Developmental Restriction of Retrotransposition Activated in Arabidopsis by Environmental Stress [Genome and Systems Biology]
Retrotransposons (RTs) can rapidly increase in copy number due to periodic bursts of transposition. Such bursts are mutagenic and thus potentially deleterious. However, certain transposition-induced gain-of-function or regulatory mutations may be of selective advantage. How an optimal balance between these opposing effects arises is not well characterized. Here, we studied transposition bursts of a heat-activated retrotransposon family in Arabidopsis. We recorded a high inter and intraplant variation in the number and chromosomal position of new insertions, which usually did not affect plant fertility and were equally well...
Source: Genetics - October 4, 2017 Category: Genetics & Stem Cells Authors: Gaubert, H., Sanchez, D. H., Drost, H.-G., Paszkowski, J. Tags: Genome and Systems Biology Source Type: research
Identification of trans Protein QTL for Secreted Airway Mucins in Mice and a Causal Role for Bpifb1 [Genetics of Complex Traits]
Mucus hyper-secretion is a hallmark feature of asthma and other muco-obstructive airway diseases. The mucin proteins MUC5AC and MUC5B are the major glycoprotein components of mucus and have critical roles in airway defense. Despite the biomedical importance of these two proteins, the loci that regulate them in the context of natural genetic variation have not been studied. To identify genes that underlie variation in airway mucin levels, we performed genetic analyses in founder strains and incipient lines of the Collaborative Cross (CC) in a house dust mite mouse model of asthma. CC founder strains exhibited significant di...
Source: Genetics - October 4, 2017 Category: Genetics & Stem Cells Authors: Donoghue, L. J., Livraghi-Butrico, A., McFadden, K. M., Thomas, J. M., Chen, G., Grubb, B. R., ONeal, W. K., Boucher, R. C., Kelada, S. N. P. Tags: Genetics of Complex Traits Source Type: research
A Mixed Model Approach to Genome-Wide Association Studies for Selection Signatures, with Application to Mice Bred for Voluntary Exercise Behavior [Genetics of Complex Traits]
Selection experiments and experimental evolution provide unique opportunities to study the genetics of adaptation because the target and intensity of selection are known relatively precisely. In contrast to natural selection, where populations are never strictly "replicated," experimental evolution routinely includes replicate lines so that selection signatures—genomic regions showing excessive differentiation between treatments—can be separated from possible founder effects, genetic drift, and multiple adaptive solutions. We developed a mouse model with four lines within a high running (HR) selection treatment...
Source: Genetics - October 4, 2017 Category: Genetics & Stem Cells Authors: Xu, S., Garland, T. Tags: Genetics of Complex Traits Source Type: research
Variation in Recombination Rate and Its Genetic Determinism in Sheep Populations [Genetics of Complex Traits]
Recombination is a complex biological process that results from a cascade of multiple events during meiosis. Understanding the genetic determinism of recombination can help to understand if and how these events are interacting. To tackle this question, we studied the patterns of recombination in sheep, using multiple approaches and data sets. We constructed male recombination maps in a dairy breed from the south of France (the Lacaune breed) at a fine scale by combining meiotic recombination rates from a large pedigree genotyped with a 50K SNP array and historical recombination rates from a sample of unrelated individuals ...
Source: Genetics - October 4, 2017 Category: Genetics & Stem Cells Authors: Petit, M., Astruc, J.-M., Sarry, J., Drouilhet, L., Fabre, S., Moreno, C. R., Servin, B. Tags: Genetics of Complex Traits Source Type: research
Selection During Maize Domestication Targeted a Gene Network Controlling Plant and Inflorescence Architecture [Genetics of Complex Traits]
Selection during evolution, whether natural or artificial, acts through the phenotype. For multifaceted phenotypes such as plant and inflorescence architecture, the underlying genetic architecture is comprised of a complex network of interacting genes rather than single genes that act independently to determine the trait. As such, selection acts on entire gene networks. Here, we begin to define the genetic regulatory network to which the maize domestication gene, teosinte branched1 (tb1), belongs. Using a combination of molecular methods to uncover either direct or indirect regulatory interactions, we identified a set of g...
Source: Genetics - October 4, 2017 Category: Genetics & Stem Cells Authors: Studer, A. J., Wang, H., Doebley, J. F. Tags: Genetics of Complex Traits Source Type: research
Significant Synteny and Colocalization of Ecologically Relevant Quantitative Trait Loci Within and Across Species of Salmonid Fishes [Genetics of Complex Traits]
The organization of functional regions within genomes has important implications for evolutionary potential. Considerable research effort has gone toward identifying the genomic basis of phenotypic traits of interest through quantitative trait loci (QTL) analyses. Less research has assessed the arrangement of QTL in the genome within and across species. To investigate the distribution, extent of colocalization, and the synteny of QTL for ecologically relevant traits, we used a comparative genomic mapping approach within and across a range of salmonid species. We compiled 943 QTL from all available species [lake whitefish (...
Source: Genetics - October 4, 2017 Category: Genetics & Stem Cells Authors: Jacobs, A., Womack, R., Chen, M., Gharbi, K., Elmer, K. R. Tags: Genetics of Complex Traits Source Type: research
Cross-Species Y Chromosome Function Between Malaria Vectors of the Anopheles gambiae Species Complex [Population and Evolutionary Genetics]
Y chromosome function, structure and evolution is poorly understood in many species, including the Anopheles genus of mosquitoes—an emerging model system for studying speciation that also represents the major vectors of malaria. While the Anopheline Y had previously been implicated in male mating behavior, recent data from the Anopheles gambiae complex suggests that, apart from the putative primary sex-determiner, no other genes are conserved on the Y. Studying the functional basis of the evolutionary divergence of the Y chromosome in the gambiae complex is complicated by complete F1 male hybrid sterility. Here, we u...
Source: Genetics - October 4, 2017 Category: Genetics & Stem Cells Authors: Bernardini, F., Galizi, R., Wunderlich, M., Taxiarchi, C., Kranjc, N., Kyrou, K., Hammond, A., Nolan, T., Lawniczak, M. N. K., Papathanos, P. A., Crisanti, A., Windbichler, N. Tags: Population and Evolutionary Genetics Source Type: research
Drift-Induced Selection Between Male and Female Heterogamety [Population and Evolutionary Genetics]
Evolutionary transitions between male and female heterogamety are common in both vertebrates and invertebrates. Theoretical studies of these transitions have found that, when all genotypes are equally fit, continuous paths of intermediate equilibria link the two sex chromosome systems. This observation has led to a belief that neutral evolution along these paths can drive transitions, and that arbitrarily small fitness differences among sex chromosome genotypes can determine the system to which evolution leads. Here, we study stochastic evolutionary dynamics along these equilibrium paths. We find non-neutrality, both in tr...
Source: Genetics - October 4, 2017 Category: Genetics & Stem Cells Authors: Veller, C., Muralidhar, P., Constable, G. W. A., Nowak, M. A. Tags: Population and Evolutionary Genetics Source Type: research
Selection Constrains High Rates of Tandem Repetitive DNA Mutation in Daphnia pulex [Population and Evolutionary Genetics]
A long-standing evolutionary puzzle is that all eukaryotic genomes contain large amounts of tandemly-repeated DNA whose sequence motifs and abundance vary greatly among even closely related species. To elucidate the evolutionary forces governing tandem repeat dynamics, quantification of the rates and patterns of mutations in repeat copy number and tests of its selective neutrality are necessary. Here, we used whole-genome sequences of 28 mutation accumulation (MA) lines of Daphnia pulex, in addition to six isolates from a non-MA population originating from the same progenitor, to both estimate mutation rates of abundances ...
Source: Genetics - October 4, 2017 Category: Genetics & Stem Cells Authors: Flynn, J. M., Caldas, I., Cristescu, M. E., Clark, A. G. Tags: Population and Evolutionary Genetics Source Type: research
Hill-Robertson Interference Reduces Genetic Diversity on a Young Plant Y-Chromosome [Genetics of Sex]
X and Y chromosomes differ in effective population size (Ne), rates of recombination, and exposure to natural selection, all of which can affect patterns of genetic diversity. On Y chromosomes with suppressed recombination, natural selection is expected to eliminate linked neutral variation, and lower the Ne of Y compared to X chromosomes or autosomes. However, female-biased sex ratios and high variance in male reproductive success can also reduce Y-linked Ne, making it difficult to infer the causes of low Y-diversity. Here, we investigate the factors affecting levels of polymorphism during sex chromosome evolution in the ...
Source: Genetics - October 4, 2017 Category: Genetics & Stem Cells Authors: Hough, J., Wang, W., Barrett, S. C. H., Wright, S. I. Tags: Genetics of Sex Source Type: research
Accumulation of Deleterious Mutations During Bacterial Range Expansions [Population and Evolutionary Genetics]
Recent theory predicts that the fitness of pioneer populations can decline when species expand their range, due to high rates of genetic drift on wave fronts making selection less efficient at purging deleterious variants. To test these predictions, we studied the fate of mutator bacteria expanding their range for 1650 generations on agar plates. In agreement with theory, we find that growth abilities of strains with a high mutation rate (HMR lines) decreased significantly over time, unlike strains with a lower mutation rate (LMR lines) that present three to four times fewer mutations. Estimation of the distribution of fit...
Source: Genetics - October 4, 2017 Category: Genetics & Stem Cells Authors: Bosshard, L., Dupanloup, I., Tenaillon, O., Bruggmann, R., Ackermann, M., Peischl, S., Excoffier, L. Tags: Population and Evolutionary Genetics Source Type: research
When Does Frequency-Independent Selection Maintain Genetic Variation? [Population and Evolutionary Genetics]
Frequency-independent selection is generally considered as a force that acts to reduce the genetic variation in evolving populations, yet rigorous arguments for this idea are scarce. When selection fluctuates in time, it is unclear whether frequency-independent selection may maintain genetic polymorphism without invoking additional mechanisms. We show that constant frequency-independent selection with arbitrary epistasis on a well-mixed haploid population eliminates genetic variation if we assume linkage equilibrium between alleles. To this end, we introduce the notion of frequency-independent selection at the level of all...
Source: Genetics - October 4, 2017 Category: Genetics & Stem Cells Authors: Novak, S., Barton, N. H. Tags: Population and Evolutionary Genetics Source Type: research
Predicting Amino Acid Substitution Probabilities Using Single Nucleotide Polymorphisms [Population and Evolutionary Genetics]
Fast genome sequencing offers invaluable opportunities for building updated and improved models of protein sequence evolution. We here show that Single Nucleotide Polymorphisms (SNPs) can be used to build a model capable of predicting the probability of substitution between amino acids in variants of the same protein in different species. The model is based on a substitution matrix inferred from the frequency of codon interchanges observed in a suitably selected subset of human SNPs, and predicts the substitution probabilities observed in alignments between Homo sapiens and related species at 85–100% of sequence iden...
Source: Genetics - October 4, 2017 Category: Genetics & Stem Cells Authors: Rizzato, F., Rodriguez, A., Biarnes, X., Laio, A. Tags: Population and Evolutionary Genetics Source Type: research
Lipocalins Are Required for Apical Extracellular Matrix Organization and Remodeling in Caenorhabditis elegans [Developmental and Behavioral Genetics]
A lipid and glycoprotein-rich apical extracellular matrix (aECM) or glycocalyx lines exposed membranes in the body, and is particularly important to protect narrow tube integrity. Lipocalins ("fat cups") are small, secreted, cup-shaped proteins that bind and transport lipophilic cargo and are often found in luminal or aECM compartments such as mammalian plasma, urine, or tear film. Although some lipocalins can bind known aECM lipids and/or matrix metalloproteinases, it is not known if and how lipocalins affect aECM structure due to challenges in visualizing the aECM in most systems. Here we show that two Caenorhabditis ele...
Source: Genetics - October 4, 2017 Category: Genetics & Stem Cells Authors: Forman-Rubinsky, R., Cohen, J. D., Sundaram, M. V. Tags: Developmental and Behavioral Genetics Source Type: research
Genetic Screen for Postembryonic Development in the Zebrafish (Danio rerio): Dominant Mutations Affecting Adult Form [Developmental and Behavioral Genetics]
Large-scale forward genetic screens have been instrumental for identifying genes that regulate development, homeostasis, and regeneration, as well as the mechanisms of disease. The zebrafish, Danio rerio, is an established genetic and developmental model used in genetic screens to uncover genes necessary for early development. However, the regulation of postembryonic development has received less attention as these screens are more labor intensive and require extensive resources. The lack of systematic interrogation of late development leaves large aspects of the genetic regulation of adult form and physiology unresolved. ...
Source: Genetics - October 4, 2017 Category: Genetics & Stem Cells Authors: Henke, K., Daane, J. M., Hawkins, M. B., Dooley, C. M., Busch-Nentwich, E. M., Stemple, D. L., Harris, M. P. Tags: Developmental and Behavioral Genetics Source Type: research
