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Journal articles on the topic 'Variation (Genetics)'

Author: Grafiati

Published: 4 June 2021

Last updated: 1 August 2024

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1

Bedge, Kiran, and Pratima Salunkhe. "Population Genetics : A Review." International Journal of Scientific Research in Science and Technology 11, no. 2 (April 20, 2024): 746–48. http://dx.doi.org/10.32628/ijsrst24112109.

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Genetics is the study of genes and genetic variations alongwith the hereditary characteristics of an organism. Genetics is a central pillar of biology. It overlaps with other areas, such as: Agriculture, Medicine, Biotechnology. Genetics involves studying: Gene structure and function Gene variation and changes How genes affect health, appearance, and personality. Population genetics studies genetic variation within and among populations, based on the Hardy-Weinberg law, which remains constant in large populations with random mating and minimal mutation, selection, and migration.

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2

Paaby, Annalise, and Greg Gibson. "Cryptic Genetic Variation in Evolutionary Developmental Genetics." Biology 5, no. 2 (June 13, 2016): 28. http://dx.doi.org/10.3390/biology5020028.

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3

Varvio, Sirkka-Liisa, Ranajit Chakraborty, and Masatoshi Nei. "Genetic variation in subdivided populations and conservation genetics." Heredity 57, no. 2 (October 1986): 189–98. http://dx.doi.org/10.1038/hdy.1986.109.

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4

Miyashita, Naohiko, Cathy C. Laurie-Ahlberg, Alan N. Wilton, and Ted H. Emigh. "QUANTITATIVE ANALYSIS OF X CHROMOSOME EFFECTS ON THE ACTIVITIES OF THE GLUCOSE 6-PHOSPHATE AND 6-PHOSPHOGLUCONATE DEHYDROGENASES OF DROSOPHILA MELANOGASTER." Genetics 113, no. 2 (June 1, 1986): 321–35. http://dx.doi.org/10.1093/genetics/113.2.321.

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ABSTRACT By combining 20 X chromosomes with five autosomal backgrounds, the relative importance of these factors with respect to the activity variations of G6PD and 6PGD in Drosophila melanogaster were investigated. Analysis of variance revealed that there exist significant X chromosome, autosomal background and genetic interaction effects. The effect of the X chromosome was due mainly to the two allozymic forms of each enzyme, but some within-allozyme effects were also detected. From the estimated variance components, it was concluded that the variation attributed to the autosomal background is much larger than the variation attributed to the X chromosome, even when the effect of the allozymes is included. The segregation of the allozymes seems to account for about 10% of the total activity variation of each enzyme. The variation due to the interaction between the X chromosome and the autosomal background is much smaller than variations attributed either to the X chromosome or to the autosomal background. The interaction effect is indicated by the change of the ranking of the X chromosomes for different autosomal backgrounds. Highly significant and positive correlation between G6PD and 6PGD activities was detected. Again, the contribution of the autosomal background to the correlation was much larger than that attributed to the X chromosome.

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Zahn, L. M. "GENETICS: The Variation Within." Science 314, no. 5802 (November 17, 2006): 1050a. http://dx.doi.org/10.1126/science.314.5802.1050a.

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6

Wagner, Günter P. "Evolutionary Genetics: The Nature of Hidden Genetic Variation Unveiled." Current Biology 13, no. 24 (December 2003): R958—R960. http://dx.doi.org/10.1016/j.cub.2003.11.042.

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7

Brown, Patrick O., and Leland Hartwell. "Genomics and human disease—variations on variation." Nature Genetics 18, no. 2 (February 1998): 91–93. http://dx.doi.org/10.1038/ng0298-91.

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8

Barton, N. H. "Pleiotropic models of quantitative variation." Genetics 124, no. 3 (March 1, 1990): 773–82. http://dx.doi.org/10.1093/genetics/124.3.773.

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Abstract It is widely held that each gene typically affects many characters, and that each character is affected by many genes. Moreover, strong stabilizing selection cannot act on an indefinitely large number of independent traits. This makes it likely that heritable variation in any one trait is maintained as a side effect of polymorphisms which have nothing to do with selection on that trait. This paper examines the idea that variation is maintained as the pleiotropic side effect of either deleterious mutation, or balancing selection. If mutation is responsible, it must produce alleles which are only mildly deleterious (s approximately 10(-3)), but nevertheless have significant effects on the trait. Balancing selection can readily maintain high heritabilities; however, selection must be spread over many weakly selected polymorphisms if large responses to artificial selection are to be possible. In both classes of pleiotropic model, extreme phenotypes are less fit, giving the appearance of stabilizing selection on the trait. However, it is shown that this effect is weak (of the same order as the selection on each gene): the strong stabilizing selection which is often observed is likely to be caused by correlations with a limited number of directly selected traits. Possible experiments for distinguishing the alternatives are discussed.

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Reinhardt, Josie A., Bryan Kolaczkowski, Corbin D. Jones, David J. Begun, and Andrew D. Kern. "Parallel Geographic Variation inDrosophila melanogaster." Genetics 197, no. 1 (March 7, 2014): 361–73. http://dx.doi.org/10.1534/genetics.114.161463.

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10

Slater, Garett P., Nicholas M. A. Smith, and Brock A. Harpur. "Prospects in Connecting Genetic Variation to Variation in Fertility in Male Bees." Genes 12, no. 8 (August 16, 2021): 1251. http://dx.doi.org/10.3390/genes12081251.

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Bees are economically and ecologically important pollinating species. Managed and native bee species face increasing pressures from human-created stressors such as habitat loss, pesticide use, and introduced pathogens. There has been increasing attention towards how each of these factors impacts fertility, especially sperm production and maintenance in males. Here, we turn our attention towards another important factor impacting phenotypic variation: genetics. Using honey bees as a model, we explore the current understanding of how genetic variation within and between populations contributes to variation in sperm production, sperm maintenance, and insemination success among males. We conclude with perspectives and future directions in the study of male fertility in honey bees and non-Apis pollinators more broadly, which still remain largely understudied.

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11

Molenaar, Peter C. M. "Estimating the actual subject-specific genetic correlations in behavior genetics." Behavioral and Brain Sciences 35, no. 5 (October 2012): 373–74. http://dx.doi.org/10.1017/s0140525x12001069.

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AbstractGeneralization of the standard behavior longitudinal genetic factor model for the analysis of interindividual phenotypic variation to a genetic state space model for the analysis of intraindividual variation enables the possibility to estimate subject-specific heritabilities.

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12

Zahn, Laura L. "How genetics affect phenotypic variation." Science 347, no. 6222 (February 5, 2015): 623.17–625. http://dx.doi.org/10.1126/science.347.6222.623-q.

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13

Borst, Piet. "Molecular genetics of antigenic variation." Immunology Today 12, no. 3 (January 1991): A29—A33. http://dx.doi.org/10.1016/s0167-5699(05)80009-x.

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Borst, Piet. "Molecular genetics of antigenic variation." Parasitology Today 7, no. 3 (March 1991): 29–33. http://dx.doi.org/10.1016/0169-4758(91)90026-k.

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15

Vihinen, Mauno. "Individual Genetic Heterogeneity." Genes 13, no. 9 (September 10, 2022): 1626. http://dx.doi.org/10.3390/genes13091626.

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Genetic variation has been widely covered in literature, however, not from the perspective of an individual in any species. Here, a synthesis of genetic concepts and variations relevant for individual genetic constitution is provided. All the different levels of genetic information and variation are covered, ranging from whether an organism is unmixed or hybrid, has variations in genome, chromosomes, and more locally in DNA regions, to epigenetic variants or alterations in selfish genetic elements. Genetic constitution and heterogeneity of microbiota are highly relevant for health and wellbeing of an individual. Mutation rates vary widely for variation types, e.g., due to the sequence context. Genetic information guides numerous aspects in organisms. Types of inheritance, whether Mendelian or non-Mendelian, zygosity, sexual reproduction, and sex determination are covered. Functions of DNA and functional effects of variations are introduced, along with mechanism that reduce and modulate functional effects, including TARAR countermeasures and intraindividual genetic conflict. TARAR countermeasures for tolerance, avoidance, repair, attenuation, and resistance are essential for life, integrity of genetic information, and gene expression. The genetic composition, effects of variations, and their expression are considered also in diseases and personalized medicine. The text synthesizes knowledge and insight on individual genetic heterogeneity and organizes and systematizes the central concepts.

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16

Hill, William G. "Sewall Wright and quantitative genetics." Genome 31, no. 1 (January 1, 1989): 190–95. http://dx.doi.org/10.1139/g89-033.

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Some aspects of Wright's great contribution to quantitative genetics and animal breeding are reviewed in relation to current research and practice. Particular aspects discussed are as follows: the utility of his definition of inbreeding coefficient in terms of the correlation of uniting gametes; the maintenance of genetic variation in the optimum model; the inter-relations between past and present animal-breeding practice and the shifting-balance theory of evolution.Key words: quantitative genetics, inbreeding coefficient, genetic variation, evolution.

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17

Sankar, P. "GENETICS: Enhanced: Toward a New Vocabulary of Human Genetic Variation." Science 298, no. 5597 (November 15, 2002): 1337–38. http://dx.doi.org/10.1126/science.1074447.

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18

Bost, Bruno, Christine Dillmann, and Dominique de Vienne. "Fluxes and Metabolic Pools as Model Traits for Quantitative Genetics. I. The L-Shaped Distribution of Gene Effects." Genetics 153, no. 4 (December 1, 1999): 2001–12. http://dx.doi.org/10.1093/genetics/153.4.2001.

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Abstract The fluxes through metabolic pathways can be considered as model quantitative traits, whose QTL are the polymorphic loci controlling the activity or quantity of the enzymes. Relying on metabolic control theory, we investigated the relationships between the variations of enzyme activity along metabolic pathways and the variations of the flux in a population with biallelic QTL. Two kinds of variations were taken into account, the variation of the average enzyme activity across the loci, and the variation of the activity of each enzyme of the pathway among the individuals of the population. We proposed analytical approximations for the flux mean and variance in the population as well as for the additive and dominance variances of the individual QTL. Monte Carlo simulations based on these approximations showed that an L-shaped distribution of the contributions of individual QTL to the flux variance (R2) is consistently expected in an F2 progeny. This result could partly account for the classically observed L-shaped distribution of QTL effects for quantitative traits. The high correlation we found between R2 value and flux control coefficients variance suggests that such a distribution is an intrinsic property of metabolic pathways due to the summation property of control coefficients.

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19

Zeng, Z. B., and C. C. Cockerham. "Mutation models and quantitative genetic variation." Genetics 133, no. 3 (March 1, 1993): 729–36. http://dx.doi.org/10.1093/genetics/133.3.729.

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Abstract Analyses of evolution and maintenance of quantitative genetic variation depend on the mutation models assumed. Currently two polygenic mutation models have been used in theoretical analyses. One is the random walk mutation model and the other is the house-of-cards mutation model. Although in the short term the two models give similar results for the evolution of neutral genetic variation within and between populations, the predictions of the changes of the variation are qualitatively different in the long term. In this paper a more general mutation model, called the regression mutation model, is proposed to bridge the gap of the two models. The model regards the regression coefficient, gamma, of the effect of an allele after mutation on the effect of the allele before mutation as a parameter. When gamma = 1 or 0, the model becomes the random walk model or the house-of-cards model, respectively. The additive genetic variances within and between populations are formulated for this mutation model, and some insights are gained by looking at the changes of the genetic variances as gamma changes. The effects of gamma on the statistical test of selection for quantitative characters during macroevolution are also discussed. The results suggest that the random walk mutation model should not be interpreted as a null hypothesis of neutrality for testing against alternative hypotheses of selection during macroevolution because it can potentially allocate too much variation for the change of population means under neutrality.

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Toro, M. A., A. Fernández, L. A. García-Cortés, J. Rodrigáñez, and L. Silió. "Sex Ratio Variation in Iberian Pigs." Genetics 173, no. 2 (April 2, 2006): 911–17. http://dx.doi.org/10.1534/genetics.106.055939.

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Nagylaki, T. "Geographical variation in a quantitative character." Genetics 136, no. 1 (January 1, 1994): 361–81. http://dx.doi.org/10.1093/genetics/136.1.361.

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Abstract A model for the evolution of the local averages of a quantitative character under migration, selection, and random genetic drift in a subdivided population is formulated and investigated. Generations are discrete and nonoverlapping; the monoecious, diploid population mates at random in each deme. All three evolutionary forces are weak, but the migration pattern and the local population numbers are otherwise arbitrary. The character is determined by purely additive gene action and a stochastically independent environment; its distribution is Gaussian with a constant variance; and it is under Gaussian stabilizing selection with the same parameters in every deme. Linkage disequilibrium is neglected. Most of the results concern the covariances of the local averages. For a finite number of demes, explicit formulas are derived for (i) the asymptotic rate and pattern of convergence to equilibrium, (ii) the variance of a suitably weighted average of the local averages, and (iii) the equilibrium covariances when selection and random drift are much weaker than migration. Essentially complete analyses of equilibrium and convergence are presented for random outbreeding and site homing, the Levene and island models, the circular habitat and the unbounded linear stepping-stone model in the diffusion approximation, and the exact unbounded stepping-stone model in one and two dimensions.

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22

Swain-Lenz, Devjanee, Igor Nikolskiy, Jiye Cheng, Priya Sudarsanam, Darcy Nayler, Max V. Staller, and Barak A. Cohen. "Causal Genetic Variation Underlying Metabolome Differences." Genetics 206, no. 4 (June 26, 2017): 2199–206. http://dx.doi.org/10.1534/genetics.117.203752.

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23

Roth, E. J., B. L. Frazier, N. R. Apuya, and K. G. Lark. "Genetic variation in an inbred plant: variation in tissue cultures of soybean [Glycine max (L.) Merrill]." Genetics 121, no. 2 (February 1, 1989): 359–68. http://dx.doi.org/10.1093/genetics/121.2.359.

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Abstract Although soybean [Glycine max (L.) Merrill] grows as an inbreeding, generally homozygous, plant, the germplasm of the species contains large amounts of genetic variation. Analysis of soybean DNA has indicated that variation of RFLP (restriction fragment length polymorphism) markers within the species usually entails only two alleles at any one locus and that mixtures of such dimorphic loci account for virtually all of the restriction fragment variation seen in soybean (G. max), and in its ancestors, G. soja and G. gracilis. We report here that tissue cultures prepared from root tissue of individual soybean plants develop RFLP allelic differences at various loci. However, these newly generated alleles are almost always the same as ones previously found and characterized in other varieties of cultivated soybean (cultivars). This repeated generation of particular alleles suggests that much of the genetic variation seen in soybean could be the consequence of specific, relatively frequently employed, recombinational events. Such a mechanism would allow inbred cultivars to generate genetic variation (in the form of alternative alleles) in a controlled manner, perhaps in response to stress.

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Riddle, Russel A., Peter S. Dawson, and Dave F. Zirkle. "AN EXPERIMENTAL TEST OF THE RELATIONSHIP BETWEEN GENETIC VARIATION AND ENVIRONMENTAL VARIATION IN TRIBOLIUM FLOUR BEETLES." Genetics 113, no. 2 (June 1, 1986): 391–404. http://dx.doi.org/10.1093/genetics/113.2.391.

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ABSTRACT The hypothesis that a component of genetic variation for polygenic fitness traits is maintained by environmental heterogeneity was tested using an experimental system involving two species of flour beetles, Tribolium castaneum and T. confusum. Replicated populations of each species from a number of environmental treatments were analyzed for various fitness components following almost 60 generations of natural selection. Environmental differences consisted of flours of cereals commonly invaded by natural populations of these insects.—Tests for adaptation to environments were based on experiments in which populations were reared factorially on each flour, such that population treatment x flour interactions could be detected. Measurements were made of survival, growth rate, larval weight, pupal weight, developmental time, fecundity of individuals at low density and fecundity and cannibalism at high density in both fresh and conditioned media.—Flour differences were found to have significant effects on most traits. Evidence for significant genetic variation and significant genotype x environment interaction was also found. However, no evidence could be found to support the hypothesis that genetic variation was maintained by environmental heterogeneity in food resources. The absence of adaptation to the experimental treatments despite the presence of genetic variation in fitness components suggests that pleiotropy may assume an important role in determining net fitness values of polygenes.

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Schoenebeck, Jeffrey J., and Elaine A. Ostrander. "The Genetics of Canine Skull Shape Variation." Genetics 193, no. 2 (February 2013): 317–25. http://dx.doi.org/10.1534/genetics.112.145284.

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Innan, Hideki, Fumio Tajima, Ryohei Terauchi, and Naohiko T. Miyashita. "Intragenic Recombination in the Adh Locws of the Wild Plant Arabidopsis thaliana." Genetics 143, no. 4 (August 1, 1996): 1761–70. http://dx.doi.org/10.1093/genetics/143.4.1761.

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Abstract Nucleotide variation in the Adh region of the wild plant Arabidopsis thaliana was analyzed in 17 ecotypes sampled worldwide to investigate DNA polymorphism in natural plant populations. The investigated 2.4kb Adh region was divided into four blocks by intragenic recombinations between two parental sequence types that diverged 6.3 million years (Myr) ago, if the nucleotide mutation rate μ = 10−9 is assumed. Within each block, dimorphism of segregating variations was observed with intermediate frequencies, which caused a substantial amount of nucleotide variation in A. thaliana at the species level. The first recombination introduced the divergent variation that resulted in dimorphism in this plant species ~3.3 Myr ago, and three subsequent intragenic recombinations have occurred sporadically in ~1.1-Myr intervals. It was shown that there was only a limited number (six) of sequence types in this species and that no clear association was observed between sequence type and geographic origin. Taken together, these results suggest that A. thaliana has spread over the world only recently. It can be concluded that recombination played an important role in the evolutionary history of A. thaliana, especially through the generation of DNA polymorphism in the natural populations of this plant species.

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Gooding, R. H. "Genetic variation in arthropod vectors of disease-causing organisms: obstacles and opportunities." Clinical Microbiology Reviews 9, no. 3 (July 1996): 301–20. http://dx.doi.org/10.1128/cmr.9.3.301.

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An overview of the genetic variation in arthropods that transmit pathogens to vertebrates is presented, emphasizing the genetics of vector-pathogen relationships and the biochemical genetics of vectors. Vector-pathogen interactions are reviewed briefly as a prelude to a discussion of the genetics of susceptibility and refractoriness in vectors. Susceptibility to pathogens is controlled by maternally inherited factors, sex-linked dominant alleles, and dominant and recessive autosomal genes. There is widespread interpopulation (including intercolony) and temporal variation in susceptibility to pathogens. The amount of biochemical genetic variation in vectors is similar to that found in other invertebrates. However, the amount varies widely among species, among populations within species, and temporally within populations. Biochemical genetic studies show that there is considerable genetic structuring of many vectors at the local, regional, and global levels. It is argued that genetic variation in vectors is critical in understanding vector-pathogen interactions and that genetic variation in vectors creates both obstacles to and opportunities for application of genetic techniques to the control of vectors.

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Österberg, Marita Kruskopf, Oksana Shavorskaya, Martin Lascoux, and Ulf Lagercrantz. "Naturally Occurring Indel Variation in the Brassica nigra COL1 Gene Is Associated With Variation in Flowering Time." Genetics 161, no. 1 (May 1, 2002): 299–306. http://dx.doi.org/10.1093/genetics/161.1.299.

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Abstract Previous QTL mapping identified a Brassica nigra homolog to Arabidopsis thaliana CO as a candidate gene affecting flowering time in B. nigra. Transformation of an A. thaliana co mutant with two different alleles of the B. nigra CO (Bni COa) homolog, one from an early-flowering B. nigra plant and one from a late one, did not show any differential effect of the two alleles on flowering time. The DNA sequence of the coding region of the two alleles was also identical, showing that nucleotide variation influencing flowering time must reside outside the coding region of Bni COa. In contrast, the nucleotide sequence of the B. nigra COL1 (Bni COL1) gene located 3.5 kb upstream of Bni COa was highly diverged between the alleles from early and late plants. One indel polymorphism in the Bni COL1 coding region, present in several natural populations of B. nigra, displayed a significant association with flowering time within a majority of these populations. These data indicate that a quantitative trait nucleotide (QTN) affecting flowering time is located within or close to the Bni COL1 gene. The intergenic sequence between Bni COL1 and Bni COa displayed a prominent peak of divergence 1 kb downstream of the Bni COL1 coding region. This region could contain regulatory elements for the downstream Bni COa gene. Our data suggest that a naturally occurring QTN for flowering time affects the function or expression of either Bni COL1 or Bni COa.

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Saïdou, Abdoul-Aziz, Cédric Mariac, Vivianne Luong, Jean-Louis Pham, Gilles Bezançon, and Yves Vigouroux. "Association Studies Identify Natural Variation at PHYC Linked to Flowering Time and Morphological Variation in Pearl Millet." Genetics 182, no. 3 (May 11, 2009): 899–910. http://dx.doi.org/10.1534/genetics.109.102756.

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Ellsworth, Katarzyna A., Irene Moon, Bruce W. Eckloff, Brooke L. Fridley, Gregory D. Jenkins, Anthony Batzler, Joanna M. Biernacka, et al. "FKBP5 genetic variation." Pharmacogenetics and Genomics 23, no. 3 (March 2013): 156–66. http://dx.doi.org/10.1097/fpc.0b013e32835dc133.

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Melo, Diogo, Gabriel Marroig, and Jason B. Wolf. "Genomic Perspective on Multivariate Variation, Pleiotropy, and Evolution." Journal of Heredity 110, no. 4 (April 15, 2019): 479–93. http://dx.doi.org/10.1093/jhered/esz011.

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AbstractMultivariate quantitative genetics provides a powerful framework for understanding patterns and processes of phenotypic evolution. Quantitative genetics parameters, like trait heritability or the G-matrix for sets of traits, can be used to predict evolutionary response or to understand the evolutionary history of a population. These population-level approaches have proven to be extremely successful, but the underlying genetics of multivariate variation and evolutionary change typically remain a black box. Establishing a deeper empirical understanding of how individual genetic effects lead to genetic (co)variation is then crucial to our understanding of the evolutionary process. To delve into this black box, we exploit an experimental population of mice composed from lineages derived by artificial selection. We develop an approach to estimate the multivariate effect of loci and characterize these vectors of effects in terms of their magnitude and alignment with the direction of evolutionary divergence. Using these estimates, we reconstruct the traits in the ancestral populations and quantify how much of the divergence is due to genetic effects. Finally, we also use these vectors to decompose patterns of genetic covariation and examine the relationship between these components and the corresponding distribution of pleiotropic effects. We find that additive effects are much larger than dominance effects and are more closely aligned with the direction of selection and divergence, with larger effects being more aligned than smaller effects. Pleiotropic effects are highly variable but are, on average, modular. These results are consistent with pleiotropy being partly shaped by selection while reflecting underlying developmental constraints.

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Parker, Katherine, A. Mesut Erzurumluoglu, and Santiago Rodriguez. "The Y Chromosome: A Complex Locus for Genetic Analyses of Complex Human Traits." Genes 11, no. 11 (October 29, 2020): 1273. http://dx.doi.org/10.3390/genes11111273.

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The Human Y chromosome (ChrY) has been demonstrated to be a powerful tool for phylogenetics, population genetics, genetic genealogy and forensics. However, the importance of ChrY genetic variation in relation to human complex traits is less clear. In this review, we summarise existing evidence about the inherent complexities of ChrY variation and their use in association studies of human complex traits. We present and discuss the specific particularities of ChrY genetic variation, including Y chromosomal haplogroups, that need to be considered in the design and interpretation of genetic epidemiological studies involving ChrY.

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Charlesworth, Deborah, Nicholas H. Barton, and Brian Charlesworth. "The sources of adaptive variation." Proceedings of the Royal Society B: Biological Sciences 284, no. 1855 (May 31, 2017): 20162864. http://dx.doi.org/10.1098/rspb.2016.2864.

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The role of natural selection in the evolution of adaptive phenotypes has undergone constant probing by evolutionary biologists, employing both theoretical and empirical approaches. As Darwin noted, natural selection can act together with other processes, including random changes in the frequencies of phenotypic differences that are not under strong selection, and changes in the environment, which may reflect evolutionary changes in the organisms themselves. As understanding of genetics developed after 1900, the new genetic discoveries were incorporated into evolutionary biology. The resulting general principles were summarized by Julian Huxley in his 1942 book Evolution: the modern synthesis . Here, we examine how recent advances in genetics, developmental biology and molecular biology, including epigenetics, relate to today's understanding of the evolution of adaptations. We illustrate how careful genetic studies have repeatedly shown that apparently puzzling results in a wide diversity of organisms involve processes that are consistent with neo-Darwinism. They do not support important roles in adaptation for processes such as directed mutation or the inheritance of acquired characters, and therefore no radical revision of our understanding of the mechanism of adaptive evolution is needed.

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Ballad, J. William O., Joy Hatzidakis, Timothy L. Karr, and Martin Kreitman. "Reduced Variation in Drosophila simulans Mitochondrial DNA." Genetics 144, no. 4 (December 1, 1996): 1519–28. http://dx.doi.org/10.1093/genetics/144.4.1519.

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We investigated the evolutionary dynamics of infection of a Drosophila simulans population by a maternally inherited insect bacterial parasite, Wolbachia, by analyzing nucleotide variability in three regions of the mitochondrial genome in four infected and 35 uninfected lines. Mitochondrial variability is significantly reduced compared to a noncoding region of a nuclear-encoded gene in both uninfected and pooled samples of flies, indicating a sweep of genetic variation. The selective sweep of mitochondrial DNA may have been generated by the fixation of an advantageous mitochondrial gene mutation in the mitochondrial genome. Alternatively, the dramatic reduction in mitochondrial diversity may be related to Wolbachia.

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Xu, Hongyan, Ranajit Chakraborty, and Yun-Xin Fu. "Mutation Rate Variation at Human Dinucleotide Microsatellites." Genetics 170, no. 1 (February 16, 2005): 305–12. http://dx.doi.org/10.1534/genetics.104.036855.

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Greenspan, G., and D. Geiger. "Modeling Haplotype Block Variation Using Markov Chains." Genetics 172, no. 4 (December 15, 2005): 2583–99. http://dx.doi.org/10.1534/genetics.105.042978.

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Kuittinen, Helmi, and Montserrat Aguadé. "Nucleotide Variation at theCHALCONE ISOMERASELocus inArabidopsis thaliana." Genetics 155, no. 2 (June 1, 2000): 863–72. http://dx.doi.org/10.1093/genetics/155.2.863.

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AbstractAn ~1.9-kb region encompassing the CHI gene, which encodes chalcone isomerase, was sequenced in 24 worldwide ecotypes of Arabidopsis thaliana (L.) Heynh. and in 1 ecotype of A. lyrata ssp. petraea. There was no evidence for dimorphism at the CHI region. A minimum of three recombination events was inferred in the history of the sampled ecotypes of the highly selfing A. thaliana. The estimated nucleotide diversity (θTOTAL = 0.004, θSIL = 0.005) was on the lower part of the range of the corresponding estimates for other gene regions. The skewness of the frequency spectrum toward an excess of low-frequency polymorphisms, together with the bell-shaped distribution of pairwise nucleotide differences at CHI, suggests that A. thaliana has recently experienced a rapid population growth. Although this pattern could also be explained by a recent selective sweep at the studied region, results from the other studied loci and from an AFLP survey seem to support the expansion hypothesis. Comparison of silent polymorphism and divergence at the CHI region and at the Adh1 and ChiA revealed in some cases a significant deviation of the direct relationship predicted by the neutral theory, which would be compatible with balancing selection acting at the latter regions.

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Huddleston, John, and Evan E. Eichler. "An Incomplete Understanding of Human Genetic Variation." Genetics 202, no. 4 (April 2016): 1251–54. http://dx.doi.org/10.1534/genetics.115.180539.

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Sundström, Hannah, Matthew T. Webster, and Hans Ellegren. "Reduced Variation on the Chicken Z Chromosome." Genetics 167, no. 1 (May 2004): 377–85. http://dx.doi.org/10.1534/genetics.167.1.377.

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Salcedo, Tovah, Armando Geraldes, and Michael W. Nachman. "Nucleotide Variation in Wild and Inbred Mice." Genetics 177, no. 4 (December 2007): 2277–91. http://dx.doi.org/10.1534/genetics.107.079988.

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Langley, Charles H., Kristian Stevens, Charis Cardeno, Yuh Chwen G. Lee, Daniel R. Schrider, John E. Pool, Sasha A. Langley, et al. "Genomic Variation in Natural Populations ofDrosophila melanogaster." Genetics 192, no. 2 (June 5, 2012): 533–98. http://dx.doi.org/10.1534/genetics.112.142018.

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Keightley, Peter D., and William G. Hill. "Directional Selection and Variation in Finite Populations." Genetics 117, no. 3 (November 1, 1987): 573–82. http://dx.doi.org/10.1093/genetics/117.3.573.

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ABSTRACT Predictions are made of the equilibrium genetic variances and responses in a metric trait under the joint effects of directional selection, mutation and linkage in a finite population. The "infinitesimal model" is analyzed as the limiting case of many mutants of very small effect, otherwise Monte Carlo simulation is used. If the effects of mutant genes on the trait are symmetrically distributed and they are unlinked, the variance of mutant effects is not an important parameter. If the distribution is skewed, unless effects or the population size is small, the proportion of mutants that have increasing effect is the critical parameter. With linkage the distribution of genotypic values in the population becomes skewed downward and the equilibrium genetic variance and response are smaller as disequilibrium becomes important. Linkage effects are greater when the mutational variance is contributed by many genes of small effect than few of large effect, and are greater when the majority of mutants increase rather than decrease the trait because genes that are of large effect or are deleterious do not segregate for long. The most likely conditions for "Muller's ratchet" are investigated.

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Hill, William G. "Understanding and using quantitative genetic variation." Philosophical Transactions of the Royal Society B: Biological Sciences 365, no. 1537 (January 12, 2010): 73–85. http://dx.doi.org/10.1098/rstb.2009.0203.

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Quantitative genetics, or the genetics of complex traits, is the study of those characters which are not affected by the action of just a few major genes. Its basis is in statistical models and methodology, albeit based on many strong assumptions. While these are formally unrealistic, methods work. Analyses using dense molecular markers are greatly increasing information about the architecture of these traits, but while some genes of large effect are found, even many dozens of genes do not explain all the variation. Hence, new methods of prediction of merit in breeding programmes are again based on essentially numerical methods, but incorporating genomic information. Long-term selection responses are revealed in laboratory selection experiments, and prospects for continued genetic improvement are high. There is extensive genetic variation in natural populations, but better estimates of covariances among multiple traits and their relation to fitness are needed. Methods based on summary statistics and predictions rather than at the individual gene level seem likely to prevail for some time yet.

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Amini, Dara Suci, and Afifatul Achyar. "Analysis of Genetic Variation of MatK Gene Sequences in Ammothamnus lehmannii NCBI Popset 2440747918 Using In Silico RFLP." Tropical Genetics 3, no. 2 (November 29, 2023): 53–59. http://dx.doi.org/10.24036/tg.v3i2.49.

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Genetic diversity or genetic variation is variation that occurs in an organism due to differences in the sequence of nucleotide bases (adenine, thymine, guanine and cytosine) that form DNA in cells. Variation genetics can be studied in silico using available gene sequences in the NCBI genbank database. This study used the MatK (Maturase-K) gene sequence with the identity number Popset 2440747918 which was downloaded in fasta format from NCBI . Then screening of restriction enzyme candidates was carried out to determine the restriction enzymes prior to in silico RFLP. The restriction enzyme selected from the screening was the restriction enzyme HindIII which has the recognition site A'AGC_T. The results obtained from 79 samples of DNA sequences, 76 samples were cut and 3 samples were not. And found three allele variations with the percentage of the presence of fragments A1 (86.07%), A2 (10.12%) and A3 (3.79%). The percentage values and frequencies of these A1, A2 and A3 alleles indicate a low level of genetic variation.

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Biros, Erik, Mirko Karan, and Jonathan Golledge. "Genetic Variation and Atherosclerosis." Current Genomics 9, no. 1 (March 1, 2008): 29–42. http://dx.doi.org/10.2174/138920208783884856.

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Ryan, Stephen G. "Human Genetic Variation." Pharmacogenomics 3, no. 1 (January 2002): 9–11. http://dx.doi.org/10.1517/14622416.3.1.9.

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Kemper, Kathryn. "59 Insights into Complex Traits from Human Genetics." Journal of Animal Science 99, Supplement_3 (October 8, 2021): 30–31. http://dx.doi.org/10.1093/jas/skab235.052.

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Abstract Genomic selection has been implemented successfully in many livestock industries for genetic improvement. However, genomic selection provides limited insight into the genetic mechanisms underlying variation in complex traits. In contrast, human genetics has a focus on understanding genetic architecture and the origins of quantitative trait variation. This presentation will discuss a number of examples from human genetics which can inform our understanding of the nature of variation in complex traits. So-called ‘monogenic’ conditions, for example, are proving to have more complex genetic architecture than naïve expectations might suggest. Massive data sets of millions of people are also enabling longstanding questions to be addressed. Traits such as height, for example, are affected by a very large but finite number of loci. We can reconcile seemingly disparate heritability estimates from different experimental designs by accounting for assortative mating. The presentation will provide a brief update on current approaches to genomic prediction in human genetics and discuss the implications of these findings for understanding and predicting complex traits in livestock.

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Karczewski, Konrad J., and Alicia R. Martin. "Analytic and Translational Genetics." Annual Review of Biomedical Data Science 3, no. 1 (July 20, 2020): 217–41. http://dx.doi.org/10.1146/annurev-biodatasci-072018-021148.

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Understanding the influence of genetics on human disease is among the primary goals for biology and medicine. To this end, the direct study of natural human genetic variation has provided valuable insights into human physiology and disease as well as into the origins and migrations of humans. In this review, we discuss the foundations of population genetics, which provide a crucial context to the study of human genes and traits. In particular, genome-wide association studies and similar methods have revealed thousands of genetic loci associated with diseases and traits, providing invaluable information into the biology of these traits. Simultaneously, as the study of rare genetic variation has expanded, so-called human knockouts have elucidated the function of human genes and the therapeutic potential of targeting them.

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Eichten, Steven R., Akanksha Srivastava, Adam J. Reddiex, Diep R. Ganguly, Alison Heussler, Jared C. Streich, Pip B. Wilson, and Justin O. Borevitz. "Extending the Genotype in Brachypodium by Including DNA Methylation Reveals a Joint Contribution with Genetics on Adaptive Traits." G3: Genes|Genomes|Genetics 10, no. 5 (March 4, 2020): 1629–37. http://dx.doi.org/10.1534/g3.120.401189.

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Epigenomic changes have been considered a potential missing link underlying phenotypic variation in quantitative traits but is potentially confounded with the underlying DNA sequence variation. Although the concept of epigenetic inheritance has been discussed in depth, there have been few studies attempting to directly dissect the amount of epigenomic variation within inbred natural populations while also accounting for genetic diversity. By using known genetic relationships between Brachypodium lines, multiple sets of nearly identical accession families were selected for phenotypic studies and DNA methylome profiling to investigate the dual role of (epi)genetics under simulated natural seasonal climate conditions. Despite reduced genetic diversity, appreciable phenotypic variation was still observable in the measured traits (height, leaf width and length, tiller count, flowering time, ear count) between as well as within the inbred accessions. However, with reduced genetic diversity there was diminished variation in DNA methylation within families. Mixed-effects linear modeling revealed large genetic differences between families and a minor contribution of DNA methylation variation on phenotypic variation in select traits. Taken together, this analysis suggests a limited but significant contribution of DNA methylation toward heritable phenotypic variation relative to genetic differences.

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Laurie, C. C., J. T. Bridgham, and M. Choudhary. "Associations between DNA sequence variation and variation in expression of the Adh gene in natural populations of Drosophila melanogaster." Genetics 129, no. 2 (October 1, 1991): 489–99. http://dx.doi.org/10.1093/genetics/129.2.489.

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Abstract A large part of the genetic variation in alcohol dehydrogenase (ADH) activity level in natural populations of Drosophila melanogaster is associated with segregation of an amino acid replacement polymorphism at nucleotide 1490, which generates a difference in electrophoretic mobility. Part of the allozymic difference in activity level is due to a catalytic efficiency difference, which is also caused by the amino acid replacement, and part is due to a difference in the concentration of ADH protein. A previous site-directed in vitro mutagenesis experiment clearly demonstrated that the amino acid replacement has no effect on the concentration of ADH protein, nor does a strongly associated silent polymorphism at nucleotide 1443. Here we analyze associations between polymorphisms within the Adh gene and variation in ADH protein level for a number of chromosomes derived from natural populations. A sequence length polymorphism within the first intron of the distal (adult) transcript, 1, is in strong linkage disequilibrium with the amino acid replacement. Among a sample of 46 isochromosomal lines analyzed, all but one of the 14 Fast lines have 1 and all but one of the 32 Slow lines lack 1. The exceptional Fast line has an unusually low level of ADH protein (typical of Slow lines) and the exceptional Slow line has an unusually high level (typical of Fast lines). These results suggest that the 1 polymorphism may be responsible for the average difference in ADH protein between the allozymic classes. A previous experiment localized the effect on ADH protein to a 2.3-kb restriction fragment. DNA sequences of this fragment from several alleles of each allozymic type indicate that no other polymorphisms within this region are as closely associated with the ADH protein level difference as the 1 polymorphism.

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