24 Works

Data for: PickMe: sample selection for species tree reconstruction using coalescent weighted quartets

Joseph Rusinko, Yu Cai, Allison Doherty, Katherine Thompson, Julien Boutte, Mark Fishbein & Shannon Straub
After collecting large data sets of many genes for many species for phylogenomics studies, researchers may make ad hoc decisions about which genes or samples to include in a species tree reconstruction analysis based on various parameters, including the amount of missing data. Optimally, sampling would be maximized, but it can be difficult for empiricists to determine where to draw the line for sample inclusion when data sets are incomplete. Under the multispecies coalescent model,...

Visceral organ growth in pigs from birth through 150 kg bodyweight

Merlin Lindemann
Visceral organs (VO) are essential for their role in the metabolism and distribution of consumed nutrients as well as other life functions in animals. Two experiments were conducted to assess the natural longitudinal changes that the VO undergo from birth through 150 kg body weight (BW). Results showed that both absolute and relative measurements (weight, volume, and length) of VO were dependent on the BW (age) of the pig.

The impact of life stage and pigment source on the evolution of novel warning signal traits

Carita Lindstedt, Robin Bagley, Sarah Calhim, Mackenzie Jones & Catherine Linnen
Our understanding of how novel warning color traits evolve in natural populations is largely based on studies of reproductive stages and organisms with endogenously produced pigmentation. In these systems, genetic drift is often required for novel alleles to overcome strong purifying selection stemming from frequency-dependent predation and positive assortative mating. Here, we integrate data from field surveys, predation experiments, population genomics, and phenotypic correlations to explain the origin and maintenance of geographic variation in a...

The unfolded protein response regulates hepatic autophagy by sXBP1-mediated activation of TFEB

Zeyuan Zhang, Qingwen Qian, Mark Li, Fan Shao, Wen-Xing Ding, Vitor A. Lira, Sophia X. Chen, Sara C. Sebag, Gökhan S. Hotamisligil, Huojun Cao & Ling Yang
Defective macroautophagy/autophagy and a failure to initiate the adaptive unfolded protein response (UPR) in response to the endoplasmic reticulum (ER) stress contributes to obesity-associated metabolic dysfunction. However, whether and how unresolved ER stress leads to defects in the autophagy pathway and to the progression of obesity-associated hepatic pathologies remains unclear. Obesity suppresses the expression of hepatic spliced XBP1 (X-box binding protein 1; sXBP1), the key transcription factor that promotes the adaptive UPR. Our RNA-seq analysis...

Deepest Observed Fresh Groundwater Contour Lines for the Cumberland Plateau of Eastern Kentucky

Ethan Davis, Thomas Parris & Jerrad Grider
These contour lines detail the estimated depth of the base of fresh groundwater—i.e., deepest observed fresh water. These contours were created using the deepest domestic water well depths in each 11-digit HUC watershed of a 14-county study area in the Cumberland Plateau of eastern Kentucky.

A shift to shorter cuticular hydrocarbons accompanies sexual isolation among Drosophila americana group populations

Jeremy S Davis, Matthew Pearcy, Joanne Yew & Leonie Moyle
Because sensory signals often evolve rapidly, they could be instrumental in the emergence of reproductive isolation between species. However, pinpointing their specific contribution to isolating barriers, and the mechanisms underlying their divergence, remains challenging. Here we demonstrate sexual isolation due to divergence in chemical signals between two populations of Drosophila americana (SC and NE) and one population of D. novamexicana, and dissect its underlying phenotypic and genetic mechanisms. Mating trials revealed strong sexual isolation between...

Do tradeoffs govern plant species responses to different global change treatments?

J. Adam Langley, Emily Grman, Kevin Wilcox, Meghan Avolio, Kimberly Komatsu, Scott Collins, Sally Koerner, Melinda Smith, Andrew Baldwin, William Bowman, Nona Chiariello, Anu Eskelinen, Harry Harmens, Mark Hovenden, Kari Klanderud, Rebecca McCulley, Vladimir Onipchenko, Clare Robinson & Katharine Suding
Plants are subject to tradeoffs among growth strategies such that adaptations for optimal growth in one condition can preclude optimal growth in another. Thus, we hypothesized that the response of plant species abundance to one global change treatment would relate inversely to the response to a second treatment, particularly for treatment combinations that accentuate distinct traits. To address this hypothesis, we examined plant species abundances in 39 global change experiments manipulating CO2, nitrogen, phosphorus, water,...

Elastic Thickness and Crust-Mantle Interface Models of Tharsis Bulge on Mars and Surrounding Areas

Ratheesh Kumar R.T, Dhananjay Ravat & Paul morgan
The datasets contain the final models of spatial variation of elastic thickness (Te) and the depth to Moho or the Crust-Mantle Interface (CMI) of the Tharsis Bulge and the surrounding regions derived from the software package LithoFLEX. The models are based on the crustal density of 2900 kg/m3, which was selected from analyzing results of a range of densities, and other standard lithospheric parameters. The models are useful for understanding the nature and evolution of...

Intraspecific genetic variation in Dendroctonus alters efficacy of molecular approaches to population suppression

Bethany Kyre & Lynne Rieske
Genetic variability among geographically distinct populations of widely distributed insect species is commonplace and, in the case of southern pine beetle (SPB), Dendroctonus frontalis, has been well documented. This genetic variability could have consequences for beetle susceptibility to an emerging molecular approach to population suppression: RNA interference (RNAi). The use of RNAi for gene silencing in forest pest management is in its infancy, but its effectiveness in SPB has been demonstrated. RNAi is a naturally...

Which peer reviewers voluntarily reveal their identity to authors? Insights into the consequences of open-identities peer review

Charles Fox
Identifying reviewers is argued to improve quality and fairness of peer review, but is generally disfavored by reviewers. To gain some insight into the factors that influence when reviewers are willing to have their identity revealed, I examine which reviewers voluntarily reveal their identities to authors at the journal Functional Ecology, at which reviewer identities are confidential unless reviewers sign their comments to authors. 5.6% of reviewers signed their comments to authors. This proportion increased...

GeoDatabase and Modeling Code used for Landslide Hazard and Susceptibility Mapping in Eastern and Northern Kentucky

Lindsey Bryson, batmyagmar dashbold & Matt Crawford
We created a landslide susceptibility map using spatial soil property features extracted from the NRCS WSS that include percent sand, percent silt, percent clay, saturated hydraulic conductivity, available water capacity, one third bar water content, plasticity index, and liquid limit, all of which were used as features in the logistic regression analysis. We also used satellite soil moisture data, and a high-resolution (1.5 m) LiDAR-derived digital elevation map (DEM) which include slope, aspect, curvature, elevation,...

Multi-Temporal UAV Images and GeoDatabase Used to Estimate Temporal and Spatial Soil Moisture Content

Lindsey Bryson & batmyagmar dashbold
We used small unmanned aerial vehicle (UAV) with optical digital camera to detect a land movement and to extract soil parameters. Using multi-temporal images in Garrard County, Kentucky, we detected land movement on three pairs of images that were captured one month apart. The multi-temporal images and the result of the movement analysis are available in folders. In addition, vertical displacement analysis is carried out using Differential Interferometry technique (DinSAR) to a pair of Synthetic...

Patterns of recent natural selection on genetic loci associated with sexually differentiated human body size and shape phenotypes

Audrey M. Arner, Kathleen E. Grogan, Mark Grabowski, Hugo Reyes-Centeno & George H. Perry
Levels of sex differences for human body size and shape phenotypes are hypothesized to have adaptively reduced following the agricultural transition as part of an evolutionary response to relatively more equal divisions of labor and new technology adoption. In this study, we tested this hypothesis by studying genetic variants associated with five sexually differentiated human phenotypes: height, body mass, hip circumference, body fat percentage, and waist circumference. We first analyzed genome-wide association (GWAS) results for...

Landslide Soil Hydrology Data for Three Landslides in Kentucky

Matt Crawford & Lindsey Bryson
This data is from three landslides monitored in Kentucky between October 2015 and September 2020. The purpose was to capture and analyze subsurface hydrologic conditions within the landslides at different slope positions over time. The site descriptions, field methodology, data-acquisition techniques, and observations provide a general picture of soil moisture in hillslope soils. Data collected includes volumetric water content, soil water potential, bulk electrical conductivity, bulk dielectric permittivity, temperature. Water potential is the energy state...

Opposing community assembly patterns for dominant and non-dominant plant species in herbaceous ecosystems globally

Carlos Alberto Arnillas, Elizabeth Borer, Eric Seabloom, Juan Alberti, Selene Baez, Jonathon Bakker, Elizabeth Boughton, Yvonne Buckley, Miguel Bugalho, Ian Donohue, John Dwyer, Jennifer Firn, Riley Gridzak, Nicole Hagenah, Yann Hautier, Aveliina Helm, Anke Jentsch, , Kimberly Komatsu, Lauri Laanisto, Ramesh Laungani, Rebecca McCulley, Joslin Moore, John Morgan, Pablo Peri … & Marc Cadotte
Biotic and abiotic factors interact with dominant plants —the locally most frequent or with the largest coverage— and non-dominant plants differently, partially because dominant plants modify the environment where non-dominant plants grow. For instance, if dominant plants compete strongly, they will deplete most resources, forcing non-dominant plants into a narrower niche space. Conversely, if dominant plants are constrained by the environment, they might not exhaust available resources but instead may ameliorate environmental stressors that usually...

Proteomic Analysis of Human Sural Nerve

Craig van Horne , Monica Chau & Jorge Quintero
A proteomic analysis, using mass spectrometry and immunoassays, of the human peripheral nervous system's response to a transection injury. We obtained, from the same participants, the protein levels in freshly cut and degenerating human sural nerve tissue.

Bee Assemblages Data [2021]

Daniel A. Potter & Bernadette M. Mach
Plant characteristics, sample sites, and non-native bee assemblages for a bee survey conducted in 2014-2017 by Bernadette Mach in the Daniel A. Potter lab at the University of Kentucky.

Irreproducibility in searches of scientific literature: a comparative analysis

Gabor Pozsgai, Gabor Lövei, Liette Vasseur, Geoff Gurr, Péter Batáry, Janos Korponai, Nick Littlewood, Jian Liu, Arnold Móra, John Obrycki, Olivia Reynolds, Jenni Stockan, Heather VanVolkenburg, Jie Zhang, Wenwu Zhou & Minsheng You
1. Repeatability is the cornerstone of science and it is particularly important for systematic reviews. However, little is known on how researchers’ choice of database and search platform influence the repeatability of systematic reviews. Here, we aim to unveil how the computer environment and the location where the search was initiated from influence hit results. 2. We present a comparative analysis of time-synchronized searches at different institutional locations in the world, and evaluate the consistency...

Pathotype complexity and genetic characterization of Phytophthora sojae populations in Illinois, Indiana, Kentucky, and Ohio

Linda Hebb, Carl A. Bradley, Santiago Xavier Mideros, Darcy E. P. Telenko, Kiersten Wise & Anne Elizabeth Dorrance
Phytophthora sojae, the causal agent of Phytophthora root and stem rot of soybean, has been managed with single Rps genes since the 1960’s, but has subsequently adapted to many of these resistance genes, rendering them ineffective. The objective of this study was to examine the pathotype and genetic diversity of P. sojae from soil samples across Illinois, Indiana, Kentucky, and Ohio by assessing which Rps gene(s) were still effective and identifying possible population clusters. There...

StateMap 2020-2021

Matthew Massey, Antonia E. Bottoms, Maxwell L., III Hammond & Michele M. McHugh
This dataset characterizes the types and distributions of surficial geologic materials in the Cecilia, Constantine, Howe Valley, and Sonora 7.5-minute quadrangles. The primary goal for this mapping project was to identify and map the spatial distribution and understand the mechanical and chemical properties of surficial geologic materials in a rapidly developing area of Kentucky. This new dataset will have immediate utility to a range of users in local, state, and Federal agencies that are working...

Longer telomeres during early life predict higher lifetime fitness in females but not males

David Westneat & Britt Heidinger
The mechanisms that contribute to variation in lifetime reproductive success are not well understood. One possibility is that telomeres, conserved DNA sequences at chromosome ends that often shorten with age and stress exposures, may reflect differences in vital processes or themselves influence fitness. Telomere length often predicts longevity, but longevity is only one component of fitness and little is known about how longevity and lifetime reproductive success relate to telomere dynamics in wild populations. We...

A trait-based framework for predicting foodborne pathogen risk from wild birds

Olivia Smith, Elissa Olimpi, Nora Navarro-González, Kevin Cornell, Luke Frishkoff, Tobin Northfield, Timothy Bowles, Max Edworthy, Johnna Eilers, Zhen Fu, Karina Garcia, David Gonthier, Matthew Jones, Christina Kennedy, Christopher Latimer, Jeb Owen, Chika Sato, Joseph Taylor, Erin Wilson Rankin, William Snyder & Daniel Karp
Recent foodborne illness outbreaks have heightened pressures on growers to deter wildlife from farms, jeopardizing conservation efforts. However, it remains unclear which species, particularly birds, pose the greatest risk to food safety. Using >11,000 pathogen tests and 1,565 bird surveys covering 139 bird species from across the western U.S.A., we examined the importance of 11 traits in mediating wild bird risk to food safety. We tested whether traits associated with pathogen exposure (e.g., habitat associations,...

Innate immune activation by checkpoint inhibition in patient-derived lung cancer tissues

Andrew Lane, Teresa Fan, Richard Higashi, Huan Song, Saeed Daneshmandi, Angela Mahan, Matthew Purdom, Thomas Pittman, Daheng He & Chi Wang
Although Pembrolizumab-based immunotherapy has significantly improved lung cancer patient survival, many patients show variable efficacy and resistance development. A better understanding of the drug’s action is needed to improve patient outcomes. Functional heterogeneity of the tumor microenvironment (TME) is crucial to modulating drug resistance; understanding of individual patients’ TME that impacts drug response is hampered by lack of appropriate models. Lung organotypic tissue slice cultures (OTC) with patients’ native TME procured from primary and brain-metastasized...

Data from: Evaluating otter reintroduction outcomes using genetic spatial capture-recapture modified for dendritic networks

Sean Murphy & John Cox
River otters (Lontra canadensis) were extirpated from New Mexico by the 1950s. A limited reintroduction occurred during 2008–2010 in which 33 otters sourced from Washington (WA) were translocated to the Upper Rio Grande Basin (URG) of New Mexico. We conducted a noninvasive genetic capture-recapture survey during the winter of 2018 by collecting fecal DNA samples from river otter scats found at latrines in the URG dendritic network of perennial waterways. Our objectives were to: 1)...

Registration Year

  • 2021

Resource Types

  • Dataset


  • University of Kentucky
  • Charles Sturt University
  • Smithsonian Environmental Research Center
  • Helmholtz Centre for Environmental Research
  • National Research Institute for Agriculture, Food and Environment
  • Hobart and William Smith Colleges
  • Zhejiang University
  • University of Washington
  • Stanford University
  • University of Pretoria