200 Works

Elevational niche-shift migration: Why the degree of elevational change matters for the ecology, evolution, and physiology of migratory birds

Jessie Williamson & Christopher Witt
Abstract Elevational migration can be defined as roundtrip seasonal movement that involves upward and downward shifts in elevation. These shifts incur physiological challenges that are proportional to the degree of elevational change. Larger shifts in elevation correspond to larger shifts in partial pressure of oxygen, air density, temperature, and ultraviolet (UV) exposure. Although most avian examples of elevational migration involve subtle shifts that would have minimal impacts on physiology, shifts of any magnitude have previously...

Repository Analytics and Metrics Portal (RAMP) 2021 data

Jonathan Wheeler & Kenning Arlitsch
The Repository Analytics and Metrics Portal (RAMP) is a web service that aggregates use and performance use data of institutional repositories. The data are a subset of data from RAMP, the Repository Analytics and Metrics Portal (http://rampanalytics.org), consisting of data from all participating repositories for the calendar year 2021. For a description of the data collection, processing, and output methods, please see the "methods" section below. The record will be revised periodically to make new...

Mining the first 100 days: Human and data ethics in Twitter research

Jonathan Wheeler & Teresa Neely
This dataset consists of tweet identifiers for tweets harvested between November 28, 2016, following the election of Donald Trump through the end of the first 100 days of his administration. Data collection ended May 1, 2017. Tweets were harvested using multiple methods described below. The total dataset consists of 218,273,152 tweets. Because of the different methods used to harvest tweets, there may be some duplication.

Data from: Demography predicts genetic effective size in a desert stream fish community

Tyler Pilger
Demographic data collected during long-term diversity monitoring and short-term ecological surveys were used to calculate summary statistics to compare with estimates of genetic effective size for nine species occurring in the Gila River, New Mexico, USA. Diversity survey data collected by New Mexico Department of Game and Fish from 1988 to 2010 were converted to presence/absence data to create detection histories for each of the nine focal species. Simple occupancy models of detection histories implemented...

Gila Trout neutral and outlier SNP genotype matrices

David Camak, Megan Osborne & Thomas Turner
Many salmonid species exist in highly structured and isolated populations, and are susceptible to habitat fragmentation and disturbances. Gila Trout (Oncorhynchus gilae) is a threatened species found in the Southwestern United States, and is managed to preserve relict populations (i.e., lineages) distributed across a fragmented landscape. We evaluated genomic variation within and among remaining lineages of Gila Trout using RADseq to assess how drift and selection have structured populations using neutral and outlier loci. We...

Repository Analytics and Metrics Portal (RAMP) 2020 data

Jonathan Wheeler & Kenning Arlitsch
Version update: The originally uploaded versions of the CSV files in this dataset included an extra column, "Unnamed: 0," which is not RAMP data and was an artifact of the process used to export the data to CSV format. This column has been removed from the revised dataset. The data are otherwise the same as in the first version. The Repository Analytics and Metrics Portal (RAMP) is a web service that aggregates use and performance...

Analysis of paralogs in target enrichment data pinpoints multiple ancient polyploidy events in Alchemilla s.l. (Rosaceae)

Diego F. Morales-Briones, Berit Gehrke, Chien-Hsun Huang, Aaron Liston, Hong Ma, Hannah Marx, David Tank & Ya Yang
Target enrichment is becoming increasingly popular for phylogenomic studies. Although baits for enrichment are typically designed to target single-copy genes, paralogs are often recovered with increased sequencing depth, sometimes from a significant proportion of loci, especially in groups experiencing whole-genome duplication (WGD) events. Common approaches for processing paralogs in target enrichment data sets include random selection, manual pruning, and mainly, the removal of entire genes that show any evidence of paralogy. These approaches are prone...

A lightweight backpack harness for tracking hummingbirds

Jessie L. Williamson & Christopher C. Witt
Hummingbirds and other lightweight bird species are challenging to track because they have limited capacity to carry devices for data-logging. We present a simple and customizable three-loop ‘backpack’ harness for studying hummingbird migration and movement, with step-by-step instructions for harness construction and attachment. The harness has negligible weight and cost (< $0.50 USD/each), is easy for a single person to make and apply in the field, and it requires no complicated setup or equipment. We...

Data from: Social selectivity in aging wild chimpanzees

Alexandra Rosati, Lindsey Hagberg, Drew Enigk, Emily Otali, Melissa Emery Thompson, Martin Muller, Richard Wrangham & Zarin Machanda
Humans prioritize close, positive relationships during aging, and socioemotional selectivity theory proposes that this shift causally depend on capacities for thinking about personal future time horizons. To examine this theory, we tested for key elements of human social aging in longitudinal data on wild chimpanzees. Aging male chimpanzees have more mutual friendships characterized by high, equitable investment, whereas younger males have more one-sided relationships. Older males are more likely to be alone, but they also...

Context-dependent variability in the population prevalence and individual fitness effects of plant-fungal symbiosis

Marion Donald, Teresa Bohner, Kory Kolis, Alan Shadow, Jennifer Rudgers & Tom Miller
1. Heritable symbionts, found within a diverse array of flora and fauna, are often observed at intermediate prevalence within host populations, despite expectations that positive fitness feedbacks should drive beneficial symbionts to fixation. Intermediate prevalence may reflect neutral dynamics of symbionts with weak fitness effects, transient dynamics of symbionts trending toward fixation (or elimination), or a stable intermediate outcome determined by the balance of fitness effects and failed symbiont transmission. Theory suggests these outcomes should...

Accelerated brain shape evolution is associated with rapid diversification in an avian radiation

Chad Eliason, Jenna McCullough, Michael Andersen & Shannon Hackett
Niche expansion is a critical step in the speciation process. Large brains linked to improved cognitive ability may enable species to expand their niches and forage in new ways, thereby promoting speciation. Despite considerable work on ecological divergence in brain size and its importance in speciation, relatively little is known about how brain shape relates to behavioral, ecological, and taxonomic diversity at macroevolutionary scales. This is due, in part, to inherent challenges with quantifying brain...

LADPU Smart Meter Data

Vinicius Souza, Trilce Estrada, Adnan Bashir & Abdullah Mueen
This dataset contains the electric power consumption data from the Los Alamos Public Utility Department (LADPU) in New Mexico, USA. The data was collected by Landis+Gyr smart meters devices on 1,757 households at North Mesa, Los Alamos, NM. The sampling rate is one observation every fifteen minutes (i.e., 96 observations per day). For most customers, the data spans about six years, from July 30, 2013 to December 30, 2019. However, for some customers, the period...

Data from: Changes in the diet and body size of a small herbivorous mammal (Sigmodon hispidus, hispid cotton rat) following the Late Pleistocene megafauna extinction

Catalina P. Tome, Emma A. Elliott Smith, S. Kathleen Lyons, Seth D. Newsome & Felisa A. Smith
The catastrophic loss of large-bodied mammals during the terminal Pleistocene likely led to cascading effects within communities. While the extinction of the top consumers probably expanded the resources available to survivors of all body sizes, little work has focused on the responses of the smallest mammals. Here, we use a detailed fossil record from the southwestern United States to examine the response of the hispid cotton rat (Sigmodon hispidus) to biodiversity loss and climatic change...

Data from: Mother's social status is associated with child health in a horticulturalist population

Sarah Alami, Christopher Von Rueden, Edmond Seabright, Thomas S. Kraft, Aaron D. Blackwell, Jonathan Stieglitz, Hillard Kaplan & Michael Gurven
High social status is often associated with greater mating opportunities and fertility for men, but do women also obtain fitness benefits of high status? Greater resource access and child survivorship may be principal pathways through which social status increases women’s fitness. Here we examine whether peer-rankings of women’s social status (indicated by political influence, project leadership and respect) positively covaries with child nutritional status and health in a community of Amazonian horticulturalists. We find that...

Core Characteristics of Learning Resource Collectors

Nancy J. Hoebelheinrich, Elizabeth Newbold, Angus Whyte, Maria Johnsson, Kerstin Helbig, Margareta Hellström, Iryna Kuchma & Mijke Jetten
As part of the Education And Training On Handling Of Research Data IG (ETHRD-IG) activities, the Learning Resource Collectors Focus Group studied the evolving landscape of learning resources on RDM topics. As we collected and listed a snapshot of current catalogues or registries of learning resources for review, we realized that a set of core characteristics could describe these types of organisations that would be useful to help people evaluate and understand the resources they...

Wallacean and Melanesian islands promote higher rates of diversification within the global passerine radiation Corvides: Supplementary information

Jenna McCullough, Carl Oliveros, Brett Benz, Rosana Zenil-Ferguson, Joel Cracraft, Robert Moyle & Michael Andersen
The complex island archipelagoes of Wallacea and Melanesia have provided empirical data behind integral theories in evolutionary biology, including allopatric speciation and island biogeography. Yet, questions regarding the relative impact of the layered biogeographic barriers, such as deep-water trenches and isolated island systems, on faunal diversification remain underexplored. One such barrier is Wallace’s Line, a significant biogeographic boundary that largely separates Australian and Asian biodiversity. To assess the relative roles of biogeographic barriers—specifically isolated island...

Data from: QTL mapping identifies candidate alleles involved in adaptive introgression and range expansion in a wild sunflower

Kenneth D. Whitney, Karl W. Broman, Nolan C. Kane, Stephen M. Hovick, Rebecca A. Randell & Loren H. Rieseberg
The wild North American sunflowers Helianthus annuus and H. debilis are participants in one of the earliest identified examples of adaptive trait introgression, and the exchange is hypothesized to have triggered a range expansion in H. annuus. However, the genetic basis of the adaptive exchange has not been examined. Here, we combine quantitative trait locus (QTL) mapping with field measurements of fitness to identify candidate H. debilis QTL alleles likely to have introgressed into H....

Data from: Genetic monitoring and complex population dynamics: insights from a 12-year study of the Rio Grande silvery minnow

Megan J. Osborne, Evan W. Carson & Thomas F. Turner
The endangered Rio Grande silvery minnow persists as a remnant population in a highly fragmented and regulated arid-land river system. The species is subject to dramatic fluctuations in density. Since 2003, the wild population has been supplemented by hatchery-reared fish. We report on a 12-year (1999 – 2010) monitoring study of genetic diversity and effective population size (Ne) of wild and hatchery stocks. Our goals were to evaluate how genetic metrics responded to changes in...

Data from: Loss of genetic diversity, recovery, and allele surfing in a colonizing parasite, Geomydoecus aurei

James W. Demastes, David J. Hafner, Mark S. Hafner, Jessica E. Light & Theresa A. Spradling
Understanding the genetic consequences of changes in species distributions has wide-ranging implications for predicting future outcomes of climate change, for protecting threatened or endangered populations, and for understanding the history that has led to current genetic patterns within species. Herein, we examine the genetic consequences of range expansion over a 25-year period in a parasite (Geomydoecus aurei) that is in the process of expanding its geographic range via invasion of a novel host. By sampling...

Data from: Earth history and the passerine superradiation

Carl H. Oliveros, Daniel J. Field, Daniel T. Ksepka, F. Keith Barker, Alexandre Aleixo, Michael J. Andersen, Per Alström, Brett W. Benz, Edward L. Braun, Michael J. Braun, Gustavo A. Bravo, Robb T. Brumfield, R. Terry Chesser, Santiago Claramunt, Joel Cracraft, Andrés M. Cuervo, Elizabeth P. Derryberry, Travis C. Glenn, Michael G. Harvey, Peter A. Hosner, Leo Joseph, Rebecca T. Kimball, Andrew L. Mack, Colin M. Miskelly, A. Townsend Peterson … & Brant C. Faircloth
Avian diversification has been influenced by global climate change, plate tectonic movements, and mass extinction events. However, the impact of these factors on the diversification of the hyperdiverse perching birds (passerines) is unclear because family level relationships are unresolved and the timing of splitting events among lineages is uncertain. We analyzed DNA data from 4,060 nuclear loci and 137 passerine families using concatenation and coalescent approaches to infer a comprehensive phylogenetic hypothesis that clarifies relationships...

Data from: Convergence in resource use efficiency across trees with differing hydraulic strategies in response to ecosystem precipitation manipulation

Jean-Marc Limousin, Enrico A. Yepez, Nate G. McDowell & William T. Pockman
1. Plants are expected to respond to drought by maximizing the efficiency of the most limiting resource, the water use efficiency (WUE), at the expense of nitrogen and carbon use efficiencies (NUE and CUE). Therefore, plants resource use efficiencies are viewed as indicators of species drought tolerance. 2. We tested these predictions by measuring leaf-level intrinsic WUE (WUEi, the ratio of net assimilation to stomatal conductance), photosynthetic NUE (PNUE, the ratio of daily maximum net...

Data from: River network architecture, genetic effective size and distributional patterns predict differences in genetic structure across species in a dryland stream fish community

Tyler J. Pilger, Keith B. Gido, David L. Propst, James E. Whitney & Thomas F. Turner
Dendritic ecological network (DEN) architecture can be a strong predictor of spatial genetic patterns in theoretical and simulation studies. Yet, interspecific differences in dispersal capabilities and distribution within the network may equally affect species’ genetic structuring. We characterized patterns of genetic variation from up to ten microsatellite loci for nine numerically dominant members of the upper Gila River fish community, New Mexico, USA. Using comparative landscape genetics, we evaluated the role of network architecture for...

Data from: Using historical biogeography models to study color pattern evolution

Chad Eliason, Michael Andersen & Shannon Hackett
Color is among the most striking features of organisms, varying not only in spectral properties like hue and brightness, but also in where and how it is produced on the body. Different combinations of colors on a bird’s body are important in both environmental and social contexts. Previous comparative studies have treated plumage patches individually or derived plumage complexity scores from color measurements across a bird’s body. However, these approaches do not consider the multivariate...

Data from: Isolation with asymmetric gene flow during the nonsynchronous divergence of dry forest birds

Jessica A. Oswald, Isaac Overcast, , Michael J. Andersen & Brian Tilston Smith
Dry forest bird communities in South America are often fragmented by intervening mountains and rainforests, generating high local endemism. The historical assembly of dry forest communities likely results from dynamic processes linked to numerous population histories among codistributed species. Nevertheless, species may diversify in the same way through time if landscape and environmental features, or species ecologies, similarly structure populations. Here we tested whether six co-distributed taxon pairs that occur in the dry forests of...

Genetic confirmation of a hybrid between two highly divergent cardinalid species: A Rose-breasted Grosbeak (Pheucticus ludovicianus) and a Scarlet Tanager (Piranga olivacea)

David Toews, Tessa Rhinehart, Robert Mulvihill, Spencer Galen, Stephen Gosser, Tom Johnson, Jessie Williamson, Andrew Wood & Steven Latta
Using low-coverage whole-genome sequencing, analysis of vocalizations, and inferences from natural history, we document a first-generation hybrid between a rose-breasted grosbeak (Pheucticus ludovicianus) and a scarlet tanager (Piranga olivacea). These two species occur sympatrically throughout much of eastern North America, although were not previously known to interbreed. Following the field identification of a putative hybrid, we use genetic and bioacoustic data to show that a rose-breasted grosbeak was the maternal parent and a scarlet tanager...

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