19 Works

Data from: Mechanical feedback and robustness of apical constrictions in Drosophila embryo ventral furrow formation

Michael C. Holcomb, Guo-Jie Jason Gao, Mahsa Servati, Dylan Schneider, Presley K. McNeely, Jeffrey H. Thomas & Jerzy Blawzdziewicz
Formation of the ventral furrow in the Drosophila embryo relies on the apical constriction of cells in the ventral region to produce bending forces that drive tissue invagination. Recently [J Phys Condens Matter. 2016;28(41):414021], we observed that apical constrictions during the initial phase of ventral furrow formation produce elongated patterns of cellular constriction chains prior to invagination, and argued that these are indicative of tensile stress feedback. Here, we quantitatively analyze the constriction patterns preceding...

Supporting data for: Gene-rich UV sex chromosomes harbor conserved regulators of sexual development (Carey et al., 2021)

Sarah Carey, Shenqiang Shu, John Lovell, Avinash Shenqiang, Florian Maumus, George Tiley, Noe Fernandez-Pozo, Kerrie Barry, Cindy Chen, Mei Wang, Anna Lipzen, Chris Daum, Christopher Saski, Adam Payton, Jordan McBreen, Roth Conrad, Leslie Kollar, Sanna Olsson, Sanna Huttunen, Jacob Landis, Norman Wickett, Matthew Johnson, Stefan Rensing, Jane Grimwood, Jeremy Schmutz … & Adam Healey
Non-recombining sex chromosomes, like the mammalian Y, often lose genes and accumulate transposable elements, a process termed degeneration. The correlation between suppressed recombination and degeneration is clear in animal XY systems, but the absence of recombination is confounded with other asymmetries between the X and Y. In contrast, UV sex chromosomes, like those found in bryophytes, experience symmetrical population genetic conditions. Here we generate and use nearly gapless female and male chromosome-scale reference genomes of...

Data related to: Open-system evolution of a crustal-scale magma column, Klamath Mountains, California

Calvin Barnes, Nolwenn Coint, Melanie Barnes, Ariel Strickland, John Cottle, O. Ramo, Kevin Chamberlain & John Valley
Granitic magmas commonly display evidence for some level of interaction with and/or origins from crustal rocks. There is fundamental debate in the community as to the processes that control the origins of these magmas and the potential for their contamination as they pass through the crust. One approach to addressing these issues involves a combination of detailed field mapping combined with geochemical analysis of bulk-rock samples and their constituent minerals. In particular, resolution of debates...

Core genome phylogenetic tree of two Campylobacter novaezeelandiae and four unclassified thermophilic Campylobacter isolates from Canadian agricultural surface water

Mirena Ivanova, Bonnie Oh, Izhar Khan, Kendra Nightingale, Marie Bugarel, Amanda Brown & Guy Loneragan
This dataset includes 1) concatenated alignment of 135 core gene sequences and 2) phylogenomic tree of the 38 currently described Campylobacter spp., including Campylobacter novaezeelandiae and four additional novel Campylobacter species isolated from agricultural water in Canada. The original alignment of 120 kb was produced by Roary v.3.13.0. Gblocks v.0.91b was used to remove ambiguous alignments and phylogenetically uninformative positions. The final alignment (110 kb) was used as input to RAxML-NG v.0.9.0 to infer a...

Phylogenomics in the hard pines (Pinus subsection Ponderosae; Pinaceae) confirms paraphyly in Pinus ponderosa, and places Pinus jeffreyi with the California big cone pines

Ann Willyard, David S. Gernandt, Blake Cooper, Connor Douglas, Kristen Finch, Hassan Karemera, Erik Lindberg, Stephen K. Langer, Julia Lefler, Paula Marquardt, Dakota Pouncey & Frank Telewski
We sampled 130 individuals (2 to 25 per taxon) of subsections Ponderosae and Sabinianae. Nucleotide sequences were obtained by targeting 703 low copy nuclear genes. From the unenriched portion of the short reads, we assembled nearly complete plastome nucleotide sequences. We used 600 nuclear genes and the plastome sequences to create phylogenies and species trees that we compared to evaluate cytonuclear concordance and reticulation. We found that Pinus jeffreyi belongs with subsect. Sabinianae based on...

Data for: Reflections of Grinnellian and Eltonian niches on the distribution of phyllostomid bats in Atlantic Forest of South America

Richard Stevens
Abstract Aim: Ecological niches are complex and the product of interactions with biotic and abiotic environments across the entire geographic range of species. One recent distinction is between Grinnellian niche characteristics that reflect influences at large spatial scales such as climate and Eltonian niche characteristics that reflect influences at the local level such as distribution of resources and how they are shared among species. Aims of this research were to estimate Grinnellian and Eltonian niche...

Are Palmer’s elm-leaf goldenrod and the smooth elm-leaf goldenrod real? The Angiosperms353 kit provides within-species signal in Solidago ulmifolia s.l.

James Beck, Morgan Markley, Mackenzie Zielke, Justin Thomas, Haley Hale, Lindsay Wiliams & Matthew Johnson
Abstract — The genus Solidago represents a taxonomically challenging group due to its sheer number of species, putative hybridization, polyploidy, and shallow genetic divergence among species. Here we use a dataset obtained exclusively from herbarium specimens to evaluate the status of Solidago ulmifolia var. palmeri, a morphologically subtle taxon potentially confined to Alabama, Arkansas, Mississippi, and Missouri. A multivariate analysis of both discrete and continuous morphological data revealed no clear distinction between S. ulmifolia var....

Mammals on mountainsides revisited: trait-based tests of assembly reveal the importance of abiotic filters

Brooks Kohli, Richard Stevens, Eric Rickart & Rebecca Rowe
Aim: Mountains provide uniquely informative systems for examining how biodiversity is distributed and identifying the causes of those patterns. Elevational patterns of species richness are well-documented for many taxa but comparatively few studies have investigated patterns in multiple dimensions of biodiversity along mountainsides, which can reveal the underlying processes at play. Here, we use trait-based diversity patterns to determine the role of abiotic filters and competition in the assembly of communities of small mammals across...

Analytic dataset informing modeling of winter species distributions of North American bat species

Sarah Olson, Meredith McClure, Catherine Haase, Carter Hranac, David Hayman, Brett Dickson, Liam McGuire, Daniel Crowley, Nathan Fuller, Cori Lausen & Raina Plowright
The fungal pathogen Pseudogymnoascus destructans and resultant white-nose syndrome (WNS) continues to advance across North America, infecting new bat populations, species, and hibernacula. Western North America hosts the highest bat diversity in the U.S. and Canada, yet little is known about hibernacula and hibernation behavior in this region. An improved understanding of where bats hibernate and the conditions that create suitable hibernacula is critical if land managers are to anticipate and address the conservation needs...

Data from: Invasion-induced root-fungal disruptions alter plant water and nitrogen economies

Lalasia Bialic-Murphy, Nick Smith, Priya Voothuluru, Robert McElderry, Morgan Roche, Steven Cassidy, Stephanie Kivlin & Susan Kaliz
Despite widespread evidence that biological invasion influences both the biotic and abiotic soil environments, the extent to which these two pathways underpin the effects of invasion on plant traits and performance is unknown. Leveraging a long-term (14-yr) field experiment, we show that an allelochemical-producing invader affects plants through biotic mechanisms, altering the soil fungal community composition, with no apparent shifts in soil nutrient availability. Changes in belowground fungal communities resulted in high costs of nutrient...

A comprehensive phylogenomic platform for exploring the angiosperm tree of life

William Baker, Paul Bailey, Vanessa Barber, Abigail Barker, Sidonie Bellot, David Bishop, Laura Botigue, Grace Brewer, Tom Carruthers, James Clarkson, Jeffrey Cook, Robyn Cowan, Steven Dodsworth, Niroshini Epitawalage, Elaine Françoso, Berta Gallego, Matthew Johnson, Jan Kim, Kevin Leempoel, Olivier Maurin, Catherine McGinnie, Lisa Pokorny, Shyamali Roy, Malcolm Stone, Eduardo Toledo … & Félix Forest
The tree of life is the fundamental biological roadmap for navigating the evolution and properties of life on Earth, and yet remains largely unknown. Even angiosperms (flowering plants) are fraught with data gaps, despite their critical role in sustaining terrestrial life. Today, high-throughput sequencing promises to significantly deepen our understanding of evolutionary relationships. Here, we describe a comprehensive phylogenomic platform for exploring the angiosperm tree of life, comprising a set of open tools and data...

Large‐scale genome sampling reveals unique immunity and metabolic adaptations in bats

Diana Daniela Moreno Santillan, Tanya Lama, Yocelyn T Gutierrez Guerrero, Zixia Huang, Graham Hughes, Alexis Brown, Paul Donat, Huabin Zhao, Stephen Rossiter, Laurel Yohe, Joshua Potter, Emma Teeling, Sonja Vernes, Kalina Davies, Eugene Myers, Federico Hoffmann, Angelique Corthals, David Ray & Liliana Davalos
Comprising more than 1,400 species, bats possess adaptations unique among mammals including powered flight, unexpected longevity given small body size, and extraordinary immunity. Some of the molecular mechanisms underlying these unique adaptations includes DNA repair, metabolism and immunity. However, analyses have been limited to a few divergent lineages, reducing the scope of inferences on gene family evolution across the Order Chiroptera. We conducted an exhaustive comparative genomic study of 37 bat species encompassing a large...

Supporting Data and Code for \"Managing to Climatology: Improving semi-arid agricultural risk management using crop models and a dense meteorological network\"

Steven Mauget & Donna Mitchell-McCallister
Without reliable seasonal climate forecasts, farmers and managers in other weather-sensitive sectors might adopt practices that are optimal for recent climate conditions. To demonstrate this principle, crop simulation models driven by a dense meteorological network were used to identify climate-optimal planting dates for U.S. Southern High Plains (SHP) un-irrigated agriculture. This method converted large samples of SHP growing season weather outcomes into climate-representative cotton and sorghum yield distributions over a range of planting dates. Best...

Paralogs and off-target sequences improve phylogenetic resolution in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae)

Elliot Gardner, Matthew Johnson, Joan Pereira, Aida Shafreena Ahmad Puad, Deby Arifiani, Sahromi Sahromi, Norman Wickett & Nyree Zerega
We present a 517-gene phylogenetic framework for the breadfruit genus Artocarpus (ca. 70 spp., Moraceae), making use of silica-dried leaves from recent fieldwork and herbarium specimens (some up to 106 years old) to achieve 96% taxon sampling. We explore issues relating to assembly, paralogous loci, partitions, and analysis method to reconstruct a phylogeny that is robust to variation in data and available tools. While codon partitioning did not result in any substantial topological differences, the...

Data from: Effects of Bark Beetle Outbreaks on Forest Landscape Pattern in the Southern Rocky Mountains, U.S.A.

Kyle Rodman, Robert Andrus, Cori Butkiewicz, Teresa Chapman, Nathan Gill, Brian Harvey, Dominik Kulakowski, Niko Tutland, Thomas Veblen & Sarah Hart
Since the late 1990s, extensive outbreaks of native bark beetles (Curculionidae: Scolytinae) have affected coniferous forests throughout Europe and North America, driving changes in carbon storage, wildlife habitat, nutrient cycling, and water resource provisioning. Remote sensing is a crucial tool for quantifying the effects of these disturbances across broad landscapes. In particular, Landsat time series (LTS) are increasingly used to characterize outbreak dynamics, including the presence and severity of bark beetle-caused tree mortality, though broad-scale...

Temperature alone is insufficient to understand hibernation energetics

Liam McGuire, Emily Johnson, Winifred Frick & Justin Boyles
Energy conservation has long been a focal point in hibernation research. A long-standing assumption is that ambient temperature (Ta) largely defines the rate of energy expenditure because of well-known relationships between Ta, metabolic rate and frequency of arousal from torpor. Body condition and humidity also affect energy expenditure but are usually considered secondary factors. We held tricolored bats (Perimyotis subflavus) in captivity under multiple environmental conditions to directly compare the importance of Ta, fat mass...

Population connectivity across a highly fragmented distribution: Phylogeography of the Chalcophaps doves

Devon DeRaad, Joseph Manthey, Emily Ostrow, Lucas DeCicco, Michael Andersen, Peter Hosner, Hannah Shult, Leo Joseph, John Dumbacher & Robert Moyle
Chalcophaps is a morphologically conserved genus of ground-walking doves distributed from India to mainland China, south to Australia, and across the western Pacific to Vanuatu. Here, we reconstruct the evolutionary history of this genus using DNA sequence data from two nuclear genes and one mitochondrial gene, sampled from throughout the geographic range of Chalcophaps. We find support for three major evolutionary lineages in our phylogenetic reconstruction, each corresponding to the three currently recognized Chalcophaps species....

Data from: Bayesian analysis of a single gamete recognition gene yields a robust Eutherian phylogeny at all taxonomic levels

Emma Roberts
The extraordinary morphological diversity among extant mammals poses a challenge for studies of speciation, adaptation, molecular evolution, and reproductive isolation. Despite the recent wealth of molecular studies on mammalian phylogenetics, remaining uncertainties surrounding both ancestral and more recent divergence events have proven difficult to resolve. Multi-gene datasets often provide increased support for higher-level affinities within Mammalia, but such analyses require vast amounts of information (genomic-level sequence data) and computational effort (high-performance computing). This study presents...

Registration Year

  • 2021

Resource Types

  • Dataset
  • Output Management Plan


  • Texas Tech University
  • University of Wisconsin-Madison
  • Agricultural Research Service
  • Northwestern University
  • University of Kansas
  • Max Planck Institute for Psycholinguistics
  • Wichita State University
  • University of Washington
  • The Nature Conservancy
  • Duke University