scholarly journals Disruption of genetic identity for genebank maize accessions during conservation

Genetika ◽  
2017 ◽  
Vol 49 (3) ◽  
pp. 853-864
Author(s):  
Vojka Babic ◽  
Violeta Andjelkovic ◽  
Ana Nikolic ◽  
Marija Milivojevic ◽  
Jelena Srdic ◽  
...  
Keyword(s):  
Genetic Drift ◽  
Seed Viability ◽  
Random Genetic Drift ◽  
Effective Population ◽  
Medium Term ◽  
Viability Kernel ◽  
Maize Landraces ◽  
Identity Disruption ◽  
Maize Research Institute ◽  
Kernel Type

Maintenance of the original accessions identity and integrity is one of the priorities among genebank activities. Different factors related to conservation may result in accessions disruption. Regeneration is the most frequent critical point in this process, due to bottlenecks, inbreeding, random genetic drift and unintentional mixing or contamination. On the other hand, genetic drift may occur due to seed viability loss. Therefore, it is very important to establish the balance between the frequency of regeneration and the duration of accession conservation. The aim of the present study was to estimate whether the identity of accessions regenerated after 27 years of medium-term conservation was disrupted. Phenotypic markers were applied on three Maize Research Institute ?Zemun Polje? (MRIZP) genebank maize landraces (K2026, K768 and K86), differing in seed viability, kernel type and effective population size. It was estimated that, after the regeneration, there had been no significant changes in the landrace K2026. There were some parameters indicating that genetic drift had occurred in the landrace K768, and that there had been even a certain degree of inbreeding in the landrace K86. According to the results, accession K2026 could still be kept under the same ID number. Due to the genuine identity disruption, assignment of new ID numbers for K768 and K86 should be suggested.

Analysis of genetic diversity in four Canadian swine breeds using pedigree data

2010 ◽  
Vol 90 (3) ◽  
pp. 331-340 ◽  
Author(s):  
M G Melka ◽  
F. Schenkel
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Effective Population Size ◽  
Genetic Drift ◽  
Relative Proportion ◽  
Random Genetic Drift ◽  
Pedigree Data ◽  
Effective Population ◽  
Animal Genetic Resources ◽  
Loss Of Genetic Diversity

Conservation of animal genetic resources entails judicious assessment of genetic diversity as a first step. The objective of this study was to analyze the trend of within-breed genetic diversity and identify major causes of loss of genetic diversity in four swine breeds based on pedigree data. Pedigree files from Duroc (DC), Hampshire (HP), Lacombe (LC) and Landrace (LR) containing 480 191, 114 871, 51 397 and 1 080 144 records, respectively, were analyzed. Pedigree completeness, quality and depth were determined. Several parameters derived from the in-depth pedigree analyses were used to measure trends and current levels of genetic diversity. Pedigree completeness indexes of the four breeds were 90.4, 52.7, 89.6 and 96.1%, respectively. The estimated percentage of genetic diversity lost within each breed over the last three decades was approximately 3, 22, 12 and 2%, respectively. The relative proportion of genetic diversity lost due to random genetic drift in DC, HP, LC and LR was 74.5, 63.6, 72.9 and 60.0%, respectively. The estimated current effective population size for DC, HP, LC and LR was 72, 14, 36 and 125, respectively. Therefore, HP and LC have been found to have lost considerable genetic diversity, demanding priority for conservation. Key words: Genetic drift, effective population size

scholarly journals Genetic differentiation of quantitative characters between populations or species: I. Mutation and random genetic drift

1982 ◽  
Vol 39 (3) ◽  
pp. 303-314 ◽  
Author(s):  
Ranajit Chakraborty ◽  
Masatoshi Nei
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Genetic Drift ◽  
Genetic Variance ◽  
Genetic Model ◽  
Neutral Evolution ◽  
Random Genetic Drift ◽  
Effective Population ◽  
Quantitative Characters ◽  
Allelic State

SummaryIntroducing a new genetic model called the discrete allelic-state model, the evolutionary change of genetic variation of quantitative characters within and between populations is studied under the assumption of no selection. This model allows us to study the effects of mutation and random genetic drift in detail. It is shown that when the allelic effects on phenotype are additive, the rate of approach of the genetic variance within populations to the equilibrium value depends only on the effective population size. It is also shown that the distribution of genotypic value often deviates from normality particularly when the effective population size and the number of loci concerned are small. On the other hand, the interpopulational variance increases linearly with time, if the intrapopu-lational variance remains constant. Therefore, the ratio of interpopulational variance to intrapopulational variance can be used for testing the hypothesis of neutral evolution of quantitative characters.

scholarly journals Estimation of the Effective Number of Founders That Initiate an Infection after Aphid Transmission of a Multipartite Plant Virus

2008 ◽  
Vol 82 (24) ◽  
pp. 12416-12421 ◽  
Author(s):  
Mónica Betancourt ◽  
Alberto Fereres ◽  
Aurora Fraile ◽  
Fernando García-Arenal
Keyword(s):  
Genetic Drift ◽  
Rna Virus ◽  
Horizontal Transmission ◽  
Aphis Gossypii ◽  
Virus Evolution ◽  
Population Bottlenecks ◽  
Random Genetic Drift ◽  
Effective Number ◽  
Effective Population ◽  
Deterministic Models

ABSTRACT The fecundity of RNA viruses can be very high. Thus, it is often assumed that viruses have large populations, and RNA virus evolution has been mostly explained using purely deterministic models. However, population bottlenecks during the virus life cycle could result in effective population numbers being much smaller than reported censuses, and random genetic drift could be important in virus evolution. A step at which population bottlenecks may be severe is host-to-host transmission. We report here an estimate of the size of the population that starts a new infection when Cucumber mosaic virus (CMV) is transmitted by the aphid Aphis gossypii, based on the segregation of two CMV genotypes in plants infected by aphids that acquired the virus from plants infected by both genotypes. Results show very small effective numbers of founders, between one and two, both in experiments in which the three-partite genome of CMV was aphid transmitted and in experiments in which a fourth RNA, CMV satellite RNA, was also transmitted. These numbers are very similar to those published for Potato virus Y, which has a monopartite genome and is transmitted by aphids according to a different mechanism than CMV. Thus, the number of genomic segments seems not to be a major determinant of the effective number of founders. Also, our results suggest that the occurrence of severe bottlenecks during horizontal transmission is general for viruses nonpersistently transmitted by aphids, indicating that random genetic drift should be considered when modeling virus evolution.

scholarly journals Linkage disequilibrium due to random genetic drift

1969 ◽  
Vol 13 (1) ◽  
pp. 47-55 ◽  
Author(s):  
Tomoko Ohta ◽  
Motoo Kimura
Keyword(s):  
Stochastic Process ◽  
Linkage Disequilibrium ◽  
Genetic Drift ◽  
Recombination Fraction ◽  
Random Genetic Drift ◽  
Effective Population ◽  
Finite Populations ◽  
Population Number ◽  
Backward Equation ◽  
Expected Values

The behaviour of linkage disequilibrium between two segregating loci in finite populations has been studied as a continuous stochastic process for different intensity of linkage, assuming no selection. By the method of the Kolmogorov backward equation, the expected values of the square of linkage disequilibrium z2, and other two quantities, xy(1 − x) (1 − y) and z(1 − 2x) (1 − 2y), were obtained in terms of T, the time measured in Ne as unit, and R, the product of recombination fraction (c) and effective population number (Ne). The rate of decrease of the simultaneous heterozygosity at two loci and also the asymptotic rate of decrease of the probability for the coexistence of four gamete types within a population were determined. The eigenvalues λ1, λ2 and λ3 related to the stochastic process are tabulated for various values of R = Nec.

scholarly journals Unexpectedly high mutation rate of a deep-sea hyperthermophilic anaerobic archaeon

2020 ◽  
Author(s):  
Jiahao Gu ◽  
Xiaojun Wang ◽  
Xiaopan Ma ◽  
Ying Sun ◽  
Xiang Xiao ◽  
...  
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Genome Size ◽  
Mutation Rate ◽  
Genetic Drift ◽  
Deep Sea ◽  
High Mutation Rate ◽  
Random Genetic Drift ◽  
Effective Population ◽  
Free Living

AbstractDeep-sea hydrothermal vents resemble the early Earth, and thus the dominant Thermococcaceae inhabitants, which occupy an evolutionarily basal position of the archaeal tree and take an obligate anaerobic hyperthermophilic free-living lifestyle, are likely excellent models to study the evolution of early life. Here, we determined that unbiased mutation rate of a representative species, Thermococcus eurythermalis, exceeded that of all known free-living prokaryotes by 1-2 orders of magnitude, and thus rejected the long-standing hypothesis that low mutation rates were selectively favored in hyperthermophiles. We further sequenced multiple and diverse isolates of this species and calculated that T. eurythermalis has a lower effective population size than other free-living prokaryotes by 1-2 orders of magnitude. These data collectively indicate that the high mutation rate of this species is not selectively favored but instead driven by random genetic drift. The availability of these unusual data also helps explore mechanisms underlying microbial genome size evolution. We showed that genome size is negatively correlated with mutation rate and positively correlated with effective population size across 30 bacterial and archaeal lineages, suggesting that increased mutation rate and random genetic drift are likely two important mechanisms driving microbial genome reduction. Future determinations of the unbiased mutation rate of more representative lineages with highly reduced genomes such as Prochlorococcus and Pelagibacterales that dominate marine microbial communities are essential to test these hypotheses.

CYTO-NUCLEAR EPISTASIS: TWO-LOCUS RANDOM GENETIC DRIFT IN HERMAPHRODITIC AND DIOECIOUS SPECIES

Evolution ◽  
2006 ◽  
Vol 60 (4) ◽  
pp. 643 ◽  
Author(s):  
Michael J. Wade ◽  
Charles J. Goodnight
Keyword(s):  
Genetic Drift ◽  
Random Genetic Drift ◽  
Dioecious Species

scholarly journals Influence of Random Genetic Drift on Human Immunodeficiency Virus Type 1envEvolution During Chronic Infection

Genetics ◽  
2004 ◽  
Vol 166 (3) ◽  
pp. 1155-1164 ◽  
Author(s):  
Daniel Shriner ◽  
Raj Shankarappa ◽  
Mark A. Jensen ◽  
David C. Nickle ◽  
John E. Mittler ◽  
...  
Keyword(s):  
Human Immunodeficiency Virus ◽  
Human Immunodeficiency Virus Type ◽  
Virus Type ◽  
Genetic Drift ◽  
Chronic Infection ◽  
Random Genetic Drift ◽  
Immunodeficiency Virus

scholarly journals A General Solution of the Wright–Fisher Model of Random Genetic Drift

2016 ◽  
Vol 27 (4) ◽  
pp. 467-492 ◽  
Author(s):  
Tat Dat Tran ◽  
Julian Hofrichter ◽  
Jürgen Jost
Keyword(s):  
General Solution ◽  
Genetic Drift ◽  
Random Genetic Drift ◽  
Fisher Model

scholarly journals GENETIC VARIABILITY MAINTAINED BY MUTATION AND OVERDOMINANT SELECTION IN FINITE POPULATIONS

Genetics ◽  
1981 ◽  
Vol 98 (2) ◽  
pp. 441-459 ◽  
Author(s):  
Takeo Maruyama ◽  
Masatoshi Nei
Keyword(s):  
Mutation Rate ◽  
Allozyme Polymorphism ◽  
Random Genetic Drift ◽  
Effective Population ◽  
Mathematical Properties ◽  
Overdominant Selection ◽  
Mean And Variance ◽  
The Mean ◽  
Neutral Mutations ◽  
The Relationship

ABSTRACT Mathematical properties of the overdominance model with mutation and random genetic drift are studied by using the method of stochastic differential equations (Itô and McKean 1974). It is shown that overdominant selection is very powerful in increasing the mean heterozygosity as compared with neutral mutations, and if 2Ns (N = effective population size; s = selective disadvantage for homozygotes) is larger than 10, a very low mutation rate is sufficient to explain the observed level of allozyme polymorphism. The distribution of heterozygosity for overdominant genes is considerably different from that of neutral mutations, and if the ratio of selection coefficient (s) to mutation rate (ν) is large and the mean heterozygosity (h) is lower than 0.2, single-locus heterozygosity is either approximately 0 or 0.5. If h increases further, however, heterozygosity shows a multiple-peak distribution. Reflecting this type of distribution, the relationship between the mean and variance of heterozygosity is considerably different from that for neutral genes. When s/v is large, the proportion of polymorphic loci increases approximately linearly with mean heterozygosity. The distribution of allele frequencies is also drastically different from that of neutral genes, and generally shows a peak at the intermediate gene frequency. Implications of these results on the maintenance of allozyme polymorphism are discussed.

scholarly journals Evolution of gene regulatory networks by means of selection and random genetic drift

2018 ◽  
Author(s):  
Antonios Kioukis ◽  
Pavlos Pavlidis
Keyword(s):  
Natural Selection ◽  
Positive Selection ◽  
Genetic Drift ◽  
Regulatory Networks ◽  
Fitness Landscape ◽  
Random Genetic Drift ◽  
Maturation Period ◽  
Evolutionary Forces ◽  
Gene Regulatory

The evolution of a population by means of genetic drift and natural selection operating on a gene regulatory network (GRN) of an individual has not been scrutinized in depth. Thus, the relative importance of various evolutionary forces and processes on shaping genetic variability in GRNs is understudied. Furthermore, it is not known if existing tools that identify recent and strong positive selection from genomic sequences, in simple models of evolution, can detect recent positive selection when it operates on GRNs. Here, we propose a simulation framework, called EvoNET, that simulates forward-in-time the evolution of GRNs in a population. Since the population size is finite, random genetic drift is explicitly applied. The fitness of a mutation is not constant, but we evaluate the fitness of each individual by measuring its genetic distance from an optimal genotype. Mutations and recombination may take place from generation to generation, modifying the genotypic composition of the population. Each individual goes through a maturation period, where its GRN reaches equilibrium. At the next step, individuals compete to produce the next generation. As time progresses, the beneficial genotypes push the population higher in the fitness landscape. We examine properties of the GRN evolution such as robustness against the deleterious effect of mutations and the role of genetic drift. We confirm classical results from Andreas Wagner’s work that GRNs show robustness against mutations and we provide new results regarding the interplay between random genetic drift and natural selection.

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