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https://www.readbyqxmd.com/read/28811388/hill-robertson-interference-reduces-genetic-diversity-on-a-young-plant-y-chromosome
#1
Josh Hough, Wei Wang, Spencer C H Barrett, Stephen I Wright
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...
August 15, 2017: Genetics
https://www.readbyqxmd.com/read/28811387/selection-constrains-high-rates-of-tandem-repetitive-dna-mutation-in-daphnia-pulex
#2
Jullien M Flynn, Ian Caldas, Melania E Cristescu, Andrew G Clark
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 of repeat sequences and evaluate the selective regime acting upon them...
August 15, 2017: Genetics
https://www.readbyqxmd.com/read/28801530/rhythmic-behavior-is-controlled-by-the-srm160-splicing-factor-in-drosophila-melanogaster
#3
Esteban J Beckwith, Carlos E Hernando, Sofía Polcowñuk, Agustina P Bertolin, Estefania Mancini, M Fernanda Ceriani, Marcelo J Yanovsky
Circadian clocks organize the metabolism, physiology, and behavior of organisms throughout the day-night cycle by controlling daily rhythms in gene expression at the transcriptional and post-transcriptional levels. While many transcription factors underlying circadian oscillations are known, the splicing factors that modulate these rhythms remain largely unexplored. A genome-wide assessment of the alterations of gene expression in a null mutant of the alternative splicing regulator SR-related matrix protein of 160 kD (SRm160) revealed the extent to which alternative splicing impacts on behavior-related genes...
August 11, 2017: Genetics
https://www.readbyqxmd.com/read/28801529/silencing-of-repetitive-dna-is-controlled-by-a-member-of-an-unusual-caenorhabditis-elegans-gene-family
#4
Eduardo Leyva-Díaz, Nikolaos Stefanakis, Inés Carrera, Lori Glenwinkel, Guoqiang Wang, Monica Driscoll, Oliver Hobert
Repetitive DNA sequences are subject to gene silencing in various animal species. Under specific circumstances repetitive DNA sequences can escape such silencing. For example, when exogenously added, extrachromosomal DNA sequences that are stably inherited in multicopy repetitive arrays in the nematode Caenorhabditis elegans are frequently silenced in the germline, whereas such silencing often does not occur in the soma. This indicates that somatic cells might utilize factors that prevent repetitive DNA silencing...
August 11, 2017: Genetics
https://www.readbyqxmd.com/read/28798062/when-does-frequency-independent-selection-maintain-genetic-variation
#5
Sebastian Novak, Nicholas H Barton
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...
August 10, 2017: Genetics
https://www.readbyqxmd.com/read/28794107/variation-in-recombination-rate-and-its-genetic-determinism-in-sheep-populations
#6
Morgane Petit, Jean-Michel Astruc, Julien Sarry, Laurence Drouilhet, Stéphane Fabre, Carole Moreno, Bertrand Servin
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 datasets. 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 genotyped with a 600K SNP array...
August 9, 2017: Genetics
https://www.readbyqxmd.com/read/28774882/developmental-restriction-of-retrotransposition-activated-in-arabidopsis-by-environmental-stress
#7
Hervé Gaubert, Diego H Sanchez, Hajk-Georg Drost, Jerzy Paszkowski
Retrotransposons (RTs) may 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 intra-plant variation in the number and chromosomal position of new insertions, which usually did not affect plant fertility and were equally well transmitted through male and female gametes, even though 90% of them were within active genes...
August 3, 2017: Genetics
https://www.readbyqxmd.com/read/28774881/a-mixed-model-approach-to-genome-wide-association-studies-for-selection-signatures-with-application-to-mice-bred-for-voluntary-exercise-behavior
#8
Shizhong Xu, Theodore Garland
Selection experiments and experimental evolution (EE) 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," EE 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...
August 3, 2017: Genetics
https://www.readbyqxmd.com/read/28760747/significant-synteny-and-co-localization-of-ecologically-relevant-quantitative-trait-loci-within-and-across-species-of-salmonid-fishes
#9
Arne Jacobs, Robyn Womack, Mel Chen, Karim Gharbi, Kathryn Elmer
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 co-localization, and the synteny of QTL for ecologically relevant traits, we used a comparative genomic mapping approach within and across a range of salmonid species...
July 31, 2017: Genetics
https://www.readbyqxmd.com/read/28760746/insights-into-the-evolution-and-function-of-auxin-signaling-f-box-proteins-in-arabidopsis-thaliana-through-synthetic-analysis-of-natural-variants
#10
R Clay Wright, Mollye L Zahler, Stacey R Gerben, Jennifer L Nemhauser
The evolution of complex body plans in land plants has been paralleled by gene duplication and divergence within nuclear auxin-signaling networks. A deep mechanistic understanding of auxin signaling proteins therefore may allow rational engineering of novel plant architectures. Towards that end, we analyzed natural variation in the auxin receptor F-box family of wild accessions of the reference plant Arabidopsis thaliana and used this information to populate a structure/function map. We employed a synthetic assay to identify natural hypermorphic F-box variants, and then assayed auxin-associated phenotypes in accessions expressing these variants...
July 31, 2017: Genetics
https://www.readbyqxmd.com/read/28754661/predicting-amino-acid-substitution-probabilities-using-single-nucleotide-polymorphisms
#11
Francesca Rizzato, Alex Rodriguez, Xevi Biarnés, Alessandro Laio
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 identity better than any other approach we are aware of...
July 28, 2017: Genetics
https://www.readbyqxmd.com/read/28754660/selection-during-maize-domestication-targeted-a-gene-network-controlling-plant-and-inflorescence-architecture
#12
Anthony J Studer, Huai Wang, John F Doebley
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 composed 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 genes that lie downstream of tb1 in a gene network regulating both plant and inflorescence architecture...
July 28, 2017: Genetics
https://www.readbyqxmd.com/read/28754659/stress-induced-sleep-after-exposure-to-ultraviolet-light-is-promoted-by-p53-in-caenorhabditis-elegans
#13
Hilary DeBardeleben, Lindsey E Lopes, Mark P Nessel, David M Raizen
Stress-induced sleep (SIS) in C. elegans is important for restoration of cellular homeostasis and is a useful model to study the function and regulation of sleep. SIS is triggered when epidermal growth factor (EGF) activates the ALA neuron, which then releases neuropeptides to promote sleep. To further understand this behavior, we established a new model of stress-induced sleep using irradiation by ultraviolet C (UVC) light. While UVC irradiation requires ALA signaling and leads to a sleep state similar to that induced by heat and other stressors, it does not induce the proteostatic stress seen with heat exposure...
July 28, 2017: Genetics
https://www.readbyqxmd.com/read/28751423/sid-1-functions-in-multiple-roles-to-support-parental-rnai-in-caenorhabditis-elegans
#14
Eddie Wang, Craig P Hunter
Systemic RNA interference (RNAi) in Caenorhbaditis elegans requires sid-1, sid-3, and sid-5 Injected, expressed, or ingested double-stranded RNA (dsRNA) is transported between cells, enabling RNAi in most tissues, including the germline and progeny (parental RNAi). A recent report claims that parental RNAi also requires the yolk receptor rme-2 Here, we characterize the role of the sid genes and rme-2 in parental RNAi. We identify multiple independent paths for maternal dsRNA to reach embryos and initiate RNAi...
July 27, 2017: Genetics
https://www.readbyqxmd.com/read/28751422/analysis-of-large-scale-mutagenesis-data-to-assess-the-impact-of-single-amino-acid-substitutions
#15
Vanessa E Gray, Ronald J Hause, Douglas M Fowler
Mutagenesis is a widely-used method for identifying protein positions that are important for function or ligand binding. Advances in high-throughput DNA sequencing and mutagenesis techniques have enabled measurement of the effects of nearly all possible amino acid substitutions in many proteins. The resulting large-scale mutagenesis data sets offer a unique opportunity to draw general conclusions about the effects of different amino acid substitutions. Thus, we analyzed 34,373 mutations in fourteen proteins whose effects were measured using large-scale mutagenesis approaches...
July 27, 2017: Genetics
https://www.readbyqxmd.com/read/28751421/the-recombination-landscape-in-wild-house-mice-inferred-using-population-genomic-data
#16
Tom R Booker, Rob W Ness, Peter D Keightley
Characterizing variation in the rate of recombination across the genome is important for understanding several evolutionary processes. Previous analysis of the recombination landscape in laboratory mice has revealed that the different subspecies have different suites of recombination hotspots. It is unknown, however, whether hotspots identified in laboratory strains reflect the hotspot diversity of natural populations or whether broad-scale variation in the rate of recombination is conserved between subspecies...
July 27, 2017: Genetics
https://www.readbyqxmd.com/read/28751420/recombination-driven-genome-evolution-and-stability-of-bacterial-species
#17
Purushottam D Dixit, Tin Y Pang, Sergei Maslov
While bacteria divide clonally, horizontal gene transfer followed by homologous recombination is now recognized as an important contributor to their evolution. However, the details of how the competition between clonality and recombination shapes genome diversity remains poorly understood. Using a computational model, we find two principal regimes in bacterial evolution and identify two composite parameters that dictate the evolutionary fate of bacterial species. In the divergent regime, characterized by either a low recombination frequency or strict barriers to recombination, cohesion due to recombination is not sufficient to overcome the mutational drift...
July 27, 2017: Genetics
https://www.readbyqxmd.com/read/28743762/mitotic-gene-conversion-tracts-associated-with-repair-of-a-defined-double-strand-break-in-saccharomyces-cerevisiae
#18
Yee Fang Hum, Sue Jinks-Robertson
Mitotic recombination between homologous chromosomes leads to the uncovering of recessive alleles through loss of heterozygosity. In the current study, a defined double-strand break was used to initiate reciprocal loss of heterozygosity between diverged homologs of chromosome IV in Saccharomyces cerevisiae These events resulted from the repair of two broken chromatids, one of which was repaired as a crossover and the other as a noncrossover. Associated gene conversion tracts resulting from the donor-directed repair of mismatches formed during strand exchange (heteroduplex DNA) were mapped using microarrays...
July 25, 2017: Genetics
https://www.readbyqxmd.com/read/28743761/naturally-segregating-variation-at-ugt86dd-contributes-to-nicotine-resistance-in-drosophila-melanogaster
#19
Chad A Highfill, Jonathan H Tran, Samantha K T Nguyen, Taylor R Moldenhauer, Xiaofei Wang, Stuart J Macdonald
Identifying the sequence polymorphisms underlying complex trait variation is a key goal of genetics research, since knowing the precise causative molecular events allows insight into the pathways governing trait variation. Genetic analysis of complex traits in model systems regularly starts by constructing QTL maps, but generally fails to identify causative sequence polymorphisms. Previously we mapped a series of QTL contributing to resistance to nicotine in a Drosophila melanogaster multiparental mapping resource, and here use a battery of functional tests to resolve QTL to the molecular level...
July 25, 2017: Genetics
https://www.readbyqxmd.com/read/28739661/histone-acetylation-not-stoichiometry-regulates-linker-histone-binding-in-saccharomyces-cerevisiae
#20
Mackenzie B D Lawrence, Nicolas Coutin, Jennifer K Choi, Benjamin J E Martin, Nicholas A T Irwin, Barry Young, Christopher Loewen, LeAnn J Howe
Linker histones play a fundamental role in shaping chromatin structure, but how their interaction with chromatin is regulated is not well understood. In this study, we used a combination of genetic and genomic approaches to explore the regulation of linker histone binding in the yeast, Saccharomyces cerevisiae We found that increased expression of Hho1, the yeast linker histone, resulted in a severe growth defect, despite only subtle changes in chromatin structure. Further, this growth defect was rescued by mutations that increase histone acetylation...
July 24, 2017: Genetics
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