478 Works

Data from: Valuable habitat and low deforestation can reduce biodiversity gains from development rights markets

Kate J. Helmstedt & Matthew D. Potts
1. Illegal private land deforestation threatens global biodiversity, even in areas with native habitat requirements stipulated by law. Compliance can be improved by allowing landholders to meet legal reserve requirements by buying and selling the rights to have deforested land through a Tradeable Development Rights system (TDR). While this policy mechanism may prevent native habitat area loss, the spatial pattern of reserved areas will shift, creating novel landscape patterns. The resulting altered fragmentation and connectivity...

Data from: Synopsis and taxonomic revision of three genera in the snake tribe Sonorini

Christian L. Cox, Alison R. Davis Rabosky, Iris A. Holmes, Jacobo Reyes-Velasco, Corey E. Roelke, Eric N. Smith, Oscar Flores-Villel, Jimmy A. McGuire & Jonathan A. Campbell
Delimiting species is a crucial goal of integrative biology, and yet can be misled by homoplasy and high levels of morphological variation. The snake tribe Sonorini contains three genera that have long confounded taxonomists: Chilomeniscus, Chionactis and Sonora. Dynamic colour evolution in this group, including rampant geographic variation in colour and colour polymorphism, has led to a chaotic taxonomy. We used mitochondrial and high-throughput nuclear data (ddRADseq) and complete taxonomic sampling of each genus to...

Data from: Chaparral bird community responses to prescribed fire and shrub removal in three management seasons

Erica A. Newman, Jennifer B. Potts, Morgan W. Tingley, Charles Vaughn & Scott L. Stephens
Chaparral, a type of shrubland common throughout the California Floristic Province, is subject to management and removal in regions where wildfire threatens human lives and property. Management practices include conducting prescribed burns outside of the historical fire season and employing mechanical fuel reduction (mastication). As the wildland–urban interface grows, particularly in coastal California, more of this ecosystem is subject to active management. To understand the ecological implications of current California chaparral fire management practices, we...

Data for Cold adaptation does not alter ATP homeostasis during cold exposure in Drosophila melanogaster

Caroline Williams
Data and analysis scripts for Williams et al. 2018 Integrative Zoology:

Data from: Pleistocene diversification in an ancient lineage: a role for glacial cycles in the evolutionary history of Dioon Lindl. (Zamiaceae).

Brian L. Dorsey, Timothy J Gregory, Chodon Sass & Chelsea D. Specht
Premise of the study: Recent estimates of crown ages for cycad genera (Late Miocene) challenge us to consider what processes have produced the extant diversity of this ancient group in such relatively little time. Pleistocene climate change has driven major shifts in species distributions in Mexico and may have led to speciation in the genus Dioon by forcing populations to migrate up in elevation thereby becoming separated by topography. Methods: We inferred orthologs from transcriptomes...

Data from: Consumption of carotenoids not increased by bacterial infection in brown trout embryos (Salmo trutta)

Lucas Marques Da Cunha, Laetitia G.E. Wilkins, Laure Menin, Daniel Ortitz, Véronique Vocat-Mottier, Claus Wedekind & Laetitia G. E. Wilkins
Carotenoids are organic pigment molecules that play important roles in signalling, control of oxidative stress, and immunity. Fish allocate carotenoids to their eggs, which gives them the typical yellow to red colouration and supports their resistance against microbial infections. However, it is still unclear whether carotenoids act mainly as a shield against infection or are used up during the embryos' immune defence. We investigated this question with experimental families produced from wild-caught brown trout (Salmo...

Data from: Scaling up DNA barcoding - primer sets for simple and cost efficient arthropod systematics by multiplex PCR and Illumina amplicon sequencing

Henrik Krehenwinkel, Susan R. Kennedy, Alexandra Rueda, Athena Lam & Rosemary G. Gillespie
1. The simplicity and cost efficiency of Illumina amplicon sequencing has greatly contributed to the advancement of DNA barcoding and metabarcoding applications. However, current amplicon sequencing based barcoding approaches are usually restricted to short, single-locus fragments, limiting their taxonomic and phylogenetic resolution. 2. Here, we establish a cost efficient and simple multiplex PCR protocol for arthropod systematics by Illumina amplicon sequencing. We introduce primer sets, including several new, generic primers, to reliably amplify nine loci...

Data from: A genotypic trade-off between constitutive resistance to viral infection and host growth rate

Lewis J. Bartlett, Lena Wilfert & Mike Boots
Genotypic trade-offs are fundamental to the understanding of the evolution of life-history traits. In particular, the evolution of optimal host defence and the maintenance of variation in defence against infectious disease is thought to be underpinned by such evolutionary trade-offs. However, empirical demonstrations of these trade-offs that satisfy the strict assumptions made by theoretical models are rare. Additionally, none of these trade-offs have yet been shown to be robustly replicable using a variety of different...

Data from: Dense infraspecific sampling reveals rapid and independent trajectories of plastome degradation in a heterotrophic orchid complex

Craig F. Barrett, Susann Wicke & Chodon Sass
Heterotrophic plants provide excellent opportunities to study the effects of altered selective regimes on genome evolution. Plastid genome (plastome) studies in heterotrophic plants are often based on one or a few highly divergent species or sequences as representatives of an entire lineage, thus missing important evolutionary-transitory events. Here we present the first infraspecific analysis of plastome evolution in any heterotrophic plant. By combining genome skimming and targeted sequence capture, we address hypotheses on the degree...

Data from: Opening the file drawer: Unexpected insights from a chytrid infection experiment

Allison Q. Byrne, Thomas J. Poorten, Jamie Voyles, Craig K.R. Willis, Erica Bree Rosenblum & Craig K. R. Willis
Infection experiments are critical for understanding wildlife disease dynamics. Although infection experiments are typically designed to reduce complexity, disease outcomes still result from complex interactions between host, pathogen, and environmental factors. Cryptic variation across factors can lead to decreased repeatability of infection experiments within and between research groups and hinder research progress. Furthermore, studies with unexpected results are often relegated to the “file drawer” and potential insights gained from these experimental outcomes are lost. Here,...

Data from: Moving like a model: mimicry of hymenopteran flight trajectories by clearwing moths of Southeast Asian rainforests

Marta A. Skowron Volponi, Donald J. McLean, Paolo Volponi, Robert Dudley & Donald James McLean
Clearwing moths are known for their physical resemblance to hymenopterans, but the extent of their behavioural mimicry is unknown. We describe zigzag flights of sesiid bee mimics which are nearly indistinguishable from those of sympatric bees, whereas sesiid wasp mimics display faster, straighter flights more akin to those of wasps. In particular, the flight of the sesiids Heterosphecia pahangensis, Aschistophleps argentifasciata and Pyrophleps cruentata resembles both Tetragonilla collina and T. atripes stingless bees and, to...

Data from: Collective behavior and colony persistence of social spiders depends on their physical environment

Ambika Kamath, Skylar D. Primavera, Colin M. Wright, Grant N. Doering, Kirsten A. Sheehy, Noa Pinter-Wollman, Jonathan N. Pruitt, Colin M Wright, Jonathan N Pruitt, Skylar D Primavera, Grant N Doering & Kirsten A Sheehy
The physical environment occupied by group-living animals can profoundly affect their cooperative social interactions and therefore their collective behavior and success. These effects can be especially apparent in human-modified habitats, which often harbor substantial variation in the physical environments available within them. For nest-building animal societies, this influence of the physical environment on collective behavior can be mediated by the construction of nests—nests could either buffer animal behavior from changes in the physical environment or...

Data from: Dry season survival of juvenile salmonids in an intermittent coastal stream

Jason L. Hwan, Albert Fernández-Chacón, Matt Buoro, Stephanie M. Carlson & Mathieu Buoro
We estimated dry season survival of imperiled salmonids in an intermittent coastal stream in California across four years (2009-2012). Our study encompassed two dry and two wet winters allowing us to explore patterns of survival across and within dry seasons with different antecedent precipitation. Apparent survival of age-0+ steelhead trout (Oncorhynchus mykiss) was higher following wet winters compared to dry winters. Moreover, antecedent precipitation was positively correlated with cumulative survival of age-0+ steelhead. Within years,...

Data from: Phylogenomics reveals rapid, simultaneous diversification of three major clades of Gondwanan frogs at the Cretaceous–Paleogene boundary

Yan-Jie Feng, David C. Blackburn, Dan Liang, David M. Hillis, David B. Wake, David C. Cannatella & Peng Zhang
Frogs (Anura) are one of the most diverse groups of vertebrates and comprise nearly 90% of living amphibian species. Their worldwide distribution and diverse biology make them well-suited for assessing fundamental questions in evolution, ecology, and conservation. However, despite their scientific importance, the evolutionary history and tempo of frog diversification remain poorly understood. By using a molecular dataset of unprecedented size, including 88-kb characters from 95 nuclear genes of 156 frog species, in conjunction with...

Data from: Range instability leads to cytonuclear discordance in a morphologically cryptic ground squirrel species complex

Mark A. Phuong, Ke Bi & Craig Moritz
The processes responsible for cytonuclear discordance frequently remain unclear. Here, we employed an exon capture dataset and demographic methods to test hypotheses generated by species distribution models to examine how contrasting histories of range stability vs. fluctuation have caused cytonuclear concordance and discordance in ground squirrel lineages from the Otospermophilus beecheyi species complex. Previous studies in O. beecheyi revealed three morphologically cryptic and highly divergent mitochondrial DNA lineages (named the Northern, Central, and Southern lineages...

Data from: Inferring the timing of long-distance dispersal between Rail metapopulations using genetic and isotopic assignments

Laurie A. Hall & Steven R. Beissinger
The stochastic and infrequent nature of long-distance dispersal often makes it difficult to detect. We quantified the frequency, distance, and timing of long-distance dispersal in a non-migratory, secretive wetland bird, the California black rail (Laterallus jamaicensis coturniculus), between an inland and a coastal metapopulation separated by greater than 100 km. Using 15 microsatellites in conjunction with stable carbon, nitrogen, and sulfur isotopes, we classified rails as: residents of their capture population, recent migrants that dispersed...

Data from: Modeling effects of nonbreeders on population growth estimates

Aline M. Lee, Jane M. Reid & Steven R. Beissinger
Adult individuals that do not breed in a given year occur in a wide range of natural populations. However, such nonbreeders are often ignored in theoretical and empirical population studies, limiting our knowledge of how nonbreeders affect realized and estimated population dynamics and potentially impeding projection of deterministic and stochastic population growth rates. We present and analyse a general modelling framework for systems where breeders and nonbreeders differ in key demographic rates, incorporating different forms...

Data from: Changes in spatial variance during a grassland to shrubland state transition

Zak Ratajczak, Paolo D'Odorico, Jesse B. Nippert, Scott L. Collins, Nathaniel A. Brunsell & Sujith Ravi
State transitions are changes in ecosystem structure and self-reinforcing feedbacks that are initiated when an exogenous driver variable crosses a threshold. Reversing state transitions is difficult and costly. While some state transitions are relatively rapid, many take years to decades. Outside of theoretical models, very little is known about slower state transitions and how they unfold in time and space. We quantified changes in spatial variance as a mesic grassland ecosystem shifts to a shrub-dominated...

Data from: The influence of spatially structured soil properties on tree community assemblages at a landscape scale in the tropical forests of southern Cameroon

Jason Vleminckx, Jean-Louis Doucet, Julie Morin-Rivat, Achille Biwolé, David Bauman, Olivier J. Hardy, Adeline Fayolle, Jean-François Gillet, Kasso Daïnou, Anaïs Gorel & Thomas Drouet
Species distribution within plant communities results from both the influence of deterministic processes, related to environmental conditions, and neutral processes related to dispersal limitation and stochastic events, the relative importance of each factor depending on the observation scale. Assessing the relative contribution of environment necessitates controlling for spatial dependences among data points. Recent methods, combining multiple regression and Moran's eigenvectors maps (MEM), have been proved successful in disentangling the influence of pure spatial processes related...

Data from: Precipitation alters interactions in a grassland ecological community

Nicolas Deguines, Justin S. Brashares & Laura R. Prugh
Climate change is transforming precipitation regimes world-wide. Changes in precipitation regimes are known to have powerful effects on plant productivity, but the consequences of these shifts for the dynamics of ecological communities are poorly understood. This knowledge gap hinders our ability to anticipate and mitigate the impacts of climate change on biodiversity. Precipitation may affect fauna through direct effects on physiology, behaviour or demography, through plant-mediated indirect effects, or by modifying interactions among species. In...

Data from: Survival by genotype: patterns at Mc1r are not black and white at the White Sands ecotone

Simone Des Roches, Rahel Sollmann, Kendall Calhoun, A. P. Rothstein, Erica B. Rosenblum, S. Des Roches, K. Calhoun, E. B. Rosenblum & R. Sollmann
Measuring links among genotype, phenotype and survival in the wild has long been a focus of studies of adaptation. We conducted a 4-year capture–recapture study to measure survival by genotype and phenotype in the Southwestern Fence Lizard (Sceloporus cowlesi) at the White Sands ecotone (transition area between white sands and dark soil habitats). We report several unanticipated findings. First, in contrast with previous work showing that cryptic blanched coloration in S. cowlesi from the heart...

Data from: Interaction between stimulus contrast and pre-saccadic crowding

Mehmet N. Agaoglu, Susana T.L. Chung & Susana T. L. Chung
Objects that are briefly flashed around the time of saccades are mislocalized. Previously, robust interactions between saccadic perceptual distortions and stimulus contrast have been reported. It is also known that crowding depends on the contrast of the target and flankers. Here, we investigated how stimulus contrast and crowding interact with pre-saccadic perception. We asked observers to report the orientation of a tilted Gabor presented in the periphery, with or without four flanking vertically oriented Gabors....

Data from: Minimal variation in eutherian brain growth rates during fetal neurogenesis

Andrew C. Halley
A central question in the evolution of brain development is whether species differ in rates of brain growth during fetal neurogenesis. Studies of neonatal data have found allometric evidence for brain growth rate differences according to physiological variables such as relative metabolism and placental invasiveness, but these findings have not been tested against fetal data directly. Here, we measure rates of exponential brain growth acceleration in 10 eutherian mammals, two marsupials, and two birds. Eutherian...

Data from: Precipitation drives global variation in natural selection

Adam Siepielski, Michael B. Morrissey, Mathieu Buoro, Stephanie M. Carlson, Christina M. Caruso, Sonya M. Clegg, Tim Coulson, Joseph DiBattista, Kiyoko M. Gotanda, Clinton D. Francis, Joe Hereford, Joel G. Kingsolver, Kate E. Augustine, Loeske E. B. Kruuk, Ryan A. Martin, Ben C. Sheldon, Nina Sletvold, Erik I. Svensson, Michael J. Wade & Andrew D. C. MacColl
Climate change has the potential to affect the ecology and evolution of every species on Earth. Although the ecological consequences of climate change are increasingly well documented, the effects of climate on the key evolutionary process driving adaptation—natural selection—are largely unknown. We report that aspects of precipitation and potential evapotranspiration, along with the North Atlantic Oscillation, predicted variation in selection across plant and animal populations throughout many terrestrial biomes, whereas temperature explained little variation. By...

Data from: Catecholaminergic regulation of learning rate in a dynamic environment

Marieke Jepma, Peter R. Murphy, Matthew R. Nassar, Mauricio Rangel-Gomez, Martijn Meeter & Sander Nieuwenhuis
Adaptive behavior in a changing world requires flexibly adapting one’s rate of learning to the rate of environmental change. Recent studies have examined the computational mechanisms by which various environmental factors determine the impact of new outcomes on existing beliefs (i.e., the ‘learning rate’). However, the brain mechanisms, and in particular the neuromodulators, involved in this process are still largely unknown. The brain-wide neurophysiological effects of the catecholamines norepinephrine and dopamine on stimulus-evoked cortical responses...

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