bluuebunny/crossref_metadata_2025 huggingface dataset:
A SYMMETRIC TWO-LOCUS FERTILITY MODEL
Authors: Feldman Marcus W , Liberman Uri
Published: January 2021

A model in which selection is mediated by differential fertilities among the genotypes at two diallelic loci is proposed. Fertility depends only on the number of heterozygous loci participating in the mating. Classes analogous to symmetric equilibria in symmetric viability models are determined explicitly and shown to exhibit stability behavior very different from the viability results. Linkage equilibrium is shown to occur in a relatively asymmetric fashion and to overlap in stability with linkage disequilibrium. In many cases single-locus or two-locus polymorphism is shown to be stable simultaneously with chromosome fixation even under very tight linkage. It is suggested that historical effects may be of great significance in the evolution of systems in which fertility is the primary agent of natural selection.
EXTRANUCLEAR DIFFERENTIATION AND GENE FLOW IN THE FINITE ISLAND MODEL
Authors: Takahata Naoyuki , Palumbi Stephen R
Published: January 2021

Use of sequence information from extranuclear genomes to examine deme structure in natural populations has been hampered by lack of clear linkage between sequence relatedness and rates of mutation and migration among demes. Here, we approach this problem in two complementary ways. First, we develop a model of extranuclear genomes in a population divided into a finite number of demes. Sex-dependent migration, neutral mutation, unequal genetic contribution of separate sexes and random genetic drift in each deme are incorporated for generality. From this model, we derive the relationship between gene identity probabilities (between and within demes) and migration rate, mutation rate and effective deme size. Second, we show how within- and between-deme identity probabilities may be calculated from restriction maps of mitochondrial (mt) DNA. These results, when coupled with our results on gene flow and genetic differentiation, allow estimation of relative interdeme gene flow when deme sizes are constant and genetic variants are selectively neutral. We illustrate use of our results by reanalyzing published data on mtDNA in mouse populations from around the world and show that their geographic differentiation is consistent with an island model of deme structure.
IDENTIFICATION AND CHARACTERIZATION OF 22 GENES THAT AFFECT THE VULVAL CELL LINEAGES OF THE NEMATODE CAENORHABDITIS ELEGANS
Authors: Ferguson Edwin L , Horvitz H Robert
Published: January 2021

Ninety-five mutants of the nematode Caenorhabditis elegans altered in the cell lineages of the vulva have been isolated on the basis of their displaying one of two phenotypes, Vulvaless or Multivulva. In Vulvaless mutants, which define 12 genes, no vulva is present. In Multivulva mutants, which define ten genes, one or more supernumerary vulva-like protrusions are located along the ventral side of the animal. A single recessive mutation is responsible for the phenotypes of most, but not all, of these strains. Fifteen of these 22 genes are represented by multiple alleles. We have shown by a variety of genetic criteria that mutations that result in a Vulvaless or Multivulva phenotype in six of the 22 genes most likely eliminate gene function. In addition, Vulvaless or Multivulva mutations in seven of the other genes most likely result in a partial reduction of gene function; the absence of the activity of any of these genes probably results in lethality or sterility. Our results suggest that we may have identified most, or all, genes of these two classes.
GENETIC VARIATION FOR THE SEX RATIO IN NASONIA VITRIPENNIS
Authors: Parker E Davis , Orzack Steven Hecht
Published: January 2021

We detected genetic variation for the sex ratio in the parasitoid wasp Nasonia vitripennis by analysis of inbred lines and with an artificial selection experiment. Sex ratios differed significantly among five independently isolated lines. Furthermore, sex ratio in broods produced by single females in single hosts shifted from 80-90% female to 50-55% female in 13 to 15 generations in each of two replicate selection lines. The final sex ratios of both selection lines were significantly lower than any of the inbred line sex ratios. Backcrosses revealed that the selection response was due to nuclear genes acting through the female parent. In light of known facultative sex ratio behavior and major genes affecting sex ratio in Nasonia, our results suggest that population and individual sex ratios in this species are molded by processes at both genetic and behavioral levels.
A DIRECT ASSESSMENT OF THE ROLE OF GENETIC DRIFT IN DETERMINING ALLELE FREQUENCY VARIATION IN POPULATIONS OF EUPHYDRYAS EDITHA
Authors: Mueller Laurence D , Wilcox Bruce A , Ehrlich Paul R , Heckel David G , Murphy Dennis D
Published: January 2021

Estimates of allele frequencies at six polymorphic loci were collected over eight generations in two populations of Euphydryas editha. We have estimated, in addition, the effective population size for each generation for both populations with results from mark-recapture and other field data. The variation in allele frequencies generated by random genetic drift was then studied using computer simulations and our direct estimates of effective population size. Substantial differences between observed values and computer-generated expected values assuming drift alone were found for three loci (Got, Hk, Pgi) in one population. These observations are consistent with natural selection in a variable environment.
FINE STRUCTURE AND INSTABILITY OF THE Ml-a LOCUS IN BARLEY
Authors: Wise Roger P , Ellingboe Albert H
Published: January 2021

There are many naturally occurring variants at the Ml-a locus in barley that confer resistance to the powdery mildew fungus Erysiphe graminis f. sp. hordei. Since the Ml-a locus is bracketed by Hor-1 and Hor-2, genes that encode storage proteins in the endosperm, the Ml-a locus is amenable to fine structure analysis. Rare susceptible recombinants, as judged by exchange of flanking markers, were recovered in F3 families from the Ml-a10 × Ml-a1, Ml-a1 × Ml-a15 and Ml-a6 × Ml-a13 crosses. Some susceptible recombinants were recovered from the Ml-a6 × Ml-a13 cross that did not fit the expected F3 family segregation ratios. The Ml-a6/Ml-a13 recombinants often reverted to resistance in subsequent generations. No recombinants were recovered in the reciprocal cross, Ml-a13 × Ml-a6. The possibility of a transposable element and a possible linear order of six "alleles" at the Ml-a locus is discussed.
HETEROGENEITY OF LETHALS IN A "SIMPLE" LETHAL COMPLEMENTATION GROUP
Authors: Janca Frank C , Woloshyn Effie P , Nash David
Published: January 2021

Of 24 ethyl methanesulphonate-induced, recessive-lethal mutations in the region 9E1-9F13 of the X chromosome of Drosophila melanogaster, eight fall into a typically homogeneous lethal complementation group associated with the raspberry (ras) locus. Mutations in this group have previously been shown to be pleiotropic, affecting not only ras but also two other genetic entities, gua1 and pur1, which yield auxotrophic mutations.—The eight new mutations have been characterized phenotypically in double heterozygotes with gua1, pur1 and ras mutations. Despite their homogeneity in lethal complementation tests, the mutations prove quite diverse. For example, two mutations have little or no effect on eye color in double heterozygotes with ras  2. The differences between the lethals are allele-specific and cannot be explained as a trivial outcome of a hypomorphic series.—Taken alone, the lethal complementation studies mask the complexity of the locus and the diversity of its recessive lethal alleles. By extension, we argue that the general use of lethal saturation studies provides an unduly simplified image of genetic organization. We suggest that the reason why recessive lethal mutations rarely present complex complementation patterns is that complex loci tend to produce mutations that affect several subfunctions.
TEMPERATURE-DEPENDENT EXPRESSION OF THE APTEROUS PHENOTYPE IN DROSOPHILA MELANOGASTER
Authors: Stevens Mary E , Bryant Peter J
Published: January 2021

Mutations at the apterous (ap) locus in Drosophila melanogaster produce a variety of developmental defects, including several classes of wing abnormalities. We describe the wing phenotype produced by homozygotes and hemizygotes of three different temperature-sensitive apterous alleles grown at 16, 18, 20, 22, 25, and 29°. We also describe the phenotype produced by each of these three alleles when heteroallelic with the non-temperature-sensitive apc allele. Constant-temperature and temperature-shift experiments show that each of the heteroallelic genotypes can produce several of the previously described apterous phenotypes and that the length of the temperature-sensitive period for a given phenotype depends on the allelic combinations used to measure it. We suggest that the stage-specific requirements of the tissue for gene product, rather than the time of gene expression per se, determine the temperature-sensitive periods for apterous and other loci. The results support the hypothesis that the various wing phenotypes produced by apterous mutations are due to quantitative reductions in the activity of gene product and that failure to meet specific threshold requirements for gene product can lead to qualitatively different phenotypes.
ACTIVITY OF CHI RECOMBINATIONAL HOTSPOTS IN SALMONELLA TYPHIMURIUM
Authors: Smith Gerald R , Roberts Christine M , Schultz Dennis W
Published: January 2021

Chi sites have previously been shown to stimulate homologous recombination by the Escherichia coli RecBC pathway. To test the activity of Chi in another organism, bacteriophage λ crosses were carried out in Salmonella typhimurium strains bearing the E. coli λ receptor protein. Chi is active in these crosses in S. typhimurium, but is less active than in the same crosses carried out in E. coli. The lower Chi activity in S. typhimurium appears to be intrinsic to the S. typhimurium RecBC enzyme, since the Chi activity in E. coli-S. typhimurium hybrids depends on the species of origin of their RecBC enzyme. For these studies we constructed an F' factor and a pBR322-derived plasmid carrying the thyA  +  recC  +  recB  +  argA  + region of the S. typhimurium chromosome.
COMPLEX CIS-ACTING REGULATORS AND LOCUS STRUCTURE OF DROSOPHILA TISSUE-SPECIFIC ADH VARIANTS
Authors: Rabinow Leonard , Dickinson W J
Published: January 2021

Diverse patterns of tissue-specific expression of alcohol dehydrogenase (ADH) among species of the grimshawi subgroup of Hawaiian picture-winged Drosophila suggests control by complex or multiple, independently acting regulatory elements. These elements act by controlling Adh mRNA accumulation in individual tissue types. Restriction mapping of the Adh loci from these species reveals several insertion/deletion differences, one of which lies just outside the 5' end of the structural sequences and correlates with differences in larval patterns of ADH expression. No tissue-specific rearrangement of Adh sequences was observed.
GENETIC VARIATION AND GEOGRAPHIC DIFFERENTIATION IN MITOCHONDRIAL DNA OF THE HORSESHOE CRAB, LIMULUS POLYPHEMUS
Authors: Saunders Nancy C , Kessler Louis G , Avise John C
Published: January 2021

Restriction site variation in mitochondrial DNA (mtDNA) of the horseshoe crab (Limulus polyphemus) was surveyed in populations ranging from New Hampshire to the Gulf Coast of Florida. MtDNA clonal diversity was moderately high, particularly in southern samples, and a major genetic "break" (nucleotide sequence divergence approximately 2%) distinguished all sampled individuals which were north vs. south of a region in northeastern Florida. The area of genotypic divergence in Limulus corresponds to a long-recognized zoogeographic boundary between warm-temperate and tropical marine faunas, and it suggests that selection pressures and/or gene flow barriers associated with water mass differences may also influence the evolution of species widely distributed across such transition zones. On the other hand, a comparison of the mtDNA divergence patterns in Limulus with computer models involving stochastic lineage extinction in species with limited gene flow demonstrates that deterministic explanations need not necessarily be invoked to account for the observations. Experiments to distinguish stochastic from deterministic possibilities are suggested. Overall, the pattern and magnitude of mtDNA differentiation in horseshoe crabs is very similar to that typically reported for freshwater and terrestrial species assayed over a comparable geographic range. Results demonstrate for the first time that, geographically, at least some continuously distributed marine organisms can show considerable mtDNA genetic differentiation.
ADDITIVE VARIATION MAINTAINED UNDER STABILIZING SELECTION: A TWO-LOCUS MODEL OF PLEIOTROPY FOR TWO QUANTITATIVE CHARACTERS
Authors: Gimelfarb A
Published: January 2021

A model with two diallelic loci controlling two additive quantitative characters is suggested. One of the loci has a similar effect on both characters, whereas the second locus has an antagonistic effect on the two characters. Both characters experience direct stabilizing selection. The model yields a stable polymorphic state, with both characters maintaining genetic variation. The genetic correlation between the characters at the equilibrium is zero, in spite of the pleiotropic effects of the loci controlling them.
GENE FLOW IN NATURAL POPULATIONS OF DROSOPHILA MELANOGASTER WITH SPECIAL REFERENCE TO LETHAL ALLELISM RATES AND PROTEIN VARIATION
Authors: Yamazaki Tsuneyuki , Choo Jong-Kil , Watanabe Takao K , Takahata Naoyuki
Published: January 2021

A simultaneous survey of 14 protein loci, together with frequencies and within- and between-population allelism rates of lethal chromosomes, was carried out in five (four Japanese and one Korean) natural populations and one cage population of Drosophila melanogaster. It was found that lethal allelism rates decrease rapidly as geographic distance between two populations increases, while variation at protein loci shows a remarkable similarity over all populations examined. These findings suggest that there are very high levels of gene flow in these natural populations and that selection at protein loci which can maintain substantial geographic variation, if present, is overshadowed by gene flow. There is no indication that invasion of D. melanogaster to the Far East occurred so recently that the frequencies of lethal chromosomes are still in nonequilibrium.
DNA SEQUENCE COMPARISON AMONG CLOSELY RELATED DROSOPHILA SPECIES IN THE MULLERI COMPLEX
Authors: Schulze Dan H , Lee C S
Published: January 2021

DNA hybridization was used to establish DNA sequence relationships among seven Drosophila species. Single-copy DNA was isolated from four species within the Drosophila mulleri complex, D. mojavensis, D. arizonensis, D. ritae and D. starmeri. These single-copy DNAs were used as tracers to be hybridized with each other and one additional member of the mulleri complex, D. aldrichi, a member of a closely related complex, D. hydei, and a distantly related species, D. melanogaster. Two methods have been used to determine the relatedness between these species: (1) the extent of duplex formed as measured by binding to hydroxyapatite and (2) the thermal stability of the duplexed DNA. Moderately repetitive DNA was purified from these species and used similarly to determine the divergence of this family of sequences. The rate of nucleotide substitution was estimated to be 0.2 ± 0.1% base pair change per million years for both single-copy and middle-repetitive DNAs. The size of the D. arizonensis genome, a representative of the mulleri complex, was calculated to be 2.2 × 108 base pairs from its kinetic complexity similar to that of D. hydei. The relative amounts (18%) and average reiteration frequency (100 copies) of the middle-repetitive DNA are similar for all Drosophila species studied. Finally, the data are presented in a phylogenetic tree.
TRANSITORY DEREPRESSION AND THE MAINTENANCE OF CONJUGATIVE PLASMIDS
Authors: Lundquist Peter D , Levin Bruce R
Published: January 2021

It has been proposed that bacterial plasmids cannot be maintained by infectious transfer alone and that their persistence requires positive selection for plasmid-borne genes. To test this hypothesis, the population dynamics of two laboratory and five naturally occurring conjugative plasmids were examined in chemostat cultures of E. coli K-12. Both laboratory plasmids and three of the five wild plasmids failed to increase in frequency when introduced at low frequencies. However, two of the naturally occurring plasmids rapidly increased in frequency, and bacteria carrying them achieved dominance in the absence of selection for known plasmid-borne genes. Three hypotheses for the invasion and persistence of these two plasmids were examined. It is concluded that although these two extrachromsomal genetic elements are repressed for conjugative pili synthesis, as a consequence of high rates of transfer during periods of transitory derepression in newly formed transconjugants, they become established and are maintained by infectious transfer alone. The implications of these observations to the theory of plasmid maintenance and the evolution of repressible conjugative pili synthesis are discussed.
EXCESS POLYMORPHISM AT THE Adh LOCUS IN DROSOPHILA MELANOGASTER
Authors: Kreitman Martin E , Aguadé Montserrat
Published: January 2021

The evolutionary history of a region of DNA encompassing the Adh locus is studied by comparing patterns of variation in Drosophila melanogaster and its sibling species, D. simulans. An unexpectedly high level of silent polymorphism in the Adh coding region relative to the 5' and 3' flanking regions in D. melanogaster is revealed by a populational survey of restriction polymorphism using a four-cutter filter hybridization technique as well as by direct sequence comparisons. In both of these studies, a region of the Adh gene encompassing the three coding exons exhibits a frequency of polymorphism equal to that of a 4-kb 5' flanking region. In contrast, an interspecific sequence comparison shows a two-fold higher level of divergence in the 5' flanking sequence compared to the structural locus. Analysis of the patterns of variation suggest an excess of polymorphism within the D. melanogaster Adh locus, rather than lack of polymorphism in the 5' flanking region. An approach is outlined for testing neutral theory predictions about patterns of variation within and between species. This approach indicates that the observed patterns of variation are incompatible with an infinite site neutral model.
MEIOTIC SEGREGATION AND MALE RECOMBINATION IN INTERSPECIFIC HYBRIDS OF DROSOPHILA
Authors: Coyne Jerry A
Published: January 2021

Male hybrids between three pairs of Drosophila species show no substantial distortion of Mendelian segregation and no appreciable male recombination. These results do not support the theories that meiotic drive alleles of large effect are often fixed within species and that transposable genetic elements cause speciation.
LATENT NONSTRUCTURAL DIFFERENTIATION AMONG HOMOLOGOUS CHROMOSOMES AT THE DIPLOID LEVEL: CHROMOSOME 6Be OF AEGILOPS LONGISSIMA
Authors: Kota Rama S , McGuire Patrick E , Dvořák Jan
Published: January 2021

Previous work has shown that chromosome pairing at metaphase I (MI) of wheat homologous chromosomes from different inbred lines (heterohomologous chromosomes) is reduced relative to that between homologous chromosomes within an inbred line (euhomologous chromosomes). In order to determine if a potential for this phenomenon exists in diploid species closely related to the wheat B genome, MI chromosome pairing was investigated between euhomologous and heterohomologous 6Be (=6Se) chromosomes, each from a different population of Aegilops longissima Schweinf. et Muschl. (2n = 2x = 14) substituted for chromosome 6B of Chinese Spring wheat (Triticum aestivum L., 2n = 6x = 42). Euhomologous and heterohomologous monotelodisomics, i.e., plants with one complete chromosome 6Be and a telosome of either 6Bep or 6Beq, were constructed in the isogenic background of Chinese Spring. Pairing at MI of the Ae. longissima chromosomes was reduced in heterohomologous monotelodisomics compared to that in the corresponding euhomologous monotelodisomics. The remaining 20 pairs of Chinese Spring chromosomes paired equally well in the euhomologous and heterohomologous monotelodisomics. Thus, the cause of the reduced pairing must reside specifically in the Ae. longissima heterohomologues. In the hybrids between the Ae. longissima lines that contributed the substituted chromosomes, pairing between the heterohomologous chromosomes was normal and did not differ from that of the euhomologous chromosomes. These data provide evidence that a potential for reduced pairing between the heterohomologues is present in the diploid species, but is expressed only in the polyploid wheat genetic background. The reduction in heterohomologous chromosome pairing was greater in the p arm than in the q arm, exactly as in chromosome 6B of wheat. It is concluded that the reduced pairing between Ae. longissima heterohomologues has little to do with constitutive heterochromatin. The value of chromosome pairing as an unequivocal means of determining the origin of genomes in polyploid plants is questioned.
GENE CONVERSION DISPARITY: FACTORS INFLUENCING ITS DIRECTION AND EXTENT, WITH TESTS OF ASSUMPTIONS AND PREDICTIONS IN ITS EVOLUTIONARY EFFECTS
Authors: Lamb Bernard C
Published: January 2021

The evolutionarily important characteristics of gene conversion disparity extent and direction are surveyed in fungi. Temperature and background genotype can have small or large effects, sometimes even changing the direction of disparity. Disparity results from Sordaria and Ascobolus were very similar, with between-strain, between-data set and between-locus differences being larger than those between species or genera. In general, different loci in an organism show similar disparity properties when comparable types of mutation are considered, but may not do so in pooled results containing different proportions of different mutation types. Frameshifts typically have strong disparities, usually with negative signs for single base additions and positive signs for single base deletions. Base substitutions tend to have moderate disparities, favoring wild type more often than mutant in most data sets. Large deletions usually have significant disparity, either positive or negative. For comparable molecular types of mutation, spontaneous and induced mutations had roughly similar disparity properties.—Experimental tests and theoretical considerations generally failed to support a number of assumptions and predictions made in previous treatments of gene conversion in evolution. In general, a mutation's conversion properties depend much more on its molecular type in relation to wild type than on any evolved conversion advantages or disadvantages.
MORPHOMETRIC DIFFERENTIATION AMONG EXPERIMENTAL LINES OF THE HOUSEFLY IN RELATION TO A BOTTLENECK
Authors: Bryant Edwin H , Combs Lisa M , McCommas Steven A
Published: January 2021

Differentiation in morphometric traits among experimental populations of the housefly subjected to an experimental bottleneck was examined for replicate lines founded with one, four or 16 pairs of flies. Differentiation among lines within a bottleneck size was significantly greater than predicted by drift in relation to the additive genetic variation for these traits within the founding population. Two models of nonadditive genetic variance were investigated to interpret these results, one involving dominance of allelic effects within loci and another incorporating multiplicative epistasis. Both models generated more variation among lines as a direct result of sampling during the bottleneck than predicted by a model with additive gene action. The pattern of differentiation among our experimental lines in relation to these models conformed more to the model incorporating epistasis. Nevertheless, it may be difficult to distinguish differentiation among lines occurring during a bottleneck as a result of nonadditive gene action from that caused by diversifying selection among lines after the bottleneck.
Studies on the Recombination Genes of Bacteriophage T4: Suppression of uvsX and uvsY Mutations by uvsW Mutations
Authors: Yonesaki Tetsuro , Minagawa Teiichi
Published: January 2021

Genes uvsW, uvsX and uvsY are dispensable for T4 growth but are implicated in recombination and in the repair of damaged DNA. We found that large-plaque mutants arose efficiently from small-plaque uvsX and uvsY mutants at 42° and were pseudorevertants containing a new mutation in uvsW. Using reconstructed double mutants, we confirmed that a mutation in uvsW partially increases the burst size and UV resistance of uvsX and uvsY mutants. At 41° the uvsW mutation completely restores the arrest in DNA synthesis caused by mutations in genes uvsX, uvsY and 46, but at 30° it only partially restores DNA synthesis in a gene 46 mutant and does not restore DNA synthesis in uvsX and uvsY mutants. Restored DNA synthesis at 41° was paralleled by the overproduction of single-stranded DNA and gene 32 protein. Based on these findings, we propose that the uvsW gene regulates the production of single-stranded DNA and we discuss the phenotype of uvsW mutants and their suppression of some uvsX and uvsY phenotypes. Infection of restrictive cells with am uvsW mutants revealed a defect in the synthesis of a protein of molecular weight 53,000 daltons, suggesting that this protein is the uvsW gene product.
The Regulation of Aldehyde Oxidase in Imaginal Wing Discs of Drosophila Hybrids: Evidence for cis- and trans-Acting Control Elements
Authors: Sprey Th E , Kuhn David T
Published: January 2021

The aldehyde oxidase (Aldox) distribution pattern was determined for wing discs of partial hybrids between D. melanogaster and D. simulans. In these animals the regulation of Aldox activity is not uniform over the disc epithelium as both cis-dominant and trans -acting control were evident in different regions of the disc. The Aldox expression was shown to be regulated by loci on the X chromosome, 2L and 3R of D. melanogaster and 2R and 3R of D. simulans.
Covariance of Inbred Relatives with Special Reference to Selfing
Authors: Wright A J
Published: January 2021

The covariance of inbred relatives from a population in linkage and identity equilibrium in the presence of dominance and epistasis is formulated using a similar procedure to that which B. S. Weir and C. C. Cockerham used to derive a general expression for the genotypic variance. An alternative model based on the description of a genotype in terms of the homozygotes of its constituent alleles is defined which leads to an equivalent set of 21 quadratic components, but when the relatives are descended from a common ancestor by selfing some confounding occurs and only 12 are necessary. This covariance can be subdivided into components arising among families at different levels of the hierarchy generated by a selfing series, and the component among descendants of distinct members of the base population has a different form from those arising at lower levels of the hierarchy. The 12 quadratic components together with an error variance can be estimated using the 20 statistics provided by analyses of variance and covariance of families generated by four generations of selfing.
Persistence of Tandem Arrays: Implications for Satellite and Simple-Sequence DNAs
Authors: Walsh James Bruce
Published: January 2021

Recombination processes acting on tandem arrays are suggested here to have probable intrinsic biases, producing an expected net decrease in array size following each event, in contrast to previous models which assume no net change in array size. We examine the implications of this by modeling copy number dynamics in a tandem array under the joint interactions of sister-strand unequal crossing over (rate γ per generation per copy) and intrastrand recombination resulting in deletion (rate ∊ per generation per copy). Assuming no gene amplification or selection, the expected mean persistence time of an array starting with z excess copies (i.e., array size z + 1) is z(1 + γ/∊) recombinational events. Nontrivial equilibrium distributions of array sizes exist when gene amplification or certain forms of selection are considered. We characterize the equilibrium distribution for both a simple model of gene amplification and under the assumption that selection imposes a minimal array size, n. For the latter case, n + 1/03B1 is an upper bound for mean array size under fairly general conditions, where α(=2∊/γ) is the scaled deletion rate. Further, the distribution of excess copies over n is bounded above by a geometric distribution with parameter α/(1 + α). Tandem arrays are unlikely to be greatly expanded by unequal crossing over unless α << 1, implying that other mechanisms, such as gene amplification, are likely important in the evolution of large arrays. Thus unequal crossing over, by itself, is likely insufficient to account for satellite DNA.
Mutations that Improve the pRE Promoter of Coliphage Lambda
Authors: Mahoney Michael E , Wulff Daniel L
Published: January 2021

The dya5 mutation, a C→T change at position -43 of the λ pRE promoter, results in a twofold increase in pRE activity in vivo. Smaller increases in pRE activity are found for the dya2 mutation, a T→C change at position -1 of pRE, and the dya3 mutation, an A→G change at +5 of pRE· The mutant pRE promoters retain complete dependence on cII protein for activity. These observations argue, at least for pRE-like promoters, that promoter activities are influenced by nucleotide sequences at least eight nucleotides to the 5′-side of the conventional -35 region consensus sequence, and by nucleotide sequences near the start-site of transcription. Although Hawley and McClure (1983) found A·T pairs more frequently than G·TC pairs in the region of -40 to -45 of prokaryotic promoters, other mutations that change a G·TC pair to an A·T pair at positions -41, -44 and -45 of pRE do not result in increased promoter activity. We also found that a T→C change at position -42 results in a mild decrease in promoter activity. These observations argue that Ts at positions -42 and -43 of pRE are required for maximum promoter activity, but do not support the hypothesis that As and Ts in the -40 to -45 region generally lead to higher promoter activities.
Molecular Evolution and Nucleotide Sequences of the Maize Plastid Genes for the α Subunit of CF1 (atpA) and the Proteolipid Subunit of CF0 (atpH)
Authors: Rodermel Steven R , Bogorad Lawrence
Published: January 2021

The nucleotide sequences of the maize plastid genes for the α subunit of CF1 (atpA) and the proteolipid subunit of CF 0 (atpH) are presented. The evolution of these genes among higher plants is characterized by a transition mutation bias of about 2:1 and by rates of synonymous and nonsynonymous substitution which are much lower than similar rates for genes from other sources. This is consistent with the notion that the plastid genome is evolving conservatively in primary sequence. Yet, the mode and tempo of sequence evolution of these and other plastid-encoded coupling factor genes are not the same. In particular, higher rates of nonsynonymous substitution in atpE (the gene for the ∊ subunit of CF1) and higher rates of synonymous substitution in atpH in the dicot vs. monocot lineages of higher plants indicate that these sequences are likely subject to different evolutionary constraints in these two lineages. The 5′- and 3′ transcribed flanking regions of atpA and atpH from maize, wheat and tobacco are conserved in size, but contain few putative regulatory elements which are conserved either in their spatial arrangement or sequence complexity. However, these regions likely contain variable numbers of "species-specific" regulatory elements. The present studies thus suggest that the plastid genome is not a passive participant in an evolutionary process governed by a more rapidly changing, readily adaptive, nuclear compartment, but that novel strategies for the coordinate expression of genes in the plastid genome may arise through rapid evolution of the flanking sequences of these genes.
Variation in Male Fertilities and Pairwise Mating Probabilities in Picea glauca
Authors: Schoen D J , Stewart S C
Published: January 2021

Frequencies of multilocus male gametes in seeds collected from clones in several blocks of a white spruce seed orchard were analyzed as part of a 2-yr study of mating system variation in this species. Observed frequencies of male gamete types departed significantly from those expected assuming equal male fertilities among clones. Male gamete frequencies in seed crops were significantly heterogeneous among clones within blocks, and among blocks within clones. Clonal male fertilities were estimated from male gamete frequency data. These estimates were highly skewed, with a small proportion of the clones contributing male gametes to the majority of the seed. The estimates were significantly heterogeneous among clones within blocks, and among blocks within clones. Between-year variation in clonal male fertilities was also pronounced, with male fertilities of some clones changing by as much as three orders of magnitude. Clonal male fertility was significantly correlated with clonal male cone production in both years. These results are important with regard to assumptions made for the estimation of general combining ability, average genetic correlation among progeny from single parents, and expected response to selection in open-pollinated plant populations.
X-Y Exchange and the Coevolution of the X and Y rDNA Arrays in Drosophila melanogaster
Authors: Gillings M R , Frankham R , Speirs J , Whalley M
Published: January 2021

The nucleolus organizers on the X and Y chromosomes of Drosophila melanogaster are the sites of 200-250 tandemly repeated genes for ribosomal RNA. As there is no meiotic crossing over in male Drosophila, the X and Y chromosomal rDNA arrays should be evolutionarily independent, and therefore divergent. The rRNAs produced by X and Y are, however, very similar, if not identical. Molecular, genetic and cytological analyses of a series of X chromosome rDNA deletions (bb alleles) showed that they arose by unequal exchange through the nucleolus organizers of the X and Y chromosomes. Three separate exchange events generated compound X·YL chromosomes carrying mainly Y-specific rDNA. This led to the hypothesis that X-Y exchange is responsible for the coevolution of X and Y chromosomal rDNA. We have tested and confirmed several of the predictions of this hypothesis: First, X·YL chromosomes must be found in wild populations. We have found such a chromosome. Second, the X·YL chromosome must lose the YL arm, and/or be at a selective disadvantage to normal X+ chromosomes, to retain the normal morphology of the X chromosome. Six of seventeen sublines founded from homozygous X·YLbb stocks have become fixed for chromosomes with spontaneous loss of part or all of the appended YL. Third, rDNA variants on the X chromosome are expected to be clustered within the X+ nucleolus organizer, recently donated ("Y") forms being proximal, and X-specific forms distal. We present evidence for clustering of rRNA genes containing Type 1 insertions. Consequently, X-Y exchange is probably responsible for the coevolution of X and Y rDNA arrays.
Homoeosis in Drosophila: The Lethal Syndrome of the Regulator of bithorax (or trithorax) Locus and Its Interaction With Other Homoeotic Loci
Authors: Sato Takashi , Denell Robin E
Published: January 2021

Regulator of bithorax (Rg-bx)- [or trithorax (trx)-] lethal zygotes show anterior transformations of various cuticular features of the larval thorax and abdomen. The Rg-bx  - lethal syndrome depends on the dosage of the bithorax gene complex (BX-C), and lack of Rg-bx+ function is antagonistic to posterior transformations displayed by Polycomb (Pc)- embryos. Significantly, when the BX-C is deleted, the Rg-bx  - embryos disclose homoeosis of mesothoracic to prothoracic cuticular structures. This homoeotic transformation is due to a reduction in Antennapedia (Antp)+ gene activity and is consequently dependent on the dosage of the Antennapedia gene complex (ANT-C), suggesting that the Rg-bx  + activity is necessary for proper expression of the Antp  + gene. However, the functional relationship between the Rg-bx and Sex combs reduced (Scr) loci in embryogenesis is still to be established.
Linkage of the Steroid Sulfatase Gene to the Sex-Reversed Mutation in the Mouse
Authors: Keitges Elisabeth A , Schorderet Daniel F , Gartler Stanley M
Published: January 2021

Dosage studies and the inheritance pattern of the gene for steroid sulfatase (Sts) in the mouse have previously provided indirect evidence for a functional Y-linked allele which recombines obligatorily with its X-linked allele in male meiosis. In this study, we have investigated the linkage relationship of Sts and the sex-reversed mutation (Sxr), a gene which is known to reside in the pairing region of the Y chromosome. The results clearly demonstrate that Sxr and Sts are linked in a region of obligatory recombination and Sts maps proximal to Sxr with most recombinants occurring proximal to the two genes.
Characterization and in Vivo Cloning of prlC, a Suppressor of Signal Sequence Mutations in Escherichia coli K12
Authors: Trun Nancy J , Silhavy Thomas J
Published: January 2021

The prlC gene of E. coli was originally identified as an allele, prlC1, which suppresses certain signal sequence mutations in the genes for several exported proteins. We have isolated six new alleles of prlC that also confer this phenotype. These mutations can be placed into three classes based on the degree to which they suppress the lamBsignal sequence deletion, lamBs78. Genetic mapping reveals that the physical location of the mutations in prlC correlates with the strength of the suppression, suggesting that different regions of the gene can be altered to yield a suppressor phenotype. We also describe an in vivo cloning procedure using λplacMu9H. The procedure relies on transposition and illegitimate recombination to generate a specialized transducing phage that carries prlC1. This method should be applicable to any gene for which there is a mutant phenotype.
The Cloning and Mapping of ADR6, a Gene Required for Sporulation and for Expression of the Alcohol Dehydrogenase II Isozyme From Saccharomyces cerevisiae
Authors: Taguchi Aileen K W , Young Elton T
Published: January 2021

The alcohol dehydrogenase II (ADH2) gene of the yeast, Saccharomyces cerevisiae, is not transcribed during growth on fermentable carbon sources such as glucose. Growth of yeast cells in a medium containing only nonfermentable carbon sources leads to a marked increase or derepression of ADH2 expression. The recessive mutation, adr6-1, leads to an inability to fully derepress ADH2 expression and to an inability to sporulate. The ADR6 gene product appears to act directly or indirectly on ADH2 sequences 3' to or including the presumptive TATAA box. The upstream activating sequence (UAS) located 5' to the TATAA box is not required for the Adr6- phenotype. Here, we describe the isolation of a recombinant plasmid containing the wild-type ADR6 gene. ADR6 codes for a 4.4-kb RNA which is present during growth both on glucose and on nonfermentable carbon sources. Disruption of the ADR6 transcription unit led to viable cells with decreased ADHII activity and an inability to sporulate. This indicates that both phenotypes result from mutations within a single gene and that the adr6-1 allele was representative of mutations at this locus. The ADR6 gene mapped to the left arm of chromosome XVI at a site 18 centimorgans from the centromere.
Genomic Organization and Developmental Fate of Adjacent Repeated Sequences in a Foldback DNA Clone of Tetrahymena thermophila
Authors: Tschunko Almuth H , Loechel Robert H , McLaren Ning C , Allen Sally Lyman
Published: January 2021

DNA sequence elimination and rearrangement occurs during the development of somatic cell lineages of eukaryotes and was first discovered over a century ago. However, the significance and mechanism of chromatin elimination are not understood. DNA elimination also occurs during the development of the somatic macronucleus from the germinal micronucleus in unicellular ciliated protozoa such as Tetrahymena thermophila. In this study foldback DNA from the micronucleus was used as a probe to isolate ten clones. All of those tested (4/4) contained sequences that were repetitive in the micronucleus and rearranged in the macronucleus. The presence of inverted repeated sequences was clearly demonstrated in one of them by electron microscopy. DNA sequence analysis showed that the left portion of this clone contains three tandem, directly repeated copies of a 340-bp sequence, a 120-bp portion of which appears in inverted orientation at a 1.6-kb distance. This clone, pTtFB1, was subjected to a detailed analysis of its developmental fate. Subregions were subcloned and used as probes against Southern blots of micronuclear and macronuclear DNA. We found that all subregions defined repeated sequence families in the micronuclear genome. A minimum of four different families was defined, two of which are retained in the macronucleus and two of which are completely eliminated. The inverted repeat family is retained with little rearrangement. Two of the families, defined by subregions that do not contain parts of the inverted repeat, one in the "loop" and one in the "right flanking region," are totally eliminated during macronuclear development–and contain open reading frames. A fourth family occurs in the "loop" region and is rearranged extensively during development. The two gene families that are eliminated are stable in the micronuclear genome but are not clustered together as evidenced by experiments in which DNAs from nullisomic strains are used to map family members to specific micronuclear chromosomes. The inverted repeat family is also stable in the micronuclear genome and is dispersed among several chromosomes. The significance of retained inverted repeats to the process of elimination is discussed.
Assessment of X Chromosome Dosage Compensation in Caenorhabditis elegans by Phenotypic Analysis of lin-14
Authors: DeLong Leslie , Casson Lawrence P , Meyer Barbara J
Published: January 2021

Caenorhabditis elegans compensates for the difference in X chromosome gene dose between males (XO) and hermaphrodites (XX) through a mechanism that equalizes the levels of X-specific mRNA transcripts between the two sexes. We have devised a sensitive and quantitative genetic assay to measure perturbations in X chromosome gene expression caused by mutations that affect this process of dosage compensation. The assay is based on quantitating the precocious alae phenotype caused by a mutation that reduces but does not eliminate the function of the X-linked gene lin-14. We demonstrate that in diploid animals the lin-14 gene is dosage compensated between XO and XX animals. In XXX diploid animals, however, lin-14 expression is not compensated, implying that the normal dosage compensation mechanism in C. elegans lacks the capacity to compensate completely for the additional X chromosome in triplex animals. Using the lin-14 assay we compare the effects of mutations in the genes dpy-21, dpy-26, dpy-27, dpy-28, and dpy-22 on X-linked gene expression. Additionally, in the case of dpy-21 we correlate the change in phenotypic expression of lin-14 with a corresponding change in the lin-14 mRNA transcript level.
A Comprehensive Study of Genic Variation in Natural Populations of Drosophila melanogaster. III. Variations in Genetic Structure and Their Causes Between Drosophila melanogaster and Its Sibling Species Drosophila simulans
Authors: Choudhary M , Singh Rama S
Published: January 2021

The natural populations of Drosophila melanogaster and Drosophila simulans were compared for their genetic structure. A total of 114 gene-protein loci were studied in four mainland (from Europe and Africa) and an island (Seychelle) populations of D. simulans and the results were compared with those obtained on the same set of homologous loci in fifteen worldwide populations of D. melanogaster. The main results are as follows: (1) D. melanogaster shows a significantly higher proportion of loci polymorphic than D. simulans (52% vs. 39%, P < 0.05), (2) both species have similar mean heterozygosity and mean number of alleles per locus, (3) the two species share some highly polymorphic loci but they do not share loci that show high geographic differentiation, and (4) D. simulans shows significantly less geographic differentiation than D. melanogaster. The differences in genetic differentiation between the two species are limited to loci located on the X and second chromosomes only; loci on the third chromosome show similar level of geographic differentiation in both species. These two species have previously been shown to differ in their pattern of variation for chromosomal polymorphisms, quantitative and physiological characters, two-dimensional electrophoretic (2DE) proteins, middle repetitive DNA and mitochondrial DNA. Variation in niche-widths and/or genetic "strategies" of adaptation appear to be the main causes of differences in the genetic structure of these two species.
Definition and Estimation of Higher-Order Gene Fixation Indices
Authors: Ritland Kermit
Published: January 2021

Fixation indices summarize the associations between genes that arise from the joint effects of inbreeding and selection. In this paper, fixation indices are derived for pairs, triplets and quadruplets of genes at a single multiallelic locus. The fixation indices are obtained by dividing cumulants by constants; the cumulants describe the statistical distribution of alleles and the constants are functions of gene frequency. The use of cumulants instead of moments is necessary only for four-gene indices, when the fourth cumulant is used. A second type of four-gene index is also required, and this index is based upon the covariation of second-order cumulants. At multiallelic loci, a large number of indices is possible. If alleles are selectively neutral, the number of indices is reduced and the relationship between gene identity and gene cumulants is shown.—Two-gene indices can always be estimated from genotypic frequency data at a single polymorphic locus. Three-gene indices are also estimable except when allele frequency equals one-half. Four-gene indices are not estimable unless selection is assumed to have an equal effect upon each allele (such as under selective neutrality) and the locus contains at least three alleles of unequal frequency. For diallelic or selected loci, an alternative four- gene fixation index is proposed. This index incorporates both types of four-gene associations but cannot be related to gene identity.