Prophage Provide a Safe Haven for Adaptive Exploration in Temperate Viruses [Population and Evolutionary Genetics]
Prophage sequences constitute a substantial fraction of the temperate virus gene pool. Although subject to mutational decay, prophage sequences can also be an important source of adaptive mutations for these viral populations. Here we develop a life-history model for temperate viruses, including both the virulent (lytic) and the temperate phases of the life cycle. We then examine the survival of mutations that increase fitness during the lytic phase (attachment rate, burst size), increase fitness in the temperate phase (increasing host survival), or affect transitions between the two phases (integration or induction probab...
Source: Genetics - May 5, 2017 Category: Genetics & Stem Cells Authors: Wahl, L. M., Pattenden, T. Tags: Population and Evolutionary Genetics Source Type: research
Rapid Adaptation of a Polygenic Trait After a Sudden Environmental Shift [Population and Evolutionary Genetics]
Although a number of studies have shown that natural and laboratory populations initially well adapted to their environment can evolve rapidly when conditions suddenly change, the dynamics of rapid adaptation are not well understood. Here a population genetic model of polygenic selection is analyzed to describe the short-term response of a quantitative trait after a sudden shift of the phenotypic optimum. We provide explicit analytical expressions for the timescales over which the trait mean approaches the new optimum. We find that when the effect sizes are small relative to a scaled mutation rate, small to moderate allele...
Source: Genetics - May 5, 2017 Category: Genetics & Stem Cells Authors: Jain, K., Stephan, W. Tags: Population and Evolutionary Genetics Source Type: research
Spiraling Complexity: A Test of the Snowball Effect in a Computational Model of RNA Folding [Population and Evolutionary Genetics]
Genetic incompatibilities can emerge as a byproduct of genetic divergence. According to Dobzhansky and Muller, an allele that fixes in one population may be incompatible with an allele at a different locus in another population when the two alleles are brought together in hybrids. Orr showed that the number of Dobzhansky-Muller incompatibilities (DMIs) should accumulate faster than linearly—i.e., snowball—as two lineages diverge. Several studies have attempted to test the snowball effect using data from natural populations. One limitation of these studies is that they have focused on predictions of the Orr mode...
Source: Genetics - May 5, 2017 Category: Genetics & Stem Cells Authors: Kalirad, A., Azevedo, R. B. R. Tags: Population and Evolutionary Genetics Source Type: research
Comparative Analyses of Selection Operating on Nontranslated Intergenic Regions of Diverse Bacterial Species [Population and Evolutionary Genetics]
Nontranslated intergenic regions (IGRs) compose 10–15% of bacterial genomes, and contain many regulatory elements with key functions. Despite this, there are few systematic studies on the strength and direction of selection operating on IGRs in bacteria using whole-genome sequence data sets. Here we exploit representative whole-genome data sets from six diverse bacterial species: Staphylococcus aureus, Streptococcus pneumoniae, Mycobacterium tuberculosis, Salmonella enterica, Klebsiella pneumoniae, and Escherichia coli. We compare patterns of selection operating on IGRs using two independent methods: the proportion o...
Source: Genetics - May 5, 2017 Category: Genetics & Stem Cells Authors: Thorpe, H. A., Bayliss, S. C., Hurst, L. D., Feil, E. J. Tags: Population and Evolutionary Genetics Source Type: research
Inference of the Distribution of Selection Coefficients for New Nonsynonymous Mutations Using Large Samples [Population and Evolutionary Genetics]
The distribution of fitness effects (DFE) has considerable importance in population genetics. To date, estimates of the DFE come from studies using a small number of individuals. Thus, estimates of the proportion of moderately to strongly deleterious new mutations may be unreliable because such variants are unlikely to be segregating in the data. Additionally, the true functional form of the DFE is unknown, and estimates of the DFE differ significantly between studies. Here we present a flexible and computationally tractable method, called Fitai, to estimate the DFE of new mutations using the site frequency spectrum from a...
Source: Genetics - May 5, 2017 Category: Genetics & Stem Cells Authors: Kim, B. Y., Huber, C. D., Lohmueller, K. E. Tags: Population and Evolutionary Genetics Source Type: research
The Bacterial Sequential Markov Coalescent [Population and Evolutionary Genetics]
We present a new model that approximates the coalescent with gene conversion: the bacterial sequential Markov coalescent (BSMC). Our approach is based on a similar idea to the sequential Markov coalescent (SMC)—an approximation of the coalescent with crossover recombination. However, bacterial recombination poses hurdles to a sequential Markov approximation, as it leads to strong correlations and linkage disequilibrium across very distant sites in the genome. Our BSMC overcomes these difficulties, and shows a considerable reduction in computational demand compared to the exact CGC, and very similar patterns in simula...
Source: Genetics - May 5, 2017 Category: Genetics & Stem Cells Authors: De Maio, N., Wilson, D. J. Tags: Population and Evolutionary Genetics Source Type: research
Population Genomics of Daphnia pulex [Population and Evolutionary Genetics]
Using data from 83 isolates from a single population, the population genomics of the microcrustacean Daphnia pulex are described and compared to current knowledge for the only other well-studied invertebrate, Drosophila melanogaster. These two species are quite similar with respect to effective population sizes and mutation rates, although some features of recombination appear to be different, with linkage disequilibrium being elevated at short ($$ 0.05$$ appear to evolve in a nearly neutral fashion. All forms of genomic sites (including replacement sites within codons, and intergenic and UTR regions) appear to be experien...
Source: Genetics - May 5, 2017 Category: Genetics & Stem Cells Authors: Lynch, M., Gutenkunst, R., Ackerman, M., Spitze, K., Ye, Z., Maruki, T., Jia, Z. Tags: Population and Evolutionary Genetics Source Type: research
Regulation of Hyphal Growth and N-Acetylglucosamine Catabolism by Two Transcription Factors in Candida albicans [Developmental and Behavioral Genetics]
The amino sugar N-acetylglucosamine (GlcNAc) is increasingly recognized as an important signaling molecule in addition to its well-known structural roles at the cell surface. In the human fungal pathogen Candida albicans, GlcNAc stimulates several responses including the induction of the genes needed for its catabolism and a switch from budding to filamentous hyphal growth. We identified two genes needed for growth on GlcNAc (RON1 and NGS1) and found that mutants lacking these genes fail to induce the genes needed for GlcNAc catabolism. NGS1 was also important for growth on other sugars, such as maltose, but RON1 appeared ...
Source: Genetics - May 5, 2017 Category: Genetics & Stem Cells Authors: Naseem, S., Min, K., Spitzer, D., Gardin, J., Konopka, J. B. Tags: Developmental and Behavioral Genetics Source Type: research
Locomotion Behavior Is Affected by the G{alpha}S Pathway and the Two-Pore-Domain K+ Channel TWK-7 Interacting in GABAergic Motor Neurons in Caenorhabditis elegans [Developmental and Behavioral Genetics]
Adjusting the efficiency of movement in response to environmental cues is an essential integrative characteristic of adaptive locomotion behavior across species. However, the modulatory molecules and the pathways involved are largely unknown. Recently, we demonstrated that in Caenorhabditis elegans, a loss-of-function of the two-pore-domain potassium (K2P) channel TWK-7 causes a fast, coordinated, and persistent forward crawling behavior in which five central aspects of stimulated locomotion—velocity, direction, wave parameters, duration, and straightness—are affected. Here, we isolated the reduction-of-functio...
Source: Genetics - May 5, 2017 Category: Genetics & Stem Cells Authors: Gottschling, D.-C., Doring, F., Luersen, K. Tags: Developmental and Behavioral Genetics Source Type: research
The NCA-1 and NCA-2 Ion Channels Function Downstream of Gq and Rho To Regulate Locomotion in Caenorhabditis elegans [Developmental and Behavioral Genetics]
The heterotrimeric G protein Gq positively regulates neuronal activity and synaptic transmission. Previously, the Rho guanine nucleotide exchange factor Trio was identified as a direct effector of Gq that acts in parallel to the canonical Gq effector phospholipase C. Here, we examine how Trio and Rho act to stimulate neuronal activity downstream of Gq in the nematode Caenorhabditis elegans. Through two forward genetic screens, we identify the cation channels NCA-1 and NCA-2, orthologs of mammalian NALCN, as downstream targets of the Gq-Rho pathway. By performing genetic epistasis analysis using dominant activating mutation...
Source: Genetics - May 5, 2017 Category: Genetics & Stem Cells Authors: Topalidou, I., Chen, P.-A., Cooper, K., Watanabe, S., Jorgensen, E. M., Ailion, M. Tags: Developmental and Behavioral Genetics Source Type: research
Molecular Determinants of the Regulation of Development and Metabolism by Neuronal eIF2{alpha} Phosphorylation in Caenorhabditis elegans [Developmental and Behavioral Genetics]
Cell-nonautonomous effects of signaling in the nervous system of animals can influence diverse aspects of organismal physiology. We previously showed that phosphorylation of Ser49 of the α-subunit of eukaryotic translation initiation factor 2 (eIF2α) in two chemosensory neurons by PEK-1/PERK promotes entry of Caenorhabditis elegans into dauer diapause. Here, we identified and characterized the molecular determinants that confer sensitivity to effects of neuronal eIF2α phosphorylation on development and physiology of C. elegans. Isolation and characterization of mutations in eif-2Ba encoding the α-su...
Source: Genetics - May 5, 2017 Category: Genetics & Stem Cells Authors: Kulalert, W., Sadeeshkumar, H., Zhang, Y. K., Schroeder, F. C., Kim, D. H. Tags: Developmental and Behavioral Genetics Source Type: research
A Search for Genes Mediating the Growth-Promoting Function of TGF{beta} in the Drosophila melanogaster Wing Disc [Developmental and Behavioral Genetics]
Transforming Growth Factor β (TGFβ) signaling has a complex influence on cell proliferation, acting to stop cell division in differentiating cells, but also promoting cell division in immature cells. The activity of the pathway in Drosophila is mostly required to stimulate the proliferation of neural and epithelial tissues. Most interestingly, this function is not absolutely required for cell division, but it is needed for these tissues to reach their correct size. It is not known how TGFβ signaling promotes cell division in imaginal discs, or what the interactions between TGFβ activity and other signal...
Source: Genetics - May 5, 2017 Category: Genetics & Stem Cells Authors: Hevia, C. F., Lopez-Varea, A., Esteban, N., de Celis, J. F. Tags: Developmental and Behavioral Genetics Source Type: research
Extrinsic Repair of Injured Dendrites as a Paradigm for Regeneration by Fusion in Caenorhabditis elegans [Developmental and Behavioral Genetics]
Injury triggers regeneration of axons and dendrites. Research has identified factors required for axonal regeneration outside the CNS, but little is known about regeneration triggered by dendrotomy. Here, we study neuronal plasticity triggered by dendrotomy and determine the fate of complex PVD arbors following laser surgery of dendrites. We find that severed primary dendrites grow toward each other and reconnect via branch fusion. Simultaneously, terminal branches lose self-avoidance and grow toward each other, meeting and fusing at the tips via an AFF-1-mediated process. Ectopic branch growth is identified as a step in t...
Source: Genetics - May 5, 2017 Category: Genetics & Stem Cells Authors: Oren-Suissa, M., Gattegno, T., Kravtsov, V., Podbilewicz, B. Tags: Developmental and Behavioral Genetics Source Type: research
Adult Muscle Formation Requires Drosophila Moleskin for Proliferation of Wing Disc-Associated Muscle Precursors [Developmental and Behavioral Genetics]
Adult muscle precursor (AMP) cells located in the notum of the larval wing disc undergo rapid amplification and eventual fusion to generate the Drosophila melanogaster indirect flight muscles (IFMs). Here we find that loss of Moleskin (Msk) function in these wing disc-associated myoblasts reduces the overall AMP pool size, resulting in the absence of IFM formation. This myoblast loss is due to a decrease in the AMP proliferative capacity and is independent of cell death. In contrast, disruption of Msk during pupal myoblast proliferation does not alter the AMP number, suggesting that Msk is specifically required for larval ...
Source: Genetics - May 5, 2017 Category: Genetics & Stem Cells Authors: Vishal, K., Brooks, D. S., Bawa, S., Gameros, S., Stetsiv, M., Geisbrecht, E. R. Tags: Developmental and Behavioral Genetics Source Type: research
Germline Proliferation Is Regulated by Somatic Endocytic Genes via JNK and BMP Signaling in Drosophila [Cellular Genetics]
Signals derived from the microenvironment contribute greatly to tumorigenesis . The underlying mechanism requires thorough investigation. Here, we use Drosophila testis as a model system to address this question, taking the advantage of the ease to distinguish germline and somatic cells and to track the cell numbers. In an EMS mutagenesis screen, we identified Rab5, a key factor in endocytosis, for its nonautonomous role in germline proliferation. The disruption of Rab5 in somatic cyst cells, which escort the development of germline lineage, induced the overproliferation of underdifferentiated but genetically wild-type ger...
Source: Genetics - May 5, 2017 Category: Genetics & Stem Cells Authors: Tang, Y., Geng, Q., Chen, D., Zhao, S., Liu, X., Wang, Z. Tags: Cellular Genetics Source Type: research
