Zeitschriftenartikel: „Theoretical population genetics“

1

Ewens, W. J. „Theoretical population genetics“. Genome 31, Nr. 2 (15.01.1989): 1088–89. http://dx.doi.org/10.1139/g89-188.

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2

Chakraborty, Ranajit. „Theoretical Population Genetics“. Trends in Ecology & Evolution 6, Nr. 2 (Februar 1991): 68. http://dx.doi.org/10.1016/0169-5347(91)90132-h.

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3

Wakeley, John. „The Limits of Theoretical Population Genetics“. Genetics 169, Nr. 1 (01.01.2005): 1–7. http://dx.doi.org/10.1093/genetics/169.1.1.

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4

Couvet, D. „Introduction to theoretical population genetics“. Trends in Ecology & Evolution 8, Nr. 5 (Mai 1993): 192. http://dx.doi.org/10.1016/0169-5347(93)90152-f.

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5

WAKELEY, J. „John Wakeley discusses theoretical population genetics“. Biosilico 1, Nr. 3 (Juli 2003): 84–85. http://dx.doi.org/10.1016/s1478-5382(03)02344-8.

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6

Sarkar, Sahotra. „The Origins of Theoretical Population Genetics“. Endeavour 26, Nr. 2 (Juni 2002): 77. http://dx.doi.org/10.1016/s0160-9327(02)01414-x.

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7

Al Ghafri, Mataab K. „The theoretical approach to population genetics“. Ology: Reviews in Applied Sciences 1 (03.10.2018): 10–11. http://dx.doi.org/10.14297/ras.v1i1.3.

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8

Kretschmer, Hildrun, und B. M. Gupta. „Collaboration patterns in theoretical population genetics“. Scientometrics 43, Nr. 3 (November 1998): 455–62. http://dx.doi.org/10.1007/bf02457409.

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9

Gupta, B. M., und C. R. Karisiddappa. „Collaboration in theoretical population genetics speciality“. Scientometrics 42, Nr. 3 (Oktober 1998): 349–76. http://dx.doi.org/10.1007/bf02458377.

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10

Charlesworth, Brian. „The Origins of Theoretical Population Genetics: How population and quantitative genetics began“. Trends in Genetics 18, Nr. 6 (Juni 2002): 324–25. http://dx.doi.org/10.1016/s0168-9525(02)02680-x.

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11

Haigh, John. „INTRODUCTION TO THEORETICAL POPULATION GENETICS (Biomathematics 21)“. Bulletin of the London Mathematical Society 26, Nr. 3 (Mai 1994): 318–20. http://dx.doi.org/10.1112/blms/26.3.318.

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12

Gupta, B. M., Suresh Kumar und C. R. Karisiddappa. „Collaboration profile of theoretical population genetics speciality“. Scientometrics 39, Nr. 3 (Juli 1997): 293–314. http://dx.doi.org/10.1007/bf02458532.

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13

Dung, Samantha Kristin, Andrea López, Ezequiel Lopez Barragan, Rochelle-Jan Reyes, Ricky Thu, Edgar Castellanos, Francisca Catalan, Emilia Huerta-Sánchez und Rori V. Rohlfs. „Illuminating Women’s Hidden Contribution to Historical Theoretical Population Genetics“. Genetics 211, Nr. 2 (Februar 2019): 363–66. http://dx.doi.org/10.1534/genetics.118.301277.

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14

Ohta, T., und H. Tachida. „Theoretical study of near neutrality. I. Heterozygosity and rate of mutant substitution.“ Genetics 126, Nr. 1 (01.09.1990): 219–29. http://dx.doi.org/10.1093/genetics/126.1.219.

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Abstract In order to clarify the nature of "near neutrality" in molecular evolution and polymorphism, extensive simulation studies were performed. Selection coefficients of new mutations are assumed to be small so that both random genetic drift and selection contribute to determining the behavior of mutants. The model also incorporates normally distributed spatial fluctuation of selection coefficients. If the system starts from "average neutrality," it will move to a better adapted state, and most new mutations will become "slightly deleterious." Monte Carlo simulations have indicated that such adaptation is attained, but that the rate of such "progress" is very low for weak selection. In general, the larger the population size, the more effective the selection becomes. Also, as selection becomes weaker, the behavior of the mutants approaches that of completely neutral genes. Thus, the weaker the selection, the smaller is the effect of population size on mutant dynamics. Increase of heterozygosity with population size is very pronounced for subdivided populations. The significance of these results is discussed in relation to various observed facts on molecular evolution and polymorphism, such as generation-time dependency and overdispersion of the molecular clock, or contrasting patterns of DNA and protein polymorphism among some closely related species.

15

Werren, John H., und Leo W. Beukeboom. „Population Genetics of a Parasitic Chromosome: Theoretical Analysis of PSR in Subdivided Populations“. American Naturalist 142, Nr. 2 (August 1993): 224–41. http://dx.doi.org/10.1086/285536.

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16

Sherry, Stephen T., Henry C. Harpending, Mark A. Batzer und Mark Stoneking. „Alu Evolution in Human Populations: Using the Coalescent to Estimate Effective Population Size“. Genetics 147, Nr. 4 (01.12.1997): 1977–82. http://dx.doi.org/10.1093/genetics/147.4.1977.

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Abstract There are estimated to be ~1000 members of the Ya5 Alu subfamily of retroposons in humans. This Subfamily has a distribution restricted to humans, with a few copies in gorillas and chimpanzees. Fifty-seven Ya5 elements were previously cloned from a HeLaderived randomly sheared total genomic library, sequenced, and screened for polymorphism in a panel of 120 unrelated humans. Forty-four of the 57 cloned Alu repeats were monomorphic in the sample and 13 Alu repeats were dimorphic for insertion presence/absence. The observed distribution of sample frequencies of the 13 dimorphic elements is consistent with the theoretical expectation for elements ascertained in a single diploid cell line. Coalescence theory is used to compute expected total pedigree branch lengths for monomorphic and dimorphic elements, leading to an estimate of human effective population size of ~18,000 during the last one to two million years.

17

Orr, H. Allen. „The population genetics of beneficial mutations“. Philosophical Transactions of the Royal Society B: Biological Sciences 365, Nr. 1544 (27.04.2010): 1195–201. http://dx.doi.org/10.1098/rstb.2009.0282.

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The population genetic study of advantageous mutations has lagged behind that of deleterious and neutral mutations. But over the past two decades, a number of significant developments, both theoretical and empirical, have occurred. Here, I review two of these developments: the attempt to determine the distribution of fitness effects among beneficial mutations and the attempt to determine their average dominance. Considering both theory and data, I conclude that, while considerable theoretical progress has been made, we still lack sufficient data to draw confident conclusions about the distribution of effects or the dominance of beneficial mutations.

18

Ghosh, Atiyo, Patrick G. Meirmans und Patsy Haccou. „Quantifying introgression risk with realistic population genetics“. Proceedings of the Royal Society B: Biological Sciences 279, Nr. 1748 (10.10.2012): 4747–54. http://dx.doi.org/10.1098/rspb.2012.1907.

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Introgression is the permanent incorporation of genes from the genome of one population into another. This can have severe consequences, such as extinction of endemic species, or the spread of transgenes. Quantification of the risk of introgression is an important component of genetically modified crop regulation. Most theoretical introgression studies aimed at such quantification disregard one or more of the most important factors concerning introgression: realistic genetical mechanisms, repeated invasions and stochasticity. In addition, the use of linkage as a risk mitigation strategy has not been studied properly yet with genetic introgression models. Current genetic introgression studies fail to take repeated invasions and demographic stochasticity into account properly, and use incorrect measures of introgression risk that can be manipulated by arbitrary choices. In this study, we present proper methods for risk quantification that overcome these difficulties. We generalize a probabilistic risk measure, the so-called hazard rate of introgression, for application to introgression models with complex genetics and small natural population sizes. We illustrate the method by studying the effects of linkage and recombination on transgene introgression risk at different population sizes.

19

Ohta, T. „Theoretical study of near neutrality. II. Effect of subdivided population structure with local extinction and recolonization.“ Genetics 130, Nr. 4 (01.04.1992): 917–23. http://dx.doi.org/10.1093/genetics/130.4.917.

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Abstract There are several unsolved problems concerning the model of nearly neutral mutations. One is the interaction of subdivided population structure and weak selection that spatially fluctuates. The model of nearly neutral mutations whose selection coefficient spatially fluctuates has been studied by adopting the island model with periodic extinction-recolonization. Both the number of colonies and the migration rate play significant roles in determining mutants' behavior, and selection is ineffective when the extinction-recolonization is frequent with low migration rate. In summary, the number of mutant substitutions decreases and the polymorphism increases by increasing the total population size, and/or decreasing the extinction-recolonization rate. However, by increasing the total size of the population, the mutant substitution rate does not become as low when compared with that in panmictic populations, because of the extinction-recolonization, especially when the migration rate is limited. It is also found that the model satisfactorily explains the contrasting patterns of molecular polymorphisms observed in sibling species of Drosophila, including heterozygosity, proportion of polymorphism and fixation index.

20

Gupta, B. M., und C. R. Karisiddappa. „Author productivity patterns in theoretical population genetics (1900–1980)“. Scientometrics 36, Nr. 1 (Mai 1996): 19–41. http://dx.doi.org/10.1007/bf02126643.

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21

Gupta, B. M. „Growth and obsolescence of literature in theoretical population genetics“. Scientometrics 42, Nr. 3 (Oktober 1998): 335–47. http://dx.doi.org/10.1007/bf02458376.

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22

Luo, Z. W., R. Thompson und J. A. Woolliams. „A Population Genetics Model of Marker-Assisted Selection“. Genetics 146, Nr. 3 (01.07.1997): 1173–83. http://dx.doi.org/10.1093/genetics/146.3.1173.

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A deterministic two-loci model was developed to predict genetic response to marker-assisted selection (MAS) in one generation and in multiple generations. Formulas were derived to relate linkage disequilibrium in a population to the proportion of additive genetic variance used by MAS, and in turn to an extra improvement in genetic response over phenotypic selection. Predictions of the response were compared to those predicted by using an infinite-loci model and the factors affecting efficiency of MAS were examined. Theoretical analyses of the present study revealed the nonlinearity between the selection intensity and genetic response in MAS. In addition to the heritability of the trait and the proportion of the marker-associated genetic variance, the frequencies of the selectively favorable alleles at the two loci, one marker and one quantitative trait locus, were found to play an important role in determining both the short- and long-term efficiencies of MAS. The evolution of linkage disequilibrium and thus the genetic response over several generations were predicted theoretically and examined by simulation. MAS dissipated the disequilibrium more quickly than drift alone. In some cases studied, the rate of dissipation was as large as that to be expected in the circumstance where the true recombination fraction was increased by three times and selection was absent.

23

Tenaillon, Olivier, Bruno Toupance, Hervé Le Nagard, François Taddei und Bernard Godelle. „Mutators, Population Size, Adaptive Landscape and the Adaptation of Asexual Populations of Bacteria“. Genetics 152, Nr. 2 (01.06.1999): 485–93. http://dx.doi.org/10.1093/genetics/152.2.485.

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Abstract Selection of mutator alleles, increasing the mutation rate up to 10,000-fold, has been observed during in vitro experimental evolution. This spread is ascribed to the hitchhiking of mutator alleles with favorable mutations, as demonstrated by a theoretical model using selective parameters corresponding to such experiments. Observations of unexpectedly high frequencies of mutators in natural isolates suggest that the same phemonemon could occur in the wild. But it remains questionable whether realistic in natura parameter values could also result in selection of mutators. In particular, the main parameters of adaptation, the size of the adapting population and the height and steepness of the adaptive peak characterizing adaptation, are very variable in nature. By simulation approach, we studied the effect of these parameters on the selection of mutators in asexual populations, assuming additive fitness. We show that the larger the population size, the more likely the fixation of mutator alleles. At a large population size, at least four adaptive mutations are needed for mutator fixation; moreover, under stronger selection stronger mutators are selected. We propose a model based on multiple mutations to illustrate how second-order selection can optimize population fitness when few favorable mutations are required for adaptation.

24

Nagylaki, T. „Gustave Malécot and the transition from classical to modern population genetics.“ Genetics 122, Nr. 2 (01.06.1989): 253–68. http://dx.doi.org/10.1093/genetics/122.2.253.

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Abstract The contributions of Gustave Malécot to theoretical population genetics are described, discussed, and put into perspective relative to earlier and later work. In this context, certain aspects of the theory of inbreeding, the correlation between relatives, the evolution of finite panmictic populations, and (in more depth) spatial variation are reviewed. A brief biographical sketch of Malécot is also presented.

25

Ouborg, N. Joop. „Integrating population genetics and conservation biology in the era of genomics“. Biology Letters 6, Nr. 1 (02.09.2009): 3–6. http://dx.doi.org/10.1098/rsbl.2009.0590.

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As one of the final activities of the ESF-CONGEN Networking programme, a conference entitled ‘Integrating Population Genetics and Conservation Biology’ was held at Trondheim, Norway, from 23 to 26 May 2009. Conference speakers and poster presenters gave a display of the state-of-the-art developments in the field of conservation genetics. Over the five-year running period of the successful ESF-CONGEN Networking programme, much progress has been made in theoretical approaches, basic research on inbreeding depression and other genetic processes associated with habitat fragmentation and conservation issues, and with applying principles of conservation genetics in the conservation of many species. Future perspectives were also discussed in the conference, and it was concluded that conservation genetics is evolving into conservation genomics, while at the same time basic and applied research on threatened species and populations from a population genetic point of view continues to be emphasized.

26

Ohta, Tomoko. „POPULATION GENETICS OF AN EXPANDING FAMILY OF MOBILE GENETIC ELEMENTS“. Genetics 113, Nr. 1 (01.05.1986): 145–59. http://dx.doi.org/10.1093/genetics/113.1.145.

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ABSTRACT A model of an expanding family of dispersed repetitive DNA was studied. Based on the previous result of the model of duplicative transposition, an approximate solution to give allelism and identity coefficients as functions of time was obtained, and theoretical predictions were verified by Monte Carlo experiments. The results show that, even if the copy number per genome increases very rapidly, allelism and identity coefficients may take a long time to reach equilibrium. The changes of allelism and allelic identity are similar to that of homozygosity at an ordinary single locus, whereas that of nonallelic identity can be much slower, particularly when the copy number per genome is large. Thus, many existing families of highly repetitive sequences may represent nonequilibrium states for nonallelic identity. The present model may be extended to include other evolutionary forces such as gene conversion or the recurrent insertion from normal gene copies.

27

Antonovics, Janis, Kara O'Keefe und Michael E. Hood. „Theoretical Population Genetics of Mating-Type Linked Haplo-Lethal Alleles“. International Journal of Plant Sciences 159, Nr. 2 (März 1998): 192–98. http://dx.doi.org/10.1086/297538.

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28

Sarkar, Sahotra. „Haldane and the emergence of theoretical population genetics, 1924–1932“. Journal of Genetics 71, Nr. 3 (Dezember 1992): 73–79. http://dx.doi.org/10.1007/bf02927888.

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29

Sawyer, S. A., und D. L. Hartl. „Population genetics of polymorphism and divergence.“ Genetics 132, Nr. 4 (01.12.1992): 1161–76. http://dx.doi.org/10.1093/genetics/132.4.1161.

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Abstract Frequencies of mutant sites are modeled as a Poisson random field in two species that share a sufficiently recent common ancestor. The selective effect of the new alleles can be favorable, neutral, or detrimental. The model is applied to the sample configurations of nucleotides in the alcohol dehydrogenase gene (Adh) in Drosophila simulans and Drosophila yakuba. Assuming a synonymous mutation rate of 1.5 x 10(-8) per site per year and 10 generations per year, we obtain estimates for the effective population size (N(e) = 6.5 x 10(6)), the species divergence time (tdiv = 3.74 million years), and an average selection coefficient (sigma = 1.53 x 10(-6) per generation for advantageous or mildly detrimental replacements), although it is conceivable that only two of the amino acid replacements were selected and the rest neutral. The analysis, which includes a sampling theory for the independent infinite sites model with selection, also suggests the estimate that the number of amino acids in the enzyme that are susceptible to favorable mutation is in the range 2-23 at any one time. The approach provides a theoretical basis for the use of a 2 x 2 contingency table to compare fixed differences and polymorphic sites with silent sites and amino acid replacements.

30

Cherry, Joshua L. „Selection in a Subdivided Population With Local Extinction and Recolonization“. Genetics 164, Nr. 2 (01.06.2003): 789–95. http://dx.doi.org/10.1093/genetics/164.2.789.

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Abstract In a subdivided population, local extinction and subsequent recolonization affect the fate of alleles. Of particular interest is the interaction of this force with natural selection. The effect of selection can be weakened by this additional source of stochastic change in allele frequency. The behavior of a selected allele in such a population is shown to be equivalent to that of an allele with a different selection coefficient in an unstructured population with a different size. This equivalence allows use of established results for panmictic populations to predict such quantities as fixation probabilities and mean times to fixation. The magnitude of the quantity Nese, which determines fixation probability, is decreased by extinction and recolonization. Thus deleterious alleles are more likely to fix, and advantageous alleles less likely to do so, in the presence of extinction and recolonization. Computer simulations confirm that the theoretical predictions of both fixation probabilities and mean times to fixation are good approximations.

31

Hu, Zhongwen, Fangyuan Yang, Deping Zhang, Shimeng Zhang, Xiaofei Yu und Maofa Yang. „Genetic Diversity and Fine-Scale Genetic Structure of Spodoptera litura Fabricius (Lepidoptera: Noctuidae) in Southern China Based on Microsatellite Markers“. Animals 13, Nr. 4 (05.02.2023): 560. http://dx.doi.org/10.3390/ani13040560.

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Population genetic structure is strongly affected by dispersal events, especially for migratory species. The investigation of population structure is therefore conducive to increasing our understanding of species dispersal. Spodoptera litura (Fabricius) (Lepidoptera: Noctuidae) is an important tobacco pest in China causing serious damage to multiple crops. In this study, we explore its dispersal dynamics by clarifying the fine-scale population genetics using 545 S. litura samples collected from tobacco plantations at 24 locations (mainly in Baise, Hechi, and Hezhou, Southern China). We analyzed the genetic diversity, genetic structure, and gene flow of these populations using seven microsatellite loci. Our results revealed high genetic diversity and low population genetic structure among S. litura. The genetic distance was uncorrelated with geographical distance, indicating the complete randomness of dispersal among the local populations. Our results suggest that the movement scope of contemporary S. litura might be much higher than the local-level spatial scale, which will provide a theoretical basis for pest management.

32

Griffing, B. „Genetic analysis of plant mixtures.“ Genetics 122, Nr. 4 (01.08.1989): 943–56. http://dx.doi.org/10.1093/genetics/122.4.943.

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Abstract Plant mixtures are difficult to analyze genetically because of possible interactions between neighboring plants (i.e., between plants in the same biological group). However, a genetic modeling scheme has been devised which, theoretically, can accommodate such interactions. This study was an attempt to put the theoretical modeling procedure to an experimental test. To this end an experimental procedure was devised that generated biological groups from a well defined base population. A cultural system was used which permitted growing plant mixtures in controlled environmental facilities. This allowed the experiment to be conducted over a wide range of temperature and nutrient conditions. Application of the theoretical gene model to the experimental data permitted identification of those classes of gene effects that were responsible for genetic variation exhibited by the mixtures. Adequacy of the genetic modeling description was corroborated by precise prediction of an independent genetic response. The genetic analyses also identified statistically significant temperature-and nutrient-dependent forms of heterosis. It was concluded that the study demonstrated the suitability of the theoretical group gene model for describing complexities inherent in plant mixtures.

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Bergelson, Joy, Eli Stahl, Scott Dudek und Martin Kreitman. „Genetic Variation Within and Among Populations of Arabidopsis thaliana“. Genetics 148, Nr. 3 (01.03.1998): 1311–23. http://dx.doi.org/10.1093/genetics/148.3.1311.

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Abstract We investigated levels of nucleotide polymorphism within and among populations of the highly self-fertilizing Brassicaceous species, Arabidopsis thaliana. Four-cutter RFLP data were collected at one mitochondrial and three nuclear loci from 115 isolines representing 11 worldwide population collections, as well as from seven commonly used ecotypes. The collections include multiple populations from North America and Eurasia, as well as two pairs of collections from locally proximate sites, and thus allow a hierarchical geographic analysis of polymorphism. We found no variation at the mitochondrial locus Nad5 and very low levels of intrapopulation nucleotide diversity at Adh, Dhs1, and Gpa1. Interpopulation nucleotide diversity was also consistently low among the loci, averaging 0.0014. gst, a measure of population differentiation, was estimated to be 0.643. Interestingly, we found no association between geographical distance between populations and genetic distance. Most haplotypes have a worldwide distribution, suggesting a recent expansion of the species or long-distance gene flow. The low level of polymorphism found in this study is consistent with theoretical models of neutral mutations and background selection in highly self-fertilizing species.

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Jarne, Philippe. „Mating system, bottlenecks and genetic polymorphism in hermaphroditic animals“. Genetical Research 65, Nr. 3 (Juni 1995): 193–207. http://dx.doi.org/10.1017/s0016672300033279.

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SummaryA loss of neutral genetic polymorphism is theoretically expected for many reasons in inbreeding organisms when compared to outbreeders. The first reason derives from the decrease of the effective population size, down to a halving, in purely selfing species. Other genetical reasons include hitchhiking and background selection. A loss can also be caused by ecological processes, that is by any kind of process provoking a genetic bottleneck. These theoretical expectations have been empirically confirmed in hermaphroditic plants for which selfing species exhibit both a lower gene diversity and number of alleles per population. Here I extend the analysis to hermaphroditic animals, mainly terrestrial and freshwater snails. The decrease of variability in selfers is far greater than what is expected under the halving of the effective size of populations only. Hitchhiking and background selection certainly cannot be rejected as causes of this extra loss. Bottlenecks can clearly be invoked in tropical freshwater snails. However a crude theoretical analysis using Ewens's sampling formulae shows that the relative loss of variability estimated by the number of alleles is smaller in inbreeders than in outbreeders assuming populations with the same number of individuals. This suggests that bottlenecks contribute less to the loss in selfers than in outcrossers. Variability lost within selfing populations of hermaphroditic animals is also lost at the level of a group of populations (metapopulation). This is theoretically not always expected. Indeed, I calculate the ratio of the effective size of a selfing metapopulation to be greater than that of an outcrossing one using previously derived equations. The large variation of this ratio which depends on both migration and effective size of subpopulations prevents prediction of the relative amount of genetic variability stored by selfing and outcrossing metapopulations.

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Tachida, Hidenori. „A Population Genetic Study of the Evolution of SINEs. II. Sequence Evolution Under the Master Copy Model“. Genetics 143, Nr. 2 (01.06.1996): 1033–42. http://dx.doi.org/10.1093/genetics/143.2.1033.

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Abstract A transient population genetic model of SINE (short interspersed repetitive element) evolution assuming the master copy model is theoretically investigated. Means and variances of consensus frequency of nucleotides, nucleotide homozygosity, and the number of shared differences that are considered to have caused by mutations occurring in the master copy lineages are computed. All quantities investigated are shown to be monotone functions of the duration of the expansion period. Thus, they can be used to estimate the expansion period although their sampling variances are generally large. Using the theoretical results, the Sb subfamily of human Alu sequences is analyzed. First, the expansion period is estimated from the observed mean and variance of homozygosity. The expansion period is shown to be short compared to the time since the end of the expansion of the subfamily. However, the observed number of the shared differences is more than twice that expected under the master copy model with the estimated expansion period. Alternative models including that with multiple master copy loci to explain this observation are discussed.

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Tsitrone, Anne, François Rousset und Patrice David. „Heterosis, Marker Mutational Processes and Population Inbreeding History“. Genetics 159, Nr. 4 (01.12.2001): 1845–59. http://dx.doi.org/10.1093/genetics/159.4.1845.

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AbstractGenotype-fitness correlations (GFC) have previously been studied using allozyme markers and have often focused on short-term processes such as recent inbreeding. Thus, models of GFC usually neglect marker mutation and only use heterozygosity as a genotypic index. Recently, GFC have also been reported (i) with DNA markers such as microsatellites, characterized by high mutation rates and specific mutational processes and (ii) using new individual genotypic indices assumed to be more precise than heterozygosity. The aim of this article is to evaluate the theoretical impact of marker mutation on GFC. We model GFC due to short-term processes generated by the current breeding system (partial selfing) and to long-term processes generated by past population history (hybridization). Various mutation rates and mutation models corresponding to different kinds of molecular markers are considered. Heterozygosity is compared to other genotypic indices designed for specific marker types. Highly mutable markers (such as microsatellites) are particularly suitable for the detection of GFC that evolve in relation to short-term processes, whereas GFC due to long-term processes are best observed with intermediate mutation rates. Irrespective of the marker type and population scenario, heterozygosity usually provides higher correlations than other genotypic indices under most biologically plausible conditions.

37

Epperson, B. K. „Spatial and space-time correlations in systems of subpopulations with genetic drift and migration.“ Genetics 133, Nr. 3 (01.03.1993): 711–27. http://dx.doi.org/10.1093/genetics/133.3.711.

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Abstract The geographic distribution of genetic variation is an important theoretical and experimental component of population genetics. Previous characterizations of genetic structure of populations have used measures of spatial variance and spatial correlations. Yet a full understanding of the causes and consequences of spatial structure requires complete characterization of the underlying space-time system. This paper examines important interactions between processes and spatial structure in systems of subpopulations with migration and drift, by analyzing correlations of gene frequencies over space and time. We develop methods for studying important features of the complete set of space-time correlations of gene frequencies for the first time in population genetics. These methods also provide a new alternative for studying the purely spatial correlations and the variance, for models with general spatial dimensionalities and migration patterns. These results are obtained by employing theorems, previously unused in population genetics, for space-time autoregressive (STAR) stochastic spatial time series. We include results on systems with subpopulation interactions that have time delay lags (temporal orders) greater than one. We use the space-time correlation structure to develop novel estimators for migration rates that are based on space-time data (samples collected over space and time) rather than on purely spatial data, for real systems. We examine the space-time and spatial correlations for some specific stepping stone migration models. One focus is on the effects of anisotropic migration rates. Partial space-time correlation coefficients can be used for identifying migration patterns. Using STAR models, the spatial, space-time, and partial space-time correlations together provide a framework with an unprecedented level of detail for characterizing, predicting and contrasting space-time theoretical distributions of gene frequencies, and for identifying features such as the pattern of migration and estimating migration rates in experimental studies of genetic variation over space and time.

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Gupta, B. M. „Analysis of distribution of the age of citations in theoretical population genetics“. Scientometrics 40, Nr. 1 (September 1997): 139–62. http://dx.doi.org/10.1007/bf02459265.

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39

Fox, Keolu, Kartik Lakshmi Rallapalli und Alexis C. Komor. „Rewriting Human History and Empowering Indigenous Communities with Genome Editing Tools“. Genes 11, Nr. 1 (12.01.2020): 88. http://dx.doi.org/10.3390/genes11010088.

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Appropriate empirical-based evidence and detailed theoretical considerations should be used for evolutionary explanations of phenotypic variation observed in the field of human population genetics (especially Indigenous populations). Investigators within the population genetics community frequently overlook the importance of these criteria when associating observed phenotypic variation with evolutionary explanations. A functional investigation of population-specific variation using cutting-edge genome editing tools has the potential to empower the population genetics community by holding “just-so” evolutionary explanations accountable. Here, we detail currently available precision genome editing tools and methods, with a particular emphasis on base editing, that can be applied to functionally investigate population-specific point mutations. We use the recent identification of thrifty mutations in the CREBRF gene as an example of the current dire need for an alliance between the fields of population genetics and genome editing.

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Koots, Kenneth R., und John P. Gibson. „Realized Sampling Variances of Estimates of Genetic Parameters and the Difference Between Genetic and Phenotypic Correlations“. Genetics 143, Nr. 3 (01.07.1996): 1409–16. http://dx.doi.org/10.1093/genetics/143.3.1409.

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Abstract A data set of 1572 heritability estimates and 1015 pairs of genetic and phenotypic correlation estimates, constructed from a survey of published beef cattle genetic parameter estimates, provided a rare opportunity to study realized sampling variances of genetic parameter estimates. The distribution of both heritability estimates and genetic correlation estimates, when plotted against estimated accuracy, was consistent with random error variance being some three times the sampling variance predicted from standard formulae. This result was consistent with the observation that the variance of estimates of heritabilities and genetic correlations between populations were about four times the predicted sampling variance, suggesting few real differences in genetic parameters between populations. Except where there was a strong biological or statistical expectation of a difference, there was little evidence for differences between genetic and phenotypic correlations for most trait combinations or for differences in genetic correlations between populations. These results suggest that, even for controlled populations, estimating genetic parameters specific to a given population is less useful than commonly believed. A serendipitous discovery was that, in the standard formula for theoretical standard error of a genetic correlation estimate, the heritabilities refer to the estimated values and not, as seems generally assumed, the true population values.

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Montchamp-Moreau, Catherine, und Mariano Katz. „A theoretical analysis of linkage disequilibrium produced by genetic drift in Drosophila populations“. Genetical Research 48, Nr. 3 (Dezember 1986): 161–66. http://dx.doi.org/10.1017/s0016672300024952.

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SummaryWe analyse the progression of linkage disequilibrium produced by random genetic drift in populations subject to cyclical fluctuations in size. Our model is applied to natural populations of Drosophila which show an annual demographic cycle of bottleneck (finite size) and demographic burst (size supposed to be infinite). In these populations, linkage disequilibrium stabilizes in such a way that, at equilibrium, the expected square of the correlation of gene frequencies E(r2) shows a stable cycle from year to year. If two loci are tightly linked, E(r2) barely varies during the annual cycle. Its values remain close to the value expected in a population of the same but constant effective size. If two loci are loosely linked, fluctuations in E(r2) are large. The maximum value, reached at the end of the bottleneck, is 10 to 100 times greater than the value obtained at the end of the burst. Our results show that the interpretation of observed linkage disequilibrium, by means of statistical tests, requires an accurate knowledge of population demography.

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Unckless, Robert L., und H. Allen Orr. „The Population Genetics of Adaptation: Multiple Substitutions on a Smooth Fitness Landscape“. Genetics 183, Nr. 3 (07.09.2009): 1079–86. http://dx.doi.org/10.1534/genetics.109.106757.

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Much recent work in the theoretical study of adaptation has focused on the so-called strong selection–weak mutation (SSWM) limit, wherein adaptation is due to new mutations of definite selective advantage. This work, in turn, has focused on the first step (substitution) during adaptive evolution. Here we extend this theory to allow multiple steps during adaptation. We find analytic solutions to the probability that adaptation follows a certain path during evolution as well as the probability that adaptation arrives at a given genotype regardless of the path taken. We also consider the probability of parallel adaptation and the proportion of the total increase in fitness caused by the first substitution. Our key assumption is that there is no epistasis among beneficial mutations.

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Joost, Stéphane, Séverine Vuilleumier, Jeffrey D. Jensen, Sean Schoville, Kevin Leempoel, Sylvie Stucki, Ivo Widmer, Christelle Melodelima, Jonathan Rolland und Stéphanie Manel. „Uncovering the genetic basis of adaptive change: on the intersection of landscape genomics and theoretical population genetics“. Molecular Ecology 22, Nr. 14 (04.06.2013): 3659–65. http://dx.doi.org/10.1111/mec.12352.

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44

Hill Jr., R. R., und J. H. Elgin Jr. „Analysis of pest resistance in alfalfa with a new autotetraploid genetic model“. Canadian Journal of Genetics and Cytology 27, Nr. 1 (01.02.1985): 39–46. http://dx.doi.org/10.1139/g85-008.

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A genetic model for the analysis of crosses and advanced generations between autotetraploid populations had been developed and applied to an analysis of pest resistance data in an experiment on alfalfa (Medicago sativa L.). The model had the form [Formula: see text] where [Formula: see text] is the observed mean of combination ij in generation n, C is a constant, u, is a parameter for the mean of parent population i, kn and mn are constants computed from the theoretical approach to equilibrium in the population, Gij is the digenic parameter in the equilibrium population that would arise from the population cross, and Qij is the quadrigenic parameter for that population. Nonadditive genetic effects were observed for most of the traits subjected to analysis under the model. The mode of gene action varied from one population to another in many cases. Variances of estimates of Gij were small, but those of Qij were very large. The large covariance between estimates of Gij and Qij was caused by a correlation between coefficients of these parameters.Key words: pest resistance, Medicago, autotetraploid, additive effects, population genetics.

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Tanaka, Mark M., Carl T. Bergstrom und Bruce R. Levin. „The Evolution of Mutator Genes in Bacterial Populations: The Roles of Environmental Change and Timing“. Genetics 164, Nr. 3 (01.07.2003): 843–54. http://dx.doi.org/10.1093/genetics/164.3.843.

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Abstract Recent studies have found high frequencies of bacteria with increased genomic rates of mutation in both clinical and laboratory populations. These observations may seem surprising in light of earlier experimental and theoretical studies. Mutator genes (genes that elevate the genomic mutation rate) are likely to induce deleterious mutations and thus suffer an indirect selective disadvantage; at the same time, bacteria carrying them can increase in frequency only by generating beneficial mutations at other loci. When clones carrying mutator genes are rare, however, these beneficial mutations are far more likely to arise in members of the much larger nonmutator population. How then can mutators become prevalent? To address this question, we develop a model of the population dynamics of bacteria confronted with ever-changing environments. Using analytical and simulation procedures, we explore the process by which initially rare mutator alleles can rise in frequency. We demonstrate that subsequent to a shift in environmental conditions, there will be relatively long periods of time during which the mutator subpopulation can produce a beneficial mutation before the ancestral subpopulations are eliminated. If the beneficial mutation arises early enough, the overall frequency of mutators will climb to a point higher than when the process began. The probability of producing a subsequent beneficial mutation will then also increase. In this manner, mutators can increase in frequency over successive selective sweeps. We discuss the implications and predictions of these theoretical results in relation to antibiotic resistance and the evolution of mutation rates.

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Liddell, Erin, Carly N. Cook und Paul Sunnucks. „Evaluating the use of risk assessment frameworks in the identification of population units for biodiversity conservation“. Wildlife Research 47, Nr. 3 (2020): 208. http://dx.doi.org/10.1071/wr18170.

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Abstract ContextManaging small, isolated populations requires conservation practitioners to weigh up the risks of inbreeding depression and outbreeding depression when assessing alternative management actions aimed at preventing species extinction. Accordingly, it is important that research intended to guide these management decisions provides the relevant evidence to inform them. AimsTo determine the extent to which studies that use genetic analyses to characterise population units for conservation consider the key theoretical concepts necessary for making sound management recommendations regarding the desirability of gene flow among units, notably the consequences and relative risks of inbreeding depression and outbreeding depression. MethodsA systematic search was conducted of peer-reviewed literature for studies that attempted to identify population units of threatened birds and mammals. Using content analysis, the theoretical framing of these studies was assessed, based on the discussion of key concepts concerning differences among populations. Key resultsThere has been a significant increase over time in the number of published studies that use genetics to identify population units for conservation. Many do not consider theoretical concepts relevant to the effective management of fragmented populations of threatened species. Mammals were more common than birds as focal species of studies, but the number of concepts used in the framing of the studies was similar for these two taxa, despite differences in their ecology and biology that might be expected to affect perceptions of distinctiveness. Nevertheless, species of greater conservation concern tended to have a slightly more comprehensive theoretical framing. ConclusionsThere is great potential for more studies to implement theoretical guidelines and practical decision support tools when considering the best course of action for identifying appropriate population units for conservation management. ImplicationsThe gap in the identified literature is likely to be impacting the ability of conservation practitioners to make evidence-informed decisions about how to manage the genetic health of threatened species; it would be valuable to improve this situation.

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DeWoody, J. Andrew, DeEtte Walker und John C. Avise. „Genetic Parentage in Large Half-Sib Clutches: Theoretical Estimates and Empirical Appraisals“. Genetics 154, Nr. 4 (01.04.2000): 1907–12. http://dx.doi.org/10.1093/genetics/154.4.1907.

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Abstract Nearly all of the 906 embryos from a male-tended nest of the sand goby (Pomatoschistus minutus) were genotyped at two hypervariable microsatellite loci to document conclusively the number of mothers and their relative genetic contributions to the nest. The true number of mothers determined by this nearly exhaustive genetic appraisal was compared to computer simulation treatments based on allele frequencies in the population, assumptions about reproductive skew, and statistical sampling strategies of progeny subsets. The “ground-truthed” appraisal and the theoretical estimates showed good agreement, indicating that for this nest a random sample of ~20 offspring would have sufficed for assessing the true number of biological parents (but not necessarily their relative genetic contributions). Also, a general dilocus matrix procedure is suggested for organizing and interpreting otherwise cumbersome data sets when extremely large numbers of full-sib and half-sib embryos from a nest are genotyped at two or more hypervariable loci.

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Cherry, Joshua L. „Selection, Subdivision and Extinction and Recolonization“. Genetics 166, Nr. 2 (01.02.2004): 1105–14. http://dx.doi.org/10.1093/genetics/166.2.1105.

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Abstract In a subdivided population, the interaction between natural selection and stochastic change in allele frequency is affected by the occurrence of local extinction and subsequent recolonization. The relative importance of selection can be diminished by this additional source of stochastic change in allele frequency. Results are presented for subdivided populations with extinction and recolonization where there is more than one founding allele after extinction, where these may tend to come from the same source deme, where the number of founding alleles is variable or the founders make unequal contributions, and where there is dominance for fitness or local frequency dependence. The behavior of a selected allele in a subdivided population is in all these situations approximately the same as that of an allele with different selection parameters in an unstructured population with a different size. The magnitude of the quantity Nese, which determines fixation probability in the case of genic selection, is always decreased by extinction and recolonization, so that deleterious alleles are more likely to fix and advantageous alleles less likely to do so. The importance of dominance or frequency dependence is also altered by extinction and recolonization. Computer simulations confirm that the theoretical predictions of both fixation probabilities and mean times to fixation are good approximations.

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Benson, John F., Peter J. Mahoney, Jeff A. Sikich, Laurel E. K. Serieys, John P. Pollinger, Holly B. Ernest und Seth P. D. Riley. „Interactions between demography, genetics, and landscape connectivity increase extinction probability for a small population of large carnivores in a major metropolitan area“. Proceedings of the Royal Society B: Biological Sciences 283, Nr. 1837 (31.08.2016): 20160957. http://dx.doi.org/10.1098/rspb.2016.0957.

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The extinction vortex is a theoretical model describing the process by which extinction risk is elevated in small, isolated populations owing to interactions between environmental, demographic, and genetic factors. However, empirical demonstrations of these interactions have been elusive. We modelled the dynamics of a small mountain lion population isolated by anthropogenic barriers in greater Los Angeles, California, to evaluate the influence of demographic, genetic, and landscape factors on extinction probability. The population exhibited strong survival and reproduction, and the model predicted stable median population growth and a 15% probability of extinction over 50 years in the absence of inbreeding depression. However, our model also predicted the population will lose 40–57% of its heterozygosity in 50 years. When we reduced demographic parameters proportional to reductions documented in another wild population of mountain lions that experienced inbreeding depression, extinction probability rose to 99.7%. Simulating greater landscape connectivity by increasing immigration to greater than or equal to one migrant per generation appears sufficient to largely maintain genetic diversity and reduce extinction probability. We provide empirical support for the central tenet of the extinction vortex as interactions between genetics and demography greatly increased extinction probability relative to the risk from demographic and environmental stochasticity alone. Our modelling approach realistically integrates demographic and genetic data to provide a comprehensive assessment of factors threatening small populations.

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Steiner, Margaret C., und John Novembre. „Population genetic models for the spatial spread of adaptive variants: A review in light of SARS-CoV-2 evolution“. PLOS Genetics 18, Nr. 9 (22.09.2022): e1010391. http://dx.doi.org/10.1371/journal.pgen.1010391.

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Theoretical population genetics has long studied the arrival and geographic spread of adaptive variants through the analysis of mathematical models of dispersal and natural selection. These models take on a renewed interest in the context of the COVID-19 pandemic, especially given the consequences that novel adaptive variants have had on the course of the pandemic as they have spread through global populations. Here, we review theoretical models for the spatial spread of adaptive variants and identify areas to be improved in future work, toward a better understanding of variants of concern in Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) evolution and other contemporary applications. As we describe, characteristics of pandemics such as COVID-19—such as the impact of long-distance travel patterns and the overdispersion of lineages due to superspreading events—suggest new directions for improving upon existing population genetic models.

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