39 Works

Data from: Pseudomonas syringae enhances herbivory by suppressing the reactive oxygen burst in Arabidopsis

Simon C. Groen, Parris T. Humphrey, Daniela Chevasco, Frederick M. Ausubel, Naomi E. Pierce & Noah K. Whiteman
Plant-herbivore interactions have evolved in the presence of plant-colonizing microbes. These microbes can have important third-party effects on herbivore ecology, as exemplified by drosophilid flies that evolved from ancestors feeding on plant-associated microbes. Leaf-mining flies in the genus Scaptomyza, which is nested within the paraphyletic genus Drosophila, show strong associations with bacteria in the genus Pseudomonas, including Pseudomonas syringae. Adult females are capable of vectoring these bacteria between plants and larvae show a preference for...

Data from: Evf2 lncRNA/BRG1/DLX1 interactions reveal RNA-dependent inhibition of chromatin remodeling

Ivelisse Cajigas, David E. Leib, Jesse Cochrane, Hao Luo, Kelsey R. Swyter, Sean Chen, Brain S. Clark, James Thompson, , Robert E. Kingston & Jhumku D. Kohtz
Transcription-regulating long non-coding RNAs (lncRNAs) have the potential to control the site-specific expression of thousands of target genes. Previously, we showed that Evf2, the first described ultraconserved lncRNA, increases the association of transcriptional activators (DLX homeodomain proteins) with key DNA enhancers but represses gene expression. In this report, mass spectrometry shows that the Evf2-DLX1 ribonucleoprotein (RNP) contains the SWI/SNF-related chromatin remodelers Brahma-related gene 1 (BRG1, SMARCA4) and Brahma-associated factor (BAF170, SMARCC2) in the developing mouse...

Data from: Accounting for experimental noise reveals that mRNA levels, amplified by post-transcriptional processes, largely determine steady-state protein levels in yeast

Gábor Csárdi, Alexander Franks, David S. Choi, Edoardo M. Airoldi & David Allan Drummond
Cells respond to their environment by modulating protein levels through mRNA transcription and post-transcriptional control. Modest observed correlations between global steady-state mRNA and protein measurements have been interpreted as evidence that mRNA levels determine roughly 40% of the variation in protein levels, indicating dominant post-transcriptional effects. However, the techniques underlying these conclusions, such as correlation and regression, yield biased results when data are noisy, missing systematically, and collinear---properties of mRNA and protein measurements---which motivated us...

Data from: Reversible, specific, active aggregates of endogenous proteins assemble upon heat stress

Edward W. J. Wallace, Jamie L. Kear-Scott, Evgeny V. Pilipenko, Michael H. Schwartz, Pawel R. Laskowski, Alexandra E. Rojek, Christopher D. Katanski, Joshua A. Riback, Michael F. Dion, Alexander M. Franks, Edoardo M. Airoldi, Tao Pan, Bogdan A. Budnik & D. Allan Drummond
Heat causes protein misfolding and aggregation and in eukaryotic cells triggers aggregation of proteins and RNA into stress granules. We have carried out extensive proteomic studies to quantify heat-triggered aggregation and subsequent disaggregation in budding yeast, identifying >170 endogenous proteins aggregating within minutes of heat shock in multiple subcellular compartments. We demonstrate that these aggregated proteins are not misfolded and destined for degradation. Stable-isotope labeling reveals that even severely aggregated endogenous proteins are disaggregated without...

Data from: Nuclear genomic signals of the \"microturbellarian\" roots of platyhelminth evolutionary innovation

Christopher E. Laumer, Andreas Hejnol & Gonzalo Giribet
Flatworms number among the most diverse invertebrate phyla, and represent the most biomedically significant branch of the major bilaterian clade Spiralia, but to date, deep evolutionary relationships within this group have been studied using only a single locus (the rRNA operon), leaving the origins of many key clades unclear. Here, using a survey of genomes and transcriptomes representing all free-living flatworm orders, we provide resolution of platyhelminth interrelationships based on hundreds of nuclear protein-coding genes,...

Data from: Only accessible information is useful: insights from gradient-mediated patterning

Mikhail Tikhonov, Shawn C. Little & Thomas Gregor
Information theory is gaining popularity as a tool to characterise performance of biological systems. However, information is commonly quantified without reference to whether or how a system could extract and use it; as a result, information-theoretic quantities are easily misinterpreted. Here we take the example of pattern-forming developmental systems which are commonly structured as cascades of sequential gene expression steps. Such a multi-tiered structure appears to constitute sub-optimal use of the positional information provided by...

Data from: Hard and soft selection on phenology through seasonal shifts in the general and social environments: a study on plant emergence time

Arthur E. Weis, Kyle M. Turner, Bergita Petro, Emily J. Austen & Susana M. Wadgymar
The timing of transition out of one life history phase determines where in the seasonal succession of environments the next phase is spent. Shifts in the general environment (e.g., seasonal climate) affect the expected fitness for particular transition dates. Variation in transition date also leads to temporal variation in the social environment. For instance, early transition may confer a competitive advantage over later individuals. If so, the social environment will impose frequency- and density-dependent selection...

Data from: Protein pheromone expression levels predict and respond to the formation of social dominance networks

Adam C. Nelson, Christopher B. Cunningham, James S. Ruff & Wayne K. Potts
Communication signals are key regulators of social networks and are thought to be under selective pressure to honestly reflect social status, including dominance status. The odours of dominants and nondominants differentially influence behaviour, and identification of the specific pheromones associated with, and predictive of, dominance status is essential for understanding the mechanisms of network formation and maintenance. In mice, major urinary proteins (MUPs) are excreted in extraordinary large quantities and expression level has been hypothesized...

Data from: Why close relatives make bad neighbors: phylogenetic conservatism in niche preferences and dispersal disproves Darwin’s Naturalization Hypothesis in the thistle tribe

Daniel S. Park & Daniel Potter
The number of exotic plant species that have been introduced into the United States far exceeds that of other groups of organisms, and many of these have become invasive. As in many regions of the globe, invasive members of the thistle tribe, Cardueae, are highly problematic in the California Floristic Province, an established biodiversity hotspot. While Darwin's naturalization hypothesis posits that plant invaders closely related to native species would be at a disadvantage, evidence has...

Data from: Evolutionary novelty in a butterfly wing pattern through enhancer shuffling

Richard W. R. Wallbank, Simon W. Baxter, Carolina Pardo-Diaz, Joseph J. Hanly, Simon H. Martin, James Mallet, Kanchon K. Dasmahapatra, Camilo Salazar, Mathieu Joron, Nicola Nadeau, W. Owen McMillan & Chris D. Jiggins
An important goal in evolutionary biology is to understand the genetic changes underlying novel morphological structures. We investigated the origins of a complex wing pattern found among Amazonian Heliconius butterflies. Genome sequence data from 142 individuals across 17 species identified narrow regions associated with two distinct red colour pattern elements, dennis and ray. We hypothesise that these modules in non-coding sequence represent distinct cis-regulatory loci that control expression of the transcription factor optix, which in...

Data from: How obstacles perturb population fronts and alter their genetic structure

Wolfram Möbius, Andrew W. Murray & David R. Nelson
As populations spread into new territory, environmental heterogeneities can shape the population front and genetic composition. We focus here on the effects of an important building block of heterogeneous environments, isolated obstacles. With a combination of experiments, theory, and simulation, we show how isolated obstacles both create long-lived distortions of the front shape and amplify the effect of genetic drift. A system of bacteriophage T7 spreading on a spatially heterogeneous Escherichia coli lawn serves as...

Data from: Selection of Pairings Reaching Evenly Across the Data (SPREAD): a simple algorithm to design maximally informative fully crossed mating experiments

Kolea Zimmerman, Daniel Levitis, Ethan Addicott & Anne Pringle
We present a novel algorithm for the design of crossing experiments. The algorithm identifies a set of individuals (a "crossing-set") from a larger pool of potential crossing-sets by maximizing the diversity of traits of interest, for example, maximizing the range of genetic and geographic distances between individuals included in the crossing-set. To calculate diversity, we use the mean nearest neighbor distance of crosses plotted in trait space. We implement our algorithm on a real dataset...

Data from: Morphological and genomic comparisons of Hawaiian and Japanese Black-footed Albatrosses (Phoebastria nigripes) using double digest RADseq: implications for conservation

Elisa G. Dierickx, Allison J. Shultz, Fumio Sato, Takashi Hiraoka & Scott V. Edwards
Evaluating the genetic and demographic independence of populations of threatened species is important for determining appropriate conservation measures, but different technologies can yield different conclusions. Despite multiple studies, the taxonomic status and extent of gene flow between the main breeding populations of Black-footed Albatross (Phoebastria nigripes), a Near-Threatened philopatric seabird, are still controversial. Here, we employ double digest RADseq to quantify the extent of genomewide divergence and gene flow in this species. Our genomewide data...

Data from: Breeding system evolution influenced the geographic expansion and diversification of the core Corvoidea (Aves: Passeriformes)

Petter Z. Marki, Pierre-Henri Fabre, Knud A. Jønsson, Carsten Rahbek, Jon Fjeldså & Jonathan D. Kennedy
Birds vary greatly in their life-history strategies, including their breeding systems, which range from brood parasitism to a system with multiple non-breeding helpers at the nest. By far the most common arrangement, however, is where both parents participate in raising the young. The traits associated with parental care have been suggested to affect dispersal propensity and lineage diversification, but to date tests of this potential relationship at broad temporal and spatial scales have been limited....

Data from: Placing cryptic, recently extinct, or hypothesized taxa into an ultrametric phylogeny using continuous character data: A case study with the lizard Anolis roosevelti

Liam J. Revell, D. Luke Mahler, Robert Graham Reynolds & Graham James Slater
In recent years, enormous effort and investment has been put into assembling the tree of life: a phylogenetic history for all species on Earth. Overwhelmingly, this progress toward building an ever increasingly complete phylogeny of living things has been accomplished through sophisticated analysis of molecular data. In the modern genomic age, molecular genetic data have become very easy and inexpensive to obtain for many species. However, some lineages are poorly represented in or absent from...

Data from: Axial allometry in a neutrally buoyant environment: effects of the terrestrial-aquatic transition on vertebral scaling

Katrina E. Jones & Stephanie E. Pierce
Ecological diversification into new environments presents new mechanical challenges for locomotion. An extreme example of this is the transition from a terrestrial to an aquatic lifestyle. Here, we examine the implications of life in a neutrally buoyant environment on adaptations of the axial skeleton to evolutionary increases in body size. On land, mammals must use their thoracolumbar vertebral column for body support against gravity and thus exhibit increasing stabilization of the trunk as body size...

Data from: Phylogenomic resolution of scorpions reveals multilevel discordance with morphological phylogenetic signal

Prashant P. Sharma, Rosa Fernández, Lauren A. Esposito, Edmundo González-Santillán, Lionel Monod, E. Gonzalez-Santillan & R. Fernandez
Scorpions represent an iconic lineage of arthropods, historically renowned for their unique bauplan, ancient fossil record and venom potency. Yet, higher level relationships of scorpions, based exclusively on morphology, remain virtually untested, and no multilocus molecular phylogeny has been deployed heretofore towards assessing the basal tree topology. We applied a phylogenomic assessment to resolve scorpion phylogeny, for the first time, to our knowledge, sampling extensive molecular sequence data from all superfamilies and examining basal relationships...

Data from: Cognitive capacities for cooking in chimpanzees

Felix Warneken & Alexandra G. Rosati
The transition to a cooked diet represents an important shift in human ecology and evolution. Cooking requires a set of sophisticated cognitive abilities, including causal reasoning, self-control and anticipatory planning. Do humans uniquely possess the cognitive capacities needed to cook food? We address whether one of humans' closest relatives, chimpanzees (Pan troglodytes), possess the domain-general cognitive skills needed to cook. Across nine studies, we show that chimpanzees: (i) prefer cooked foods; (ii) comprehend the transformation...

Data from: Trans-Pacific RAD-Seq population genomics confirms introgressive hybridization in Eastern Pacific Pocillopora corals.

David J. Combosch & Steven V. Vollmer
Discrepancies between morphology-based taxonomy and phylogenetic systematics are common in Scleractinian corals. In Pocillopora corals, nine recently identified genetic lineages disagree fundamentally with the 17 recognized Pocillopora species, including 5 major Indo-Pacific reef-builders. Pocillopora corals hybridize in the Tropical Eastern Pacific, so it is possible that some of the disagreement between the genetics and taxonomy may be due to introgressive hybridization. Here we used 6769 genome-wide SNPs from Restriction-site Associated DNA sequencing (RAD-Seq) to conduct...

Data from: De novo sequencing and variant calling with nanopores using PoreSeq

Tamas Szalay & Jene A. Golovchenko
The accuracy of sequencing single DNA molecules with nanopores is continually improving, but de novo genome sequencing and assembly using only nanopore data remain challenging. Here we describe PoreSeq, an algorithm that identifies and corrects errors in nanopore sequencing data and improves the accuracy of de novo genome assembly with increasing coverage depth. The approach relies on modeling the possible sources of uncertainty that occur as DNA transits through the nanopore and finds the sequence...

Data from: Optimisation of next generation sequencing transcriptome annotation for species lacking sequenced genomes

Nina F. Ockendon, Lauren A. O'Connell, Stephen J. Bush, Jimena Monzon-Sandoval, Holly Barnes, Tamás Székely, Hans A. Hofmann, Steve Dorus & Araxi O. Urrutia
Next generation sequencing methods, such as RNA-seq, have permitted the exploration of gene expression in a range of organisms which have been studied in ecological contexts but lack a sequenced genome. However, the efficacy and accuracy of RNA-seq annotation methods using reference genomes from related species have yet to be robustly characterised. Here we conduct a comprehensive power analysis employing RNA-seq data from Drosophila melanogaster in conjunction with 11 additional genomes from related Drosophila species...

Data from: Limits on information transduction through amplitude and frequency regulation of transcription factor activity

Anders S. Hansen & Erin K. O'Shea
Signaling pathways often transmit multiple signals through a single shared transcription factor (TF) and encode signal information by differentially regulating TF dynamics. However, signal information will be lost unless it can be reliably decoded by downstream genes. To understand the limits on dynamic information transduction, we apply information theory to quantify how much gene expression information the yeast TF Msn2 can transduce to target genes in the amplitude or frequency of its activation dynamics. We...

Data from: Globally, functional traits are weak predictors of juvenile tree growth, and we do not know why

C. E. Timothy Paine, Lucy Amissah, Harald Auge, Christopher Baraloto, Martin Baruffol, Nils Bourland, Helge Bruelheide, Kasso Daïnou, Roland C. De Gouvenain, Jean-Louis Doucet, Susan Doust, Paul V. A. Fine, Claire Fortunel, Josephine Haase, Karen D. Holl, Hervé Jactel, Xuefei Li, Kaoru Kitajima, Julia Koricheva, Cristina Martínez-Garza, Christian Messier, Alain Paquette, Christopher Philipson, Daniel Piotto, Lourens Poorter … & Andy Hector
1. Plant functional traits, in particular specific leaf area (SLA), wood density and seed mass, are often good predictors of individual tree growth rates within communities. Individuals and species with high SLA, low wood density and small seeds tend to have faster growth rates. 2. If community-level relationships between traits and growth have general predictive value, then similar relationships should also be observed in analyses that integrate across taxa, biogeographic regions and environments. Such global...

Data from: Izumo1 and Juno: the evolutionary origins and coevolution of essential sperm-egg binding partners

Phil Grayson
Reproductive proteins are among the most rapidly evolving classes of proteins. For a subset of these, rapid evolution is driven by positive Darwinian selection despite vital, well-conserved, reproductive functions. Izumo1 is the only essential sperm–egg fusion protein currently known on mammalian sperm, and its egg receptor (Juno; formerly Folr4) was recently discovered. Male knockout mice for Izumo1 and female knockout mice for Juno are both healthy but sterile. Here, both sperm–egg binding proteins are shown...

Data from: Context-dependent effects of Y chromosome and mitochondrial haplotype on male locomotive activity in Drosophila melanogaster

Rebecca Dean, Bernardo Lemos & Damian K. Dowling
Some regions of the genome exhibit sexual asymmetries in inheritance, and are thus subjected to sex-biased evolutionary forces. Maternal inheritance of mitochondrial DNA (mtDNA) enables mtDNA mutations harmful to males, but not females, to accumulate. In the face of male-harmful mtDNA mutation accumulation, selection will favour the evolution of compensatory modifiers in the nuclear genome that offset fitness losses to males. The Y chromosome is a candidate to host these modifiers, because it is paternally-inherited,...

Registration Year

  • 2015

Resource Types

  • Dataset


  • Harvard University
  • The University of Texas at Austin
  • University of Georgia
  • Del Rosario University
  • University of Cambridge
  • University of Alberta
  • University of California, Berkeley
  • Smithsonian Institution
  • University of Oslo
  • University of Chicago