90 Works

Globally, plant-soil feedbacks are weak predictors of plant abundance

Kurt Reinhart, Jonathan Bauer, Sarah McCarthy-Neumann, Andrew MacDougall, José Hierro, Mariana Chiuffo, Scott Mangan, Johannes Heinze, Joana Bergmann, Jasmin Joshi, Richard Duncan, Jeff Diaz, Paul Kardol, Gemma Rutten, Markus Fischer, Wim Van Der Putten, T. Bezemer & John Klironomos
Plant-soil feedbacks (PSFs) have been shown to strongly affect plant performance under controlled conditions, and PSFs are thought to have far reaching consequences for plant population dynamics and the structuring of plant communities. However, thus far the relationship between PSF and plant species abundance in the field is not consistent. Here, we synthesize PSF experiments from tropical forests to semiarid grasslands, and test for a positive relationship between plant abundance in the field and PSFs...

Data from: A novel landscape genetics approach demonstrates the effects of human disturbance on the Udzungwa red colobus monkey (Procolobus gordonorum)

Maria Jose Ruiz-Lopez, Claudia Barelli, Francesco Rovero, Keith Hodges, Christian Roos, William E. Peterman & Nelson Ting
A comprehensive understanding of how human disturbance affects tropical forest ecosystems is critical for the mitigation of future losses in global biodiversity. Although many genetic studies of tropical forest fragmentation have been conducted to provide insight into this issue, relatively few have incorporated landscape data to explicitly test the effects of human disturbance on genetic differentiation among populations. In this study, we use a newly developed landscape genetic approach that relies on a genetic algorithm...

Data from: The geography of divergence-with-gene-flow facilitates multi-trait adaptation and the evolution of pollinator isolation in Mimulus aurantiacus

Sean Stankowski, Matthew A. Streisfeld & James M. Sobel
Ecological adaptation is the driving force during divergence-with-gene-flow and generates reproductive isolation early in speciation. Although gene flow opposes divergence, local adaptation can be facilitated by factors that prevent the breakup of favorable allelic combinations. We investigated how selection, genetic architecture, and geography have contributed to the maintenance of floral trait divergence and pollinator isolation between parapatric ecotypes of Mimulus aurantiacus. Combining greenhouse, field, and genomic studies, we show that sharp clines in floral traits...

Data from: Temporal and phylogenetic evolution of the sauropod dinosaur body plan

Karl T. Bates, Philip D. Mannion, Peter L. Falkingham, Stephen L. Brusatte, John R. Hutchinson, Alexandros Otero, William I. Sellers, Corwin Sullivan, Kent A. Stevens & Vivian Allen
The colossal size and body plan of sauropod dinosaurs are unparalleled in terrestrial vertebrates. However, to date, there have been only limited attempts to examine temporal and phylogenetic patterns in the sauropod bauplan. Here, we combine three-dimensional computational models with phylogenetic reconstructions to quantify the evolution of whole-body shape and body segment properties across the sauropod radiation. Limitations associated with the absence of soft tissue preservation in fossils result in large error bars about mean...

Data from: A redescription and phylogenetic analysis based on new material of the fossil newts Taricha oligocenica Van Frank, 1955 and Taricha lindoei Naylor, 1979 (Amphibia, Salamandridae) from the Oligocene of Oregon.

John J. Jacisin & Samantha S.B. Hopkins
Complete body fossils of salamanders are relatively rare, but provide critical information on the evolutionary roots of extant urodele clades. We describe new specimens of the fossil salamandrids Taricha oligocenica Van Frank, 1955, and Taricha lindoei Naylor, 1979, from the Oligocene Mehama and John Day Formations of Oregon that illustrate aspects of skeletal morphology previously unseen in these taxa, and contribute to our understanding of population-level variation. Morphological analysis of these specimens supports the classification...

Data from: Genomewide variation provides insight into evolutionary relationships in a monkeyflower species complex (Mimulussect.Diplacus)

Madeline A. Chase, Sean Stankowski & Matthew A. Streisfeld
PREMISE OF THE STUDY: Evolutionary radiations provide excellent opportunities to study the origins of biodiversity, but rapid divergence and ongoing gene flow make inferring evolutionary relationships among taxa difficult. Consequently, multiple tools that combine morphological and genomic analyses may be necessary to provide a clear picture of relationships. We used an integrative approach to shed light on relationships within a diverse radiation of monkeyflowers (Mimulus section Diplacus) with a controversial taxonomic history. METHODS: Using genome-wide...

Data from: A rich diversity of opercle bone shape among teleost fishes

Charles B. Kimmel, Clayton M. Small & Matthew L. Knope
The opercle is a prominent craniofacial bone supporting the gill cover in all bony fish and has been the subject of morphological, developmental, and genetic investigation. We surveyed the shapes of this bone among 110 families spanning the teleost tree and examined its pattern of occupancy in a principal component-based morphospace. Contrasting with expectations from the literature that suggest the local morphospace would be only sparsely occupied, we find primarily dense, broad filling of the...

Data from: Temporal identity establishes columnar neuron morphology, connectivity, and function in a Drosophila navigation circuit

Luis F. Sullivan, Timothy L. Warren & Chris Q. Doe
The insect central complex (CX) is a conserved brain region containing 60+ neuronal subtypes, several of which contribute to navigation. It is not known how CX neuronal diversity is generated or how developmental origin of subtypes relates to function. We mapped the developmental origin of four key CX subtypes and found that neurons with similar origin have similar axon/dendrite targeting. Moreover, we found that the temporal transcription factor (TTF) Eyeless/Pax6 regulates the development of two...

Data from: Genomic patterns of introgression in rainbow and westslope cutthroat trout illuminated by overlapping paired-end RAD sequencing

Paul A. Hohenlohe, Mitch D. Day, Stephen J. Amish, Michael R. Miller, Nicholas Kamps-Hughes, Matthew C. Boyer, Clint C. Muhlfeld, Fred W. Allendorf, Eric A. Johnson, Gordon Luikart & Nick Kamps-Hughes
Rapid and inexpensive methods for genomewide single nucleotide polymorphism (SNP) discovery and genotyping are urgently needed for population management and conservation. In hybridized populations, genomic techniques that can identify and genotype thousands of species-diagnostic markers would allow precise estimates of population- and individual-level admixture as well as identification of ‘super invasive’ alleles, which show elevated rates of introgression above the genomewide background (likely due to natural selection). Techniques like restriction-site-associated DNA (RAD) sequencing can discover...

Data from: The biogeography of marine invertebrate life histories

Dustin J. Marshall, Patrick J. Krug, Elena K. Kupriyanova, Maria Byrne & Richard B. Emlet
Biologists have long sought to identify and explain patterns in the diverse array of marine life histories. The most famous speculation about such patterns is Gunnar Thorson’s suggestion that species producing planktonic larvae are rarer at higher latitudes (Thorson’s rule). Although some elements of Thorson’s rule have proven incorrect, other elements remain untested. With a wealth of new life-history data, statistical approaches, and remote-sensing technology, new insights into marine reproduction can be generated. We gathered...

Data from: Population genomics of divergence within an obligate pollination mutualism: selection maintains differences between Joshua tree species

Anne M. Royer, Matthew A. Streisfeld & Christopher Irwin Smith
PREMISE OF THE STUDY: Speciation is a complex process that can be shaped by many factors, from geographic isolation to interspecific interactions. In Joshua trees, selection from pollinators on style length has been hypothesized to contribute to the maintenance of differentiation between two hybridizing sister species. We used population genomics approaches to measure the extent of genetic differentiation between these species, test whether selection maintains differences between them, and determine whether genetic variants associated with...

Audio Cartography

Megen Brittell
Rendered maps (audioCartography-maps); Prepare Data (audioCartography-prepare); Present Stimuli (audioCartography-present); Process Data (audioCartography-process)

Climate Change Maps in the US Media 2012-2017 and Content Analysis

Carolyn S. Fish

Shifting Practices for a Stronger Tomorrow: Local Journalism in the Pacific Northwest (2019)

Damian Radcliffe

Data from: \"De novo assembly transcriptome for the rostrum dace (Leuciscus burdigalensis, Cyprinidae: fish) naturally infected by a copepod ectoparasite\" in Genomic Resources Notes accepted 1 December 2014 to 31 January 2015

Olivier Rey, Géraldine Loot, Olivier Bouchez, Simon Blanchet, Maria Jose Ruiz-Lopez, Nelson Ting, Paul D. Etter, Eric A. Johnson, Tony L. Goldberg, Colin A. Chapman, James H. Jones, Patrick A. Omeja & William M. Switzer
The emergence of pathogens represents substantial threats to public health, livestock, domesticated animals, and biodiversity. How wild populations respond to emerging pathogens has generated a lot of interest in the last two decades. With the recent advent of high-throughput sequencing technologies it is now possible to develop large transcriptomic resources for non-model organisms, hence allowing new research avenues on the immune responses of hosts from a large taxonomic spectra. We here focused on a wild...

Data from: Geographic cline analysis as a tool for studying genome-wide variation: a case study of pollinator-mediated divergence in a monkeyflower

Sean Stankowski, James M. Sobel & Matthew A. Streisfeld
A major goal of speciation research is to reveal the genomic signatures that accompany the speciation process. Genome scans are routinely used to explore genome-wide variation and identify highly differentiated loci that may contribute to ecological divergence, but they do not incorporate spatial, phenotypic or environmental data that might enhance outlier detection. Geographic cline analysis provides a potential framework for integrating diverse forms of data in a spatially explicit framework, but has not been used...

Data from: Patterns of transposable element variation and clinality in Drosophila

Jeffrey R. Adrion, David J. Begun & Matthew W. Hahn
Natural populations often exist in spatially diverse environments and may experience variation in the strength and targets of natural selection across their ranges. Drosophila provides an excellent opportunity to study the effects of spatially varying selection in natural populations, as both D. melanogaster and D. simulans live across a wide range of environments in North America. Here, we characterize patterns of variation in transposable elements (TEs) from six populations of D. melanogaster and nine populations...

Data from: Evolution of stickleback in 50 years on earthquake-uplifted islands

Emily A. Lescak, Susan L. Bassham, Julian Catchen, Ofer Gelmond, Mary L. Sherbick, Frank A. Von Hippel & William A. Cresko
How rapidly can animal populations in the wild evolve when faced with sudden environmental shifts? Uplift during the 1964 Great Alaska Earthquake abruptly created freshwater ponds on multiple islands in Prince William Sound and the Gulf of Alaska. In the short time since the earthquake, the phenotypes of resident freshwater threespine stickleback fish on at least three of these islands have changed dramatically from their oceanic ancestors. To test the hypothesis that these freshwater populations...

Data from: Phylogenomics provides new insight into evolutionary relationships and genealogical discordance in the reef-building coral genus Acropora

Natalie L. Rosser, Luke Thomas, Sean Stankowski, Zoe T. Richards, W. Jason Kennington & Michael S. Johnson
Understanding the genetic basis of reproductive isolation is a long-standing goal of speciation research. In recently diverged populations, genealogical discordance may reveal genes and genomic regions that contribute to the speciation process. Previous work has shown that conspecific colonies of Acropora that spawn in different seasons (spring and autumn) are associated with highly diverged lineages of the phylogenetic marker PaxC. Here, we used 10 034 single-nucleotide polymorphisms to generate a genome-wide phylogeny and compared it...

Data from: MycoDB, a global database of plant response to mycorrhizal fungi

V. Bala Chaudhary, Megan A. Rúa, Anita Antoninka, James D. Bever, Jeffery Cannon, Ashley Craig, Jessica Duchicela, Alicia Frame, Monique Gardes, Catherine Gehring, Michelle Ha, Miranda Hart, Jacob Hopkins, Baoming Ji, Nancy Collins Johnson, Wittaya Kaonongbua, Justine Karst, Roger T. Koide, Louis J. Lamit, James Meadow, Brook G. Milligan, John C. Moore, , Bridget Piculell, Blake Ramsby … & Jason D. Hoeksema
Plants form belowground associations with mycorrhizal fungi in one of the most common symbioses on Earth. However, few large-scale generalizations exist for the structure and function of mycorrhizal symbioses, as the nature of this relationship varies from mutualistic to parasitic and is largely context-dependent. We announce the public release of MycoDB, a database of 4,010 studies (from 438 unique publications) to aid in multi-factor meta-analyses elucidating the ecological and evolutionary context in which mycorrhizal fungi...

Data from: Environmentally induced changes in correlated responses to selection reveal variable pleiotropy across a complex genetic network

Kristin L. Sikkink, Rose M. Reynolds, William A. Cresko & Patrick C. Phillips
Selection in novel environments can lead to a coordinated evolutionary response across a suite of characters. Environmental conditions can also potentially induce changes in the genetic architecture of complex traits, which in turn could alter the pattern of the multivariate response to selection. We describe a factorial selection experiment using the nematode Caenorhabditis remanei in which two different stress-related phenotypes (heat and oxidative stress resistance) were selected under three different environmental conditions. The pattern of...

Data from: Variation in ecophysiological traits might contribute to ecogeographic isolation and divergence between parapatric ecotypes of Mimulus aurantiacus

James M. Sobel, Sean Stankowski & Matthew A. Streisfeld
Many forms of reproductive isolation contribute to speciation, and early acting barriers may be especially important, because they have the first opportunity to limit gene flow. Ecogeographic isolation occurs when intrinsic traits of taxa contribute to disjunct geographic distributions, reducing the frequency of inter‐taxon mating. Characterizing this form of isolation requires knowledge of both the geographic arrangement of suitable habitats in nature and the identification of phenotypes involved in shaping geographic distributions. In Mimulus aurantiacus,...

Footprints of local adaptation span hundreds of linked genes in the Atlantic silverside genome

Aryn Wilder, Stephen Palumbi, David Conover & Nina Overgaard Therkildsen
The study of local adaptation in the presence of ongoing gene flow is the study of natural selection in action, revealing the functional genetic diversity most relevant to contemporary pressures. In addition to individual genes, genome-wide architecture can itself evolve to enable adaptation. Distributed across a steep thermal gradient along the east coast of North America, Atlantic silversides (Menidia menidia) exhibit an extraordinary degree of local adaptation in a suite of traits, and the capacity...

Chromonomer: a tool set for repairing and enhancing assembled genomes through integration of genetic maps and conserved synteny

Julian Catchen, Angel Amores & Susan Bassham
The pace of the sequencing and computational assembly of novel reference genomes is accelerating. Though DNA sequencing technologies and assembly software tools continue to improve, biological features of genomes such as repetitive sequence as well as molecular artifacts that often accompany sequencing library preparation can lead to fragmented or chimeric assemblies. If left uncorrected, defects like these trammel progress on understanding genome structure and function, or worse, positively mislead this research. Fortunately, integration of additional,...

Latitudinal gradients in population growth do not reflect demographic responses to climate

Megan Peterson, Graham Bailes, Lauren Hendricks, Laurel Pfeifer-Meister, Paul Reed, Scott Bridgham, Bart Johnson, Robert Shriver, Ellen Waddle, Hannah Wroton, Daniel Doak, Bitty Roy & William Morris
Spatial gradients in population growth, such as across latitudinal or elevational gradients, are often assumed to primarily be driven by variation in climate, and are frequently used to infer species’ responses to climate change. Here, we use a novel demographic, mixed model approach to dissect the contributions of climate variables vs. other latitudinal or local site effects on spatiotemporal variation in population performance in three perennial bunchgrasses. For all three species, we find that performance...

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