13 Works

Data from: Ribosome profiling reveals pervasive and regulated stop codon readthrough in Drosophila melanogaster

Joshua G. Dunn, Catherine K. Foo, Nicolette G. Belletier, Elizabeth R. Gavis & Jonathan S. Weissman
Ribosomes can read through stop codons in a regulated manner, elongating rather than terminating the nascent peptide. Stop codon readthrough is essential to diverse viruses, and phylogenetically predicted to occur in a few hundred genes in Drosophila melanogaster, but the importance of regulated readthrough in eukaryotes remains largely unexplored. Here, we present a ribosome profiling assay (deep sequencing of ribosome-protected mRNA fragments) for Drosophila melanogaster, and provide the first genome-wide experimental analysis of readthrough. Readthrough...

Data from: Transformation of stimulus correlations by the retina

Kristina D. Simmons, Jason S. Prentice, Gašper Tkačik, Jan Homann, Heather K. Yee, Stephanie E. Palmer, Philip C. Nelson & Vijay Balasubramanian
Redundancies and correlations in the responses of sensory neurons may seem to waste neural resources, but they can also carry cues about structured stimuli and may help the brain to correct for response errors. To investigate the effect of stimulus structure on redundancy in retina, we measured simultaneous responses from populations of retinal ganglion cells presented with natural and artificial stimuli that varied greatly in correlation structure; these stimuli and recordings are publicly available online....

Data from: Stigmergy, collective actions and animal social spacing

Luca Giuggioli, Jonathan R. Potts, Daniel I. Rubenstein & Simon A. Levin
Collective animal behavior studies have led the way in developing models that account for a large number of individuals, but have mostly considered situations where alignment and attraction play a key role, such as in schooling and flocking. By quantifying how animals react to each others' presence, when interaction is via conspecific avoidance rather than alignment or attraction, we present a mechanistic insight that enables us to link individual behavior and space use patterns. As...

Data from: Social environment influences the relationship between genotype and gene expression in wild baboons

Daniel E. Runcie, Ralph T. Wiedmann, Elizabeth A. Archie, Jeanne Altmann, Gregory A. Wray, Susan C. Alberts & Jenny Tung
Variation in the social environment can have profound effects on survival and reproduction in wild social mammals. However, we know little about the degree to which these effects are influenced by genetic differences among individuals, and conversely, the degree to which social environmental variation mediates genetic reaction norms. To better understand these relationships, we investigated the potential for dominance rank, social connectedness and group size to modify the effects of genetic variation on gene expression...

Data from: Endocrine phenotype, reproductive success and survival in the great tit, Parus major

Jenny Q. Ouyang, Peter Sharp, Michael Quetting & Michaela Hau
A central goal in evolutionary ecology is to characterize and identify selection patterns on the optimal phenotype in different environments. Physiological traits, such as hormonal responses, provide important mechanisms by which individuals can adapt to fluctuating environmental conditions. It is therefore expected that selection shapes hormonal traits, but the strength and the direction of selection on plastic hormonal signals are still under investigation. Here, we determined whether, and in which way, selection is acting on...

Data from: Water stress strengthens mutualism among ants, trees, and scale insects

Elizabeth G. Pringle, Erol Akçay, Ted K. Raab, Rodolfo Dirzo & Deborah M. Gordon
Abiotic environmental variables strongly affect the outcomes of species interactions. For example, mutualistic interactions between species are often stronger when resources are limited. The effect might be indirect: water stress on plants can lead to carbon stress, which could alter carbon-mediated plant mutualisms. In mutualistic ant–plant symbioses, plants host ant colonies that defend them against herbivores. Here we show that the partners' investments in a widespread ant–plant symbiosis increase with water stress across 26 sites...

Data from: Dynamic interpretation of maternal inputs by the Drosophila segmentation gene network

Feng Liu, Alexander H. Morrison & Thomas Gregor
Patterning of body parts in multicellular organisms relies on the interpretation of transcription factor (TF) concentrations by genetic networks. To determine the extent by which absolute TF concentration dictates gene expression and morphogenesis programs that ultimately lead to patterns in Drosophila embryos, we manipulate maternally supplied patterning determinants and measure readout concentration at the position of various developmental markers. When we increase the overall amount of the maternal TF Bicoid 5-fold, Bicoid concentrations in cells...

Data from: Meta-analysis reveals lower genetic diversity in overfished populations

Malin L. Pinsky & Stephen R. Palumbi
While population declines can drive the loss of genetic diversity under some circumstances, it has been unclear whether this loss is a general consequence of overharvest in highly abundant marine fishes. Here, we use a phylogenetic approach across 160 species and 11,658 loci to show that allelic richness was on average 11% lower (p < 0.0001) in overharvested populations, even after accounting for the effects of body size, latitude, and other factors. Heterozygosity was 2%...

Data from: The Oxytricha trifallax macronuclear genome: a complex eukaryotic genome with 16,000 tiny chromosomes

Estienne C. Swart, John R. Bracht, Vincent Magrini, Patrick Minx, Xiao Chen, Yi Zhou, Jaspreet S. Khurana, Aaron D. Goldman, Mariusz Nowacki, Klaas Schotanus, Seolkyoung Jung, Robert S. Fulton, Amy Ly, Sean McGrath, Kevin Haub, Jessica L. Wiggins, Donna Storton, John C. Matese, Lance Parsons, Wei-Jen Chang, Michael S. Bowen, Nicholas A. Stover, Thomas A. Jones, Sean R. Eddy, Thomas G. Doak … & Laura F. Landweber
The macronuclear genome of the ciliate Oxytricha trifallax displays an extreme and unique eukaryotic genome architecture with extensive genomic variation. During sexual genome development, the expressed, somatic macronuclear genome is whittled down to the genic portion of a small fraction (~5%) of its precursor “silent” germline micronuclear genome by a process of “unscrambling” and fragmentation. The tiny macronuclear “nanochromosomes” typically encode single, protein-coding genes (a small portion, 10%, encode 2–8 genes), have minimal noncoding regions,...

Data from: Testosterone positively associated with both male mating effort and paternal behavior in savanna baboons (Papio cynocephalus)

Patrick Ogola Onyango, Laurence R. Gesquiere, Jeanne Altmann & Susan C. Alberts
Testosterone (T) is often positively associated with male sexual behavior and negatively associated with paternal care. These associations have primarily been demonstrated in species where investment in paternal care begins well after mating activity is complete, when offspring are hatched or born. Different patterns may emerge in studies of species where investment in mating and paternal care overlap temporally, for instance in non-seasonal breeders in which males mate with multiple females sequentially and may simultaneously...

Data from: Phylogenomics reveals extensive reticulate evolution in Xiphophorus fishes

Rongfeng Cui, Molly Schumer, Karla Kruesi, Ronald Brice Walter, Peter Andolfatto, Gil G. Rosenthal & Ronald Walter
Hybridization is increasingly being recognized as a widespread process, even between ecologically and behaviorally divergent animal species. Determining phylogenetic relationships in the presence of hybridization remains a major challenge for evolutionary biologists, but advances in sequencing technology and phylogenetic techniques are beginning to address these challenges. Here we reconstruct evolutionary relationships among swordtails and platyfishes (Xiphophorus: Poeciliidae), a group of species characterized by remarkable morphological diversity and behavioral barriers to interspecific mating. Past attempts to...

Data from: When good neighbors don’t need fences: Temporal landscape partitioning among baboon social groups

A. Catherine Markham, Vishwesha Guttal, Susan C. Alberts & Jeanne Altmann
Intraspecific competition is a key factor shaping space-use strategies and movement decisions inmany species, yet how and when neighbors utilize shared areas while exhibiting active avoidance of one another is largely un- known. Here, we investigated temporal landscape partitioning in a population of wild baboons (Papio cynocephalus). We used global positioning system (GPS) collars to synchronously record the hourly locations of five baboon social groups for ∼900 days, and we used behavioral, demographic, and life...

Data from: Parasites affect food web structure primarily through increased diversity and complexity

Jennifer A. Dunne, Kevin D. Lafferty, Andrew P. Dobson, Ryan F. Hechinger, Armand M. Kuris, Neo D. Martinez, John P. McLaughlin, Kim N. Mouritsen, Robert Poulin, Karsten Reise, Daniel B. Stouffer, David W. Thieltges, Richard J. Williams & Claus Dieter Zander
Comparative research on food web structure has revealed generalities in trophic organization, produced simple models, and allowed assessment of robustness to species loss. These studies have mostly focused on free-living species. Recent research has suggested that inclusion of parasites alters structure. We assess whether such changes in network structure result from unique roles and traits of parasites or from changes to diversity and complexity. We analyzed seven highly resolved food webs that include metazoan parasite...

Registration Year

  • 2013

Resource Types

  • Dataset


  • Princeton University
  • Stanford University
  • Duke University
  • National Museums of Kenya
  • Estación Biológica de Doñana
  • Howard Hughes Medical Institute
  • University of Pennsylvania
  • University of Hamburg
  • University of Michigan-Ann Arbor
  • Aarhus University