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H E Schaffer

Publications and source records attributed to H E Schaffer.

16 recordsLinked to original sources
PubMed1988

The probabilities of similarities in DNA sequence comparisons.

We discuss the statistical significance of local similarities found between DNA sequences, and illustrate the procedure with reference to the Queen and Korn algorithm. If the longest similarity found for two sequences has length L, this length is said to be significant at the 5% level if there is a probability of no more than 0.05 of finding a length of L or greater between a pair of sequences consisting of randomly chosen bases with the same overall base frequencies. The distribution of longest lengths is related to that of lengths from any particular pair of starting positions on the two sequences. For our implementation of the Queen and Korn algorithm, this latter distribution is constructed by combining the five different blocks of bases that may be added to extend a similarity. A table is given to assess the significance of longest similarities in sequences of length up to 1000 bases. Quite long similarities are expected to occur by chance alone. The critical values we calculate for assessing significance are preferable to expected numbers of similarities used by some commercial computer packages.

Algorithms↗
PubMed1974

Isozyme allelic frequencies related to selection and gene-flow hypotheses.

Significant correlations between allelic frequencies and environmental variables in a number of insect species have been demonstrated by multivariate techniques. Since many environmental variables show a strong relationship to geographic location and since gene flow between populations can also produce patterns of gene frequencies which are related to the geographic location, both selection and gene-flow hypotheses are consistent with the observed correlations. The genetic variables can be corrected for geographic location and so for linear gene-flow patterns. If, after correction, the genetic variables still show significant correlations with similarly corrected environmental variables, then these correlations are consistent with hypotheses of selection but not of gene flow. The data of Johnson and Schaffer (1973) have been reanalyzed using the method of canonical correlation after correction for geographical location by means of multiple regression. Five of the nine loci studied exhibit significant canonical correlations. These results, under the assumption of linear gene flow, support hypotheses of selective action of environmental variables in the genotype-environment relationships observed.

Alleles↗
PubMed1973

Isozyme genotype-environment associations in natural populations of the harvester ant, Pogonomyrmex badius.

Harvester ants (P. badius) were collected from 49 localities in the southeastern U.S. Amylase and naphthylamidase activities were assayed by gel electrophoresis, and the frequencies of alleles controlling electrophoretic variation were calculated. Soil samples were analyzed and plotted against allelic frequencies. Climatographic and genetic data were analyzed by the method of principal components. Statistically significant correlations were found to occur between the patterns of genetic variation, and between the genetic and environmental patterns. These correlations are consistent with a selective basis for the maintenance of isozyme polymorphisms.

Amylases↗
PubMed1972

A study of the genetic basis of the sexual dimorphism for wing length in Drosophila melanogaster.

The genetic basis of a sexually dimorphic quantitative character in Drosophila melanogaster was investigated by means of two-way directional selection for increased and decreased differences between male and female wing length. The sex dimorphism (SD), defined as the mean wing length difference between the sexes, within families, provided the criterion for selection.-The two lines (High SD, Low SD) diverged rapidly during the 15 generations of selection, indicating the presence of extensive genetic variability for the genotype-sex interaction underlying the observed sexual dimorphism. There was evidence that genetic variability persisted in both lines when selection was relaxed. Most of the divergence between the two lines remained after 10 generations of relaxed selection.-The change in the level of sex dimorphism in the High line was due primarily to a decrease in male wing length; in the Low line most of the change in SD was the result of a decrease in female wing length. An overall reduction in wing length in both sexes in both lines is interpreted as an effect of inbreeding.-The distribution and nature of the genetic control underlying the SD characteristic of the two selection lines was investigated by chromosome substitution between selection lines using a marked inversion technique. The two lines differed by factors located on each of the three major chromosome pairs. Chromosome III had the greatest effect on the difference in SD level between lines, and showed an overall additive effect when present in homozygous versus heterozygous combination. Chromosome II had the least effect, with a significant dominance effect of the High II being evident when heterozygotes were compared with homozygotes. The effect of the X chromosome was intermediate. There was some evidence of interaction between non-homologous chromosomes.

Analysis of Variance↗
PubMedDate not supplied

The location of a mutator factor in a strain of Drosophila melanogaster by assaying male recombination.

In a set of "mutation accumulation lines," of Drosophila melanogaster that had originated from two different wild-caught lethal-carrying second chromosomes (Yamaguchi and Mukai 1974; Mukai and Cockerham 1977; Voelker, Schaffer and Mukai 1980) a correlation exists between high rates of reverse mutation at two visible loci and the ability to induce male recombination (Scobie and Schaffer 1982). The second and third chromosomes were extracted from the lines demonstrating these phenomena and tested for independent ability to induce male recombination. When the wild chromosome being tested was of male origin extracted second chromosome lines were found to induce moderate to high levels of male recombination and reduced transmission frequency of the wild chromosome (the k value). The recombinants recovered in these crosses also demonstrated a high level of double-crossover recombination without the recovery of the reciprocal double-recombinant types. In addition, identifiable portions of extracted second chromosomes of male origin have been placed on very similar, marked genetic backgrounds and tested for their ability to induce male recombination. Results of this procedure have identified two regions of the second chromosome that induce male recombination and reduce k values. These results are consistent with the hypothesis that there exist two mutator factors and the second chromosome, each associated with a "mutation accumulation line" with an unstable locus.

Animals↗
PubMedDate not supplied

A mutator factor in a strain of Drosophila melanogaster: identified by use of mutation, reversion rates and male recombination.

A set of 1,000 "mutation accumulation" lines Drosophila melanogaster, which originated from two different wild-type, lethal-bearing second chromosomes (Yamaguchi and Mukai 1974; Mukai and Cockerham 1977), was examined for evidence of a mutator factor by using the occurrence of recessive visible mutations and male recombination to identify its presence. The 1,000 lines were screened at approximately generation 240 for the presence of recessive visible mutation at twelve loci, by outcrossing to a balanced multiply marked second chromosome stock (Muller's "12ple" Bowling Green). Twenty-three lines were found to carry a visible mutation at one of the vg locus. mutations found in three lines, two at the dp locus and one at the vg locus, demonstrated instability as revertants to the wild type and were recovered and verified in these three cases. The three revertant lines, and three lines showing no reversion, were tested for their ability to induce male recombination. Male recombination was observed in the three lines in which revertants were recovered. Male and female sterility assays indicated conclusively that these "hybrid dysgenic" characteristics could not be used to identify lines potentially carrying mutator factors, whereas the consistent ability of the lines to induce high rates of reversion and male recombination was successful in determining that the "mutation accumulation lines" do possess mutator factors.

Animals↗