However, the rate at which shrubs can colonize previously glaciated terrain in a warming world is largely unknown. Reconstructions of past vegetation dynamics in conjunction with climate records can provide critical insights into shrubification rates and controls on plant migration, but paleoenvironmental reconstructions based on pollen may be...

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: Selection on multiple sexual signals in two Central- and Eastern-European populations of the barn swallow

Peter Laszlo Pap, Attila Fülöp, Marie Adamkova-Kotasova, Jaroslav Cepak, Romana Michalkova, Rebecca J. Safran, Alexandru N. Stermin, Oldrich Tomasek, Csongor I. Vágási, Orsolya Vincze, Matthew R. Wilkins & Tomas Albrecht
Variation in intensity and targets of sexual selection on multiple traits has been suggested to play a major role in promoting phenotypic differentiation between populations, although the divergence in selection may depend on year, local conditions or age. In this study, we quantified sexual selection for two putative sexual signals across two Central and East European barn swallow (Hirundo rustica rustica) populations from Czech Republic and Romania over multiple years. We then related these differences...

Data from: An effective method for ecosystem-scale manipulation of bird abundance and species richness

Chelsea Wood, Margaret Summerside & Pieter Johnson
Manipulation experiments are a cornerstone of ecological research, but can be logistically challenging to execute – particularly when they are intended to isolate the ecological role of large, vagile species, like birds. Despite indirect evidence that birds are influential in many ecosystems, large-scale, multi-year bird manipulation experiments are rare. When these studies are conducted, they are typically realized with caged or netted exclosures, an approach that can be expensive, risky for wildlife, and difficult to...

Data from: Fire-regime complacency and sensitivity to centennial- through millennial-scale climate change in Rocky Mountain subalpine forests, Colorado, U.S.A.

Philip E. Higuera, Christy E. Briles & Cathy Whitlock
1. Key uncertainties in anticipating future fire regimes are their sensitivity to climate change, and the degree to which climate will impact fire regimes directly, through increasing the probability of fire, versus indirectly, through changes in vegetation and landscape flammability. 2. We studied the sensitivity of subalpine forest fire regimes (i.e., fire frequency, fire severity) to previously documented climate variability over the past 6000 years, utilizing pollen and macroscopic charcoal from high-resolution lake-sediment records in...

Data from: Seasonality of precipitation interacts with exotic species to alter composition and phenology of a semi-arid grassland

Janet S. Prevéy & Timothy R. Seastedt
While modeling efforts suggest that invasive species will track climate changes, empirical studies are few. A relevant and largely unaddressed research question is: how will the presence of exotic species interact with precipitation change to alter ecosystem structure and function? We studied the effects of changes in seasonal timing of precipitation on species composition and resource availability in a grassland community in Colorado, USA. We examined how seasonal precipitation patterns affect the abundance of historically...

Data from: "Willing to pay?" Tax compliance in Britain and Italy: an experimental analysis

Nan Zhang, Giulia Andrighetto, Stefania Ottone, Ferruccio Ponzano & Sven Steinmo
As shown by the recent crisis, tax evasion poses a significant problem for countries such as Greece, Spain and Italy. While these societies certainly possess weaker fiscal institutions as compared to other EU members, might broader cultural differences between northern and southern Europe also help to explain citizens’ (un)willingness to pay their taxes? To address this question, we conduct laboratory experiments in the UK and Italy, two countries which straddle this North-South divide. Our design...

Data from: The evolutionary relationships and age of Homo naledi: an assessment using dated Bayesian phylogenetic methods

Mana Dembo, Davorka Radovčić, Heather M. Garvin, Myra F. Laird, Lauren Schroeder, Jill E. Scott, Juliet Brophy, Rebecca R. Ackermann, Charles M. Musiba, Darryl J. De Ruiter, Arne Ø. Mooers, Mark Collard & Chares M. Musiba
Homo naledi is a recently discovered species of fossil hominin from South Africa. A considerable amount is already known about H. naledi but some important questions remain unanswered. Here we report a study that addressed two of them: “Where does H. naledi fit in the hominin evolutionary tree?” and “How old is it?” We used a large supermatrix of craniodental characters for both early and late hominin species and Bayesian phylogenetic techniques to carry out...

Data from: Declines in low-elevation subalpine tree populations outpace growth in high-elevation populations with warming

Erin Conlisk, Cristina Castanha, Matthew J. Germino, Thomas T. Veblen, Jeremy M. Smith & Lara M. Kueppers
1. Species distribution shifts in response to climate change require that recruitment increase beyond current range boundaries. For trees with long lifespans, the importance of climate-sensitive seedling establishment to the pace of range shifts has not been demonstrated quantitatively. 2. Using spatially explicit, stochastic population models combined with data from long-term forest surveys, we explored whether the climate-sensitivity of recruitment observed in climate manipulation experiments was sufficient to alter populations and elevation ranges of two...

Data from: Environmental harshness is positively correlated with intraspecific divergence in mammals and birds

Carlos A. Botero, Roi Dor, Christy M. McCain & Rebecca J. Safran
Life on Earth is conspicuously more diverse in the tropics. Although this intriguing geographical pattern has been linked to many biotic and abiotic factors, their relative importance and potential interactions are still poorly understood. The way in which latitudinal changes in ecological conditions influence evolutionary processes is particularly controversial, as there is evidence for both a positive and a negative latitudinal gradient in speciation rates. Here, we identify and address some methodological issues (how patterns...

Data from: Moth body size increases with elevation along a complete tropical elevational gradient for two hyperdiverse clades

Gunnar Brehm, Dirk Zeuss & Robert K. Colwell
The body size of an animal is probably its most important functional trait. For arthropods, environmental drivers of body size variation are still poorly documented and understood, especially in tropical regions. We use a unique dataset for two species-rich, phylogenetically independent moth taxa (Lepidoptera: Geometridae; Arctiinae), collected along an extensive tropical elevational gradient in Costa Rica, to investigate the correlates and possible causes of body-size variation. We studied 15,047 specimens (794 species) of Geometridae and...

Data from: Stepwise Threshold Clustering: a new method for genotyping MHC loci using next-generation sequencing technology

William E. Stutz & Daniel I. Bolnick
Genes of the vertebrate major histocompatibility complex (MHC) are of great interest to biologists because of their important role in immunity and disease, and their extremely high levels of genetic diversity. Next generation sequencing (NGS) technologies are quickly becoming the method of choice for high-throughput genotyping of multi-locus templates like MHC in non-model organisms. Previous approaches to genotyping MHC genes using NGS technologies suffer from two problems: 1) a “gray zone” where low frequency alleles...

Data from: Asymmetric competition impacts evolutionary rescue in a changing environment

Courtney L. Van Den Elzen, Elizabeth J. Kleynhans & Sarah P. Otto
Interspecific competition can strongly influence the evolutionary response of a species to a changing environment, impacting the chance that the species survives or goes extinct. Previous work has shown that when two species compete for a temporally shifting resource distribution, the species lagging behind the resource peak is the first to go extinct due to competitive exclusion. However, this work assumed symmetrically distributed resources and competition. Asymmetries can generate differences between species in population sizes,...

Data from: A jungle in there: bacteria in belly buttons are highly diverse, but predictable

Jiri Hulcr, Andrew M. Latimer, Jessica B. Henley, Nina R. Rountree, Noah Fierer, Andrea Lucky, Margaret D. Lowman & Robert R. Dunn
The belly button is one of the habitats closest to us, and yet it remains relatively unexplored. We analyzed bacteria and arachaea from the belly buttons of humans from two different populations sampled within a nation-wide citizen science project. We examined bacterial and archaeal phylotypes present and their diversity using multiplex pyrosequencing of 16S rDNA libraries. We then tested the oligarchy hypothesis borrowed from tropical macroecology, namely that the frequency of phylotypes in one sample...

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