scholarly journals Genetic variation in small multigene families

1981 ◽  
Vol 37 (2) ◽  
pp. 133-149 ◽  
Author(s):  
Tomoko Ohta
Keyword(s):  
Genetic Variation ◽  
Natural Selection ◽  
Globin Gene ◽  
Gene Organization ◽  
Crossing Over ◽  
Random Genetic Drift ◽  
Cycle Model ◽  
Unequal Crossing Over ◽  
Biological Phenomena ◽  
Chromosomal Recombination

SUMMARYIn order to understand the evolution of genetic systems in which two genes are tandemly repeated (small multigene family) such as has been recently found in the haemoglobin α loci of primates, haemoglobin β loci of mouse and rarbit and other proteins, a population genetics approach was used. Special reference was made to the probarility of gene identity (identity coefficient), when unequal crossing-over is continuously occurring as well as random genetic drift, inter-chromosomal recombination and mutation. Two models were studied, cycle and selection models. The former assumes that unequal crossing-over occurs in cycles of duplication and deletion, and that the equilibrium identity coefficients were obtained. The latter is based on more realistic biological phenomena, and in this model it is assumed that natural selection is responsible for eliminating chromosomes with extra or deficient gene dose. Unequal crossing-over, inter-chromosomal recombination and natural selection lead to a duplication-deletion balance, which can then be treated as though it were a cycle model. The basic parameter is the rate of duplication-deletion which is shown to be approximately equal to 2(u + 2β)X, where u is the unequal crossing-over rate, 2β is the inter-chromosomal recombination rate and X is the frequency of chromosomes with three genes or of that with one gene. Genetic variation of the globin gene family, of which gene organization is known in most detail, is discussed in the light of the present analyses.

scholarly journals UNEQUAL CROSSING OVER AT THE rRNA TANDON AS A SOURCE OF QUANTITATIVE GENETIC VARIATION IN DROSOPHILA

Genetics ◽  
1980 ◽  
Vol 95 (3) ◽  
pp. 727-742 ◽  
Author(s):  
R Frankham ◽  
D A Briscoe ◽  
R K Nurthen
Keyword(s):  
Genetic Variation ◽  
Selection Response ◽  
Crossing Over ◽  
Wild Type ◽  
X Chromosomes ◽  
Unequal Crossing Over ◽  
Quantitative Genetic ◽  
Y Chromosomes ◽  
Homozygous Line ◽  
Minimum Estimate

ABSTRACT Abdominal bristle selection lines (three high and three low) and controls were founded from a marked homozygous line to measure the contribution of sex-linked "mutations" to selection response. Two of the low lines exhibited a period of rapid response to selection in females, but not in males. There were corresponding changes in female variance, in heritabilities in females, in the sex ratio (a deficiency of females) and in fitness, as well as the appearance of a mutant phenotype in females of one line. All of these changes were due to bb alleles (partial deficiencies for the rRNA tandon) in the X chromosomes of these lines, while the Y chromosomes remained wild-type bb+. We argue that the bb alleles arose by unequal crossing over in the rRNA tandon.—A prediction of this hypothesis is that further changes can occur in the rRNA tandon as selection is continued. This has now been shown to occur.—Our minimum estimate of the rate of occurrence of changes at the rRNA tandon is 3 × 10-4. As this is substantially higher than conventional mutation rates, the questions of the mechanisms and rates of origin of new quantitative genetic variation require careful re-examination.

scholarly journals Possible role of natural selection in the formation of tandem-repetitive noncoding DNA.

Genetics ◽  
1994 ◽  
Vol 136 (1) ◽  
pp. 333-341
Author(s):  
W Stephan ◽  
S Cho
Keyword(s):  
Natural Selection ◽  
Satellite Dna ◽  
Repeat Length ◽  
Crossing Over ◽  
Recombination Rates ◽  
Noncoding Dna ◽  
Satellite Dnas ◽  
Unequal Crossing Over ◽  
Wide Range ◽  
Long Range Ordering

Abstract A simulation model of sequence-dependent amplification, unequal crossing over and mutation is analyzed. This model predicts the spontaneous formation of tandem-repetitive patterns of noncoding DNA from arbitrary sequences for a wide range of parameter values. Natural selection is found to play an essential role in this self-organizing process. Natural selection which is modeled as a mechanism for controlling the length of a nucleotide string but not the sequence itself favors the formation of tandem-repetitive structures. Two measures of sequence heterogeneity, inter-repeat variability and repeat length, are analyzed in detail. For fixed mutation rate, both inter-repeat variability and repeat length are found to increase with decreasing rates of (unequal) crossing over. The results are compared with data on micro-, mini- and satellite DNAs. The properties of minisatellites and satellite DNAs resemble the simulated structures very closely. This suggests that unequal crossing over is a dominant long-range ordering force which keeps these arrays homogeneous even in regions of very low recombination rates, such as at satellite DNA loci. Our analysis also indicates that in regions of low rates of (unequal) crossing over, inter-repeat variability is maintained at a low level at the expense of much larger repeat units (multimeric repeats), which are characteristic of satellite DNA. In contrast, the microsatellite data do not fit the proposed model well, suggesting that unequal crossing over does not act on these very short tandem arrays.

scholarly journals FURTHER STUDY ON THE GENETIC CORRELATION BETWEEN MEMBERS OF A MULTIGENE FAMILY

Genetics ◽  
1981 ◽  
Vol 99 (3-4) ◽  
pp. 555-571
Author(s):  
Tomoko Ohta
Keyword(s):  
Natural Selection ◽  
Family Size ◽  
Multigene Family ◽  
Crossing Over ◽  
Total Size ◽  
Small Shift ◽  
Unequal Crossing Over ◽  
The Family ◽  
Number Of Genes ◽  
The Mean

ABSTRACT The extent of genetic similarity (in terms of identity coefficients) was investigated among members of a multigene family that is evolving under mutation, unequal crossing over and random genetic drift. The method of KIMURA and OHTA (1979) was used, but the possibility was incorporated that the length of the shift (in terms of the number of genes) involved in unequal crossing over can be more than one gene unit. Extensive numerical analyses show that, at equilibrium, the identity coefficients between two gene members are practically independent of their distance apart on the chromosome when the mean length of the shift at unequal crossing over is more than 10% of the total size of the family. In that case, the approximate treatment by OHTA (1980) is shown to be valid, but when the mean length of the shift is less than IO%, the average identity coefficient at equilibrium is underestimated. In order to clarify the effect of natural selection responsible for keeping the family size stable, Monte Carlo simulation studies were performed. The results indicate that the identity coefficients are not greatly influenced by natural selection on gene family size, particularly when the number of genes shifted is small compared to the family size. In addition, with sufficiently strongselection on family size, unequal crossovers with a large shift (such as with maximum shift of 90% of the family size) become ineffective and almost indisdnguishable from those with a small shift.

scholarly journals Homology requirements for unequal crossing over in humans.

Genetics ◽  
1991 ◽  
Vol 128 (1) ◽  
pp. 143-161 ◽  
Author(s):  
A B Metzenberg ◽  
G Wurzer ◽  
T H Huisman ◽  
O Smithies
Keyword(s):  
Homologous Recombination ◽  
Gene Cluster ◽  
Fusion Gene ◽  
Globin Gene ◽  
Crossing Over ◽  
Beta Globin ◽  
Unequal Crossover ◽  
Unequal Crossing Over ◽  
Beta Globin Gene

Abstract To gain insight into mechanisms of unequal homologous recombination in vivo, genes generated by homologous unequal crossovers in the human beta-globin gene cluster were examined by nucleotide sequencing and hybridization experiments. The naturally occurring genes studied included one delta-beta Lepore-Baltimore fusion gene, one delta-beta Lepore-Hollandia fusion gene, 12 delta-beta Lepore-Boston genes, one A gamma-beta fusion Kenya gene, one A gamma-G gamma fusion (the central gene of a triplication) and one G gamma-A gamma fusion. A comparison of the nucleotide sequences of three Lepore-Boston genes indicates that they were derived from at least two independent homologous but unequal crossover events, although the crossovers occurred within the same 58-bp region. Nine additional Lepore-Boston genes from individuals of various ethnic origins were shown, by hybridization to specific oligonucleotide probes, to have been generated by a crossover in the same region as the sequenced genes. Evidence for gene conversion accompanying a homologous unequal crossover event was found in only one case (although some of the single nucleotide differences observed in other genes in this study may be related to the crossover events in ways that we do not presently understand). Thus, as judged by this limited sample, concurrent gene conversions are not commonly associated with homologous but unequal exchange in humans in vivo. Classification of the recombinant chromosomes by their polymorphic restriction sites in the beta-globin gene cluster indicated that the Lepore-Boston genes are found in at least six different haplotype backgrounds. Therefore the total number of independent examples in this study is at least 6, and at most 12. We have shown that in at least six cases of genes that have arisen by homologous but unequal crossing over in vivo, each event occurred in a relatively extensive region of uninterrupted identity between the parental genes. This preference cannot be explained by a mechanism whereby crossovers occur at random within misaligned related but not identical genes. In general, crossovers occur in regions that are among the largest available stretches of identity for a particular pair of mismatched genes. Our data are in agreement with those of other types of studies of homologous recombination, and support the idea that sequence identity, rather than general homology, is a critical factor in homologous recombination.

scholarly journals The Population Genetics of Ploidy Change in Fungi

2020 ◽  
Author(s):  
Aleeza C. Gerstein ◽  
Nathaniel Sharp
Keyword(s):  
Population Genetics ◽  
Genetic Variation ◽  
Natural Selection ◽  
Genetic Variants ◽  
Natural Populations ◽  
Theoretical Work ◽  
Fungal Species ◽  
Random Genetic Drift ◽  
Lab Experiments ◽  
History Of

Ploidy is a significant type of genetic variation, describing the number of chromosome sets per cell. Ploidy evolves in natural populations, clinical populations, and lab experiments, particularly in fungi. Despite a long history of theoretical work on this topic, predicting how ploidy will evolve has proven difficult, as it is often unclear why one ploidy state outperforms another. Here, we review what is known about contemporary ploidy evolution in diverse fungal species through the lens of population genetics. As with typical genetic variants, ploidy evolution depends on the rate that new ploidy states arise by mutation, natural selection on alternative ploidy states, and random genetic drift. However, ploidy variation also has unique impacts on evolution, with the potential to alter chromosomal stability, the rate and patterns of point mutation, and the nature of selection on all loci in the genome. We discuss how ploidy evolution depends on these general and unique factors and highlight areas where additional experimental evidence is required to comprehensively explain the ploidy transitions observed in the field and the lab.

scholarly journals Simulating Evolution by Gene Duplication

Genetics ◽  
1987 ◽  
Vol 115 (1) ◽  
pp. 207-213 ◽  
Author(s):  
Tomoko Ohta
Keyword(s):  
Natural Selection ◽  
Single Gene ◽  
Genetic Load ◽  
Gene Families ◽  
Functional Gene ◽  
Gene Copy ◽  
Crossing Over ◽  
Random Drift ◽  
Unequal Crossing Over ◽  
New Gene

ABSTRACT By considering the recent finding that unequal crossing over and other molecular interactions are contributing to the evolution of multigene families, a model of the origin of repetitive genes was studied by Monte Carlo simulations. Starting from a single gene copy, how genetic systems evolve was examined under unequal crossing over, random drift and natural selection. Both beneficial and deteriorating mutations were incorporated, and the latter were assumed to occur ten times more frequently than the former. Positive natural selection favors those chromosomes with more beneficial mutations in redundant copies than others in the population, but accumulation of deteriorating mutations (pseudogenes) have no effect on fitness so long as there remains a functional gene. The results imply the following: (1) Positive natural selection is needed in order to acquire gene families with new functions. Without it, too many pseudogenes accumulate before attaining a functional gene family. (2) There is a large fluctuation in the outcome even if parameters are the same. (3) When unequal crossing over occurs more frequently, the system evolves more rapidly. It was also shown, under realistic values of parameters, that the genetic load for acquiring a new gene is not as large as J. B. S. Haldane suggested, but not so small as in a model in which a system for selection started from already redundant genes.

Biased gene conversion is not occurring among rDNA repeats in the Brassica triangle

Genome ◽  
1996 ◽  
Vol 39 (1) ◽  
pp. 150-154 ◽  
Author(s):  
Elizabeth R. Waters ◽  
Barbara A. Schaal
Keyword(s):  
Genetic Variation ◽  
Key Words ◽  
Gene Conversion ◽  
Relative Frequency ◽  
Brassica Species ◽  
Multigene Families ◽  
Crossing Over ◽  
Common Phenomenon ◽  
Unequal Crossing Over ◽  
Biased Gene Conversion

Hybridization is a common phenomenon that results in complex genomes. How ancestral genomes interact in hybrids has long been of great interest. Recombination among ancestral genomes may increase or decrease genetic variation. This study examines rDNA from members of the Brassica triangle for evidence of gene conversion across ancestral genomes. Gene conversion is a powerful force in the evolution of multigene families. It has previously been shown that biased gene conversion can act to homogenize rDNA repeats within hybrid genomes. Here, we find no evidence for biased gene conversion or unequal crossing over across ancestral genomes in allotetraploid Brassica species. We suggest that, while basic genomic processes are shared by all organisms, the relative frequency of these processes and their evolutionary importance may differ among lineages. Key words : Brassica, rDNA, gene conversion, allotetraploids.

Unequal crossing over at the rRNA locus as a source of quantitative genetic variation

Nature ◽  
1978 ◽  
Vol 272 (5648) ◽  
pp. 80-81 ◽  
Author(s):  
R. FRANKHAM ◽  
D. A. BRISCOE ◽  
R. K. NURTHEN
Keyword(s):  
Genetic Variation ◽  
Crossing Over ◽  
Unequal Crossing Over ◽  
Quantitative Genetic

The population genetics of ploidy change in unicellular fungi

2021 ◽  
Author(s):  
Aleeza C Gerstein ◽  
Nathaniel P Sharp
Keyword(s):  
Population Genetics ◽  
Genetic Variation ◽  
Natural Selection ◽  
Genetic Variants ◽  
Natural Populations ◽  
Theoretical Work ◽  
Fungal Species ◽  
Random Genetic Drift ◽  
Lab Experiments ◽  
History Of

Abstract Changes in ploidy are a significant type of genetic variation, describing the number of chromosome sets per cell. Ploidy evolves in natural populations, clinical populations, and lab experiments, particularly in fungi. Despite a long history of theoretical work on this topic, predicting how ploidy will evolve has proven difficult, as it is often unclear why one ploidy state outperforms another. Here, we review what is known about contemporary ploidy evolution in diverse fungal species through the lens of population genetics. As with typical genetic variants, ploidy evolution depends on the rate that new ploidy states arise by mutation, natural selection on alternative ploidy states, and random genetic drift. However, ploidy variation also has unique impacts on evolution, with the potential to alter chromosomal stability, the rate and patterns of point mutation, and the nature of selection on all loci in the genome. We discuss how ploidy evolution depends on these general and unique factors and highlight areas where additional experimental evidence is required to comprehensively explain the ploidy transitions observed in the field and the lab.

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