bluuebunny/crossref_metadata_2025_split huggingface dataset:
Allelic genealogy under overdominant and frequency-dependent selection and polymorphism of major histocompatibility complex loci.
Authors: Takahata N , Nei M 
Published: January 2021

Abstract
To explain the long-term persistence of polymorphic alleles (trans-specific polymorphism) at the major histocompatibility complex (MHC) loci in rodents and primates, a computer simulation study was conducted about the coalescence time of different alleles sampled under various forms of selection. At the same time, average heterozygosity, the number of alleles in a sample, and the rate of codon substitution were examined to explain the mechanism of maintenance of polymorphism at the MHC loci. The results obtained are as follows. (1) The coalescence time for neutral alleles is too short to explain the trans-specific polymorphism at the MHC loci. (2) Under overdominant selection, the coalescence time can be tens of millions of years, depending on the parameter values used. The average heterozygosity and the number of alleles observed are also high enough to explain MHC polymorphism. (3) The pathogen adaptation model proposed by Snell is incapable of explaining MHC polymorphism, since the coalescence time for this model is too short and the expected heterozygosity and the expected number of alleles are too small. (4) From the mathematical point of view, the minority advantage model of frequency-dependent selection is capable of explaining a high degree of polymorphism and trans-specific polymorphism. (5) The molecular mimicry hypothesis also gives a sufficiently long coalescence time when the mutation rate is low in the host but very high in the parasite. However, the expected heterozygosity and the expected number of alleles tend to be too small. (6) Consideration of the molecular mechanism of the function of MHC molecules and other biological observations suggest that the most important factor for the maintenance of MHC polymorphism is overdominant selection. However, some experiments are necessary to distinguish between the overdominance and frequency-dependent selection hypotheses.
Context effects in the formation of deletions in Escherichia coli.
Authors: Kazic T , Berg D E 
Published: January 2021

Abstract
We have examined the frequency with which identical deletions are formed in different chromosomal contexts. A panel of six mutant bla genes containing palindrome/direct repeat structures were moved from pBR322 to three locations: at lambda att, at chromosomal lac, and at F'lac. Deletion of the palindromes and one of the direct repeats results in reversion to Ampr. The frequency of deletion for all alleles declines beyond the reduction in copy number when they are moved from the multicopy plasmid environment to a single-copy chromosome. The magnitude of the declines varies in an allele-specific and location-specific manner. Our data support the hypothesis that context can influence the frequency of mutation independent of the immediate DNA sequence.
Transvection in the Drosophila Ultrabithorax gene: a Cbx1 mutant allele induces ectopic expression of a normal allele in trans.
Authors: Castelli-Gair J E , Micol J L , García-Bellido A 
Published: January 2021

Abstract
In wild-type Drosophila melanogaster larvae, the Ultrabithorax (Ubx) gene is expressed in the haltere imaginal discs but not in the majority of cells of the wing imaginal discs. Ectopic expression of the Ubx gene in wing discs can be elicited by the presence of Contrabithorax (Cbx) gain-of-function alleles of the Ubx gene or by loss-of-function mutations in Polycomb (Pc) or in other trans-regulatory genes which behave as repressors of Ubx gene activity. Several Ubx loss-of-function alleles cause the absence of detectable Ubx proteins (UBX) or the presence of truncated UBX lacking the homeodomain. We have compared adult wing phenotypes with larval wing disc UBX patterns in genotypes involving double mutant chromosomes carrying in cis one of those Ubx mutations and the Cbx1 mutation. We show that such double mutant genes are (1) active in the same cells in which the single mutant Cbx1 is expressed, although they are unable to yield functional proteins, and (2) able to induce ectopic expression of a normal homologous Ubx allele in a part of the cells in which the single mutant Cbx1 is active. That induction is conditional upon pairing of the homologous chromosomes (the phenomenon known as transvection), and it is not mediated by UBX. Depletion of Pc gene products by Pc3 mutation strongly enhances the induction phenomenon, as shown by (1) the increase of the number of wing disc cells in which induction of the homologous allele is detectable, and (2) the induction of not only a paired normal allele but also an unpaired one.
DNA sequence variation within maize and melon: observations from polymerase chain reaction amplification and direct sequencing.
Authors: Shattuck-Eidens D M , Bell R N , Neuhausen S L , Helentjaris T 
Published: January 2021

Abstract
While compiling genetic linkage maps in several plant species based upon restriction fragment length polymorphisms (RFLPs), it was noted that the incidence of polymorphism differs among species. The basis of this disparity was investigated in this study by examining the nucleotide sequence at homologous loci among distinct cultivars within two species which exhibit considerably different levels of RFLPs. Using the polymerase chain reaction, homologous regions from different cultivars were first amplified and the nucleotide sequence of the products were determined. Four genomic regions of seven maize cultivars and three genomic regions of eight melon cultivars were examined to compare the respective levels of sequence variation between the two species. Levels of variation for both base substitutions and insertions/deletions varied widely among the maize sequences and between maize and melon for base substitutions. Estimates of theta (a measure of polymorphism) ranged from 0 to 0.002 in melon and from 0.006 to 0.040 for base substitutions and from 0.002 to 0.023 for insertions/deletions in maize. Critical value tests and chi-squared tests suggested that in maize the underlying processes generating and maintaining neutral mutations differ among the regions. The results not only suggest that several mechanisms are necessary to explain the variation seen in these two species, but also point to some basic dissimilarities in the organization and maintenance of the genomes of different plant species.
Relationship between migration and DNA polymorphism in a local population.
Authors: Tajima F 
Published: January 2021

Abstract
The expected amount of DNA polymorphism, measured in terms of the number of nucleotide differences between the two DNA sequences randomly sampled from subpopulations, was studied by using the stepping-stone model and the finite island model, under the assumption that the migration rate is not the same among different subpopulations. The results obtained indicate that the expected amount of DNA polymorphism in the subpopulation with lower migration rate is smaller than that of higher migration rate. This suggests that marginal populations tend to have lower level of DNA polymorphism than central populations if the migration rate in the marginal populations is lower than that of the central populations.
How informative is Wright's estimator of the number of genes affecting a quantitative character?
Authors: Zeng Z B , Houle D , Cockerham C C 
Published: January 2021

Abstract
S. Wright suggested an estimator, m, of the number of loci, m, contributing to the difference in a quantitative character between two differentiated populations, which is calculated from the phenotypic means and variances in the two parental populations and their F1 and F2 hybrids. The same method can also be used to estimate m contributing to the genetic variance within a single population, by using divergent selection to create differentiated lines from the base population. In this paper we systematically examine the utility and problems of this technique under the influences of unequal allelic effects and initial allele frequencies, and linkage, which are known to lead m to underestimate m. In addition, we examine the effects of population size and selection intensity during the generations of selection. During selection, the estimator m rapidly approaches its expected value at the selection limit. With reasonable assumptions about unequal allelic effects and initial allele frequencies, the expected value of m without linkage is likely to be on the order of one-third of the number of genes. The estimates suffer most seriously from linkage. The practical maximum expectation of m is just about the number of chromosomes, considerably less than the "recombination index" which has been assumed to be the upper limit. The estimates are also associated with large sampling variances. An estimator of the variance of m derived by R. Lande substantially underestimates the actual variance. Modifications to the method can ameliorate some of the problems. These include using F3 or later generation variances or the genetic variance in the base population, and replicating the experiments and estimation procedure. However, even in the best of circumstances, information from m is very limited and can be misleading.
Detecting isolation by distance using phylogenies of genes.
Authors: Slatkin M , Maddison W P 
Published: January 2021

Abstract
We introduce a method for analyzing phylogenies of genes sampled from a geographically structured population. A parsimony method can be used to compute s, the minimum number of migration events between pairs of populations sampled, and the value of s can be used to estimate the effective migration rate M, the value of Nm in an island model with local populations of size N and a migration rate m that would yield the same value of s. Extensive simulations show that there is a simple relationship between M and the geographic distance between pairs of samples in one- and two-dimensional models of isolation by distance. Both stepping-stone and lattice models were simulated. If two demes k steps apart are sampled, then, s, the average value of s, is a function only of k/(Nm) in a one-dimensional model and is a function only of k/(Nm)2 in a two-dimensional model. Furthermore, log(M) is approximately a linear function of log(k). In a one-dimensional model, the regression coefficient is approximately -1 and in a two-dimensional model the regression coefficient is approximately -0.5. Using data from several locations, the regression of log(M) on log(distance) may indicate whether there is isolation by distance in a population at equilibrium and may allow an estimate of the effective migration rate between adjacent sampling locations. Alternative methods for analyzing DNA sequence data from a geographically structured population are discussed. An application of our method to the data of R. L. Cann, M. Stoneking and A. C. Wilson on human mitochondrial DNA is presented.
Genetic and molecular characterization of the optomotor-blind gene locus in Drosophila melanogaster.
Authors: Pflugfelder G O , Schwarz H , Roth H , Poeck B , Sigl A , Kerscher S , Jonschker B , Pak W L , Heisenberg M 
Published: January 2021

Abstract
The Drosophila gene optomotor-blind (omb) is involved in the development of a set of giant neurons in the optic lobes and possibly other structures in the imaginal brain. Adult flies have discrete defects in optomotor behavior. The gene has previously been mapped in chromomeres 4C5-6, together with three other genes, bifid, Quadroon and lacqueredgls. We have localized the gene in a genomic walk of 340 kb of DNA. By mapping seven chromosome breakpoints with omb phenotype we determined its minimum size to about 80 kb. From this region more than 20 RNAs of different size and temporal expression pattern are transcribed. Three of them (T3, T7 and T7') stem from primary transcripts of 40-80 kb in length. In its distal part the omb gene overlaps in at least 19 kb with four other complementation units, bifid, l(1)bifid, Quadroon and lacqueredgls. The three nonlethals affect the external appearance of the fly and seem to be unrelated to brain development.
Mitochondrial genetics in a natural population of the plant pathogen armillaria.
Authors: Smith M L , Duchesne L C , Bruhn J N , Anderson J B 
Published: January 2021

Abstract
Transmission and propagation of mitochondrial genotypes in fungi have not been previously investigated in the field. This study examined the distribution of nuclear and mitochondrial genotypes in a natural, local population of the fungal (Basidiomycetes) root-rot pathogen, Armillaria. Six vegetative clones, ranging in size up to 635 m, were identified on the basis of mating-type alleles. Mitochondrial DNA (mtDNA) restriction fragment patterns indicated that each vegetative clone has one, unique mtDNA type. However, as in other basidiomycetous fungi, biparental transmission of mitochondria following laboratory matings of sexually compatible haploid isolates of Armillaria resulted in a uniformly diploid mycelium that was a mosaic for both parental mitochondrial types. Therefore, either matings between monosporous, haploid isolates are uncommon in nature, or when mating does occur, cytoplasmic markers of one partner predominate during subsequent vegetative growth.
Phylogenetically informative length polymorphism and sequence variability in mitochondrial DNA of Australian songbirds (Pomatostomus).
Authors: Edwards S V , Wilson A C 
Published: January 2021

Abstract
A combination of restriction analysis and direct sequencing via the polymerase chain reaction (PCR) was used to build trees relating mitochondrial DNAs (mtDNAs) from 50 individuals belonging to five species of Australian babblers (Pomatostomus). The trees served as a quantitative framework for analyzing the direction and tempo of evolution of an intraspecific length polymorphism from a third mitochondrial ancestor. The length polymorphism lies between the cytochrome b and 12S rRNA (srRNA) genes. Screening of mtDNAs within and between the five species with restriction enzymes showed that Pomatosomus temporalis was polymorphic for two smaller size classes (M and S) that are completely segregated geographically, whereas mtDNAs from the other four species were exclusively of a third, larger size (L). Inter- and intraspecific phylogenetic trees relating mtDNAs based on restriction maps, cytochrome b sequences obtained via PCR, and the two data sets combined were compared to one another statistically and were broadly similar except for the phylogenetic position of Pomatosomus halli. Both sets of phylogenies imply that only two deletion events can account for the observed intraspecific distribution of the three length types. High levels of base-substitutional divergence were detected within and between northern and southern lineages of P. temporalis, which implies a low level of gene flow between northern and southern regions as well as a low rate of length mutation. These conclusions were confirmed by applying coalescent theory to the statistical framework provided by the phylogenetic analyses.
Using molecular markers to estimate quantitative trait locus parameters: power and genetic variances for unreplicated and replicated progeny.
Authors: Knapp S J , Bridges W C 
Published: January 2021

Abstract
Many of the progeny types used to estimate quantitative trait locus (QTL) parameters can be replicated, e.g., recombinant inbred, doubled haploid, and F3 lines. These parameters are estimated using molecular markers or QTL genotypes estimated from molecular markers as independent variables. Experiment designs for replicated progeny are functions of the number of replications per line (r) and the number of replications per QTL genotype (n). The value of n is determined by the size of the progeny population (N), the progeny type, and the number of simultaneously estimated QTL parameters (q - 1). Power for testing hypotheses about means of QTL genotypes is increased by increasing r and n, but the effects of these factors have not been quantified. In this paper, we describe how power is affected by r, n, and other factors. The genetic variance between lines nested in QTL genotypes (sigma 2n:q) is the fraction of the genetic variance between lines (sigma 2n) which is not explained by simultaneously estimated intralocus and interlocus QTL parameters (phi 2Q); thus, sigma 2n:q = sigma 2n - phi 2Q. If sigma 2n:q not equal to 0, then power is not efficiently increased by increasing r and is maximized by maximizing n and using r = 1; however, if sigma 2n:q = 0, then r and n affect power equally and power is efficiently increased by increasing r and is maximized by maximizing N.r. Increasing n efficiently increases power for a wide range of values of sigma 2n:q.sigma 2n:q = 0 when the genetic variance between lines is fully explained by QTL parameters (sigma 2n = phi 2Q).(ABSTRACT TRUNCATED AT 250 WORDS)
Characterization of enhancer-of-white-apricot in Drosophila melanogaster.
Authors: Peng X B , Mount S M 
Published: January 2021

Abstract
The white-apricot (wa) allele differs from the wild-type white gene by the presence of the retrovirus-like transposable element copia within the transcription unit. Most RNAs derived from wa have 3' termini within this insertion, and only small amounts of structurally normal RNA are produced. The activity of wa is reduced in trans by a semidominant mutation in the gene Enhancer-of-white-apricot (E(wa). Flies that are wa and heterozygous for the enhancer have eyes which are much lighter than the orange-yellow of wa alone while E(wa) homozygotes have white eyes. This semidominant effect on pigmentation is correlated with a corresponding decrease in white RNA having wild type structure, and flies homozygous for E(wa) have increased levels of aberrant RNAs. Three reverant alleles of E(wa) generated by reversion of the dominant enhancer phenotype with gamma radiation are noncomplementing recessive lethals, with death occurring during the larval stage. The effects on wa eye pigmentation of varying doses of the original E(wa) allele, the wild type allele, and the revertant alleles suggest that the original E(wa) allele produces a product that interferes with the activity of the wild type gene and that the revertants are null alleles. We propose that the E(wa) gene product influences the activity of the downstream copia long terminal repeat in 3' end formation.
The unusual sexual preferences of a chlamydomonas mutant may provide insight into mating-type evolution.
Authors: Van Winkle-Swift K P , Thuerauf D J 
Published: January 2021

Abstract
Chlamydomonas monoica undergoes intraclonal mating-type differentiation (homothallism). Although the species differs in this regard from the more commonly studied heterothallic C. reinhardtii, cell-cell interactions and progression of the sexual cycle are similar for many homothallic and heterothallic species of the genus. Regulation of chloroplast gene transmission by the nuclear mating-type alleles (mt+ and mt-) is another common denominator for Chlamydomonas species studied thus far. We have previously reported the use of chloroplast inheritance patterns to identify mutants of C. monoica that have lost the potential to function as the mt+ mating-type. A similar screening procedure led to the isolation of an unusual mutant, mtl-3 whose phenotype is less readily explained. Chloroplast gene transmission patterns in crosses involving mtl-3 suggest that the mtl-3 strain mates preferentially as mt+. However, normal mating efficiencies and high zygospore viability are observed in clonal culture, indicating the unbiased production of functional opposite mating-types. By construction of appropriately marked strains we have been able to show that mtl-3 mt- gametes prefer the mt+ gametes of their own strain. A model is presented which invokes unequal crossing over between highly homologous flagellar agglutinin genes to account for the unusual properties of the mtl-3 strain and for the evolution of mating barriers within the genus.
Isolation and characterization of Escherichia coli mutants with altered rates of deletion formation.
Authors: Whoriskey S K , Schofield M A , Miller J H 
Published: January 2021

Abstract
Using site-specific mutagenesis in vitro we constructed a genetic system to detect mutants with altered rates of deletion formation between short repeated sequences in Escherichia coli. After in vivo mutagenesis with chemical mutagens and transposons, the system allowed the identification of mutants with either increased or decreased deletion frequencies. One mutational locus, termed mutR, that results in an increase in deletion formation, was studied in detail. The mutR gene maps at 38.5 min on the E. coli genetic map. Since the precise excision of many transposable elements is also mediated at short repeated sequences, we investigated the effects of the mutant alleles, as well as recA, on precise excision of the transposon Tn9. Neither mutR nor recA affect precise excision of the transposon Tn9, from three different insertions in lacI, whereas these alleles do affect other spontaneous deletions in the same system. These results indicate that deletion events leading to precise excision occur principally via a different pathway than other random spontaneous deletions. It is suggested that, whereas precise excision occurs predominantly via a pathway involving replication enzymes (for instance template strand slippage), deletions on an F'factor are stimulated by recombination enzymes.
A novel recombinator in yeast based on gene II protein from bacteriophage f1.
Authors: Strathern J N , Weinstock K G , Higgins D R , McGill C B 
Published: January 2021

Abstract
Interchromosomal mitotic recombination in yeast can be stimulated by the protein encoded by gene II of bacteriophage f1. The normal role of the gene II enzyme is to make a site-specific cleavage of a particular strand of the duplex form of the bacteriophage DNA at the origin of DNA replication. The gene II protein was expressed in yeast in an attempt to determine the role of nicked DNA in the initiation of recombination. Stimulation of recombination in yeast by the gene II protein was dependent on the presence of a recognition site for gene II enzyme in the region being assayed. Recombination was stimulated in both directions from the gene II recognition site but showed a directional bias. The distribution of alleles among the recombinants indicated that the chromosome with the gene II recognition site acted as the recipient in gene conversion events.