55 Works

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...

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)....

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...

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: 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: 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...

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: 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...

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: 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: 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: 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...

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...

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...

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...

Data from: Targeted re-sequencing of coding DNA sequences for SNP discovery in non-model species

Daniel W. Förster, James K. Bull, Dorina Lenz, Marijke Autenrieth, Johanna L.A. Paijmans, Robert H.S. Kraus, Carsten Nowak, Helmut Bayerl, Ralph Kuehn, Alexander P. Saveljev, Magda Sindičić, Michael Hofreiter, Krzysztof Schmidt, Joerns Fickel, Johanna L. A. Paijmans & Robert H. S. Kraus
Targeted capture coupled with high throughput sequencing can be used to gain information about nuclear sequence variation at hundreds to thousands of loci. Divergent reference capture makes use of molecular data of one species to enrich target loci in other (related) species. This is particularly valuable for non-model organisms, for which often no a priori knowledge exists regarding these loci. Here, we have used targeted capture to obtain data for 809 nuclear coding DNA sequences...

Data from: Harvesting effects on wild bee communities in bioenergy grasslands depend on nesting guild

Brian J. Spiesman, Ashley Bennett, Rufus Isaacs & Claudio Gratton
Conversion of annual crops to native perennial grasslands for bioenergy production may help conserve wild bees by enhancing nest and food resources. However, bee response to the disturbance of biomass harvesting may depend on their nesting location, thus their vulnerability to nest destruction, and the response of the forb community on which they forage. Moreover, because bees have long foraging ranges, effects of local harvesting may depend on the amount of natural habitat in the...

Data from: Ecological correlates of Himalayan musk deer Moschus leucogaster

Paras Bikram Singh, Pradip Saud, Kumar Mainali, Doug Cram, Arjun Thapa, Nar Bahadur Chhetri, Laxman P. Poudyal, Hem Sagar Baral, Zhigang Jiang & Douglas Cram
Himalayan musk deer (Moschus leucogaster; hereafter musk deer) are endangered as a result of poaching and habitat loss. The species is nocturnal, crepuscular and elusive, making direct observation of habitat use and behavior difficult. However, musk deer establish and repeatedly use the same latrines for defecation. To quantify musk deer habitat correlates, we used observational spatial data based on presence-absence of musk deer latrines, as well as a range of fine spatial-scale ecological covariates. To...

Data from: Does vocal learning accelerate acoustic diversification? Evolution of contact calls in neotropical parrots

Angela Medina-García, Marcelo Araya-Salas & Timothy F. Wright
Learning has been traditionally though to accelerate the evolutionary change of behavioral traits. We evaluated the evolutionary rate of learned vocalizations and the interplay of morphology and ecology in the evolution of these signals. We examined contact calls of 51 species of Neotropical parrots from the tribe Arini. Parrots are ideal subjects due to their wide range of body sizes and habitats, and their open-ended vocal learning that allows them to modify their calls throughout...

Data from: Genetic evidence for high propagule pressure and long-distance dispersal in monk parakeet (Myiopsitta monachus) invasive populations

Anders Gonçalves Da Silva, Jessica Eberhard, Timothy Wright, Michael Avery & Michael Russello
The monk parakeet (Myiopsitta monachus) is a successful invasive species that does not exhibit life history traits typically associated with colonizing species (e.g., high reproductive rate or long-distance dispersal capacity). To investigate this apparent paradox, we examined individual and population genetic patterns of microsatellite loci at one native and two invasive sites. More specifically, we aimed to evaluate the role of propagule pressure, sexual monogamy, and long-distance dispersal in monk parakeet invasion success. Our results...

Data from: Social feedback and the emergence of rank in animal society

Elizabeth A. Hobson & Simon DeDeo
Dominance hierarchies are group-level properties that emerge from the aggression of individuals. Although individuals can gain critical benefits from their position in a hierarchy, we do not understand how real-world hierarchies form. Nor do we understand what signals and decision-rules individuals use to construct and maintain hierarchies in the absence of simple cues such as size or spatial location. A study of conflict in two groups of captive monk parakeets (Myiopsitta monachus) found that a...

Data from: Highly divergent 16S rRNA sequences in ribosomal operons of Scytonema hyalinum (Cyanobacteria)

Jeffrey R. Johansen, Jan Mareš, Nicole Pietrasiak, Markéta Bohunická, , Lenka Štenclová & Tomáš Hauer
A highly divergent 16S rRNA gene was found in one of the five ribosomal operons present in a species complex currently circumscribed as Scytonema hyalinum (Nostocales, Cyanobacteria) using clone libraries. If 16S rRNA sequence macroheterogeneity among ribosomal operons due to insertions, deletions or truncation is excluded, the sequence heterogeneity observed in S. hyalinum was the highest observed in any prokaryotic species thus far (7.3–9.0%). The secondary structure of the 16S rRNA molecules encoded by the...

Data from: Sustainability management of short-lived freshwater fish in human-altered ecosystems should focus on adult survival

David Cowley, Michael Hatch, Fitsum Abadi Gebreselassie, Wiebke J. Boeing, Sabela Lois & Michael D. Porter
Fish populations globally are susceptible to endangerment through exploitation and habitat loss. We present theoretical simulations to explore how reduced adult survival (age truncation) might affect short-lived freshwater fish species in human-altered contemporary environments. Our simulations evaluate two hypothetical "average fish" and five example fish species of age 1 or age 2 maturity. From a population equilibrium baseline representing a natural, unaltered environment we impose systematic reductions in adult survival and quantify how age truncation...

Data from: Consequences of aboveground invasion by non-native plants into restored vernal pools do not prompt changes in belowground processes

Amber Churchill & Akasha Faist
Given the frequent overlap between biological plant invasion and ecological restoration efforts it is important to investigate their interactions to sustain desirable plant communities and modify long-term legacies both above and belowground. To address this relationship, we used natural reference, invaded, and constructed vernal pools in the Central Valley of California to examine potential changes in direct and indirect plant effects on soils associated with biological invasion and active restoration ecosystem disturbances. Our results showed...

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  • New Mexico State University
  • University of British Columbia
  • University of California, Davis
  • United States Department of Agriculture
  • Brigham Young University
  • Sao Paulo State University
  • Duke University
  • University of Alberta
  • Polish Academy of Sciences
  • Oklahoma State University