94 Works

Data from: Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate

France Denoeud, Simon Henriet, Sutada Mungpakdee, Jean-Marc Aury, Corinne Da Silva, Henner Brinkmann, Jana Mikhaleva, Lisbeth C. Olsen, Claire Jubin, Cristian Cañestro, Jean-Marie Bouquet, Gemma Danks, Julie Poulain, Coen Campsteijn, Marcin Adamski, Ismael Cross, Fekadu Yadetie, Matthieu Muffato, Alexandra Louis, Stephen Butcher, Georgia Tsagkogeorga, Anke Konrad, Sarabdeep Singh, Marit F. Jensen, Evelyne Huynh Cong … & Daniel Chourrout
Genomes of animals as different as sponges and humans show conservation of global architecture. Here we show that multiple genomic features including transposon diversity, developmental gene repertoire, physical gene order, and intron-exon organization are shattered in the tunicate Oikopleura, belonging to the sister group of vertebrates and retaining chordate morphology. Ancestral architecture of animal genomes can be deeply modified and may therefore be largely nonadaptive. This rapidly evolving animal lineage thus offers unique perspectives on...

Data from: The genetic basis of a rare flower color polymorphism in Mimulus lewisii provides insight to the evolutionary mutation spectrum

Carrie A. Wu, Matthew A. Streisfeld, Laura I. Nutter & Kaitlyn A. Cross
A long-standing question in evolutionary biology asks whether the genetic changes contributing to phenotypic evolution are predictable. Here, we identify a genetic change associated with segregating variation in flower color within a population of Mimulus lewisii. To determine whether these types of changes are predictable, we combined this information with data from other species to investigate whether the spectrum of mutations affecting flower color transitions differs based on the evolutionary time-scale since divergence. We used...

Data from: Statistical analysis of dental variation in the Oligocene equid Miohippus (Mammalia, Perissodactyla) of Oregon

Nicholas A. Famoso
As many as eight species of the “anchitherine” equid Miohippus have been identified from the John Day Formation of Oregon, but no statistical analysis of variation in these horses has yet been conducted to determine if that level of diversity is warranted. Variation of the anterior-posterior length and transverse width of upper and lower teeth of Turtle Cove Member Miohippus was compared to that of M. equinanus, Mesohippus bairdii, Equus quagga, and Tapirus terrestris using...

Data from: Genome-wide analyses of the Bemisia tabaci species complex reveal contrasting patterns of admixture and complex demographic histories

Samia Elfekih, Paul Etter, Weetek T. Tay, Matteo Fumagalli, Karl Gordon, Eric Johnson & Paul De Barro
Once considered a single species, the whitefly, Bemisia tabaci, is a complex of numerous morphologically indistinguishable species. Within the last three decades, two of its members (MED and MEAM1) have become some of the world's most damaging agricultural pests invading countries across Europe, Africa, Asia and the Americas and affecting a vast range of agriculturally important food and fiber crops through both feeding-related damage and the transmission of numerous plant viruses. For some time now,...

Data from: Quantifying the dark data in museum fossil collections as palaeontology undergoes a second digital revolution

Charles R. Marshall, Seth Finnegan, Erica C. Clites, Patricia A. Holroyd, Nicole Bonuso, Crystal Cortez, Edward Davis, Gregory P. Dietl, Patrick S. Druckenmiller, Ron C. Eng, Christine Garcia, Kathryn Estes-Smargiassi, Austin Hendy, Kathy A. Hollis, Holly Little, Elizabeth A. Nesbitt, Peter Roopnarine, Leslie Skibinski, Jann Vendetti & Lisa D. White
Large-scale analysis of the fossil record requires aggregation of palaeontological data from individual fossil localities. Prior to computers these synoptic datasets were compiled by hand, a laborious undertaking that took years of effort and forced palaeontologists to make difficult choices about what types of data to tabulate. The advent of desktop computers ushered in palaeontology’s first digital revolution – online literature-based databases, such as the Paleobiology Database (PBDB). However, the published literature represents only a...

Public opinion about management strategies for a low-profile Species across multiple jurisdictions: whitebark pine in the northern Rockies

Elizabeth Shanahan, Eric Raile, Helen Naughton, Michael Wallner & Kendall Houghton
1. As public land managers seek to adopt and implement conservation measures aimed at reversing or slowing the negative effects of climate change, they are looking to understand public opinion regarding different management strategies. 2. This study explores drivers of attitudes toward different management strategies (i.e., no management, protection, and restoration) for a low-profile but keystone tree species, the whitebark pine (Pinus albicaulis), in the Greater Yellowstone Ecosystem. Since the whitebark pine species has a...

Data from: Wolbachia infection associated with increased recombination in Drosophila

Nadia D. Singh
Wolbachia is a maternally-transmitted endosymbiotic bacteria that infects a large diversity of arthropod and nematode hosts. Some strains of Wolbachia are parasitic, manipulating host reproduction to benefit themselves, while other strains of Wolbachia exhibit obligate or facultative mutualisms with their host. The effects of Wolbachia on its host are many, though primarily relate to host immune and reproductive function. Here we test the hypothesis that Wolbachia infection alters the frequency of homologous recombination during meiosis....

High-speed video recordings of Müller's larva swimming and feeding

George Von Dassow
These data form the basis for the paper "Large-scale ciliary reversal mediates capture of individual algal prey by Müller's larva" by George von Dassow and Christina I. Ellison, in press at Invertebrate Biology as of late 2019 (preprint on bioRxiv, doi.org/10.1101/709790). Wild-caught Müller's larva of several species of polyclad flatworm were observed swimming and feeding on unicellular algae using high-speed video. These videos document local ciliary reversal mediating prey capture, one cell at a time,...

Data from: Temporal structure of human gaze dynamics is invariant during free viewing

Colleen A. Marlow, Indre V. Viskontas, Alisa Matlin, Cooper Boydston, Adam Boxer & Richard P. Taylor
We investigate the dynamic structure of human gaze and present an experimental study of the frequency components of the change in gaze position over time during free viewing of computer-generated fractal images. We show that changes in gaze position are scale-invariant in time with statistical properties that are characteristic of a random walk process. We quantify and track changes in the temporal structure using a well-defined scaling parameter called the Hurst exponent, H. We find...

Data from: Species selection favors dispersive life histories in sea slugs, but higher per-offspring investment drives shifts to short-lived larvae

Patrick J. Krug, Jann E. Vendetti, Ryan A. Ellingson, Cynthia D. Trowbridge, Yayoi M. Hirano, Danielle Y. Trathen, Albert K. Rodriguez, Cornelis Swennen, Nerida G. Wilson & Ángel A. Valdés
For 40 years, paleontological studies of marine gastropods have suggested that species selection favors lineages with short-lived (lecithotrophic) larvae, which are less dispersive than long-lived (planktotrophic) larvae. Although lecithotrophs appeared to speciate more often and accumulate over time in some groups, lecithotrophy also increased extinction rates, and tests for state-dependent diversification were never performed. Molecular phylogenies of diverse groups instead suggested lecithotrophs accumulate without diversifying due to frequent, unidirectional character change. Although lecithotrophy has repeatedly...

Data from: Experimental evolution across different thermal regimes yields genetic divergence in recombination fraction but no divergence in temperature-associated plastic recombination

Kathryn P. Kohl & Nadia D. Singh
Phenotypic plasticity is pervasive in nature. One mechanism underlying the evolution and maintenance of such plasticity is environmental heterogeneity. Indeed, theory indicates that both spatial and temporal variation in the environment should favor the evolution of phenotypic plasticity under a variety of conditions. The frequency of recombination in the model system Drosophila melanogaster has long been known to exhibit phenotypic plasticity in response to temperature. Here were use a panel of replicated experimental evolution populations...

Data from: Postglacial climate and fire-mediated vegetation change on the western Olympic Peninsula, Washington

Daniel G. Gavin, Linda B. Brubaker & D. Noah Greenwald
The mode and tempo of forest compositional change during periods of rapid climate change, including the potential for the fire regime to produce non-linear relationships between climate and vegetation, is a long-standing theme of forest ecological research. In the old conifer forests of the coastal Pacific Northwest, fire disturbances are sufficiently rare that their relation to climate and their ecological effects are poorly understood. We used a 14,700-year high-resolution sediment record from Yahoo Lake on...

Data from: Disentangling visual and olfactory signals in mushroom-mimicking Dracula orchids using realistic three-dimensional printed flowers

Tobias Policha, Aleah Davis, Melinda Barnadas, Bryn T. M. Dentinger, Robert A. Raguso & Bitty A. Roy
Flowers use olfactory and visual signals to communicate with pollinators. Disentangling the relative contributions and potential synergies between signals remains a challenge. Understanding the perceptual biases exploited by floral mimicry illuminates the evolution of these signals. Here, we disentangle the olfactory and visual components of Dracula lafleurii, which mimics mushrooms in size, shape, color and scent, and is pollinated by mushroom-associated flies. To decouple signals, we used three-dimensional printing to produce realistic artificial flower molds...

Data from: A stochastic neuronal model predicts random search behaviors at multiple spatial scales in C. elegans

William M. Roberts, Steven B. Augustine, Kristy J. Lawton, Theodore H. Lindsay, Tod R. Thiele, Eduardo J. Izquierdo, Serge Faumont, Rebecca A. Lindsay, Matthew Cale Britton, Navin Pokala, Cornelia I. Bargmann & Shawn R. Lockery
Random search is a behavioral strategy used by organisms from bacteria to humans to locate food that is randomly distributed and undetectable at a distance. We investigated this behavior in the nematode Caenorhabditis elegans, an organism with a small, well-described nervous system. Here we formulate a mathematical model of random search abstracted from the C. elegans connectome and fit to a large-scale kinematic analysis of C. elegans behavior at submicron resolution. The model predicts behavioral...

Data from: Latitudinal body size trends in Oligo-Miocene mammals

John D. Orcutt & Samantha S.B. Hopkins
Paleecological data allow not only the study of trends along deep-time chronological transects but can also be used to reconstruct ecological gradients through time, which can help identify causal factors that may be strongly correlated in modern ecosystems. We have applied such an analysis to Bergmann’s rule, which posits a causal relationship between temperature and body size in mammals. Bergmann’s rule predicts that latitudinal gradients should exist during any interval of time, with larger taxa...

Data from: Climate structures genetic variation across a species' elevation range: a test of range limits hypotheses

Jason P. Sexton, Matthew B. Hufford, Ashley Bateman, David B. Lowry, Harald Meimberg, Sharon Y. Strauss, Kevin J. Rice & Ashley C.Bateman
Gene flow may influence the formation of species range limits, yet little is known about the patterns of gene flow with respect to environmental gradients or proximity to range limits. With rapid environmental change it is especially important to understand patterns of gene flow to inform conservation efforts. Here we investigate the species range of the selfing, annual plant, Mimulus laciniatus, in the California Sierra Nevada. We assessed genetic variation, gene flow, and population abundance...

Data from: Spatially explicit analysis sheds new light on the Pleistocene megafaunal extinction in North America

Meaghan M. Emery-Wetherell, Brianna K. McHorse & Edward Byrd Davis
The late Pleistocene megafaunal extinctions may have been the first extinctions directly related to human activity, but in North America the close temporal proximity of human arrival and the Younger Dryas climate event has hindered efforts to identify the ultimate extinction cause. Previous work evaluating the roles of climate change and human activity in the North American megafaunal extinction has been stymied by a reliance on geographic binning, yielding contradictory results among researchers. We used...

Data from: Context-dependent costs and benefits of tuberculosis resistance traits in a wild mammalian host

Hannah F. Tavalire, Brianna R. Beechler, Peter E. Buss, Erin E. Gorsich, Eileen G. Hoal, Nikki Le Roex, Johannie M. Spaan, Robert S. Spaan, Paul D. Van Helden, Vanessa O. Ezenwa & Anna E. Jolles
Disease acts as a powerful driver of evolution in natural host populations, yet individuals in a population often vary in their susceptibility to infection. Energetic trade-offs between immune and reproductive investment lead to the evolution of distinct life-history strategies, driven by the relative fitness costs and benefits of resisting infection. However, examples quantifying the cost of resistance outside of the laboratory are rare. Here, we observe two distinct forms of resistance to bovine tuberculosis (bTB),...

Data from: Phylogeographic analyses of American black bears (Ursus americanus) suggest four glacial refugia and complex patterns of post-glacial admixture

Emily E. Puckett, Paul D. Etter, Eric A. Johnson & Lori S. Eggert
Studies of species with continental distributions continue to identify intraspecific lineages despite continuous habitat. Lineages may form due to isolation by distance, adaptation, divergence across barriers, or genetic drift following range expansion. We investigated lineage diversification and admixture within American black bears (Ursus americanus) across their range using 22 k single nucleotide polymorphisms and mitochondrial DNA sequences. We identified three subcontinental nuclear clusters which we further divided into nine geographic regions: Alaskan (Alaska-East), eastern (Central...

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  • University of Oregon
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  • California Polytechnic State University