51 Works

Data from: An evaluation of transcriptome-based exon capture for frog phylogenomics across multiple scales of divergence (Class: Amphibia, Order: Anura)

Daniel M. Portik, Lydia L. Smith & Ke Bi
Custom sequence capture experiments are becoming an efficient approach for gathering large sets of orthologous markers in nonmodel organisms. Transcriptome-based exon capture utilizes transcript sequences to design capture probes, typically using a reference genome to identify intron–exon boundaries to exclude shorter exons (<200 bp). Here, we test directly using transcript sequences for probe design, which are often composed of multiple exons of varying lengths. Using 1260 orthologous transcripts, we conducted sequence captures across multiple phylogenetic...

Data from: Tradeoffs, spatial heterogeneity, and the maintenance of microbial diversity

Stephanie S. Porter & Kevin J. Rice
Specialization and concomitant tradeoffs are assumed to underlie the non-neutral coexistence of lineages. Tradeoffs across heterogeneous environments can promote diversity by preventing competitive exclusion. However, the importance of tradeoffs in maintaining diversity in natural microbial assemblages is unclear, as tradeoffs are frequently not detected in artificial evolution experiments. Stressful conditions associated with patches of heavy-metal enriched serpentine soils provide excellent opportunities for examining how heterogeneity may foster genetic diversity. Using a spatially-replicated design, we demonstrate...

Data from: Y-box protein 1 is required to sort microRNAs into exosomes in cells and in a cell-free reaction

Matthew J. Shurtleff, Morayma M. Temoche-Diaz, Kate V. Karfilis, Sayaka Ri & Randy Schekman
Exosomes are small vesicles that are secreted from metazoan cells and may convey selected membrane proteins and small RNAs to target cells for the control of cell migration, development and metastasis. To study the mechanisms of RNA packaging into exosomes, we devised a purification scheme based on the membrane marker CD63 to isolate a single exosome species secreted from HEK293T cells. Using immunoisolated CD63-containing exosomes we identified a set of miRNAs that are highly enriched...

Data from: Critically evaluating the theory and performance of Bayesian analyis of macroevolutionary mixtures

Brian R. Moore, Sebastian Hoehna, Michael R. May, Bruce Rannala & John P. Huelsenbeck
Bayesian analysis of macroevolutionary mixtures (BAMM) has recently taken the study of lineage diversification by storm. BAMM estimates the diversification-rate parameters (speciation and extinction) for every branch of a study phylogeny and infers the number and location of diversification-rate shifts across branches of a tree. Our evaluation of BAMM reveals two major theoretical errors: (i) the likelihood function (which estimates the model parameters from the data) is incorrect, and (ii) the compound Poisson process prior...

Data from: Rapid genetic and ecological differentiation during the northern range expansion of the venomous yellow sac spider Cheiracanthium punctorium in Europe

Henrik Krehenwinkel, Dennis Rödder, Magdalena Năpăruş-Aljančič & Matjaz Kuntner
Although poleward range expansions are commonly attributed to global change, a complex interaction of ecological and evolutionary factors might contribute to expansion success. Here, we study the expansion of the yellow sac spider Cheiracanthium punctorium, a medically important species in Central Europe. Using microsatellite markers and DNA sequences, morphological and climate niche analyses, we identify factors associated with the spider’s expansion success. Our results indicate that the species’ initial expansion has been triggered by environmental...

Data from: Climate modifies response of non-native and native species richness to nutrient enrichment

Habacuc Flores-Moreno, Peter B. Reich, Eric M. Lind, Lauren L. Sullivan, Eric W. Seabloom, Laura Yahdjian, Andrew S. MacDougall, Lara G. Reichmann, Juan Alberti, Selene Báez, Jonathan D. Bakker, Marc W. Cadotte, Maria C. Caldeira, Enrique J. Chaneton, Carla M. D'Antonio, Philip A. Fay, Jennifer Firn, Nicole Hagenah, W. Stanley Harpole, Oscar Iribarne, Kevin P. Kirkman, Johannes M. H. Knops, Kimberly J. La Pierre, Ramesh Laungani, Andrew D. B. Leakey … & Elizabeth T. Borer
Ecosystem eutrophication often increases domination by non-natives and causes displacement of native taxa. However, variation in environmental conditions may affect the outcome of interactions between native and non-native taxa in environments where nutrient supply is elevated. We examined the interactive effects of eutrophication, climate variability and climate average conditions on the success of native and non-native plant species using experimental nutrient manipulations replicated at 32 grassland sites on four continents. We hypothesized that effects of...

Data from: Directional selection effects on patterns of phenotypic (co)variation in wild populations

Ana Paula A. Assis, James L. Patton, Alex Hubbe & Gabriel Marroig
Phenotypic (co)variation is a prerequisite for evolutionary change, and understanding how (co)variation evolves is of crucial importance to the biological sciences. Theoretical models predict that under directional selection, phenotypic (co)variation should evolve in step with the underlying adaptive landscape, increasing the degree of correlation among co-selected traits as well as the amount of genetic variance in the direction of selection. Whether either of these outcomes occurs in natural populations is an open question and thus...

Data from: Large-scale recovery of an endangered amphibian despite ongoing exposure to multiple stressors

Roland A. Knapp, Gary M. Fellers, Patrick M. Kleeman, David A. W. Miller, Vance T. Vredenburg, Erica Bree Rosenblum & Cheryl J. Briggs
Amphibians are one of the most threatened animal groups, with 32% of species at risk for extinction. Given this imperiled status, is the disappearance of a large fraction of the Earth’s amphibians inevitable, or are some declining species more resilient than is generally assumed? We address this question in a species that is emblematic of many declining amphibians, the endangered Sierra Nevada yellow-legged frog (Rana sierrae). Based on >7,000 frog surveys conducted across Yosemite National...

Data from: Super-resolution ribosome profiling reveals unannotated translation events in Arabidopsis

Polly Y. Hsu, Lorenzo Calviello, Hsin-Yen Larry Wu, Fay-Wei Li, Carl J. Rothfels, Uwe Ohler & Philip N. Benfey
Deep sequencing of ribosome footprints (ribosome profiling) maps and quantifies mRNA translation. Because ribosomes decode mRNA every 3 nt, the periodic property of ribosome footprints could be used to identify novel translated ORFs. However, due to the limited resolution of existing methods, the 3-nt periodicity is observed mostly in a global analysis, but not in individual transcripts. Here, we report a protocol applied to Arabidopsis that maps over 90% of the footprints to the main...

Data from: Diabolical survival in Death Valley: recent pupfish colonization, gene flow, and genetic assimilation in the smallest species range on earth

Christopher Martin, Jacob Crawford, Bruce Turner, Lee Simons, Jacob E. Crawford & Christopher H. Martin
One of the most endangered vertebrates, the Devils Hole pupfish Cyprinodon diabolis, survives in a nearly impossible environment: a narrow subterranean fissure in the hottest desert on earth, Death Valley. This species became a conservation icon after a landmark 1976 U.S. Supreme Court case affirming federal groundwater rights to its unique habitat. However, one outstanding question about this species remains unresolved: how long has diabolis persisted in this hellish environment? We used next-generation sequencing of...

Data from: Phylogenomics at the tips: inferring lineages and their demographic history in a tropical lizard, Carlia amax

Sally Potter, Jason G. Bragg, Benjamin M. Peter, Ke Bi & Craig Moritz
High-throughput sequencing approaches offer opportunities to better understand the evolutionary processes driving diversification, particularly in nonmodel organisms. In particular, the 100–1000's of loci that can now be sequenced are providing unprecedented power in population, speciation and phylogenetic studies. Here, we apply an exon capture approach to generate >99% complete sequence and SNP data across >2000 loci from a tropical skink, Carlia amax, and exploit these data to identify divergent lineages and infer their relationships and...

Data from: The Achilles' heel hypothesis: misinformed keystone individuals impair collective learning and reduce group success

Jonathan Pruitt, Colin Wright, Carl Keiser, Alexander DeMarco, Matt Grobis, Noa Pinter-Wollman, Matthew M. Grobis, Alex E. DeMarco, Carl N. Keiser, Jonathan N. Pruitt & Colin M. Wright
Many animal societies rely on highly influential keystone individuals for proper functioning. When information quality is important for group success, such keystone individuals have the potential to diminish group performance if they possess inaccurate information. Here we test whether information quality (accurate or inaccurate) influences collective outcomes when keystone individuals are the first to acquire it. We trained keystone or generic individuals to attack or avoid novel stimuli and implanted these seed individuals within groups...

Data from: Microelastic mapping of the rat dentate gyrus

Tomas Luque, Michael S. Kang, David V. Schaffer & Sanjay Kumar
The lineage commitment of many cultured stem cells, including adult neural stem cells (NSCs), is strongly sensitive to the stiffness of the underlying extracellular matrix. However, it remains unclear how well the stiffness ranges explored in culture align with the microscale stiffness values stem cells actually encounter within their endogenous tissue niches. To address this question in the context of hippocampal NSCs, we used atomic force microscopy to spatially map the microscale elastic modulus (E)...

Data from: A cost-efficient and simple protocol to enrich prey DNA from extractions of predatory arthropods for large-scale gut content analysis by Illumina sequencing

Henrik Krehenwinkel, Susan Kennedy, Stano Pekár & Rosemary G. Gillespie
Molecular analysis of predator gut content is a popular tool to uncover food web structure and has greatly profited from the emergence of next-generation sequencing technology. However, the molecular recovery of prey spectra comes with many challenges, particularly the overabundance of predator DNA in extractions. When predator and prey are distantly related, predator-specific blocking primers can be used to preferentially amplify prey DNA. But this is difficult in the case of arthropods, where prey and...

Data from: Dead ant walking: a myrmecophilous beetle predator uses parasitoid host location cues to selectively prey on parasitized ants

Kaitlyn A. Mathis & Neil D. Tsutsui
Myrmecophiles (i.e. organisms that associate with ants) use a variety of ecological niches and employ different strategies to survive encounters with ants. Because ants are typically excellent defenders, myrmecophiles may choose moments of weakness to take advantage of their ant associates. This hypothesis was studied in the rove beetle, Myrmedonota xipe, which associates with Azteca sericeasur ants in the presence of parasitoid flies. A combination of laboratory and field experiments show that M. xipe beetles...

Data from: Monocular blur alters the tuning characteristics of stereopsis for spatial frequency and size

Roger W. Li, Kayee So, Thomas H. Wu, Ashley P. Craven, Truyet T. Tran, Kevin M. Gustafson & Dennis M. Levi
Our sense of depth perception is mediated by spatial filters at different scales in the visual brain; low spatial frequency channels provide the basis for coarse stereopsis, whereas high spatial frequency channels provide for fine stereopsis. It is well established that monocular blurring of vision results in decreased stereoacuity. However, previous studies have used tests that are broadband in their spatial frequency content. It is not yet entirely clear how the processing of stereopsis in...

Data from: Meniscus ascent by thrips (Thysanoptera)

Víctor Manuel Ortega-Jiménez, Sarahi Arriaga-Ramirez & Robert Dudley
Meniscus climbing using a fixed body posture has been well documented for various aquatic and neustonic insects, but is not known from small flying insects that inadvertently become trapped on water surfaces. Here, we show that thrips (order Thysanoptera) can ascend a meniscus by arching their non-wetting bodies to translate head-first and upward along a water surface; if initially oriented backwards, they can turn by 180° to ascend head-first, and climb upward on a surrounding...

Data from: The genetic architecture of novel trophic specialists: higher effect sizes are associated with exceptional oral jaw diversification in a pupfish adaptive radiation

Christopher H. Martin, Priscilla A. Erickson & Craig T. Miller
The genetic architecture of adaptation is fundamental to understanding the mechanisms and constraints governing diversification. However, most case studies focus on loss of complex traits or parallel speciation in similar environments. It is still unclear how the genetic architecture of these local adaptive processes compares to the architecture of evolutionary transitions contributing to morphological and ecological novelty. Here we identify quantitative trait loci (QTL) between two trophic specialists in an excellent case study for examining...

Data from: Binocular combination of stimulus orientation

Oren Yehezkel, Jian Ding, Anna Sterkin, Uri Polat & Dennis M. Levi
When two sine waves that differ slightly in orientation are presented to the two eyes separately, a single cyclopean sine wave is perceived. However, it is unclear how the brain calculates its orientation. Here, we used a signal detection rating method to estimate the perceived orientation when the two eyes were presented with Gabor patches that differed in both orientation and contrast. We found a nearly linear combination of orientation when both targets had the...

Data from: Next-generation polyploid phylogenetics: rapid resolution of hybrid polyploid complexes using PacBio single-molecule sequencing

Carl J. Rothfels, Kathleen M. Pryer & Fay-Wei Li
Difficulties in generating nuclear data for polyploids have impeded phylogenetic study of these groups. We describe a high-throughput protocol and an associated bioinformatics pipeline (PURC: “Pipeline for Untangling Reticulate Complexes”) that is able to generate these data quickly and conveniently, and demonstrate its efficacy on accessions from the fern family Cystopteridaceae. We conclude with a demonstration of the downstream utility of these data by inferring a multilabeled species tree for a subset of our accessions....

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: Autocorrelation structure at rest predicts value correlates of single neurons during reward-guided choice

Sean E. Cavanagh, Joni D. Wallis, Steven W. Kennerley & Laurence T. Hunt
Correlates of value are routinely observed in the prefrontal cortex (PFC) during reward-guided decision making. In previous work (Hunt et al., 2015), we argued that PFC correlates of chosen value are a consequence of varying rates of a dynamical evidence accumulation process. Yet within PFC, there is substantial variability in chosen value correlates across individual neurons. Here we show that this variability is explained by neurons having different temporal receptive fields of integration, indexed by...

Data from: Stronger effect of gastropods than rodents on seedling establishment, irrespective of exotic or native plant species origin

Lotte Korell, Claudia Stein, Isabell Hensen, Helge Bruelheide, Katharine N. Suding & Harald Auge
Experimental evidence about how generalist consumers affect exotic plant invasions is equivocal, but most tests have been limited to few plant species, single herbivore guilds, and single locations. Using a seed-addition experiment, we studied effects of gastropods and rodents on recruitment success of 37 exotic and 37 native plant species affiliated to three different functional groups (i.e. grasses, legumes and non-legume herbs). We replicated our seed addition x herbivore exclusion experiment at multiple grassland sites,...

Data from: An extracellular biochemical screen reveals that FLRTs and Unc5s mediate neuronal subtype recognition in the retina

Jasper J. Visser, Yolanda Cheng, Steven C. Perry, Andrew Benjamin Chastain, Bayan Parsa, Shatha S. Masri, Ray Thomas A., Jeremy N. Kay, Woj M. Wojtowicz & Thomas A Ray
In the inner plexiform layer of the mouse retina, ~70 neuronal subtypes form a stereotyped circuit that underlies visual processing. During development, subtypes organize into an intricate laminar structure. This organization is choreographed by extracellular interactions that mediate cell recognition events. To identify recognition proteins involved in lamination, we utilized microarray data from 13 subtypes to identify differentially-expressed cell surface and secreted proteins. Using these candidates, we performed a biochemical screen and identified ~50 previously-unknown...

Data from: Mosquito saliva increases endothelial permeability in the skin, immune cell migration, and dengue pathogenesis during antibody-dependent enhancement

Michael A. Schmid, Dustin R. Glasner, Sanjana Shah, Daniela Michlmayr, Laura D. Kramer, & Eva Harris
Dengue remains the most prevalent arthropod-borne viral disease in humans. While probing for blood vessels, Aedes aegypti and Ae. albopictus mosquitoes transmit the four serotypes of dengue virus (DENV1-4) by injecting virus-containing saliva into the skin. Even though arthropod saliva is known to facilitate transmission and modulate host responses to other pathogens, the full impact of mosquito saliva on dengue pathogenesis is still not well understood. Inoculating mice lacking the interferon-α/β receptor intradermally with DENV...

Registration Year

  • 2016

Resource Types

  • Dataset


  • University of California, Berkeley
  • University of California System
  • University of Florida
  • Duke University
  • United States Department of Agriculture
  • University of California, Davis
  • Helmholtz Centre for Environmental Research
  • University of Washington
  • University of North Carolina
  • University of Virginia