41 Works

Comparison of environmental inference approaches for ecometric analyses: Using hypsodonty to estimate precipitation

Rachel A. Short, Katherine Pinson & A. Michelle Lawing
Ecometrics is the study of community-level functional trait-environment relationships. We use ecometric analyses to estimate paleoenvironment and to investigate community-level functional changes through time. We evaluate four methods that have been used or have the potential to be used in ecometric analyses for estimating paleoenvironment to determine whether there have been systematic differences in paleoenvironmental estimation due to choice of the estimation method. Specifically, we evaluated linear regression, polynomial regression, nearest neighbor, and maximum likelihood...

Data from: Co-occurrence of bobcats, coyotes, and ocelots in Texas

Jason Lombardi, Darryl MacKenzie, Michael Tewes, Humberto Perotto, Jose Mata & Tyler Campbell
Interspecific competition among carnivores has been linked to differences in behavior, morphology, and resource use. Insights into these interactions can enhance understanding of local ecological processes that can have impacts on the recovery of endangered species, such as the ocelot (Leopardus pardalis). Ocelots, bobcats (Lynx rufus), and coyotes (Canis latrans) share a small geographic range overlap from South Texas to south-central Mexico but relationships among the three are poorly understood. From May 2011 to March...

Data from: Decadal heat and drought drive body size of North American bison (Bison bison) along the Great Plains

Jeff Martin & Perry S. Barboza
Large grazers are visible and valuable indicators of the effects of projected changes in temperature and drought on grasslands. The grasslands of the Great Plains has supported the greatest number of bison (Bison bison; Linnaeus, 1758) since prehistoric times. We tested the hypothesis that body mass (BM; kg) and asymptotic body mass (ABM; kg) of Bison decline with rising temperature and increasing drought over both temporal and spatial scales along the Great Plains. Temporally, we...

Adaptive associations among life history, reproductive traits, environment, and origin in the Wisconsin angiosperm flora

Ricardo Kriebel, Thomas Givnish, John Zaborsky, Jeffrey Rose, Daniel Spalink, Donald Waller, Kenneth Cameron & Kenneth Sytsma
PREMISE OF THE STUDY: We tested 25 classic and novel hypotheses regarding trait-origin, trait-trait, and trait-environment relationships to account for flora-wide variation in life history, habit, and especially reproductive traits using a plastid DNA phylogeny of most native (96.6%, or 1494/1547 species) and introduced (87.5%, or 690/789 species) angiosperms in Wisconsin, USA. METHODS: We assembled data on life history, habit, flowering, dispersal, mating system, and occurrence across open/closed/mixed habitats across species in the state phylogeny....

Lineage-specific patterns of chromosome evolution are the rule not the exception in Polyneoptera insects

Terrence Sylvester, Carl Hjelmen, Shawn Hanrahan, Paul Lenhart, Spencer Johnston & Heath Blackmon
The structure of a genome can be described at its simplest by the number of chromosomes and the sex chromosome system it contains. Despite over a century of study, the evolution of genome structure on this scale remains recalcitrant to broad generalisations that can be applied across clades. To address this issue, we have assembled a dataset of 823 karyotypes from the insect group Polyneoptera. This group contains orders with a range of variations in...

Identification and characterization of QTLs for fruit quality traits in peach through a multi-family approach

Zena Rawandoozi, Timothy P. Hartmann, Silvia Carpenedo, Ksenija Gasic, Cassia Da Silva Linge, Lichun Cai, Eric Van De Weg & David H. Byrne
Background Fruit quality traits have a significant effect on consumer acceptance and subsequently on peach (Prunus persica (L.) Batsch) consumption. Determining the genetic bases of key fruit quality traits is essential for the industry to improve fruit quality and increase consumption. Pedigree-based analysis across multiple peach pedigrees can identify the genomic basis of complex traits for direct implementation in marker-assisted selection. This strategy provides breeders with better-informed decisions and improves selection efficiency and, subsequently, saves...

An updated life history scheme for marine fishes predicts recruitment variability and sensitivity to exploitation

Colleen Petrik, Fernando González Taboada, Charles Stock & Jorge Sarmiento
Aim: Patterns of population renewal in marine fishes are often irregular and lead to volatile fluctuations in abundance that challenge management and conservation efforts. Here, we examine the relationship between life history strategies and recruitment variability in exploited marine fish species using a macroecological approach. Location: Global ocean. Time period: 1950-2018. Major taxa studied: Bony and cartilaginous fish. Methods: Based on trait data for 244 marine fish species, we objectively extend the established Equilibrium-Periodic-Opportunistic (E-P-O)...

Sun compass neurons are tuned to migratory orientation in monarch butterflies

Tu Anh Thi Nguyen, M. Jerome Beetz, Christine Merlin & Basil El Jundi
Every autumn, monarch butterflies migrate from North America to their overwintering sites in Central Mexico. To maintain their southward direction, these butterflies rely on celestial cues as orientation references. The position of the sun combined with additional skylight cues are integrated in the central complex, a region in the butterfly’s brain that acts as an internal compass. However, the central complex does not solely guide the butterflies on their migration but helps monarchs in their...

Data from: Savannas after afforestation: assessment of herbaceous community responses to wildfire versus native tree planting

Thaís M. Haddad, Ricardo A. G. Viani, Mário G. B. Cava, Giselda Durigan & Joseph V. Veldman
Afforestation and fire exclusion are pervasive threats to tropical savannas. In Brazil, laws limiting prescribed burning hinder the study of fire in the restoration of Cerrado plant communities. We took advantage of a 2017 wildfire to evaluate the potential for tree cutting and fire to promote the passive restoration of savanna herbaceous plant communities after destruction by exotic tree plantations. We sampled a burned pine plantation (Burned Plantation); a former plantation that was harvested and...

Herbivory Improves the Fitness of Predatory Beetles

Todd Ugine, Avneet Nagra, Robert Grebenok, Spencer Behmer & John Losey
While many predatory arthropods consume non-prey foods from lower trophic levels, little is known about what drives the shift from predator to omnivore. Predatory lady beetles often consume non-prey foods like plant foliage and pollen. One species, Coccinella septempunctata, eats foliage to redress sterol deficits caused by eating sterol-deficient prey. Here we explore how omnivory benefits lady beetle fitness. We reared seven species of lady beetles – from five genera distributed across the tribe Coccinellini...

Data from: Thoracic underreplication in Drosophila species estimates a minimum genome size and the dynamics of added DNA

Carl E. Hjelmen, V. Renee Holmes, Crystal G. Burrus, Elizabeth Piron, Melissa Mynes, Margaret A. Garrett, Heath Blackmon & J. Spencer Johnston
Many cells in the thorax of Drosophila were found to stall during replication, a phenomenon known as underreplication. Unlike underreplication in nuclei of salivary and follicle cells, this stall occurs with less than one complete round of replication. This stall point allows precise estimations of early-replicating euchromatin and late-replicating heterochromatin regions, providing a powerful tool to investigate the dynamics of structural change across the genome. We measure underreplication in 132 species across the Drosophila genus...

Genome-wide association mapping to identify genetic loci for cold tolerance and cold recovery during germination in rice

Michael Thomson, Ranjita Thapa & Endang Septiningsih
To investigate the genetic architecture underlying cold tolerance during germination in rice (Oryza sativa), we conducted a genome-wide association study (GWAS) using a novel diversity panel of 257 rice accessions from around the world and 5,185 SNP markers from a 7K SNP marker array. Genotyping was performed using a 7K Illumina iSelect custom-designed array by following the Infinium HD Array Ultra Protocol. The 7K array, called the C7AIR, was designed by Dr. Susan McCouch’s Lab...

Data from: Widespread variation in stable isotope trophic position estimates: patterns, causes, and potential consequences

Mackenzie Kjeldgaard, Jeremy Hewlett & Micky Eubanks
Stable isotope analysis is one of the most widely used techniques to estimate trophic position and provides fundamental insight into the structure and management of ecological communities. To account for the effects of geographic variation in isotope levels, trophic position is typically estimated relative to an isotope “baseline” (i.e., material representing geographic variation) using a methodology such as a formula or statistical analysis. There is, however, remarkable variation in the baselines and methodologies used to...

Data from: Optimising sample sizes for animal distribution analysis using tracking data

Takahiro Shimada, Michele Thums, Mark Hamann, Colin Limpus, Graeme Hays, Nancy FitzSimmons, Natalie Wildermann, Carlos Duarte & Mark Meekan
1. Knowledge of the spatial distribution of populations is fundamental to management plans for any species. When tracking data are used to describe distributions, it is sometimes assumed that the reported locations of individuals delineate the spatial extent of areas used by the target population. 2. Here, we examine existing approaches to validate this assumption, highlight caveats, and propose a new method for a more informative assessment of the number of tracked animals (i.e. sample...

C. rufifacies heat stress data

Travis Rusch
The increased severity and frequency of elevated temperatures due to climate change is changing species distributions and driving thermal selection for several species, but many potential effects are still unknown. Here, we investigated the effects of an acute thermal stress on the oviposition performance of the hairy maggot blow fly Chrysomya rufifacies (Macquart), an introduced species of ecological, economic, and forensic importance. Adult virgins were exposed to 25°C, 42°C, or 44°C for 1-h, and then...

Data from: Disparate patterns of movements and visits to points of interest located in urban hotspots across U.S. metropolitan cities during COVID-19

Qingchun Li
We examined the effect of social distancing on changes in visits to urban hotspot points of interest. In a pandemic situation, urban hotspots could be potential superspreader areas as visits to urban hotspots can increase the risk of contact and transmission of a disease among a population. We mapped origin-destination networks from census block groups to points of interest (POIs), such as restaurants, museums, and schools, in sixteen cities in the United States. We adopted...

Raw in vitro screening data and R scripts for: A Bayesian method for population-wide cardiotoxicity hazard and risk characterization using an in vitro human model

Alexander Blanchette, Sarah Burnett, Fabian Grimm, Ivan Rusyn & Weihsueh Chiu
Human induced pluripotent stem cell (iPSC)-derived cardiomyocytes are an established model for testing potential chemical hazards. Inter-individual variability in toxicodynamic sensitivity has also been demonstrated in vitro; however, quantitative characterization of the population-wide variability has not been fully explored. We sought to develop a method to address this gap by combining a population-based iPSC-derived cardiomyocyte model with Bayesian concentration-response modeling. A total of 136 compounds, including 44 pharmaceuticals and 82 environmental chemicals, were tested in...

Dityrosine formation via reactive oxygen consumption yields increasingly recalcitrant humic-like fluorescent organic matter in the ocean

Ryan Paerl, Iliana Claudio, Michael Shields, Thomas Bianchi & Christopher Osburn
Marine dissolved organic matter (DOM) is a massive elemental pool on Earth and is thought to consist of a chemically complex mixture of molecules. Part of marine DOM is fluorescent (FDOM) and includes humic-like compounds. The chemical composition of, and biochemical pathways that yield, autochthonous humic-like FDOM in the ocean is largely unknown. Inspired by medical and biochemical research detailing the formation of colored and fluorescent dityrosine via peroxidase mediated reactions, we used fluorometry and...

Maps of northern peatland extent, depth, carbon storage and nitrogen storage

Gustaf Hugelius, Julie Loisel, Sarah Chadburn, Robert B. Jackson, Miriam Jones, Glen MacDonald, Maija Marushchak, David Olefeldt, Maara Packalen, Matthias B. Siewert, Claire Treat, Merritt Turestsky, Carolina Voigt & Zicheng Yu
This dataset is grids of peatland extent, peat depth, peatland organic carbon storage, peatland total nitrogen storage and approximate extent of ombrotrophic/minerotrophic peatlands. The grids are geotiff files in 10 km pixel resolution projected in the World Azimuthal Equidistant projection. Note that the peat depth grid shows potential peat depth everywhere,also where there is no peatland cover. For files on peatland organic carbon, total nitrogen extent and extent of ombrotrophic/minerotrophic peatlands, there are separate files...

QTL × environment interactions underlie adaptive divergence in switchgrass across a large latitudinal gradient

David Lowry, John Lovell, Li Zhang, Jason Bonnette, Philip Fay, Robert Mitchell, John Lloyd-Reilley, Arvid Boe, Yanqi Wu, Francis Rouquette, Richard Wynia, Xiaoyu Weng, Kathrine Behrman, Adam Healey, Kerrie Barry, Anna Lipzen, Diane Bauer, Aditi Sharma, Jerry Jenkins, Jeremy Schmutz, Felix B. Fritschi & Thomas E. Juenger
Local adaptation is the process by which natural selection drives adaptive phenotypic divergence across environmental gradients. Theory suggests that local adaptation results from genetic trade-offs at individual genetic loci, where adaptation to one set of environmental conditions results in a cost to fitness in alternative environments. However, the degree to which there are costs associated with local adaptation is poorly understood because most of these experiments rely on two-site reciprocal transplant experiments. Here, we quantify...

Microsatellite genotypes

Lauren Chan, Charlie Painter, Michael Hill, Toby Hibbitts, Daniel Leavitt, Wade Ryberg, Danielle Walkup & Lee Fitzgerald
Phylogeographic divergence and population genetic diversity within species reflect the impacts of habitat connectivity, demographics, and landscape level processes in both the recent and distant past. Characterizing patterns of differentiation across the geographic range of a species provides insight on the roles of organismal and environmental traits, on evolutionary divergence, and future population persistence. This is particularly true of habitat specialists where habitat availability and resource dependence may result in pronounced genetic structure as well...

Under the radar: genetic assessment of Rio Grande Shiner (Notropis jemezanus) and Speckled Chub (Macrhybopsis aestivalis), two Rio Grande basin endemic cyprinids that have experienced recent range contractions

Megan Osborne, David Portnoy, Andrew Fields, Kevin Conway, Megan Bean & Christopher Hoagstrom
The Rio Grande drainage of the southwestern United States and Mexico has undergone intense anthropogenic alteration by water diversions, extraction and associated habitat changes. These alterations have disproportionately impacted the pelagic broadcast spawning guild of minnows (pelagophils). Several Rio Grande endemic pelagophils, including the co-occurring Rio Grande Shiner (Notropis jemezanus) and Speckled Chub (Macrhybopsis aestivalis), have experienced dramatic recent range-wide declines yet have slipped under the radar of conservation efforts. The status of N. jemezanus...

Data From: TERRA-REF, An open reference data set from high resolution genomics, phenomics, and imaging sensors

David LeBauer, Burnette Maxwell, Jeffrey Demieville, Noah Fahlgren, Andrew French, Roman Garnett, Zhenbin Hu, Kimberly Huynh, Rob Kooper, Zongyang Li, Maitiniyazi Maimaitijiang, Jerome Mao, Todd Mockler, Geoffrey Morris, Maria Newcomb, Michael Ottman, Philip Ozersky, Sidike Paheding, Duke Pauli, Robert Pless, Wei Qin, Kristina Riemer, Gareth Rohde, William Rooney, Vasit Sagan … & Charles Zender
The ARPA-E funded TERRA-REF project is generating open-access reference datasets for the study of plant sensing, genomics, and phenomics. Sensor data were generated by a field scanner sensing platform that captures color, thermal, hyperspectral, and active flourescence imagery as well as three dimensional structure and associated environmental measurements. This dataset is provided alongside data collected using traditional field methods in order to support calibration and validation of algorithms used to extract plot level phenotypes from...

Data from: The upper thermal tolerance for a Texas population of the hairy maggot blow fly Chrysomya rufifacies Macquart (Diptera: Calliphoridae)

Travis Rusch, Ashleigh Faris, Lauren Beebe, Jeffery Tomberlin & Aaron Tarone
The hairy maggot blow fly (Chrysomya rufifacies: Macquart) is an invasive necrophagous fly found throughout the continental United States. Chrysomya rufifacies is of medical/veterinary, forensic, and ecological importance due to its ability to cause myiasis, colonize human remains, and displace native Diptera. However, little is known about their upper thermal tolerance, which could be used to better predict their invasion potential. We investigated the upper thermal tolerance of C. rufifacies exposed to different temperatures (20...

Data from: Can ancestry and morphology be used as surrogates for species niche relationships?

Friedrich Keppeler & Kirk Winemiller
Species interactions are difficult to quantify, and, consequently, many studies have used species traits and phylogeny as proxies under an assumption of niche conservatism (i.e., closely related and morphologically similar species should have similar niches). However, few studies have investigated whether niches actually are conserved within and across diverse communities. Here, we tested the degree to which phylogenetic relatedness and morphological similarity predict diets and stable isotopic ratios (δ15N and δ13C), two common descriptors of...

Registration Year

  • 2020

Resource Types

  • Dataset


  • Texas A&M University
  • Wageningen University & Research
  • Cornell University
  • The University of Texas at Austin
  • University of Florida
  • Case Western Reserve University
  • Donald Danforth Plant Science Center
  • Texas A&M University System
  • Institute of Arctic and Alpine Research
  • Stanford University