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C W Birky

Publications and source records attributed to C W Birky.

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Biased gene conversion, copy number, and apparent mutation rate differences within chloroplast and bacterial genomes.

We investigate the possibility that differences between synonymous substitution rates of organelle and bacterial genes differing only in copy number may be due to conversion bias. We find that the rather large observed difference in the synonymous rates between genes in the single copy and inverted-repeat regions of chloroplasts can be accounted for by a very small bias against new mutants. More generally, differences in the within-organelle fixation probability result in different apparent mutation rates as measured by the expected rate of appearance of cells homoplasmic for new mutants. Thus, differences in intracellular population parameters rather than molecular mechanisms can account for some variation in the apparent mutation rates of organelle genes, and possibly in other systems with variable numbers of gene copies. On the other hand, our analysis suggests that conversion bias is not a likely explanation for relatively low mutation rates observed near the replication origin of bacterial chromosomes.

Chloroplasts

Organelle gene diversity under migration, mutation, and drift: equilibrium expectations, approach to equilibrium, effects of heteroplasmic cells, and comparison to nuclear genes.

We developed stochastic population genetic theory for mitochondrial and chloroplast genes, using an infinite alleles model appropriate for molecular genetic data. We considered the effects of mutation, random drift, and migration in a finite island model on selectively neutral alleles. Recurrence equations were obtained for the expectation of gene diversities within zygotes, within colonies, and between colonies. The variables are number and sizes of colonies, migration rates, sex ratios, degree of paternal transmission, number of germ line cell divisions, effective number of segregating organelle genomes, and mutation rate. Computer solutions of the recurrence equations were used to study the approach to equilibrium. Gene diversities equilibrate slowly, while GST, used to measure population subdivision, equilibrates rapidly. Approximate equilibrium equations for gene diversities and GST can be obtained by substituting Neo and me, simple functions of the numbers of breeding or migrating males and females and of the degree of paternal transmission, for the effective numbers of genes and migration rates in the corresponding equations for nuclear genes. The approximate equations are not valid when the diversity within individuals is large compared to that between individuals, as is often true for the D-loop of animal mtDNA. We used the exact equations to verify that organelle genes often show more subdivision than nuclear genes; however, we also identified the range of breeding and migrating sex ratios for which population subdivision is greater for nuclear genes. Finally, we show that gene diversities are higher for nuclei than for organelles over a larger range of sex ratios in a subdivided population than in a panmictic population.

Alleles

Organelle evolution.

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Animal Population Groups

Effects of linkage on rates of molecular evolution.

When an advantageous mutation is fixed in a population by selection, a closely linked selectively neutral or mildly detrimental mutation may "hitchhike" to fixation along with it. It has been suggested that hitchhiking might increase the rate of molecular evolution. Computer simulations and a mathematical argument show that complete linkage to either advantageous or deleterious mutations does not affect the substitution of selectively neutral mutations. However, the simulations show that linkage to selected background mutations decreases the rate of fixation of advantageous mutations and increases the rate of fixation of detrimental mutations. This is true whether the linked background mutations are advantageous or detrimental, and it verifies and extends previous observations that linkage tends to reduce the effects of selection on evolution. These results can be interpreted in terms of the Hill-Robertson effect: a locus linked to another locus under selection experiences a reduction in effective population size. The interpretation of differences in evolutionary rates between different genomes or different regions of a genome may be confounded by the effects of strong linkage and selection. Recombination is expected to reduce the overall rate of molecular evolution while enhancing the rate of adaptive evolution.

Biological Evolution

Chloroplast DNA diversity is low in a wild plant, Lupinus texensis.

Chloroplast DNA diversity was measured in an annual flowering plant, Lupinus texensis. Individual plants were collected from 21 local populations throughout the range of the species in Texas. Chloroplast DNA was isolated separately from each plant and digested with seven restriction enzymes. The most common form of the 150-kilobase-pair genome was cut at 134 sites, so that about 0.5% of the base pairs in the genome were sampled. Of the 100 plants examined, 88 had identical restriction fragment patterns. Three variant forms were found in different local populations. Two, represented in single plants, differed from wild type in the presence or absence of single restriction sites. The third variant was fixed in one of the local populations; it had lost a restriction site and also had a deletion of approximately equal to 100 base pairs. The data suggest that chloroplast DNA in this plant is much less polymorphic than mitochondrial DNA from animals and is probably less polymorphic than nuclear genes in the same plant or in animals.

Biological Evolution

The non-reciprocality of organelle gene recombination in Chlamydomonas reinhardtii and Saccharomyces cerevisiae: some new observations and a restatement of some old problems.

Organelle recombinant genotype frequencies, derived from analysis of individual mitotic zygote clones of Chlamydomonas reinhardtii and Saccharomyces cerevisiae, were subjected to two types of statistical tests in an attempt to detect the occurrence of reciprocal recombination: (i) calculation of correlation coefficients for the frequencies of two recombinant genotypes (reciprocal or non-reciprocal pairs) within individual zygote clones, and (ii) application of the chi-square test for independence to the frequencies of zygotes yielding one or the other, neither, or both of a given recombinant pair. Applying test (i), the strongest correlations are found for non-reciprocal rather than reciprocal pairs. When the data are analyzed by method (ii), some reciprocal as well as non-reciprocal pairs appear to be produced concurrently in zygote clones. However, such deviations from independence are greatest for non-reciprocal pairs. These tests yield comparable results for yeast mitochondrial and Chlamydomonas chloroplast gene recombination, and provide no convincing evidence for reciprocal genetic exchange. Explanations for the observed lack of reciprocality are discussed with reference both to our present understanding of the molecular events responsible for genetic recombination, and to the problems which may be unique to the analysis of organelle gene recombination.

Chlamydomonas

Uniparental inheritance of mitochondrial genes in yeast: dependence on input bias of mitochondrial DNA and preliminary investigations of the mechanism.

In Saccharomyces cerevisiae, previous studies on the inheritance of mitochondrial genes controlling antibiotic resistance have shown that some crosses produce a substantial number of uniparental zygotes, which transmit to their diploid progeny mitochondrial alleles from only one parent. In this paper, we show that uniparental zygotes are formed especially when one parent (majority parent) contributes substantially more mitochondrial DNA molecules to the zygote than does the other (minority) parent. Cellular contents of mitochondrial DNA (mtDNA) are increased in these experiments by treatment with cycloheximide, alpha-factor, or the uvsp5 nuclear mutation. In such a biased cross, some zygotes are uniparental for mitochondrial alleles from the majority parent, and the frequency of such zygotes increases with increasing bias. In two- and three-factor crosses the cap1, ery1, and oli1 loci behave coordinately, rather than independently; minority markers tend to be transmitted or lost as a unit, suggesting that the uniparental mechanism acts on entire mtDNA molecules rather than on individual loci. This rules out the possibility that uniparental inheritance can be explained by the conversion of minority markers to the majority alleles during recombination. Exceptions to the coordinate behavior of different loci can be explained by marker rescue via recombination. Uniparental inheritance is largely independent of the position of buds on the zygote. We conclude that it is due to the failure of minority markers to replicate in some zygotes, possibly involving the rapid enzymatic destruction of such markers. We have considered two general classes of mechanisms: (1) random selection of molecules for replication, as for example by competition for replicating sites on a membrane; and (2) differential marking of mtDNA molecules in the two parents, possibly by modification enzymes, followed by a mechanism that "counts" molecules and replicates only the majority type. These classes of models are distinguished genetically by the fact that the first predicts that the output frequency of a given allele among the progeny of a large number of zygotes will approximately equal the average input frequency of that allele, while the second class predicts that any input bias will be amplified in the output. The data suggest that bias amplification does occur. We hypothesize that maternal inheritance of mitochondrial or chloroplast genes in many organisms may depend upon a biased input of organelle DNA molecules, which usually favors the maternal parent, followed by failure of the minority (paternal) molecules to replicate in many or all zygotes.

Alleles

Zygote heterogeneity and uniparental inheritance of mitochondrial genes in yeast.

A number of different crosses between strains of Saccharomyces cerevisiae differing in mitochondrial genotype are analyzed with respect to the extent to which individual zygotes transmit mitochondrial genes from one parent or the other. Many crosses produce two or more distinct classes of zygotes in this respect. Some crosses produce a high frequency of uniparental zygotes, which transmit mitochondrial genes exclusively or nearly so from one parent. Such zygotes cannot be accounted for in terms of an unequal input of mitochondrial DNA molecules from the two parents; they indicate that mitochondrial DNA from one parent is selectively replicated, or mitochondrial DNA from the other parent is selectively destroyed, in the zygote. Multiple zygote classes, and uniparental zygotes, are seen in studies of mitochondrial and chloroplast inheritance in other organisms, and may have a common explanation.

DNA, Mitochondrial

Effects of glucose repression of the transmission and recombination of mitochondrial genes in yeast (Saccharomyces cerevisiae).

Matings of a number of Saccharomyces cerevisiae stocks give different output ratios of mitochondrial genotypes depending on whether the cells are glucose-repressed or derepressed. The effects of glucose repression are independent of cellular mating type and mitochondrial genotype, and take place at least in part after zygotes are formed. An explanation is proposed in terms of changes in the relative numbers of mitochondrial DNA molecules contributed by the a and alpha parents, modified by selective replication or destruction of molecules inside the zygote.

Chloramphenicol