Accuracy of Genomic Prediction in Synthetic Populations Depending on the Number of Parents, Relatedness, and Ancestral Linkage Disequilibrium [Genomic Selection]
Synthetics play an important role in quantitative genetic research and plant breeding, but few studies have investigated the application of genomic prediction (GP) to these populations. Synthetics are generated by intermating a small number of parents ($${N}_{P})$$ and thereby possess unique genetic properties, which make them especially suited for systematic investigations of factors contributing to the accuracy of GP. We generated synthetics in silico from $${N}_{P}=$$2 to 32 maize (Zea mays L.) lines taken from an ancestral population with either short- or long-range linkage disequilibrium (LD). In eight scenarios diffe...
Source: Genetics - January 2, 2017 Category: Genetics & Stem Cells Authors: Schopp, P., Muller, D., Technow, F., Melchinger, A. E. Tags: Genomic Selection Source Type: research
Fixation Probability in a Haploid-Diploid Population [Population and Evolutionary Genetics]
Classical population genetic theory generally assumes either a fully haploid or fully diploid life cycle. However, many organisms exhibit more complex life cycles, with both free-living haploid and diploid stages. Here we ask what the probability of fixation is for selected alleles in organisms with haploid-diploid life cycles. We develop a genetic model that considers the population dynamics using both the Moran model and Wright–Fisher model. Applying a branching process approximation, we obtain an accurate fixation probability assuming that the population is large and the net effect of the mutation is beneficial. W...
Source: Genetics - January 2, 2017 Category: Genetics & Stem Cells Authors: Bessho, K., Otto, S. P. Tags: Population and Evolutionary Genetics Source Type: research
Widespread Historical Contingency in Influenza Viruses [Population and Evolutionary Genetics]
In systems biology and genomics, epistasis characterizes the impact that a substitution at a particular location in a genome can have on a substitution at another location. This phenomenon is often implicated in the evolution of drug resistance or to explain why particular "disease-causing" mutations do not have the same outcome in all individuals. Hence, uncovering these mutations and their locations in a genome is a central question in biology. However, epistasis is notoriously difficult to uncover, especially in fast-evolving organisms. Here, we present a novel statistical approach that replies on a model developed in e...
Source: Genetics - January 2, 2017 Category: Genetics & Stem Cells Authors: Nshogozabahizi, J. C., Dench, J., Aris-Brosou, S. Tags: Population and Evolutionary Genetics Source Type: research
Drift Barriers to Quality Control When Genes Are Expressed at Different Levels [Population and Evolutionary Genetics]
Gene expression is imperfect, sometimes leading to toxic products. Solutions take two forms: globally reducing error rates, or ensuring that the consequences of erroneous expression are relatively harmless. The latter is optimal, but because it must evolve independently at so many loci, it is subject to a stringent "drift barrier"—a limit to how weak the effects of a deleterious mutation s can be, while still being effectively purged by selection, expressed in terms of the population size N of an idealized population such that purging requires s < –1/N. In previous work, only large populations evol...
Source: Genetics - January 2, 2017 Category: Genetics & Stem Cells Authors: Xiong, K., McEntee, J. P., Porfirio, D. J., Masel, J. Tags: Population and Evolutionary Genetics Source Type: research
Modeling Human Population Separation History Using Physically Phased Genomes [Population and Evolutionary Genetics]
Phased haplotype sequences are a key component in many population genetic analyses since variation in haplotypes reflects the action of recombination, selection, and changes in population size. In humans, haplotypes are typically estimated from unphased sequence or genotyping data using statistical models applied to large reference panels. To assess the importance of correct haplotype phase on population history inference, we performed fosmid pool sequencing and resolved phased haplotypes of five individuals from diverse African populations (including Yoruba, Esan, Gambia, Maasai, and Mende). We physically phased 98% of he...
Source: Genetics - January 2, 2017 Category: Genetics & Stem Cells Authors: Song, S., Sliwerska, E., Emery, S., Kidd, J. M. Tags: Population and Evolutionary Genetics Source Type: research
The Effects of Migration and Assortative Mating on Admixture Linkage Disequilibrium [Population and Evolutionary Genetics]
Statistical models in medical and population genetics typically assume that individuals assort randomly in a population. While this simplifies model complexity, it contradicts an increasing body of evidence of nonrandom mating in human populations. Specifically, it has been shown that assortative mating is significantly affected by genomic ancestry. In this work, we examine the effects of ancestry-assortative mating on the linkage disequilibrium between local ancestry tracks of individuals in an admixed population. To accomplish this, we develop an extension to the Wright–Fisher model that allows for ancestry-based a...
Source: Genetics - January 2, 2017 Category: Genetics & Stem Cells Authors: Zaitlen, N., Huntsman, S., Hu, D., Spear, M., Eng, C., Oh, S. S., White, M. J., Mak, A., Davis, A., Meade, K., Brigino-Buenaventura, E., LeNoir, M. A., Bibbins-Domingo, K., Burchard, E. G., Halperin, E. Tags: Population and Evolutionary Genetics Source Type: research
Spatial Gene Frequency Waves Under Genotype-Dependent Dispersal [Population and Evolutionary Genetics]
Dispersal is a crucial factor in natural evolution, since it determines the habitat experienced by any population and defines the spatial scale of interactions between individuals. There is compelling evidence for systematic differences in dispersal characteristics within the same population, i.e., genotype-dependent dispersal. The consequences of genotype-dependent dispersal on other evolutionary phenomena, however, are poorly understood. In this article we investigate the effect of genotype-dependent dispersal on spatial gene frequency patterns, using a generalization of the classical diffusion model of selection and dis...
Source: Genetics - January 2, 2017 Category: Genetics & Stem Cells Authors: Novak, S., Kollar, R. Tags: Population and Evolutionary Genetics Source Type: research
Survey of Global Genetic Diversity Within the Drosophila Immune System [Population and Evolutionary Genetics]
Numerous studies across a wide range of taxa have demonstrated that immune genes are routinely among the most rapidly evolving genes in the genome. This observation, however, does not address what proportion of immune genes undergo strong selection during adaptation to novel environments. Here, we determine the extent of very recent divergence in genes with immune function across five populations of Drosophila melanogaster and find that immune genes do not show an overall trend of recent rapid adaptation. Our population-based approach uses a set of carefully matched control genes to account for the effects of demography an...
Source: Genetics - January 2, 2017 Category: Genetics & Stem Cells Authors: Early, A. M., Arguello, J. R., Cardoso-Moreira, M., Gottipati, S., Grenier, J. K., Clark, A. G. Tags: Population and Evolutionary Genetics Source Type: research
Wolbachia in the Drosophila yakuba Complex: Pervasive Frequency Variation and Weak Cytoplasmic Incompatibility, but No Apparent Effect on Reproductive Isolation [Population and Evolutionary Genetics]
Three hybridizing species—the clade [(Drosophila yakuba, D. santomea), D. teissieri]—comprise the yakuba complex in the D. melanogaster subgroup. Their ranges overlap on Bioko and São Tomé, islands off west Africa. All three species are infected with Wolbachia—maternally inherited, endosymbiotic bacteria, best known for manipulating host reproduction to favor infected females. Previous analyses reported no cytoplasmic incompatibility (CI) in these species. However, we discovered that Wolbachia from each species cause intraspecific and interspecific CI. In D. teissieri, analyses of F1 and bac...
Source: Genetics - January 2, 2017 Category: Genetics & Stem Cells Authors: Cooper, B. S., Ginsberg, P. S., Turelli, M., Matute, D. R. Tags: Population and Evolutionary Genetics Source Type: research
Inferring Heterozygosity from Ancient and Low Coverage Genomes [Population and Evolutionary Genetics]
While genetic diversity can be quantified accurately from high coverage sequencing data, it is often desirable to obtain such estimates from data with low coverage, either to save costs or because of low DNA quality, as is observed for ancient samples. Here, we introduce a method to accurately infer heterozygosity probabilistically from sequences with average coverage $$ (Source: Genetics)
Source: Genetics - January 2, 2017 Category: Genetics & Stem Cells Authors: Kousathanas, A., Leuenberger, C., Link, V., Sell, C., Burger, J., Wegmann, D. Tags: Population and Evolutionary Genetics Source Type: research
Complex Ancient Genetic Structure and Cultural Transitions in Southern African Populations [Population and Evolutionary Genetics]
The characterization of the structure of southern African populations has been the subject of numerous genetic, medical, linguistic, archaeological, and anthropological investigations. Current diversity in the subcontinent is the result of complex events of genetic admixture and cultural contact between early inhabitants and migrants that arrived in the region over the last 2000 years. Here, we analyze 1856 individuals from 91 populations, comprising novel and published genotype data, to characterize the genetic ancestry profiles of 631 individuals from 51 southern African populations. Combining both local ancestry an...
Source: Genetics - January 2, 2017 Category: Genetics & Stem Cells Authors: Montinaro, F., Busby, G. B. J., Gonzalez-Santos, M., Oosthuitzen, O., Oosthuitzen, E., Anagnostou, P., Destro-Bisol, G., Pascali, V. L., Capelli, C. Tags: Population and Evolutionary Genetics Source Type: research
Developmental Wiring of Specific Neurons Is Regulated by RET-1/Nogo-A in Caenorhabditis elegans [Developmental and Behavioral Genetics]
Nogo-A is a membrane-bound protein that functions to inhibit neuronal migration, adhesion, and neurite outgrowth during development. In the mature nervous system, Nogo-A stabilizes neuronal wiring to inhibit neuronal plasticity and regeneration after injury. Here, we show that RET-1, the sole Nogo-A homolog in Caenorhabditis elegans, is required to control developmental wiring of a specific subset of neurons. In ret-1 deletion mutant animals, specific ventral nerve cord axons are misguided where they fail to respect the ventral midline boundary. We found that ret-1 is expressed in multiple neurons during development, and, ...
Source: Genetics - January 2, 2017 Category: Genetics & Stem Cells Authors: Torpe, N., Norgaard, S., Hoye, A. M., Pocock, R. Tags: Developmental and Behavioral Genetics Source Type: research
Conserved Ankyrin Repeat Proteins and Their NIMA Kinase Partners Regulate Extracellular Matrix Remodeling and Intracellular Trafficking in Caenorhabditis elegans [Developmental and Behavioral Genetics]
This study has thus identified a conserved NEKL–MLT protein network that regulates remodeling of the apical extracellular matrix and intracellular trafficking, functions that may be conserved across species. (Source: Genetics)
Source: Genetics - January 2, 2017 Category: Genetics & Stem Cells Authors: Lažetić, V., Fay, D. S. Tags: Developmental and Behavioral Genetics Source Type: research
Pleiotropic Effects of Loss of the D{alpha}1 Subunit in Drosophila melanogaster: Implications for Insecticide Resistance [Developmental and Behavioral Genetics]
Nicotinic acetylcholine receptors (nAChRs) are a highly conserved gene family that form pentameric receptors involved in fast excitatory synaptic neurotransmission. The specific roles individual nAChR subunits perform in Drosophila melanogaster and other insects are relatively uncharacterized. Of the 10 D. melanogaster nAChR subunits, only three have described roles in behavioral pathways; Dα3 and Dα4 in sleep, and Dα7 in the escape response. Other subunits have been associated with resistance to several classes of insecticides. In particular, our previous work has demonstrated that an allele of the D&alp...
Source: Genetics - January 2, 2017 Category: Genetics & Stem Cells Authors: Somers, J., Luong, H. N. B., Mitchell, J., Batterham, P., Perry, T. Tags: Developmental and Behavioral Genetics Source Type: research
Stage-Specific Timing of the microRNA Regulation of lin-28 by the Heterochronic Gene lin-14 in Caenorhabditis elegans [Developmental and Behavioral Genetics]
In this report, we used animals that lack lin-4 to elucidate LIN-14’s activity in this circuit. We demonstrate that three let-7 family miRNAs—miR-48, miR-84, and miR-241—inhibit lin-28 expression. Furthermore, we show genetically that these miRNAs act between lin-14 and lin-28, and that they comprise the pathway by which lin-14 positively regulates lin-28. We also show that the lin-4 family member mir-237, also regulates early cell fates. Finally, we show that the expression of these miRNAs is directly inhibited by lin-14 activity, making them the first known targets of lin-14 that act in the heterochroni...
Source: Genetics - January 2, 2017 Category: Genetics & Stem Cells Authors: Tsialikas, J., Romens, M. A., Abbott, A., Moss, E. G. Tags: Developmental and Behavioral Genetics Source Type: research
