341 Works

A new method to reconstruct quantitative food webs and nutrient flows from isotope tracer addition experiments

Andres Lopez-Sepulcre, Matthieu Bruneaux, Sarah Michelle Collins, Rana El-Sabaawi, Alexander S Flecker & Steven A Thomas
Understanding how nutrients flow through food webs is central in ecosystem ecology. Tracer addition experiments are powerful tools to reconstruct nutrient flows by adding an isotopically enriched element into an ecosystem, and tracking its fate through time. Historically, the design and analysis of tracer studies have varied widely, ranging from descriptive studies to modeling approaches of varying complexity. Increasingly, isotope tracer data is being used being used to compare ecosystems and analyze experimental manipulations. Currently,...

Data from: Modifications during early plant development promote the evolution of nature’s most complex woods

Joyce G. Chery, Marcelo R. Pace, Pedro Acevedo-Rodriguez, Chelsea D. Specht & Carl J. Rothfels
Secondary growth is the developmental process by which woody plants grow radially. The most complex presentations of secondary growth are found in lianas (woody vines) as a result of their unique demand to maintain stems that can twist without breaking. The complex woody forms in lianas arise as non-circular stem outlines, aberrant tissue configurations, and/or shifts in the relative abundance of secondary tissues. Previous studies demonstrate that abnormal activity of the vascular cambium leads to...

Regional Invasive Species & Climate Change Management Challenge: Taking Action. Managing invasive species in the context of climate change

Beaury Evelyn M., Audrey Barker-Plotkin, Carrie Brown-Lima, Emily J. Fusco, Bridget Griffin, Sydni Joubran, Brittany B. Laghina, Toni Lyn Morelli, Lara Munro, Michael Nelson, Sam Talbot & Bethany A. Bradley
Climate change is likely to alter the timing and effect of invasive species management, as well as the suite of species we are managing. Despite concern about the effects of climate change, lack of information about how and when to take action is a barrier to climate-smart invasive species management. Here, we outline strategies for incorporating climate change into management along with examples of tools that can inform proactive decision-making.

Strong sexual selection despite spatial constraints on extra-pair paternity

Emily Cramer, Emma Greig & Sara Kaiser
Extra-pair paternity should contribute to sexual selection by increasing the number of potential mates available to each individual. Potential copulation partners are, however, limited by their proximity. Spatial constraints may therefore reduce the impact of extra-pair paternity on sexual selection. We tested the effect of spatial constraints on sexual selection by simulating extra-pair copulations for 15 species of socially monogamous songbirds with varying rates of extra-pair paternity. We compared four metrics of sexual selection between...

Tracking the Near East origins and European dispersal of the house mouse

Thomas CUCCHI, Katerina Papayianni, Sophie Cersoy, Laetitia Aznar-Cormano, Antoine Zazzo, Régis Debruyne, Rémi Berthon, Adrian Bălășescu, Alan Simmons, François Valla, Yannis Hamilakis, Fanis Mavridis, Marjan Mashkour, Jamshid Darvish, Roohollah Siahsarvi, Fereidoun Biglari, Cameron A. Petrie, Lloyd Weeks, Alireza Sardari, Sepideh Maziar, Christiane Denys, David Orton, Emma Jenkins, Melinda Zeder, Jeremy B. Searle … & Jean-Denis Vigne
The house mouse (Mus musculus) is one of the most invasive mammals and an evolutionary model. However, the timing and components of its origin and dispersal remain poorly documented. To track its synanthropisation and subsequent biological invasion during the develoment of complex human societies, we analyzed 829 Mus specimens from 43 archaeological contexts in Southwestern Asia and Southeastern Europe, dating between 40,000 and 3,000 cal. BP, combining geometric morphometris numerical taxonomy with ancient mitochondrial DNA...

Data from: Divergence in DNA photorepair efficiency among genotypes from contrasting UV radiation environments in nature

Brooks E. Miner, Paige M. Kulling, Karlyn D. Beer & Benjamin Kerr
Populations of organisms routinely face abiotic selection pressures, and a central goal of evolutionary biology is to understand the mechanistic underpinnings of adaptive phenotypes. Ultraviolet radiation (UVR) is one of earth’s most pervasive environmental stressors, potentially damaging DNA in any organism exposed to solar radiation. We explored mechanisms underlying differential survival following UVR exposure in genotypes of the water flea Daphnia melanica derived from natural ponds of differing in UVR intensity. The UVR tolerance of...

Spatial proximity moderates genotype uncertainty in genetic tagging studies

Ben Augustine, J. Andrew Royle, Daniel W. Linden & Angela K. Fuller
Accelerating declines of an increasing number of animal populations worldwide necessitate methods to reliably and efficiently estimate demographic parameters such as population density and trajectory. Standard methods for estimating demographic parameters from noninvasive genetic samples are inefficient because lower quality samples cannot be used, and they do not allow for errors in individual identification. We introduce the Genotype Spatial Partial Identity Model (SPIM), which integrates a genetic classification model with a spatial population model to...

Reconciling Historical Data and Modern Computational Models in Corpus Creation

Joseph Rhyne

Unsupervised Formal Grammar Induction with Confidence

Jacob Collard

Data from: Partners coordinate territorial defense against simulated intruders in a duetting ovenbird

Pedro Diniz, Gianlucca Rech, Pedro Ribeiro, Michael Webster & Regina Macedo
Duets in breeding pairs may reflect a situation of conflict, whereby an individual answers its partner’s song as a form of unilateral acoustic mate guarding or, alternatively, it may reflect cooperation, when individuals share in territory defense or safeguard the partnership. The degree of coordination between the sexes when responding to solo versus paired intruders may elucidate the function of songs in duets. We examined this issue in a study with rufous horneros (Furnarius rufus),...

Leaf data of 101 species, varieties, forms, and cultivars of bamboo

Shuyan Lin, Karl Niklas, Yawen Wan, Dirk Hölscher, Cang Hui, Yulong Ding & Peijian Shi
The data include four comma-delimited (CSV) files and one word document. data1.csv file saves the raw data (including blade fresh mass, dry mass, area, length, width, perimeter and other measures) of 10045 leaves from 101 species, varieties, forms, and cultivars of bamboo; data2.csv file saves the results of the leaf dry mass per unit area (g/m2) comparison among 101 data sets; data3.csv file saves the results of the quotient of blade width to length comparison...

Evolution of a multifunctional trait: shared effects of foraging ecology and thermoregulation on beak morphology, with consequences for song evolution

Nicholas R. Friedman, Eliot T. Miller, Jason R. Ball, Haruka Kasuga, Vladimír Remeš & Evan P. Economo
While morphological traits are often associated with multiple functions, it remains unclear how evolution balances the selective effects of different functions. Birds' beaks function in foraging, but also in thermoregulating and singing, among other behaviours. Studies of beak evolution abound, however most focus on a single function. Thus, we quantified relative contributions of different functions over an evolutionary time scale. We measured beak shape using geometric morphometrics and compared this trait to foraging behaviour, climatic...

Natural variation for carotenoids in fresh kernels is controlled by uncommon variants in sweet corn

Matheus Baseggio, Matthew Murray, Maria Magallanes-Lundback, Nicholas Kaczmar, James Chamness, Edward Buckler, Margaret Smith, Dean DellaPenna, William Tracy & Michael Gore
Sweet corn (Zea mays L.) is highly consumed in the United States, but does not make major contributions to the daily intake of carotenoids (provitamin A carotenoids, lutein and zeaxanthin) that would help in the prevention of health complications. A genome-wide association study of seven kernel carotenoids and twelve derivative traits was conducted in a sweet corn inbred line association panel ranging from light to dark yellow in endosperm color to elucidate the genetic basis...

Water potential gradient, root conduit size and root xylem hydraulic conductivity determine the extent of hydraulic redistribution in temperate trees

Benjamin D Hafner, Benjamin D Hesse, Taryn L Bauerle & Thorsten EE Grams
1. Hydraulic redistribution (HR) of soil water through plant roots is widely described, however its extent, especially in temperate trees, remains unclear. Here, we quantified redistributed water of five temperate tree species. We hypothesized that both, HR within a plant and into the soil increases with higher water-potential gradients, larger root conduit diameters and root-xylem hydraulic conductivities. 2. Saplings of conifer (Picea abies, Pseudotsuga menziesii), diffuse-porous (Acer pseudoplatanus) and ring-porous species (Castanea sativa, Quercus robur)...

Data from: Allometric scaling laws linking biomass and rooting depth vary across ontogeny and functional groups in tropical dry forest lianas and trees

Chris M. Smith-Martin, Xiangtao Xu, David Medvigy, Stefan Schnitzer & Jennifer Powers
There are two theories about how allocation of metabolic products occurs. The allometric biomass partitioning theory (APT) suggests that all plants follow common allometric scaling rules. The optimal partitioning theory (OPT) predicts that plants allocate more biomass to the organ capturing the most limiting resource. We used whole-plant harvests of mature and juvenile tropical deciduous trees, evergreen trees, and lianas and model simulations to address the following knowledge gaps: 1) Do mature lianas comply with...

Differences in perceived predation risk associated with variation in relative size of extra-pair and within-pair offspring

Kelly Hallinger, Maren Vitousek & David Winkler
Extra-pair paternity (EPP) is a widespread phenomenon in birds. Researchers have long hypothesized that EPP must confer a fitness advantage to extra-pair offspring (EPO), but empirical support for this hypothesis is definitively mixed. This could be because genetic benefits of EPP only exist in a subset of environmental contexts to which a population is exposed. From 2013-2015, we manipulated perceived predator density in a population of tree swallows (Tachycineta bicolor) breeding in New York to...

Glacial cycles drive rapid divergence of cryptic field vole species

Nicholas Fletcher, Pelayo Acevedo, Jeremy S. Herman, Joana Pauperio, Paulo Alves & Jeremy Searle
Understanding the factors that contribute to the generation of reproductively isolated forms is a fundamental goal of evolutionary biology. Cryptic species are an especially interesting challenge to study in this context since they lack obvious morphological differentiation that provides clues to adaptive divergence that may drive reproductive isolation. Geographical isolation in refugial areas during glacial cycling is known to be important for generating genetically divergent populations, but its role in the origination of new species...

TypeTE: a tool to genotype mobile element insertions from whole genome resequencing data

Clément Goubert, Jainy Thomas, Lindsay Payer, Jeffrey Kidd, Julie Feusier, W. Scott Watkins, Kathleen Burns, Lynn Jorde & Cédric Feschotte
Alu retrotransposons account for more than 10% of the human genome, and insertions of these elements create structural variants segregating in human populations. Such polymorphic Alu are powerful markers to understand population structure, and they represent variants that can greatly impact genome function, including gene expression. Accurate genotyping of Alu and other mobile elements has been challenging. Indeed, we found that Alu genotypes previously called for the 1000 Genomes Project are sometimes erroneous, which poses...

Parallel evolution of ancient, pleiotropic enhancers underlies butterfly wing pattern mimicry

James Lewis, Rachel Geltman, Patrick Pollack, Kathleen Rondem, Steven Van Belleghem, Melissa Hubisz, Paul Munn, Linlin Zhang, Caleb Benson, Anyi Mazo-Vargas, Charles Danko, Brian Counterman, Riccardo Papa & Robert Reed
Color pattern mimicry in Heliconius butterflies is a classic case study of complex trait adaptation via selection on a few large effect genes. Association studies have linked color pattern variation to a handful of noncoding regions, yet the presumptive cis-regulatory elements (CREs) that control color patterning remain unknown. Here we combine chromatin assays, DNA sequence associations, and genome editing to functionally characterize 5 cis-regulatory elements of the color pattern gene optix. We were surprised to...

Consumer movement dynamics as hidden drivers of stream habitat structure: suckers as ecosystem engineers on the night shift

Michael Booth, Nelson Hairston & Alex Flecker
Ecosystem engineers engineering can control the spatial and temporal distribution of resources and movement by engineering organisms within an ecosystem can transport mobilize resources across boundaries and distribute engineering effects. Movement patterns of fishes can cause physical changes to stream aquatic habitats though nesting or feeding, both of which often vary in space and time. Here we present evidence of ecosystem engineering by the Sonora sucker (Catostomus insignis), a dominant fish in streams of the...

Extracting physiological information in experimental biology via Eulerian video magnification

Henrik Lauridsen, Selina Gonzales, Daniela Hedwig, Kathryn L. Perrin, Catherine J.A. Williams, Peter H. Wrege, Mads F. Bertelsen, Michael Pedersen & Jonathan T. Butcher
Background: Videographic material of animals can contain inapparent signals, such as color changes or motion that hold information about physiological functions, such as heart and respiration rate, pulse wave velocity and vocalization. Eulerian video magnification allows enhancement of such signals to enable their detection. The purpose of this study is to demonstrate how signals relevant to experimental physiology can be extracted from non-contact videographic material of animals. Results: We applied Eulerian video magnification to detect...

Data from: Social context alters spatial memory performance in free-living male prairie voles

Alexander Ophir
Spatial memory is crucial for mating success because it enables males to locate potential mates and potential competitors in space. Intraspecific competition and its varying intensity under certain conditions are potentially important for shaping spatial memory. For example, spatial memory could enable males to know where competitors are (contest competition), it could help males find mating partners (scramble competition), or both. We manipulated the intensity of intraspecific competition in two distinct contexts by altering the...

Data from: Survey completeness of a global citizen-science database of bird occurrence

Frank La Sorte & Marius Somveille
Measuring the completeness of survey inventories created by citizen-science initiatives can identify the strengths and shortfalls in our knowledge of where species occur geographically. Here, we use occurrence information from eBird to measure the survey completeness of the world’s birds in this database at three temporal resolutions and four spatial resolutions across the annual cycle during the period 2002 to 2018. Approximately 84% of the earth’s terrestrial surface contained bird occurrence information with the greatest...

Red oak seedlings as indicators of deer browse pressure: gauging the outcome of different white-tailed deer management approaches

Bernd Blossey, Paul Curtis, Jason Boulanger & Andrea Dávalos
After decades of high deer populations, North America forests have lost much of their previous biodiversity. Any landscape-level recovery requires substantial reductions in deer herds, but modern societies and wildlife management agencies appear unable to devise appropriate solutions to this chronic ecological and human health crisis. We evaluated the effectiveness of fertility control hunting in reducing deer impacts at Cornell University. We estimated spring deer populations and planted Quercus rubra seedlings to assess deer browse...

Warming and pollutants interact to modulate octocoral immunity and shape disease outcomes

Allison M. Tracy, Ernesto Weil & C. Drew Harvell
Warming environments can alter the outcome of host-parasite relationships with important consequences for biodiversity. Warming often increases disease risk, and interactions with other environmental factors can intensify impacts by modifying the underlying mechanisms, such as host immunity. In coastal ecosystems, metal pollution is a pervasive stressor that influences disease and immunity in many organisms. Despite the crisis facing coral reefs, which stems in part from warming-associated disease outbreaks, the impacts of metal pollutants on scleractinian...

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