80 Works

Data from: Evolutionary relationships within the Triops (Notostraca: Branchiopoda) using complete mitochondrial genomes

Rebekah L. Horn & David E. Cowley
The tadpole shrimp (Notostraca: Triops) have been called living fossils with conserved morphology, but subtle morphological variations within and between species has yielded confused taxonomic assignments. To aid in cryptic species detection of tadpole shrimp from southern New Mexico, USA, the first complete mitochondrial genomes for three putative species (T. longicaudatus “long,” T. l. “short,” T. newberryi) are reported. The genomes ranged in length from 15,058 bp to 15,060 bp with 13 coding genes, 22...

Data from: De novo assembly of a tadpole shrimp (Triops newberryi) transcriptome and preliminary differential gene expression analysis

Rebekah L. Horn, Thiruvarangan Ramaraj, Nicholas P. Devitt, Faye D. Schilkey & David E. Cowley
Next-generation sequencing techniques, such as RNA sequencing, have provided a wealth of genomic information for nonmodel species. Transcriptomic information can be used to quantify the patterns of gene expression, which can identify how environmental differences invoke organismal stress responses and provide a gauge in predicting species adaptability. In our study, we used RNA sequencing to characterize the first transcriptome from a naupliar tadpole shrimp (Triops newberryi) to identify the genes expressed during the early life...

Data from: Extreme precipitation variability, forage quality and large herbivore diet selection in arid environments

, Jay V. Gedir, Jason P. Marshal, Paul R. Krausman, Jamison D. Allen, Glenn C. Duff, Brian D. Jansen, John R. Morgart & James W. Cain
Nutritional ecology forms the interface between environmental variability and large herbivore behaviour, life history characteristics, and population dynamics. Forage conditions in arid and semi-arid regions are driven by unpredictable spatial and temporal patterns in rainfall. Diet selection by herbivores should be directed towards overcoming the most pressing nutritional limitation (i.e. energy, protein [nitrogen, N], moisture) within the constraints imposed by temporal and spatial variability in forage conditions. We investigated the influence of precipitation-induced shifts in...

Evaluating natural experiments in ecology: using synthetic controls in assessments of remotely-sensed land-treatments

Stephen Fick, Travis Nauman, Colby Brungard & Michael Duniway
Many important ecological phenomena occur on large spatial scales and/or are unplanned and thus do not easily fit within analytical frameworks which rely on randomization, replication, and interspersed a priori controls for statistical comparison. Analyses of such large-scale, natural experiments are common in the health and econometrics literature, where techniques have been developed to derive insight from large, noisy observational datasets. Here, we apply a technique from this literature, synthetic control, to assess landscape change...

Data from: Does urbanization ameliorate the effect of endoparasite infection in kangaroo rats?

Karen Mabry, Gizelle Hurtado & Ghislaine Mayer
Urban development can fragment and degrade remnant habitat. Such habitat alterations can have profound impacts on wildlife, including effects on population density, parasite infection status, parasite prevalence, and body condition. We investigated the influence of urbanization on populations of Merriam’s kangaroo rat (Dipodomys merriami) and their parasites. We predicted that urban development would lead to reduced abundance, increased parasite prevalence in urban populations, increased probability of parasite infection for individual animals, and decreased body condition...

Tayra (eira barbara) landscape use as a function of cover types, forest protection, and the presence of puma and free-ranging dogs

Rita Bianchi, Julianna Jenkins, Damon Lesmeister, Jéssica Gouvea, Clarice Cesário, Larissa Fornitano, Mateus Oliveira, Kimberly Morais, Renan Ribeiro & Matthew Gompper
The tayra (Eira barbara) is a common and broadly distributed Neotropical carnivore, yet is not well-studied. While this species is apparently associated with forested habitats, it also appears tolerant of some anthropogenic disturbance. We deployed 57 unbaited camera traps (n = 4,923 trap-days) in and around a protected area (Furnas do Bom Jesus State Park, São Paulo, Brazil) to survey for tayra and two potentially interactive species: puma (Puma concolor) and free-ranging dogs (Canis familiaris)....

Additional file 1 of General control nonderepressible 1 interacts with cationic amino acid transporter 1 and affects Aedes aegypti fecundity

Matthew Pinch, Theodore Muka, Yashoda Kandel, Mahesh Lamsal, Nathan Martinez, Marialuisa Teixeira, Dmitri Y. Boudko & Immo A. Hansen
Additional file 1: Table S1. Annotations of all CAT entries used for CAT annotation tree. Table S2. Potential protein interactors identified from AaCAT1 yeast two-hybrid screen. Figure S1. Ae. aegypti AaCAT1 is a transmembrane protein that localizes to the plasma membrane. a. Tertiary structure of the AaCAT1 protein was visualized using PyMOL ( https://pymol.org/2/ ). b. The TMHMM transmembrane prediction tool, Krogh et al. [39] was used to predict the transmembrane domains, and intracellular and...

Additional file 4 of Vikrahraun—the 1961 basaltic lava flow eruption at Askja, Iceland: morphology, geochemistry, and planetary analogs

Aline Y. Blasizzo, Ingrid A. Ukstins, Stephen P. Scheidt, Alison H. Graettinger, David W. Peate, Tamara L. Carley, Adam J. Moritz & Jennifer E. Thines
Additional file 4: A detailed methodology section outlining each analytical dataset individually.

Additional file 5 of Vikrahraun—the 1961 basaltic lava flow eruption at Askja, Iceland: morphology, geochemistry, and planetary analogs

Aline Y. Blasizzo, Ingrid A. Ukstins, Stephen P. Scheidt, Alison H. Graettinger, David W. Peate, Tamara L. Carley, Adam J. Moritz & Jennifer E. Thines
Additional file 5: Contains supplementary Fig. S1–S5 and associated captions

Additional file 2 of Vikrahraun—the 1961 basaltic lava flow eruption at Askja, Iceland: morphology, geochemistry, and planetary analogs

Aline Y. Blasizzo, Ingrid A. Ukstins, Stephen P. Scheidt, Alison H. Graettinger, David W. Peate, Tamara L. Carley, Adam J. Moritz & Jennifer E. Thines
Additional file 2: Textural data presented in this paper, including crystallinity, vesicularity, density, and viscosity calculations

Divergent growth-differentiation balance strategies and resource competition shape mortality patterns in ponderosa pine

Scott Ferrenberg, Carla Vazquez-Gonzalez, Steven Lee & Milda Kristupaitis
Dynamic resource availability leads to trade-offs among functions in plants. The growth-differentiation balance hypothesis (GDBH) predicts greater allocation of carbon to defense than growth when resources are scarce; with optimum defense production occurring at a point between the minimum and maximum growth rates. While the GDBH has been widely tested, consideration of phenotypic variation in rates for which defense is traded for growth and what this variation means for plant resistance remains rare. For defense,...

Data from: A single-nucleotide polymorphism-based approach for rapid and cost-effective genetic wolf monitoring in Europe based on noninvasively collected samples

Robert H. S. Kraus, Bridgett VonHoldt, Berardino Cocchiararo, Verena Harms, Helmut Bayerl, Ralph Kühn, Daniel W. Förster, Jörns Fickel, Christian Roos & Carsten Nowak
Noninvasive genetics based on microsatellite markers has become an indispensable tool for wildlife monitoring and conservation research over the past decades. However, microsatellites have several drawbacks, such as the lack of standardisation between laboratories and high error rates. Here, we propose an alternative single-nucleotide polymorphism (SNP)-based marker system for noninvasively collected samples, which promises to solve these problems. Using nanofluidic SNP genotyping technology (Fluidigm), we genotyped 158 wolf samples (tissue, scats, hairs, urine) for 192...

Data from: Multiple mating reveals complex patterns of assortative mating by personality and body size

Pierre-Olivier Montiglio, Tina W. Wey, Ann T. Chang, Sean Fogarty & Andrew Sih
1. Understanding patterns of non-random mating is central to predicting the consequences of sexual selection. Most studies quantifying assortative mating focus on testing for correlations among partners’ phenotypes in mated pairs. Few studies have distinguished between assortative mating arising from preferences for similar partners (expressed by all or a subset of the population), versus from phenotypic segregation in the environment. Also, few studies have assessed the robustness of assortative mating against temporal changes in social...

Data from: Genetic structure and effective population sizes in European red deer (Cervus elaphus) at a continental scale: insights from microsatellite DNA

Frank E. Zachos, Alain C. Frantz, Ralph Kuehn, Sabine Bertouille, Marc Colyn, Magdalena Niedzialkowska, Javier Pérez-González, Anna Skog, Nikica Šprem & Marie-Christine Flamand
We analysed more than 600 red deer (Cervus elaphus) from large parts of its European distribution range at 13 microsatellite loci, presenting the first continent-wide study of this species using nuclear markers. Populations were clearly differentiated (overall FST = 0.166, Jost’s Dest = 0.385), and the BAPS clustering algorithm yielded mainly geographically limited and adjacent genetic units. When forced into only three genetic clusters our data set produced a very similar geographic pattern as previously...

Data from: A new subfamily classification of the Leguminosae based on a taxonomically comprehensive phylogeny

, Anne Bruneau, Nasim Azani, Marielle Babineau, Edeline Gagnon, Carole Sinou, Royce Steeves, Erin Zimmerman, C. Donovan Bailey, Lynsey Kovar, Madhugiri Nageswara-Rao, Hannah Banks, RuthP. Clark, Manuel De La Estrella, Peter Gasson, GeoffreyC. Kite, BenteB. Klitgaard, GwilymP. Lewis, Danilo Neves, Gerhard Prenner, María De Lourdes Rico-Arce, ArianeR. Barbosa, Maria Cristina López-Roberts, Luciano Paganucci De Queiroz, PétalaG. Ribeiro … & Tingshuang Yi
The classification of the legume family proposed here addresses the long-known non-monophyly of the traditionally recognised subfamily Caesalpinioideae, by recognising six robustly supported monophyletic subfamilies. This new classification uses as its framework the most comprehensive phylogenetic analyses of legumes to date, based on plastid matK gene sequences, and including near-complete sampling of genera (698 of the currently recognised 765 genera) and ca. 20% (3696) of known species. The matK gene region has been the most...

Data from: Estimation of woody and herbaceous leaf area index in Sub-Saharan Africa using MODIS data

Milkah N Kahiu & Niall P Hanan
Savannas are widespread global biomes covering ~20% of terrestrial ecosystems on all continents except Antarctica. These ecosystems play a critical role in regulating terrestrial carbon cycle, ecosystem productivity, and the hydrological cycle and contribute to human livelihoods and biodiversity conservation. Despite the importance of savannas in ecosystem processes and human well-being, the presence of mixed woody and herbaceous components at scales much fin-er than most medium and coarse resolution satellite imagery poses significant challenges to...

Individual signatures outweigh social group identity in contact calls of a communally nesting parrot

Grace Smith-Vidaurre, Marcelo Araya-Salas & Timothy F. Wright
Despite longstanding interest in the evolutionary origins and maintenance of vocal learning, we know relatively little about how social dynamics influence vocal learning processes in natural populations. The “social group membership” hypothesis proposes that socially learned calls evolved and are maintained as signals of group membership. However, in fission-fusion societies, individuals can interact in social groups across various social scales. For learned calls to signal group membership over multiple social scales, they must contain information...

Allometric modelling of plant biomass from drone-acquired photographs: drone images, ground control marker coordinates and biomass data from 36 sites, 2016-2020

A. Cunliffe, K. Anderson, F. Boschetti, H. Graham, R. Brazier, I. Myers-Smith, T. Astor, M. Boer, L. Calvo, P. Clark, M. Cramer, M. Encinas-Lara, S. Escarzaga, J. Fernández-Guisuraga, A. Fisher, K. Gdulová, B. Gillespie, A. Griebel, N. Hanan, M. Hanggito, S. Haselberger, C. Havrilla, W. Ji, J. Karl, M. Kirchhoff … & R. Wojcikiewicz
This dataset contains RGB photographs acquired from drone surveys. There are 741 harvest plots from 38 surveys at 36 sites around the world. Each site was approximately 1 ha in area. Included with the photographic images are the coordinates of ground control markers, biomass, taxonomic and location data for harvest plots and ancillary metadata. The observations can be used to obtain allometric size-biomass models. This work was supported by the Natural Environment Research Council award...

Data from: Species-specific responses to warming alter community composition

Karen Mabry, Julia Tituskin & Shane Waddell
1. Species are responding to global climate change in varied and nuanced ways. However, how species-specific responses to climate change affect interactions among species remains poorly understood. It is important to understand species interactions under potential climate change scenarios because those interactions can in turn alter community dynamics. 2. In this study, we conducted two complementary experiments to examine how simulated warming might alter larval intraguild predation (IGP) rates and resulting adult assemblage composition in...

Linking camera-trap data to taxonomy: Identifying photographs of morphologically similar chipmunks

Fiona McKibben & Jennifer Frey
Remote cameras are a common method for surveying wildlife and recently have been promoted for implementing large-scale regional biodiversity monitoring programs. The use of camera-trap data depends on the correct identification of animals captured in the photographs, yet misidentification rates can be high, especially when morphologically similar species co-occur, and this can lead to faulty inferences and hinder conservation efforts. Correct identification is dependent on diagnosable taxonomic characters, photograph quality, and the experience and training...

Lehmann lovegrass and black grama drought response in the Jornada Desert 2021

Sherri Buerdsell, Brook Milligan & Erik Lehnhoff
Percent cover for Bouteloua eriopoda and Eragrostis lehmanniana was collected over four years at Mt. Summerford (latitude 32.516, longitude -106.802), New Mexico State University's Chihuahuan Desert Rangeland Research Center (CDRRC), Doña Ana County, New Mexico. In June 2016, permanent 2m × 2m plots were installed to evaluate change in percent cover of B. eriopoda and E. lehmanniana in response to precipitation manipulation treatments of +80% (irrigated), -80% (drought), and ambient (control) precipitation. We used a...

Structural determinants of tailored behavioral health services for sexual and gender minorities in the United States, 2010 to 2020: a panel analysis

Cory J. Cascalheira, Emily C. Helminen, Thomas J. Shaw & Jillian R. Scheer
Abstract Background Research indicates that tailored programming for sexual and gender minority (SGM; e.g., lesbian, gay, bisexual, transgender, queer) people, compared to non-tailored programming, is effective for reducing the disproportionate health burden SGM people experience relative to the general population. However, the availability of SGM-tailored programming is often over-reported and inconsistent across behavioral health (i.e., substance use and mental health) facilities in the United States (U.S.). Methods Using panel analysis, the National Survey of Substance...

Additional file 1 of Vikrahraun—the 1961 basaltic lava flow eruption at Askja, Iceland: morphology, geochemistry, and planetary analogs

Aline Y. Blasizzo, Ingrid A. Ukstins, Stephen P. Scheidt, Alison H. Graettinger, David W. Peate, Tamara L. Carley, Adam J. Moritz & Jennifer E. Thines
Additional file 1: Contains sample locations, an analytical summary containing a table of contents for Additional files 1-3, topographic profile data, and flow volume calculations, crystallinity, vesicularity, density, whole-rock chemistry, mineral chemistry, and additional calculations

Additional file 3 of Vikrahraun—the 1961 basaltic lava flow eruption at Askja, Iceland: morphology, geochemistry, and planetary analogs

Aline Y. Blasizzo, Ingrid A. Ukstins, Stephen P. Scheidt, Alison H. Graettinger, David W. Peate, Tamara L. Carley, Adam J. Moritz & Jennifer E. Thines
Additional file 3: Cumulative chemistry data presented in this paper, including whole-rock chemistry, mineral chemistry, thermometry, and compiled geochemistry of Vikrahraun from the literature

Additional file 5 of Vikrahraun—the 1961 basaltic lava flow eruption at Askja, Iceland: morphology, geochemistry, and planetary analogs

Aline Y. Blasizzo, Ingrid A. Ukstins, Stephen P. Scheidt, Alison H. Graettinger, David W. Peate, Tamara L. Carley, Adam J. Moritz & Jennifer E. Thines
Additional file 5: Contains supplementary Fig. S1–S5 and associated captions

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