Rarefaction, alpha diversity, and statistics, bioRxiv, 2017-12-12
AbstractUnderstanding the drivers of microbial diversity is a fundamental question in microbial ecology. Extensive literature discusses different methods for describing microbial diversity and documenting its effects on ecosystem function. However, it is widely believed that diversity depends on the number of reads that are sequenced. I discuss a statistical perspective on diversity, framing the diversity of an environment as an unknown parameter, and discussing the bias and variance of plug-in and rarefied estimates. I argue that by failing to account for both bias and variance, we invalidate analysis of alpha diversity. I describe the state of the statistical literature for addressing these problems, and suggest that measurement error modeling can address issues with variance, but bias corrections need to be utilized as well. I encourage microbial ecologists to avoid motivating their investigations with alpha diversity analyses that do not use valid statistical methodology.
biorxiv microbiology 0-100-users 2017Robust manipulation of the behavior of Drosophila melanogaster by a fungal pathogen in the laboratory, bioRxiv, 2017-12-11
AbstractMany microbes induce striking behavioral changes in their animal hosts, but how they achieve this is poorly understood, especially at the molecular level. Mechanistic understanding has been largely constrained by the lack of a model system with advanced tools for molecular manipulation. We recently discovered a strain of the behavior-manipulating fungal pathogen Entomophthora muscae infecting wild Drosophila, and established methods to infect D. melanogaster in the lab. Lab-infected flies manifest the moribund behaviors characteristic of E. muscae infection hours before death, they climb upward, extend their proboscides and affix in place, then raise their wings, clearing a path for infectious spores to launch from their abdomens. We found that E. muscae invades the fly nervous system, suggesting a direct means by which the fungus could induce behavioral changes. Given the vast molecular toolkit available for D. melanogaster, we believe this new system will enable rapid progress in understanding the mechanistic basis of E. muscae’s behavioral manipulation in the fly.
biorxiv animal-behavior-and-cognition 200-500-users 2017The ancestral animal genetic toolkit revealed by diverse choanoflagellate transcriptomes, bioRxiv, 2017-12-11
AbstractThe changes in gene content that preceded the origin of animals can be reconstructed by comparison with their sister group, the choanoflagellates. However, only two choanoflagellate genomes are currently available, providing poor coverage of their diversity. We sequenced transcriptomes of 19 additional choanoflagellate species to produce a comprehensive reconstruction of the gains and losses that shaped the ancestral animal gene repertoire. We find roughly 1,700 gene families with origins on the animal stem lineage, of which only a core set of 36 are conserved across animals. We find more than 350 gene families that were previously thought to be animal-specific actually evolved before the animal-choanoflagellate divergence, including Notch and Delta, Toll-like receptors, and glycosaminoglycan hydrolases that regulate animal extracellular matrix (ECM). In the choanoflagellate Salpingoeca helianthica, we show that a glycosaminoglycan hydrolase modulates rosette colony size, suggesting a link between ECM regulation and morphogenesis in choanoflagellates and animals.Data AvailabilityRaw sequencing reads NCBI BioProject PRJNA419411 (19 choanoflagellate transcriptomes), PRJNA420352 (S. rosetta polyA selection test)Transcriptome assemblies, annotations, and gene families <jatsext-link xmlnsxlink=httpwww.w3.org1999xlink ext-link-type=uri xlinkhref=httpsdx.doi.org10.6084m9.figshare.5686984>httpsdx.doi.org10.6084m9.figshare.5686984<jatsext-link>Protocols <jatsext-link xmlnsxlink=httpwww.w3.org1999xlink ext-link-type=uri xlinkhref=httpsdx.doi.org10.17504protocols.io.kwscxee>httpsdx.doi.org10.17504protocols.io.kwscxee<jatsext-link>
biorxiv evolutionary-biology 100-200-users 2017Optogenetic dissection of descending behavioral control in Drosophila, bioRxiv, 2017-12-10
AbstractIn most animals, the brain makes behavioral decisions that are transmitted by descending neurons to the nerve cord circuitry that produces behaviors. In insects, only a few descending neurons have been associated with specific behaviors. To explore how these neurons control an insect’s movements, we developed a novel method to systematically assay the behavioral effects of activating individual neurons on freely behaving terrestrial D. melanogaster. We calculated a two-dimensional representation of the entire behavior space explored by these flies and associated descending neurons with specific behaviors by identifying regions of this space that were visited with increased frequency during optogenetic activation. Applying this approach across a population of descending neurons, we found, that (1) activation of most of the descending neurons drove stereotyped behaviors, (2) in many cases multiple descending neurons activated similar behaviors, and (3) optogenetically-activated behaviors were often dependent on the behavioral state prior to activation.
biorxiv neuroscience 0-100-users 2017Optogenetic dissection of descending behavioral control inDrosophila, bioRxiv, 2017-12-10
AbstractIn most animals, the brain makes behavioral decisions that are transmitted by descending neurons to the nerve cord circuitry that produces behaviors. In insects, only a few descending neurons have been associated with specific behaviors. To explore how these neurons control an insect’s movements, we developed a novel method to systematically assay the behavioral effects of activating individual neurons on freely behaving terrestrialD. melanogaster. We calculated a two-dimensional representation of the entire behavior space explored by these flies and associated descending neurons with specific behaviors by identifying regions of this space that were visited with increased frequency during optogenetic activation. Applying this approach across a population of descending neurons, we found, that (1) activation of most of the descending neurons drove stereotyped behaviors, (2) in many cases multiple descending neurons activated similar behaviors, and (3) optogenetically-activated behaviors were often dependent on the behavioral state prior to activation.
biorxiv neuroscience 0-100-users 2017A deep mutational scan of an acidic activation domain, bioRxiv, 2017-12-09
AbstractTranscriptional activation domains are intrinsically disordered peptides with little primary sequence conservation. These properties have made it difficult to identify the sequence features that define activation domains. For example, although acidic activation domains were discovered 30 years ago, we still do not know what role, if any, acidic residues play in these peptides. To address this question we designed a rational mutagenesis scheme to independently test four sequence features theorized to control the strength of activation domains acidity (negative charge), hydrophobicity, intrinsic disorder, and short linear motifs. To test enough mutants to deconvolve these four features we developed a method to quantify the activities of thousands of activation domain variants in parallel. Our results with Gcn4, a classic acidic activation domain, suggest that acidic residues in particular regions keep two hydrophobic motifs exposed to solvent. We also found that the specific activity of the Gcn4 activation domain increases during amino acid starvation. Our results suggest that Gcn4 may have evolved to have low activity but high inducibility. Our results also demonstrate that high-throughput rational mutation scans will be powerful tools for unraveling the properties that control how intrinsically disordered proteins function.
biorxiv systems-biology 0-100-users 2017