41 Works

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...

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: 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...

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...

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...

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...

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...

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...

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....

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...

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...

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...

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...

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...

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)...

Whole genome analysis reveals aneuploidies in early pregnancy loss in the horse

Shilton Charlotte A., Anne Kahler, Brian W. Davis, James R. Crabtree, James Crowhurst, Andrew J. McGladdery, Claire Wathes, Terje Raudsepp & Amanda M. de Mestre

Phylogenomic analysis sheds light on the evolutionary pathways towards acoustic communication in Orthoptera

Hojun Song, Olivier Béthoux, Seunggwan Shin, Alexander Donath, Harald Letsch, Shanlin Liu, Duane D. McKenna, Guanliang Meng, Bernhard Misof, Lars Podsiadlowski, Xin Zhou, Benjamin Wipfler & Sabrina Simon
Acoustic communication is enabled by the evolution of specialised hearing and sound producing organs. In this study, we performed a large-scale macroevolutionary study to understand how both hearing and sound production evolved and affected diversification in the insect order Orthoptera, which includes many familiar singing insects, such as crickets, katydids, and grasshoppers. Using phylogenomic data, we firmly establish phylogenetic relationships among the major lineages and divergence time estimates within Orthoptera, as well as the lineage-specific...

Data from: Floral bagging differentially affects handling behaviors and single-visit pollen deposition by honey bees and native bees

Jacob Cecala, Pierre Lau & Joan Leong
Measurements of pollinator performance are crucial to pollination studies, enabling researchers to quantify the relative value of different pollinator species to plant reproduction. One of the most widely employed measures of pollinator performance is single-visit pollen deposition, the number of conspecific pollen grains deposited to a stigma after one pollinator visit. To ensure a pollen-free stigma, experimenters must first bag flowers before exposing them to a pollinator. Bagging flowers, however, may unintentionally manipulate floral characteristics...

Data from: Bee phenology is predicted by climatic variation and functional traits

Michael Stemkovski, Will Pearse, Sean Griffin, Gabriella Pardee, Jason Gibbs, Terry Griswold, John Neff, Ryan Oram, Molly RightMyer, Cory Sheffield, Karen Wright, Brian Inouye, David Inouye & Rebecca Irwin
Climate change is shifting the environmental cues that determine the phenology of interacting species. Plant-pollinator systems may be susceptible to temporal mismatch if bees and flowering plants differ in their phenological responses to warming temperatures. While the cues that trigger flowering are well-understood, little is known about what determines bee phenology. Using Generalized Additive Models, we analyzed time-series data representing 67 bee species collected over nine years in the Colorado Rocky Mountains to perform the...

Data from: Risky roots and careful herbivores: Sustained herbivory by a root-feeding herbivore attenuates indirect plant defences

John Grunseich, Morgan Thompson, Allison Hay, Zachary Gorman, Michael Kolomiets, Micky Eubanks & Anjel Helms
Abstract Aboveground plant tissues produce characteristic blends of volatile compounds in response to insect herbivory. These herbivore-induced plant volatiles (HIPVs) function in plant defence and mediate foraging decisions by herbivores and their natural enemies. The ecological roles of HIPVs as foraging cues for different trophic levels highlight an important conflict for herbivores that need to locate suitable host plants while avoiding competition and predation. Plant roots also emit HIPVs following herbivory, but our understanding of...

Data from: Genotype and male sterility phenotype data for An. coluzzii x An. quadriannulatus backcross

Kevin Deitz, Willem Takken & Michel Slotman
The Anopheles gambiae complex is comprised of eight morphologically indistinguishable species and has emerged as a model system for the study of speciation genetics due to the rapid radiation of its member species over the past two million years. Male hybrids between most An. gambiae complex species pairs are sterile, and some genotype combinations in hybrid males cause inviability. We investigated the genetic basis of hybrid male inviability and sterility between An. coluzzii and An....

Geography of artiodactyl locomotor morphology as an environmental predictor

Rachel Short & A. Michelle Lawing
Aim: We investigate locomotor function in artiodactyls, represented by calcaneal gear ratio, as it relates to multiple environments. Using an ecometrics approach, we develop a trait-environment model to investigate ecosystem level changes through time and to reconstruct past environments. We apply the trait-environment model to a case study of six sites in Kenya to evaluate changes over the past 100 years. Location: Global. Methods: Locomotor morphology was represented by calcaneal gear ratios measured as the...

The evolutionary history of sedges (Cyperaceae) in Madagascar

Isabel Larridon, Daniel Spalink, Pedro Jiménez-Mejías, José Ignacio Márquez-Corro, Santiago Martín-Bravo & Marcial Escudero
Aim: Madagascar is renowned for its unparalleled biodiversity and endemism. With many ecosystems under threat, research is urgently needed on its unique plant diversity. This applies both to Madagascar’s forests and treeless vegetation types. Sedges (Cyperaceae) are among the top ten species-richest angiosperm families in Madagascar (310 native species, 38% endemic), of which two thirds occur in open habitats. We aimed to infer the evolutionary history of sedges in Madagascar, by estimating the number, age...

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