786 Works

Data from: Characterization of a male reproductive transcriptome for Peromyscus eremicus (Cactus mouse)

Lauren L. Kordonowy, Matthew D. MacManes & Michael B. Eisen
Rodents of the genus Peromyscus have become increasingly utilized models for investigations into adaptive biology. This genus is particularly powerful for research linking genetics with adaptive physiology or behaviors, and recent research has capitalized on the unique opportunities afforded by the ecological diversity of these rodents. Well characterized genomic and transcriptomic data is intrinsic to explorations of the genetic architecture responsible for ecological adaptations. Therefore, this study characterizes the transcriptome of three male reproductive tissues...

Data from: Baby on board: olfactory cues indicate pregnancy and fetal sex in a non-human primate

Jeremy Chase Crawford & Christine M. Drea
Olfactory cues play an integral, albeit underappreciated, role in mediating vertebrate social and reproductive behaviour. These cues fluctuate with the signaller's hormonal condition, coincident with and informative about relevant aspects of its reproductive state, such as pubertal onset, change in season and, in females, timing of ovulation. Although pregnancy dramatically alters a female's endocrine profiles, which can be further influenced by fetal sex, the relationship between gestation and olfactory cues is poorly understood. We therefore...

Data from: Avoiding topsy-turvy: how Anna's Hummingbirds (Calypte anna) fly through upward gusts

Marc A. Badger, Hao Wang & Robert Dudley
Flying organisms frequently confront the challenge of maintaining stability when moving within highly dynamic airflows near the Earth's surface. Either aerodynamic or inertial forces generated by appendages and other structures, such as the tail, may be used to offset aerial perturbations, but these responses have not been well characterized. To better understand how hummingbirds modify wing and tail motions in response to individual gusts, we filmed Anna's Hummingbirds as they negotiated an upward jet of...

Data from: Estimating and mitigating amplification bias in qualitative and quantitative arthropod metabarcoding

Henrik Krehenwinkel, Madeline Wolf, Jun Ying Lim, Andrew J. Rominger, Warren B. Simison & Rosemary G. Gillespie
Amplicon based metabarcoding promises rapid and cost-efficient analyses of species composition. However, it is disputed whether abundance estimates can be derived from metabarcoding due to taxon specific PCR amplification biases. PCR-free approaches have been suggested to mitigate this problem, but come with considerable increases in workload and cost. Here, we analyze multilocus datasets of diverse arthropod communities, to evaluate whether amplification bias can be countered by (1) targeting loci with highly degenerate primers or conserved...

Data from: Novel trophic niches drive variable progress toward ecological speciation within an adaptive radiation of pupfishes

Christopher H. Martin & Laura C. Feinstein
Adaptive radiation is recognized by a rapid burst of phenotypic, ecological, and species diversification. However, it is unknown whether different species within an adaptive radiation evolve reproductive isolation at different rates. We compared patterns of genetic differentiation among nascent species within an adaptive radiation of Cyprinodon pupfishes using genotyping by sequencing. Similar to classic adaptive radiations, this clade exhibits rapid morphological diversification rates and two species are novel trophic specialists, a scale-eater and hard-shelled prey...

Data from: Comparative multi-locus phylogeography confirms multiple vicariance events in co-distributed rainforest frogs

Rayna C Bell, Jason B MacKenzie, Michael J Hickerson, Krystle L Chavarría, Michael Cunningham, Stephen Williams, Craig Moritz & K. L. Chavarria
Though Pleistocene refugia are frequently cited as drivers of species diversification, comparisons of molecular divergence among sister species typically indicate a continuum of divergence times from the late Miocene, rather than a clear pulse of speciation events at the Last Glacial Maximum (LGM). Community-scale inference methods that explicitly test for multiple vicariance events, and account for differences in ancestral effective population size and gene flow, are well suited for detecting heterogeneity of species’ responses to...

Data from: Contemporary land change alters fish communities in a San Francisco Bay drainage, California, U.S.A.

Kristina Cervantes-Yoshida, Robert A. Leidy & Stephanie M. Carlson
Urbanization is one of the leading threats to freshwater biodiversity, and urban regions continue to expand globally. Here we examined the relationship between recent urbanization and shifts in stream fish communities. We sampled fishes at 32 sites in the Alameda Creek Watershed, near San Francisco, California, in 1993–1994 and again in 2009, and we quantified univariate and multivariate changes in fish communities between the sampling periods. Sampling sites were classified into those downstream of a...

Data from: Population dynamics of an Arctiid caterpillar-tachinid parasitoid system using state-space models

Richard Karban & Perry De Valpine
1. Population dynamics of insect host–parasitoid systems are important in many natural and managed ecosystems and have inspired much ecological theory. However, ecologists have a limited knowledge about the relative strengths of species interactions, abiotic effects and density dependence in natural host–parasitoid dynamics. Statistical time-series analyses would be more informative by incorporating multiple factors, measurement error and noisy dynamics. 2. We use a novel maximum likelihood and model-selection analysis of a state-space model for host–parasitoid...

Data from: Carnivore carcasses are avoided by carnivores

Marcos Moleon, Carlos Martínez-Carrasco, Oliver Muellerklein, Wayne Getz, Carlos Muñoz-Lozano, José Antonio Sánchez-Zapata & Wayne M. Getz
1. Ecologists have traditionally focused on herbivore carcasses as study models in scavenging research. However, some observations of scavengers avoiding feeding on carnivore carrion suggest that different types of carrion may lead to differential pressures. Untested assumptions about carrion produced at different trophic levels could therefore lead ecologists to overlook important evolutionary processes and their ecological consequences. 2. Our general goal was to investigate the use of mammalian carnivore carrion by vertebrate scavengers. In particular,...

Data from: Host and habitat specialization of avian malaria in Africa

Claire Loiseau, Ryan J. Harrigan, Alexandre Robert, Rauri C. K. Bowie, Henri A. Thomassen, Thomas B. Smith & Ravinder N. M. Sehgal
Studies of both vertebrates and invertebrates have suggested that specialists, as compared to generalists, are likely to suffer more serious declines in response to environmental change. Less is known about the effects of environmental conditions on specialist vs. generalist parasites. Here, we study the evolutionary strategies of malaria parasites (Plasmodium spp.) among different bird host communities. We determined the parasite diversity and prevalence of avian malaria in three bird communities in the lowland forests in...

Data from: Urban land use limits regional bumble bee gene flow

Shalene Jha & Claire Kremen
Potential declines in native pollinator communities and increased reliance on pollinator-dependent crops have raised concerns about native pollinator conservation and dispersal across human-altered landscapes. Bumble bees are one of the the most effective native pollinators, and are often the first to be extirpated in human-altered habitats, yet little is known about how bumble bees move across fine spatial scales and what landscapes promote or limit their gene flow. In this study, we examine regional genetic...

Data from: Invasive legumes can associate with many mutualists of native legumes, but usually do not

Kimberly J. La Pierre, Ellen L. Simms, Mohsin Tariq, Marriam Zafar & Stephanie S. Porter
Mutualistic interactions can strongly influence species invasions, as the inability to form successful mutualisms in an exotic range could hamper a host’s invasion success. This barrier to invasion may be overcome if an invader either forms novel mutualistic associations or finds and associates with familiar mutualists in the exotic range. Here we ask (1) does the community of rhizobial mutualists associated with invasive legumes in their exotic range overlap with that of local native legumes...

Data from: Variation in thermal niche of a declining river-breeding frog: from counter-gradient responses to population distribution patterns

Alessandro Catenazzi & Sarah J. Kupferberg
When dams or climate change alter the thermal regimes of rivers, conditions can shift outside optimal ranges for aquatic poikilothermic vertebrates. Plasticity in thermal performance and preference, however, may allow temperature-vulnerable fauna to persist under challenging conditions. To determine the effects of thermal regime on Rana boylii (Ranidae), a threatened frog species endemic to rivers of California and Oregon, we quantified tadpole thermal preferences and performance in relation to thermal conditions. We monitored temperature and...

Data from: Evidence for ecological divergence across a mosaic of soil types in an Amazonian tropical tree: Protium subserratum (Burseraceae)

Tracy M. Misiewicz & Paul V. A. Fine
Soil gradients are known to be an important driver of divergent natural selection in plant populations. Neotropical trees have the highest diversity on earth and it is not uncommon to find soil specialist congeners distributed parapatrically. Nevertheless very little is known about the role that edaphic heterogeneity plays in the origin and maintenance of tropical tree diversity. We predict that the mosaic of different soils in the lowland Amazon rainforest play a major role in...

Data from: Diversification and phylogeographic structure in widespread Azteca plant-ants from the northern Neotropics

Elizabeth G. Pringle, Timothy C. Bonebrake, Santiago R. Ramírez, Deborah M. Gordon & Rodolfo Dirzo
The Neotropical myrmecophytic tree Cordia alliodora hosts symbiotic Azteca ants in most of its widespread range. The taxonomy of the genus Azteca is notoriously difficult, which has frequently obscured species identity in ecological studies. We used sequence data from one mitochondrial and four nuclear loci to infer phylogenetic relationships, patterns of geographic distribution, and timing of diversification for 181 colonies of Azteca from Mexico to Colombia. We identified at least eight lineages of C. alliodora-dwelling...

Data from: The utility of normalized difference vegetation index for predicting African buffalo forage quality

Sadie J. Ryan, Paul C. Cross, John Winnie, Craig Hay, Justin Bowers & Wayne M. Getz
Many studies of mammalian herbivores have employed remotely sensed vegetation greenness, in the form of Normalized Difference Vegetation Index (NDVI) as a proxy for forage quality. The assumption that reflected greenness represents forage quality often goes untested, and limited data exist on the relationships between remotely sensed and traditional forage nutrient indicators. We provide the first study connecting NDVI and forage nutrient indicators within a free-ranging African herbivore ecosystem. We examined the relationships between fecal...

Data from: Montane refugia predict population genetic structure in the Large-blotched Ensatina salamander

Thomas J. Devitt, Susan E. Cameron Devitt, Bradford D. Hollingsworth, Jimmy A. McGuire & Craig Moritz
Understanding the biotic consequences of Pleistocene range shifts and fragmentation remains a fundamental goal in historical biogeography and evolutionary biology. Here, we combine species distribution models (SDM) from the present and two late Quaternary time periods with multilocus genetic data (mitochondrial DNA and microsatellites) to evaluate the effect of climate-induced habitat shifts on population genetic structure in the Large-blotched Ensatina (Ensatina eschscholtzii klauberi), a plethodontid salamander endemic to middle and high-elevation conifer forest in the...

Data from: Genetic signature of population fragmentation varies with mobility in seven bird species of a fragmented Kenyan cloud forest

Tom Callens, Peter Galbusera, Erik Matthysen, Eric Y Durand, Mwangi Githiru, Jeroen R Huyghe & Luc Lens
Habitat fragmentation can restrict geneflow, reduce neighbourhood effective population size, and increase genetic drift and inbreeding in small, isolated habitat remnants. The extent to which habitat fragmentation leads to population fragmentation, however, differs among landscapes and taxa. Commonly, researchers use information on the current status of a species to predict population effects of habitat fragmentation. Such methods, however, do not convey information on species-specific responses to fragmentation. Here we compare levels of past population differentiation,...

Data from: Retracing the Hawaiian silversword radiation despite phylogenetic, biogeographic, and paleogeographic uncertainty

Michael J. Landis, William A. Freyman & Bruce G. Baldwin
The Hawaiian silversword alliance (Asteraceae) is an iconic adaptive radiation. However, like many island plant lineages, no fossils have been assigned to the clade. As a result, the clade's age and diversification rate are not known precisely, making it difficult to test biogeographic hypotheses about the radiation. Without fossils, paleogeographically structured biogeographic processes may inform species divergence times; for example, an island must first exist for a clade to radiate upon it. We date the...

Data from: Extensive gene tree discordance and hemiplasy shaped the genomes of North American columnar cacti

Dario Copetti, Alberto Burquez, Enriquena Bustamante, Joseph L. M. Charboneau, Kevin L. Childs, Luis E. Eguiarte, Seunghee Lee, Tiffany L. Liu, Michelle M. McMahon, Noah K. Whiteman, Rod A. Wing, Martin F. Wojciechowski & Michael J. Sanderson
Few clades of plants have proven as difficult to classify as cacti. One explanation may be an unusually high level of convergent and parallel evolution (homoplasy). To evaluate support for this phylogenetic hypothesis at the molecular level, we sequenced the genomes of four cacti in the especially problematic tribe Pachycereeae, which contains most of the large columnar cacti of Mexico and adjacent areas, including the iconic saguaro cactus (Carnegiea gigantea) of the Sonoran Desert. We...

Data from: Eco-genomic analysis of the poleward range expansion of the wasp spider Argiope bruennichi shows rapid adaptation and genomic admixture

Henrik Krehenwinkel, Dennis Rödder & Diethard Tautz
Poleward range expansions are commonly attributed to global change, but could alternatively be driven by rapid evolutionary adaptation. A well-documented example of a range expansion during the past decades is provided by the European wasp spider Argiope bruennichi. Using ecological niche modeling, thermal tolerance experiments and a genome-wide analysis of gene expression divergence, we show that invasive populations have adapted to novel climatic conditions in the course of their expansion. Their climatic niche shift is...

Data from: Parasite-mediated selection drives an immunogenetic tradeoff in plains zebras (Equus quagga)

Pauline L. Kamath, Wendy C. Turner, Martina Küsters & Wayne M. Getz
Pathogen evasion of the host immune system is a key force driving extreme polymorphism in genes of the major histocompatibility complex (MHC). Although this gene family is well characterized in structure and function, there is still much debate surrounding the mechanisms by which MHC diversity is selectively maintained. Many studies have investigated relationships between MHC variation and specific pathogens, and have found mixed support for and against the hypotheses of heterozygote advantage, frequency-dependent or fluctuating...

Data from: Genetic isolation between two recently diverged populations of a symbiotic fungus

Sara Branco, Pierre Gladieux, Christopher E. Ellison, Alan Kuo, Kurt LaButii, Anna Lipzen, Igor V. Grigoriev, Hui-Ling Liao, Rytas Vilgalys, Kabir G. Peay, John W. Taylor, Thomas D. Bruns & Kurt LaButti
Fungi are an omnipresent and highly diverse group of organisms, making up a significant part of eukaryotic diversity. Little is currently known about the drivers of fungal population differentiation and subsequent divergence of species, particularly in symbiotic, mycorrhizal fungi. Here, we investigate the population structure and environmental adaptation in Suillus brevipes (Peck) Kuntze, a wind-dispersed soil fungus that is symbiotic with pine trees. We assembled and annotated the reference genome for Su. brevipes and resequenced...

Data from: Measuring ectomycorrhizal fungal dispersal: macroecological patterns driven by microscopic propagules

Kabir G. Peay, Max G. Schubert, Nhu H. Nguyen & Thomas D. Bruns
Dispersal plays a prominent role in most conceptual models of community assembly. However, direct measurement of dispersal across a whole community is difficult at ecologically relevant spatial scales. For cryptic organisms, such as fungi and bacteria, the scale and importance of dispersal limitation has become a major point of debate. We use an experimental island biogeographic approach to measure the effects of dispersal limitation on the ecological dynamics of an important group of plant symbionts,...

Data from: A single microphone noise reduction algorithm based on the detection and reconstruction of spectro-temporal features

Tyler P. Lee & Frederic E. Theunissen
Animals throughout the animal kingdom excel at extracting individual sounds from competing background sounds, yet current state-of-the-art signal processing algorithms struggle to process speech in the presence of even modest background noise. Recent psychophysical experiments in humans and electrophysiological recordings in animal models suggest that the brain is adapted to process sounds within the restricted domain of spectro-temporal modulations found in natural sounds. Here, we describe a novel single microphone noise reduction algorithm called spectro-temporal...

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