69 Works

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...

On the potential of Angiosperms353 for population genomics studies

Matthew Johnson, Madeline Slimp, Lindsay D. Williams & Haley Hale
Premise of the Study: Targeted sequencing using Angiosperms353 has emerged as a low-cost tool for phylogenetics, with early results spanning from all flowering plants to within genera. The use of universal markers at narrower scales—within populations— would eliminate the need for specific marker development while retaining the benefits of full-gene sequences. However, whether the Angiosperms353 markers provide sufficient variation within species to calculate demographic parameters is untested. Methods: Using herbarium specimens from a 50-year-old floristic...

Data from: Suburban watershed nitrogen retention: estimating the effectiveness of stormwater management structures

Benjamin J. Koch, Catherine M. Febria, Roger M. Cooke, Jacob D. Hosen, Matthew E. Baker, Abigail R. Colson, Solange Filoso, Katharine Hayhoe, J. V. Loperfido, Anne M. K. Stoner & Margaret A. Palmer
Excess nitrogen (N) is a primary driver of freshwater and coastal eutrophication globally, and urban stormwater is a rapidly growing source of N pollution. Stormwater best management practices (BMPs) are used widely to remove excess N from runoff in urban and suburban areas, and are expected to perform under a wide variety of environmental conditions. Yet the capacity of BMPs to retain excess N varies; and both the variation and the drivers thereof are largely...

Data from: Phylogenetic community structure of North American desert bats: influence of environment at multiple spatial and taxonomic scales

Lorelei E. Patrick & Richard D. Stevens
1. Numerous processes influence community structure. The relative importance of these processes are thought to vary with spatial, temporal, and taxonomic scale: density dependent interactions are thought to be most influential at small scales, at intermediate scales environmental conditions may be the most influential factor, and biogeographic processes are thought to be of greater importance at larger scales. Additionally, the stress-dominance hypothesis suggests that communities experiencing harsher environmental conditions will be predominantly structured by habitat...

Data from: Multilocus phylogeography of a widespread savanna-woodland adapted rodent reveals the influence of Pleistocene geomorphology and climate change in Africa’s Zambezi region

Molly M. McDonough, Radim Šumbera, Vladimír Mazoch, Adam W. Ferguson, Caleb D. Phillips & Josef Bryja
Understanding historical influences of climate and physiographic barriers in shaping patterns of biodiversity remains limited for many regions of the world. For mammals of continental Africa, phylogeographic studies, particularly for West African lineages, implicate both geographic barriers and climate oscillations in shaping small mammal diversity. In contrast, studies for southern African species have revealed conflicting phylogenetic patterns for how mammalian lineages respond to both climate change and geologic events such as river formation, especially during...

Data from: Resource availability and roosting ecology shape reproductive phenology of rain forest insectivorous bats

Elias Nurul-Ain, Rosli Hashim, Tigga Kingston & Hashim Rosli
Bats in temperate and subtropical regions typically synchronize birth of a single young with peaks in resource availability driven by local climate patterns. In tropical rain forest, insects are available throughout the year, potentially allowing departures from seasonal monoestry. However, reproductive energy budgets may be constrained by the cost of commuting to foraging grounds from distant roosts. To test these hypotheses, we simultaneously tracked female reproductive activity of 11 insectivorous bat species, insect biomass, and...

Analytic dataset informing prediction of subterranean cave and mine ambient temperatures

Meredith McClure, Daniel Crowley, Catherine Haase, Liam McGuire, Nathan Fuller, David Hayman, Cori Lausen, Raina Plowright, Brett Dickson & Sarah Olson
Caves and other subterranean features provide unique environments for many species. The importance of cave microclimate is particularly relevant at temperate latitudes where bats make seasonal use of caves for hibernation. White-nose syndrome (WNS), a fungal disease that has devastated populations of hibernating bats across eastern and central North America, has brought renewed interest in bat hibernation and hibernaculum conditions. A recent review synthesized current understanding of cave climatology, exploring the qualitative relationship between cave...

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...

Data from: Target Sequence Capture of Nuclear-Encoded Genes for Phylogenetic Analysis in Ferns

Paul G. Wolf, Tanner A. Robison, Matthew G. Johnson, Michael A. Sundue, Weston L. Testo & Carl J. Rothfels
Premise of the study: Until recently, most phylogenetic studies of ferns were based on chloroplast genes. Evolutionary inferences based on these data can be incomplete because the characters are from a single linkage group and are uniparentally inherited. These limitations are particularly acute in studies of hybridization, which is prevalent in ferns; fern hybrids are common and ferns are able to hybridize across highly diverged lineages, up to 60 million years since divergence in one...

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 from: Social organisation and genetic structure: insights from co-distributed bat populations

Stephen J. Rossiter, Akbar Zubaid, Adura Mohd-Adnan, Matthew J. Struebig, Thomas H. Kunz, Sucharita Gopal, Eric J. Petit & Tigga Kingston
The impact of ecology and social organisation on genetic structure at landscape spatial scales, where gene dynamics shape evolution as well as determine susceptibility to habitat fragmentation, is poorly understood. Attempts to assess these effects must take into account the potentially confounding effects of history. We used microsatellites to compare genetic structure in seven bat species with contrasting patterns of roosting ecology and social organisation, all of which are co-distributed in an ancient forest habitat...

Data from: Context-dependent effects of large wildlife declines on small mammal communities in central Kenya

Hillary S. Young, Douglas J. McCauley, Rodolfo Dirzo, Jacob R. Goheen, Bernard Agwanda, Cara Brook, Erik O. Castillo, Adam W. Ferguson, Stephen N. Kinyua, Molly M. McDonough, Todd M. Palmer, Robert M. Pringle, Truman P. Young & Kristofer M. Helgen
Many species of large wildlife have declined drastically worldwide. These reductions often lead to profound shifts in the ecology of entire communities and ecosystems. However, the effects of these large wildlife declines on other taxa likely hinge upon both underlying abiotic properties of these systems and on the types of secondary anthropogenic changes associated with wildlife loss, making impacts difficult to predict. To better understand how these important contextual factors determine the consequences of large-wildlife...

Data from: Ontogenetic variability in crystallography and mosaicity of conodont apatite: Implications for microstructure, paleothermometry and geochemistry

Mohammad Shohel, Neo McAdams & Bradley Cramer
X-ray diffraction data from Silurian conodonts belonging to various developmental stages of the species Dapsilodus obliquicostatus demonstrate changes in crystallography and degree of nanocrystallite ordering (mosaicity) in both hyaline and albid crown tissue. The exclusive use of a single species in this study, combined with systematic testing of each element type at multiple locations, provided insight into microstructural and crystallographic differentiation between element position (Sa, Sb-c, M) as well as between juveniles and adults. A...

Experimental parasite community perturbation reveals associations between Sin Nombre virus and gastrointestinal nematodes in a rodent reservoir host

Amy Sweeny, Courtney Thomason, Edwin Carbajal, Christina Hansen, Andrea Graham & Amy Pedersen
Individuals are often co-infected with several parasite species, yet measuring within-host interactions remains difficult in the wild. Consequently, the impact of such interactions on host fitness and epidemiology are often unknown. We used anthelmintic drugs to experimentally reduce nematode infection and measured the effects on both nematodes and the important zoonosis Sin Nombre virus (SNV) in its primary reservoir (Peromyscus spp.). Treatment significantly reduced nematode infection, but increased SNV seroprevalence. Furthermore, mice that were co-infected...

Data from: Evaluating a handheld decision support device in pediatric intensive care settings

Tera L. Reynolds, Patricia R. DeLucia, Karen A. Esquibel, Todd Gage, Noah J. Wheeler, J. Adam Randell, James G. Stevenson & Kai Zheng
Objective: To evaluate end-user acceptance and the effect of a commercial handheld decision support device in pediatric intensive care settings. The technology, pac2, was designed to assist nurses in calculating medication dose volumes and infusion rates at the bedside. Materials and Methods: The devices, manufactured by InformMed Inc., were deployed in the pediatric and neonatal intensive care units in two health systems. This mixed methods study assessed end-user acceptance, as well as pac2’s effect on...

Data from: Population genomic analysis suggests strong influence of river network on spatial distribution of genetic variation in invasive saltcedar across the southwestern US

Soo-Rang Lee, Yeong-Seok Jo, Chan-Ho Park, Jonathan M. Friedman & Matthew S. Olson
Understanding the complex influences of landscape and anthropogenic elements that shape the population genetic structure of invasive species provides insight into patterns of colonization and spread. The application of landscape genomics techniques to these questions may offer detailed, previously undocumented insights into factors influencing species invasions. We investigated the spatial pattern of genetic variation and the influences of landscape factors on population similarity in the invasive riparian shrub saltcedar (Tamarix L.) by analyzing 1,997 genome-wide...

Data from: Elevated mitochondrial genome variation after 50 generations of radiation exposure in a wild rodent

Robert J. Baker, Benjamin Dickins, Jeffrey K. Wickliffe, Faisal Anwarali Khan, Sergey Gaschak, Kateryna Makova & Caleb D. Phillips
Currently, the effects of chronic, continuous low dose environmental irradiation on the mitochondrial genome of resident small mammals are unknown. Using the bank vole (Myodes glareolus) as a model system, we tested the hypothesis that approximately 50 generations of exposure to the Chernobyl environment has significantly altered genetic diversity of the mitochondrial genome. Using deep sequencing, we compared mitochondrial genomes from 131 individuals from reference sites with radioactive contamination comparable to that present in Northern...

Data from: Habitat selection and the value of information in heterogenous landscapes

Kenneth A. Schmidt & Francois Massol
Despite the wide usage of the term information in evolutionary ecology, there is no general treatise between fitness (i.e., density-dependent population growth) and selection of the environment sensu lato. Here we (1) initiate the building of a quantitative framework with which to examine the relationship between information use in spatially heterogeneous landscapes and density-dependent population growth, and (2) illustrate its utility by applying the framework to an existing model of breeding habitat selection. We begin...

Data from: Conflicting evolutionary histories of the mitochondrial and nuclear genomes in New World Myotis bats

, Brant C. Faircloth, Kevin A.M. Sullivan, Troy J. Kieran, Travis C. Glenn, Michael W. Vandewege, , Robert J. Baker, Richard D. Stevens, David A. Ray, Thomas E Lee, Roy N Platt & Kevin A M Sullivan
The rapid diversification of Myotis bats into more than 100 species is one of the most extensive mammalian radiations available for study. Efforts to understand relationships within Myotis have primarily utilized mitochondrial markers and trees inferred from nuclear markers lacked resolution. Our current understanding of relationships within Myotis is therefore biased towards a set of phylogenetic markers that may not reflect the history of the nuclear genome. To resolve this, we sequenced the full mitochondrial...

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...

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...

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...

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