70 Works

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...

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...

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: 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...

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...

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 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...

One-way nested (27km, 9km and 3km) model output of North American atmospheric CO2 simulation (full WRF-chem output)

A. Samaddar, S. Feng, T. Lauvaux, Z.R. Barkley, S. Pal & K.J. Davis
Synoptic weather systems are a major driver of spatial gradients in atmospheric CO2 mole fractions. During frontal passages air masses from different regions meet at the frontal boundary creating significant gradients in CO2 mole fractions. This study quantitatively describes the atmospheric transport of CO2 mole fractions during a mid-latitude cold front passage and explores the impact of various sources of CO2. We focus here on a cold front passage over Lincoln, Nebraska on August 4th,...

Data from: A 1,000-year-old antimicrobial remedy with antistaphylococcal activity

Freya Harrison, Aled E. L. Roberts, Rebecca Gabrilska, Kendra P. Rumbaugh, Christina Lee & Stephen P. Diggle
Plant-derived compounds and other natural substances are a rich potential source of compounds that kill or attenuate pathogens that are resistant to current antibiotics. Medieval societies used a range of these natural substances to treat conditions clearly recognizable to the modern eye as microbial infections, and there has been much debate over the likely efficacy of these treatments. Our interdisciplinary team, comprising researchers from both sciences and humanities, identified and reconstructed a potential remedy for...

Data from: Genetic data reveal mixed-stock aggregations of gray whales in the North Pacific Ocean

Anna Brüniche-Olsen, R. Jorge Urban, Vladimir V. Vertyankin, Celine A.J. Godard-Codding, John W. Bickham & J. Andrew DeWoody
Gray whales (Eschrichtius robustus) in the Western Pacific are critically endangered whereas in the Eastern Pacific they are relatively common. Holocene environmental changes and commercial whaling reduced their numbers, but gray whales in the Eastern Pacific now outnumber their Western counterparts by more than 100-fold. Herein, we investigate the genetic diversity and population structure within the species using a panel of genic SNPs. Results indicate the gray whale gene pool is differentiated into two substocks...

Data from: Multilocus characterization of a woodrat (genus Neotoma) hybrid zone

Matthew R. Mauldin, Michelle L. Haynie, J. Delton Hanson, Robert J. Baker & Robert D. Bradley
In order to investigate hybridization between 2 species of woodrats, Neotoma floridana and Neotoma micropus, 103 specimens were collected, in March of 1988, from a known area of sympatry, and compared with reference collections from areas of allopatry. Ten genetic markers, consisting of 7 microsatellite loci, 1 mitochondrial gene (cytochrome-b [Cytb]), and 2 nuclear introns (intron 2 of the vertebrate alcohol dehydrogenase gene [Adh1-I2] and intron 7 of the beta-fibrinogen gene [Fgb-I7]) were used to...

Data from: Beyond size – morphological predictors of bite force in a diverse insectivorous bat assemblage from Malaysia

Juliana Senawi, Daniela Schmieder, Björn Siemers & Tigga Kingston
1. Bite force is used to investigate feeding performance in a variety of vertebrates. In all taxa studied, bite force is strongly correlated with body and head size. Studies of bite force in bats have largely centred on neotropical species with a particular focus on species that maximize dietary differences. Little is known about the bite force of bats from the Old World tropics, nor of variation in bite force within diverse assemblages of obligate...

Data from: Threshold effect of habitat loss on bat richness in cerrado-forest landscapes

Renata L. Muylaert, Richard D. Stevens & Milton C. Ribeiro
Understanding how animal groups respond to contemporary habitat loss and fragmentation is essential for development of strategies for species conservation. Until now, there has been no consensus about how landscape degradation affects the diversity and distribution of Neotropical bats. Some studies demonstrate population declines and species loss in impacted areas, although the magnitude and generality of these effects on bat community structure are unclear. Empirical fragmentation thresholds predict an accentuated drop in biodiversity, and species...

Data from: Variation in coexisting birds to exploit spatial heterogeneity in small mammal activity

Quinn C. Emmering, Janice K. Kelly, Richard S. Ostfeld & Kenneth A. Schmidt
Breeding nest site selection is often the first defense against nest predation risk. To be effective, this mechanism requires site-specific spatial heterogeneity in predator abundance which produces predator-poor space, prey's ability to assess spatial heterogeneity in risk, and few or weak constraints on the ability to settle in within predator-poor space. We used a 15-year dataset on forested grids that provided extensive records of fledging success of veeries (Catharus fuscescens) and ovenbirds (Seiurus aurocapilla) in...

Data from: A universal probe set for targeted sequencing of 353 nuclear genes from any flowering plant designed using k-medoids clustering

Matthew G. Johnson, Lisa Pokorny, Steven Dodsworth, Laura R. Botigue, Robyn S. Cowan, Alison Devault, Wolf L. Eiserhardt, Niroshini Epitawalage, Félix Forest, Jan T. Kim, James Leebens-Mack, Ilia J. Leitch, Olivier Maurin, Doug Soltis, Pamela S. Soltis, Gane Ka-Shu Wong, William J. Baker & Norman Wickett
Sequencing of target-enriched libraries is an efficient and cost-effective method for obtaining DNA sequence data from hundreds of nuclear loci for phylogeny reconstruction. Much of the cost of developing targeted sequencing approaches is associated with the generation of preliminary data needed for the identification of orthologous loci for probe design. In plants, identifying orthologous loci has proven difficult due to a large number of whole-genome duplication events, especially in the angiosperms (flowering plants). We used...

Data from: True homoplasy of retrotransposon insertions in primates

Liliya Doronina, Olga Reising, Hiram Clawson, David A. Ray & Jürgen Schmitz
How reliable are the presence/absence insertion patterns of the supposedly homoplasy-free retrotransposons, that were randomly inserted in the quasi infinite genomic space? To systematically examine this question in an up-to-date, multi-genome comparison, we screened millions of primate transposed Alu SINE elements for incidences of homoplasious precise insertions and deletions. In genome-wide analyses, we identified and manually verified nine cases of precise parallel Alu insertions of apparently identical elements at orthologous positions in two ape lineages...

Data from: Investigating sensitivity of phylogenetic community structure metrics using North American desert bats

Lorelei E. Patrick & Richard D. Stevens
A relatively recent approach to characterizing structure of natural communities is to use phylogenies of species pools to compare patterns of relatedness between real and simulated communities. Such an approach can provide mechanistic insights into structure. Despite popularity of phylogenetic approaches, we do not yet fully understand how phylogenetic community structure (PCS) metrics might be impacted by changes to the phylogeny or community membership data from which they are calculated. We investigate metric sensitivity and...

Data from: Pleistocene speciation in the genus Populus (Salicaceae)

Nicholas D. Levsen, Peter Tiffin & Matthew S. Olson
The macro-evolutionary consequences of recent climate change remain controversial and there is little paleobotanical or morphological evidence that Pleistocene (1.8-0.12 Ma) glacial cycles acted as drivers of speciation, especially among lineages with long generation times, such as trees. We combined genetic and ecogeographic data from two closely related North American tree species, Populus balsamifera and P. trichocarpa (Salicacaeae) to determine if their divergence coincided with and was possibly caused by Pleistocene climatic events. We analyzed...

Extensive paraphyly in the typical owl family (Strigidae)

Jessie F Salter, Carl H Oliveros, Peter A Hosner, Joseph D Manthey, Mark B Robbins, Robert G Moyle, Robb T Brumfield & Brant C Faircloth
The typical owl family (Strigidae) comprises 194 species in 28 genera, 14 of which are monotypic. Relationships within and among genera in the typical owls have been challenging to discern because mitochondrial data have produced equivocal results and because many monotypic genera have been omitted from previous molecular analyses. Here, we collected and analyzed DNA sequences of ultraconserved elements (UCEs) from 43 species of typical owls to produce concatenated and multispecies coalescent-based phylogenetic hypotheses for...

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...

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...

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