38 Works

Ice-age persistence and genetic isolation of the disjunct distribution of larch in Alaska

Joseph Napier, Matias Fernandez, Guillaume De Lafontaine & Feng Sheng Hu
Larix laricina (eastern larch, tamarack) is a transcontinental North American conifer with a prominent disjunction in the Yukon isolating the Alaskan distribution from the rest of its range. We investigate whether in situ persistence during the Last Glacial Maximum (LGM) or long-distance postglacial migration from south of the ice sheets resulted in the modern-day Alaskan distribution. We analyzed variation in three chloroplast DNA regions of 840 trees from a total of 69 populations (24 new...

Pore scale study of water adsorption and subsequent methane transport in clay in the presence of wettability heterogeneity

Rui Xu, Masa Prodanovic & Christopher Landry

F2R polymorphisms and clopidogrel efficacy and safety in patients with minor stroke or TIA: supplemental figures and tables

Yuesong Pan, Runqi Wangqin, Hao Li, Yilong Wang, Xia Meng, S. Claiborne Johnston, Tabassome Simon, Jinxi Lin, Xingquan Zhao, Liping Liu, David Wang & Yongjun Wang
Objective: To investigate the association between protease-activated receptors-1 (PAR-1) gene F2R polymorphisms and efficacy of clopidogrel for minor stroke or transient ischemic attack (TIA). Methods: Three single-nucleotide polymorphisms (CYP2C19*2 [681G>A, rs4244285], CYP2C19*3 [636G>A, rs4986893] and F2R [IVSn-14 A/T, rs168753] were genotyped among 2,924 patients randomized to clopidogrel plus aspirin (n=1461) or aspirin alone (n=1463). The primary efficacy outcome was new stroke (ischemic or hemorrhagic) and the safety outcome was any bleeding. Results: Overall, 859(29.4%) were...

Data for: Landscape scale variation in the hydrologic niche of California coast redwood

Emily J. Francis, Gregory P. Asner, Katharine J. Mach & Christopher B. Field
Topoclimatic diversity within forest landscapes can underlie variation in water availability, which may correspond to patterns in habitat suitability of tree species with differing hydrologic niches. However, the trade-off between the collection of data at a fine grain size over large spatial extents has limited comprehensive analyses of landscape scale variation in habitat suitability. We present a fine scale analysis of the roles of topographic gradients in moisture availability, soil water storage, and fog frequency...

IS-mediated mutations both promote and constrain evolvability during a long-term experiment with bacteria

Jessika Consuegra, Joël Gaffé, Richard E. Lenski, Thomas Hindre, Jeffrey E. Barrick, Olivier Tenaillon & Dominique Schneider
The long-term dynamics of IS elements and their effects on bacteria are poorly understood, including whether they are primarily genomic parasites or important drivers of adaptation by natural selection. Here, we investigate the dynamics of IS elements and their contribution to genomic evolution and fitness during a long-term experiment with Escherichia coli. This data set includes the Rmd file to analyze the genomic and metagenomic data (Tenaillon et al. 2016 and Good et al. 2017)...

Combined-evidence analyses of ultraconserved elements and morphological data: an empirical example in iguanian lizards

Simon Scarpetta
Genomic datasets generated by next-generation sequencing are increasingly prevalent in phylogenetics, but morphological data are required to phylogenetically place fossils, corroborate molecular hypotheses, and date phylogenies. Combined-evidence analyses provide an integrative assessment of tree topology. However, no attempt has been made to simultaneously analyze next-generation genomic datasets and morphological data, and the future of morphology in the context of genomic data is uncertain. I conducted combined-evidence analyses that include genomic and morphological datasets, specifically, with...

Reversible diffusion-weighted imaging lesions in acute ischemic stroke: a systematic review

Nandakumar Nagaraja, John Forder, Steven Warach & Jośe Merino
Supplemental data: NNagaraja_12292019_DWI_Reversal_In_AIS_Review_Supplemental_File Supplemental Figure e-1: DWI reversal in acute ischemic stroke Supplemental Table e-1: Search Strategy Supplemental Table e-2: Variables extracted for the review Supplemental Table e-3: Imaging protocols for included studies Supplemental Table e-4: DWIR definitions used in the selected studies Supplemental Table e-5: Imaging characteristics of patients Supplemental Table e-6: QUADAS-2 tool for quality assessment of diagnostic accuracy studies by evaluating risk of bias and applicability concerns.

Cassowary gloss and a novel form of structural color in birds

Chad Eliason & Julia Clarke
One of the two lineages of extant birds resulting from its deepest split, Palaeognathae, has been reported not to exhibit structural coloration in feathers, affecting inferences of ancestral coloration mechanisms in extant birds. Structural coloration in facial skin and eggshells have been shown in the lineage, but not feathers. Here, we report the first evidence for two distinct mechanisms of structural color in palaeognath feathers. One extinct volant clade, Lithornithidae, shows evidence of elongate melanin-containing...

Data from: A new dissorophoid temnospondyl from the Allegheny Group (Late Westphalian, Carboniferous) of Five Points, Mahoning County, Ohio (USA)

Rainer Schoch, Amy Henrici & Robert Hook
A small temnospondyl skull from the Upper Carboniferous Allegheny Group of Five Points, Ohio, is referred to a new dissorophoid, Palodromeus bairdi n. gen n. sp. The complete skull with mandibles is preserved in counterparts. It is characterized by (1) elongated slit-like choana, (2) postfrontal, postorbital, and supratemporal bearing a distinct ridge, and (3) reduced parietal only two-thirds the length of the frontal. Phylogenetic analysis confirms a dichotomy between amphibamiforms and olsoniforms and places Palodromeus...

Switchgrass v5 4-way (AP13 x DAC, WBC x VS16) genetic map

John Lovell, Adam Healey, Jeremy Schmutz & Thomas Juenger
Here we present the genetic map construction methods for the switchgrass 4-way mapping population. The map spans 750 recombinant 4-way (pseudo F2) progeny genotyped at 4700 markers. These data are formatted for simple input into R/qtl and most other QTL mapping programs.

Reversible Diffusion Weighted Imaging Lesion in Acute Ischemic Stroke – A Systematic Review

Nandakumar Nagaraja, John Forder, Steven Warach & Jośe Merino
Supplemental data: NNagaraja_12292019_DWI_Reversal_In_AIS_Review_Supplemental_File Supplemental Figure e-1: DWI reversal in acute ischemic stroke Supplemental Table e-1: Search Strategy Supplemental Table e-2: Variables extracted for the review Supplemental Table e-3: Imaging protocols for included studies Supplemental Table e-4: DWIR definitions used in the selected studies Supplemental Table e-5: Imaging characteristics of patients Supplemental Table e-6: QUADAS-2 tool for quality assessment of diagnostic accuracy studies by evaluating risk of bias and applicability concerns.

Data from: Recurrent circuit dynamics underlie persistent activity in the macaque frontoparietal network

Eric Hart & Alexander Huk
During delayed oculomotor response tasks, neurons in the lateral intraparietal area (LIP) and the frontal eye fields (FEF) exhibit persistent activity that reflects the active maintenance of behaviorally relevant information. Despite many computational models of the mechanisms of persistent activity, there is a lack of circuit-level data from the primate to inform the theories. To fill this gap, we simultaneously recorded ensembles of neurons in both LIP and FEF while macaques performed a memory-guided saccade...

Groundwater recharge in Africa from ground based measurements

Alan MacDonald, Murray Lark, Richard Taylor, Tamiru Abiye, Helen Fallas, Guillaume Favreau, Ibrahim Goni, Seifu Kebede, Bridget Scanlon, James Sorenson, Moshood Tijani, Kirsty Upton & Charles West
This dataset comprises a map of groundwater recharge for Africa and a database of the 134 observations used to generate the map. The map shows long term average annual groundwater recharge in mm per annum relevant to the period 1970 to 2020. It is in the form of a GIS shapefile and is available as a layer package for ESRI and also as a georeferenced TIFF and BIL file for easy exchange with other software....

Historical biogeography of Vochysiaceae reveals an unexpected perspective of plant evolution in the Neotropics

Deise Josely Pereira Goncalves, Gustavo H. Shimizu, Edgardo M. Ortiz, Robert K. Jansen & Beryl B. Simpson
PREMISE OF THE STUDY: Despite the fast pace of exploration of the patterns and processes influencing Neotropical plant hyperdiversity, taxa explored are mostly from large groups that are widely distributed, morphologically diverse or economically important. Vochysiaceae is an example of an undersampled taxon, providing an excellent system for investigating Neotropical biogeography. We present a phylogenomic-based hypothesis of species relationships in Vochysiaceae to investigate its evolutionary history through space and time. METHODS: We inferred a phylogeny...

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...

Dataset for the transcriptome analysis of hippocampal subfields identifies gene expression profiles associated with long-term active place avoidance memory

Rayna Harris, Hsin-Yi Kao, Juan Marcos Alarcon, André Fenton & Hans Hofmann
The hippocampus plays a critical role in storing and retrieving spatial information. By targeting the dorsal hippocampus and manipulating specific “candidate” molecules using pharmacological and genetic manipulations, we have previously discovered that long-term active place avoidance memory requires transient activation of particular molecules in dorsal hippocampus. These molecules include amongst others, the persistent kinases Ca-calmodulin kinase II (CaMKII) and the atypical protein kinase C isoform PKC iota/lambda for acquisition of the conditioned behavior, whereas persistent...

7,000 years of turnover: historical contingency and human niche construction shape the Caribbean’s Anthropocene biota

Melissa Kemp, Alexis Mychajliw, Jenna Wadman & Amy Goldberg
The human-mediated movement of species across biogeographic boundaries—whether intentional or accidental—is dramatically reshaping the modern world. Conservation biologists are grappling with the present-day effects of these introductions, but humans have in fact been reshaping ecosystems and translocating species for millennia. Acknowledging the effects of human-mediated species introductions through time is important for understanding present-day biodiversity loss, ecosystem functioning, and management needs. Here, we present the first database of terrestrial vertebrate species introductions spanning the entire...

No evidence for neonicotinoid preferences in the bumblebee Bombus impatiens

Felicity Muth
Neonicotinoid pesticides can have a multitude of negative sub-lethal effects on bees. Understanding their impact on wild populations requires accurately estimating the dosages bees encounter under natural conditions. This is complicated by the possibility that bees might influence their own exposure: two recent studies found that bumblebees (Bombus terrestris) preferentially consumed neonicotinoid-contaminated nectar, even though these chemicals are thought to be tasteless and odourless. Here we used Bombus impatiens to explore two elements of these...

Data from: Evaluating Sphagnum traits in the context of resource economics and optimal partitioning theories

Tobi Oke & Merritt R. Turetsky
Trade-offs between key aspects of plant performance such as resource acquisition and allocation underpin several trait-based theories that have been derived for vascular plants. However, due to difficulty in quantifying traits in nonvascular plants, our theoretical understanding of how traits govern the physiological and ecological preferences of nonvascular plant species is quite limited. Here, we used the resource economics theory (RET) and optimal partitioning theory (OPT) to evaluate functional traits in mosses. We evaluated aspects...

Data from: Plant biomass, not plant economics traits, determines responses of soil CO2 efflux to precipitation in the C4 grass Panicum virgatum

Robert Heckman, Albina Khasanova, Nicholas Johnson, Sören Weber, Jason Bonnette, Mike Aspinwall, Lara Reichman, Thomas Juenger, Philip Fay & Christine Hawkes
1. Plant responses to major environmental drivers like precipitation can influence important aspects of carbon (C) cycling like soil CO2 efflux (JCO2). These responses may be predicted by two independent classes of drivers: plant size—larger plants respire more and produce a larger quantity of labile C, and plant economics—plants possessing more acquisitive plant economics strategies (i.e., high metabolic rate and tissue nutrient content) produce higher-quality tissue that respires rapidly and decomposes quickly. 2. At two...

Microhabitat contributes to microgeographic divergence in threespine stickleback

Meghan Maciejewski, Cynthia Jiang, Yoel Stuart & Daniel Bolnick
Since the New Synthesis, most migration-selection balance theory predicted that there should be negligible differentiation over small spatial scales (relative to dispersal), because gene flow should erode any effect of divergent selection. Nevertheless, there are classic examples of microgeographic divergence, which theory suggests can arise under specific conditions: exceptionally strong selection, phenotypic plasticity in philopatric individuals, or non-random dispersal. Here, we present evidence of microgeographic morphological variation within lake and stream populations of threespine stickleback...

Data from: Emigrating together but not establishing together: A cockroach rides ants and leaves

Zachary I. Phillips
Symbionts of ant colonies can hitchhike on winged ant reproductives (alates) during colony nuptial flights. Attaphila fungicola Wheeler, a miniature cockroach that lives in the nests of Texas leaf-cutter ants (Atta texana Buckley), hitchhikes on female alates (winged queens). Hitchhiking roaches are presumably vertically transmitted from leaf-cutter parent colony to daughter colony, remaining with female alates as they transition into foundresses (workerless queens); however, foundresses have limited resources and high mortality rates. Rather than remaining...

Do novel insecticides pose a threat to beneficial insects?

Harry Siviter & Felicity Muth
Systemic insecticides, such as neonicotinoids, are a major contributor towards beneficial insect declines. This has led to bans and restrictions on neonicotinoid use globally, most noticeably in the Europe Union, where four commonly-used neonicotinoids are banned from outside agricultural use. While this might seem like a victory for conservation, restrictions on neonicotinoid use will only benefit insect populations if newly emerging insecticides do not have similar negative impacts on beneficial insects. Flupyradifurone and sulfoxaflor are...

Fractures with variable roughness and wettability

Eric Guiltinan, Javier Estrada Santos, Qinjun Kang, Bayani Cardenas & D. Nicolas Espinoza

Data from: Chemical novelty facilitates herbivore resistance and biological invasions in some introduced plant species

Brian Sedio, John Devaney, Jamie Pullen, Geoffrey Parker, S. Joseph Wright & John Parker
Ecological release from herbivory due to chemical novelty is commonly predicted to facilitate biological invasions by plants, but has not been tested on a community scale. We used metabolomics based on mass spectrometry molecular networks to assess the novelty of foliar secondary chemistry of 15 invasive plant species compared to 46 native species at a site in eastern North America. Locally, invasive species were more chemically distinctive than natives. Among the 15 invasive species, the...

Registration Year

  • 2020

Resource Types

  • Dataset


  • The University of Texas at Austin
  • Stanford University
  • Texas A&M University
  • Georgetown University
  • Agricultural Research Service
  • University of Florida
  • University of Illinois at Urbana Champaign
  • Université du Québec à Rimouski
  • HudsonAlpha Institute for Biotechnology
  • North Carolina State University