39 Works

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: 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: 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: 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: 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: Ancient horizontal gene transfer and the last common ancestors

Gregory P. Fournier, Cheryl P. Andam & Johann Peter Gogarten
Background: The genomic history of prokaryotic organismal lineages is marked by extensive non-vertical inheritance of genes, with horizontal gene transfer (HGT) between many groups of organisms at all taxonomic levels. These HGT events have played an essential role in the origin and distribution of biological innovations. Analyses of ancient gene families show that HGT existed in the distant past, even at the time of the organismal last universal common ancestor (LUCA). Most gene transfers originated...

Data from: MHC class II assortative mate choice in European badgers (Meles meles)

Yung Wa Sin, Geetha Annavi, Chris Newman, Christina Buesching, Terry Burke, David W. Macdonald & Hannah L. Dugdale
The major histocompatibility complex (MHC) plays a crucial role in the immune system, and in some species, it is a target by which individuals choose mates to optimize the fitness of their offspring, potentially mediated by olfactory cues. Under the genetic compatibility hypothesis, individuals are predicted to choose mates with compatible MHC alleles, to increase the fitness of their offspring. Studies of MHC-based mate choice in wild mammals are under-represented currently, and few investigate more...

Data from: Size-related scaling of tree form and function in a mixed-age forest

Kristina J. Anderson-Teixeira, Jennifer C. McGarvey, Helene C. Muller-Landau, Janice Y. Park, Erika B. Gonzalez-Akre, Valentine Herrmann, Amy C. Bennett, Christopher V. So, Norman A. Bourg, Jonathan R. Thompson, Sean M. McMahon & William J. McShea
Many morphological, physiological and ecological traits of trees scale with diameter, shaping the structure and function of forest ecosystems. Understanding the mechanistic basis for such scaling relationships is key to understanding forests globally and their role in Earth's changing climate system. Here, we evaluate theoretical predictions for the scaling of nine variables in a mixed-age temperate deciduous forest (CTFS-ForestGEO forest dynamics plot at the Smithsonian Conservation Biology Institute, Virginia, USA) and compare observed scaling parameters...

Data from: Low cost, high performance processing of single particle cryo-electron microscopy data in the cloud

Michael A. Cianfrocco & Andres E. Leschziner
The advent of a new generation of electron microscopes and direct electron detectors has realized the potential of single particle cryo-electron microscopy (cryo-EM) as a technique to generate high-resolution structures. Calculating these structures requires high performance computing clusters, a resource that may be limiting to many likely cryo-EM users. To address this limitation and facilitate the spread of cryo-EM, we developed a publicly available 'off-the-shelf' computing environment on Amazon's elastic cloud computing infrastructure. This environment...

Data from: Extracting spatio-temporal patterns in animal trajectories: an ecological application of sequence analysis methods

Johannes De Groeve, Nico Van De Weghe, Nathan Ranc, Tijs Neutens, Lino Ometto, Omar Rota-Stabelli & Francesca Cagnacci
Digital tracking technologies have considerably increased the amount and quality of animal trajectories, enabling the study of habitat use and habitat selection at a fine spatial and temporal scale. However, current approaches do not yet explicitly account for a key aspect of habitat use, namely the sequential variation in the use of different habitat features. To overcome this limitation, we propose a tree-based approach that makes use of sequence analysis methods, derived from molecular biology,...

Data from: The ontogeny of fairness in seven societies

Peter R. Blake, Katherine McAuliffe, John Corbit, Tara C. Callaghan, Oumar Barry, Aleah Bowie, Lauren Kleutsch, Karen L. Kramer, Elizabeth Ross, Hurnan Vongsachang, Richard Wrangham & Felix Warneken
A sense of fairness plays a critical role in supporting human cooperation. Adult norms of fair resource sharing vary widely across societies, suggesting that culture shapes the acquisition of fairness behaviour during childhood. Here we examine how fairness behaviour develops in children from seven diverse societies, testing children from 4 to 15 years of age (n = 866 pairs) in a standardized resource decision task. We measured two key aspects of fairness decisions: disadvantageous inequity...

Data from: Apolipoprotein (ApoE) polymorphism is related to differences in potential fertility in women: a case of antagonistic pleiotropy?

Grazyna Jasienska, Peter T. Ellison, Andrzej Galbarczyk, Michal Jasienski, Malgorzata Kalemba-Drozdz, Maria Kapiszewska, Ilona Nenko, Inger Thune & Anna Ziomkiewicz
The alleles that are detrimental to health, especially in older age, are thought to persist in populations because they also confer some benefits for individuals (through antagonistic pleiotropy). The ApoE4 allele at the ApoE locus, encoding apolipoprotein E (ApoE), significantly increases risk of poor health, and yet it is present in many populations at relatively high frequencies. Why has it not been replaced by natural selection with the health-beneficial ApoE3 allele? ApoE is a major...

Data from: Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists

Annegret Kohler, Alan Kuo, Laszlo G. Nagy, Emmanuelle Morin, Kerrie W. Barry, Francois Buscot, Bjorn Canback, Cindy Choi, Nicolas Cichocki, Alicia Clum, Jan Colpaert, Alex Copeland, Mauricio D. Costa, Jeanne Dore, Dimitrios Floudas, Gilles Gay, Mariangela Girlanda, Bernard Henrissat, Sylvie Herrmann, Jaqueline Hess, Nils Hogberg, Tomas Johansson, Hassine-Radhouane Khouja, Kurt LaButti, Urs Lahrmann … & Francis Martin
To elucidate the genetic bases of mycorrhizal lifestyle evolution, we sequenced new fungal genomes, including 13 ectomycorrhizal (ECM), orchid (ORM) and ericoid (ERM) species, and five saprotrophs, which we analyzed along with other fungal genomes. Ectomycorrhizal fungi have a reduced complement of genes encoding plant cell wall–degrading enzymes (PCWDEs), as compared to their ancestral wood decayers. Nevertheless, they have retained a unique array of PCWDEs, thus suggesting that they possess diverse abilities to decompose lignocellulose....

Data from: How many routes lead to migration? Comparison of methods to assess and characterise migratory movements

Francesca Cagnacci, Stefano Focardi, Anne Ghisla, Bram Van Moorter, Eliezer Gurarie, Marco Heurich, Atle Mysterud, John Linnell, Manuela Panzacchi, Evelyn Merrill, Roel May, Torgeir Nygård, Christer Rolandsen, Mark Hebblewhite & Evelyn H. Merrill
1. Decreasing rate of migration in several species as a consequence of climate change and anthropic pressure, together with increasing evidence of space-use strategies intermediate between residency and complete migration, are very strong motivations to evaluate migration occurrence and features in animal populations. 2. The main goal of this paper was to perform a relative comparison between methods for identifying and characterising migration at the individual and population level on the basis of animal location...

Data from: Controlled measurement and comparative analysis of cellular components in E. coli reveals broad regulatory changes in response to glucose starvation

John R. Houser, Craig Barnhart, Daniel R. Boutz, Sean M. Carrol, Aurko Dasgupta, Joshua K. Michener, Brittany D. Needham, Ophelia Papoulas, Viswanadham Sridhara, Dariya K. Sydykova, Christopher J. Marx, M. Stephen Trent, Jeffery E. Barrick, Edward M. Marcotte, Claus O. Wilke, Jeffrey E. Barrick & Sean M. Carroll
How do bacteria regulate their cellular physiology in response to starvation? Here, we present a detailed characterization of Escherichia coli growth and starvation over a time-course lasting two weeks. We have measured multiple cellular components, including RNA and proteins at deep genomic coverage, as well as lipid modifications and flux through central metabolism. Our study focuses on the physiological response of E. coli in stationary phase as a result of being starved for glucose, not...

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: 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: 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: 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: 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: 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: 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: 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...

Registration Year

  • 2015
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Resource Types

  • Dataset
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Affiliations

  • Harvard University
    39
  • The University of Texas at Austin
    2
  • University of Georgia
    2
  • Del Rosario University
    2
  • University of Cambridge
    2
  • University of Alberta
    2
  • University of California, Berkeley
    2
  • Smithsonian Institution
    2
  • University of Oslo
    2
  • University of Chicago
    2