bluuebunny/crossref_metadata_2025_split huggingface dataset:
A cladistic measure of gene flow inferred from the phylogenies of alleles.
Authors: Slatkin M , Maddison W P 
Published: January 2021

Abstract
A method for estimating the average level of gene flow among populations is introduced. The method provides an estimate of Nm, where N is the size of each local population in an island model and m is the migration rate. This method depends on knowing the phylogeny of the nonrecombining segments of DNA that are sampled. Given the phylogeny, the geographic location from which each sample is drawn is treated as multistate character with one state for each geographic location. A parsimony criterion applied to the evolution of this character on the phylogeny provides the minimum number of migration events consistent with the phylogeny. Extensive simulations show that the distribution of this minimum number is a simple function of Nm. Assuming the phylogeny is accurately estimated, this method provides an estimate of Nm that is as nearly as accurate as estimates obtained using FST and other statistics when Nm is moderate. Two examples of the use of this method with mitochondrial DNA data are presented.
Analysis of yeast retrotransposon Ty insertions at the CAN1 locus.
Authors: Wilke C M , Heidler S H , Brown N , Liebman S W 
Published: January 2021

Abstract
The target site distribution for 55 independent Ty insertions that inactivate the function of the Saccharomyces cerevisiae CAN1 gene is reported. Under some selection conditions Ty elements inserted preferentially into the promoter and exhibited an orientation bias. In contrast, under other conditions no insertions were detected in the promoter region and transposition appeared to occur randomly throughout the CAN1 coding sequence. These results show that the target site distribution for Ty insertions may be a function of the selection conditions.
Allozyme-associated heterosis in Drosophila melanogaster.
Authors: Houle D 
Published: January 2021

Abstract
Two large experiments designed to detect allozyme-associated heterosis for growth rate in Drosophila melanogaster were performed. Heterosis associated with allozyme genotypes may be explained either by functional overdominance at the allozyme loci, or closely linked loci; or by genotypic correlations between allozyme loci and loci at which deleterious recessive alleles segregate. Such genotypic correlations would be favored by consanguineous mating, small effective population size, population mixing and strong natural or artificial selection. D. melanogaster is outbred, has large effective population size and there is little evidence for genotypic disequilibria. Therefore it would be unlikely to show allozyme heterosis due to genotypic correlations. In the first experiment I estimated the genotypic values of 97 replicated genotypes. In the second experiment, 500 individuals were raised in a fluctuating, stressful environment. In neither experiment was there any consistent evidence for allozyme heterosis in size or development rate, fluctuating asymmetry for size or in tendency to deviate from the population mean. In the first experiment, heterosis explained less than 5.6% of the genetic variance in growth characters. In the second, heterosis explained less than 0.1% of the phenotypic variance in growth characters. Outside of the molluscs, species which show allozyme heterosis have population structures or histories which tend to promote genotypic correlations. There is little evidence that functional overdominance is responsible for observations of allozyme-associated heterosis.
Laboratory estimates of heritabilities and genetic correlations in nature.
Authors: Riska B , Prout T , Turelli M 
Published: January 2021

Abstract
A lower bound on heritability in a natural environment can be determined from the regression of offspring raised in the laboratory on parents raised in nature. An estimate of additive genetic variance in the laboratory is also required. The estimated lower bounds on heritabilities can sometimes be used to demonstrate a significant genetic correlation between two traits in nature, if their genetic and phenotypic correlations in nature have the same sign, and if sample sizes are large, and heritabilities and phenotypic and genetic correlations are high.
Dosage effects of a Drosophila sodium channel gene on behavior and axonal excitability.
Authors: Stern M , Kreber R , Ganetzky B 
Published: January 2021

Abstract
The effects of para mutations on behavior and axonal excitability in Drosophila suggested that para specifically affects sodium channels. This hypothesis was confirmed by molecular analysis of the para locus, which demonstrates that the encoded para product is a sodium channel polypeptide. Here we characterize the effects of altered para+ dosage on behavior and axonal excitability, both in an otherwise wild-type background and in combination with two other mutations: napts, which also affects sodium channels, and ShKS133, which specifically affects potassium channels. Whereas it was previously shown that decreased dosage of para+ is unconditionally lethal in a napts background, we find that increased dosage of para+ suppresses napts. Similarly, we find that para hypomorphs or decreased dosage of para+ suppresses ShKS133, whereas increased dosage of para+ enhances ShKS133). The electrophysiological basis for these effects is investigated. Other genes in Drosophila that have sequence homology to sodium channels do not show such dosage effects, which suggests that the para+ product has a function distinct from that of other putative Drosophila sodium channel genes. We conclude that the number of sodium channels present in at least some Drosophila neurons can be affected by changes in para+ gene dosage, and that the level of para+ expression can strongly influence neuronal excitability.
Statistical genetics of an annual plant, Impatiens capensis. II. Natural selection.
Authors: Mitchell-Olds T , Bergelson J 
Published: January 2021

Abstract
Measurement of natural selection on correlated characters provides valuable information on fitness surfaces, patterns of directional, stabilizing, or disruptive selection, mechanisms of fitness variation operating in nature, and possible spatial variation in selective pressures. We examined effects of seed weight, germination date, plant size, early growth, and late growth on individual fitness. Path analysis showed that most characters had direct or indirect effects on individual fitness, indicating directional selection. For most early life-cycle characters, indirect effects via later characters exceed the direct causal effect on fitness. Selection gradients were uniform across the experimental site. There was no evidence for stabilizing or disruptive selection. We discuss several definitions of stabilizing and disruptive selection. Although early events in the life of an individual have important causal effects on subsequent characters and fitness, there is no detectable genetic variance for most of these characters, so little or no genetic response to natural selection is expected.
The SRS2 suppressor of rad6 mutations of Saccharomyces cerevisiae acts by channeling DNA lesions into the RAD52 DNA repair pathway.
Authors: Schiestl R H , Prakash S , Prakash L 
Published: January 2021

Abstract
rad6 mutants of Saccharomyces cerevisiae are defective in the repair of damaged DNA, DNA damage induced mutagenesis, and sporulation. In order to identify genes that can substitute for RAD6 function, we have isolated genomic suppressors of the UV sensitivity of rad6 deletion (rad6 delta) mutations and show that they also suppress the gamma-ray sensitivity but not the UV mutagenesis or sporulation defects of rad6. The suppressors show semidominance for suppression of UV sensitivity and dominance for suppression of gamma-ray sensitivity. The six suppressor mutations we isolated are all alleles of the same locus and are also allelic to a previously described suppressor of the rad6-1 nonsense mutation, SRS2. We show that suppression of rad6 delta is dependent on the RAD52 recombinational repair pathway since suppression is not observed in the rad6 delta SRS2 strain containing an additional mutation in either the RAD51, RAD52, RAD54, RAD55 or RAD57 genes. Possible mechanisms by which SRS2 may channel unrepaired DNA lesions into the RAD52 DNA repair pathway are discussed.
Pathways of transformation in Ustilago maydis determined by DNA conformation.
Authors: Fotheringham S , Holloman W K 
Published: January 2021

Abstract
Ustilago maydis was transformed by plasmids bearing a cloned, selectable gene but lacking an autonomously replicating sequence. Transformation was primarily through integration at nonhomologous loci when the plasmid DNA was circular. When the DNA was made linear by cleavage within the cloned gene, the spectrum of integration events shifted from random to targeted recombination at the resident chromosomal allele. In a large fraction of the transformants obtained using linear DNA, the plasmid DNA was not integrated but was maintained in an extrachromosomal state composed of a concatameric array of plasmid units joined end-to-end. The results suggest the operation of several pathways for transformation in U. maydis, and that DNA conformation at the time of transformation governs choice of pathways.
Effect of abx, bx and pbx mutations on expression of homeotic genes in Drosophila larvae.
Authors: Little J W , Byrd C A , Brower D L 
Published: January 2021

Abstract
We have examined the patterns of expression of the homeotic gene Ubx in imaginal discs of Drosophila larvae carrying mutations in the abx, bx and pbx regulatory domains. In haltere discs, all five bx insertion mutations examined led to a general reduction in Ubx expression in the anterior compartment; for a given allele, the strength of the adult cuticle phenotype correlated with the degree of Ubx reduction. Deletions mapping near or overlapping the sites of bx insertions, including three abx alleles and the bx34e-prv(bx-prv) allele, showed greatly reduced Ubx expression in parts of the anterior compartment of the haltere disc; however, anterior patches of strong Ubx expression often remained, in highly variable patterns. As expected, the pbx1 mutation led to reduced Ubx expression in the posterior compartment of the haltere disc; surprisingly, pbx1 also led to altered expression of the en protein near the compartment border in the central region of the disc. In the metathoracic leg, all the bx alleles caused extreme reduction in Ubx expression in the anterior regions, with no allele-specific differences. In contrast, abx and bx-prv alleles resulted in patchy anterior reductions in third leg discs. In the larval central nervous system, abx but not bx alleles affected Ubx expression; the bx-prv deletion gave a wild-type phenotype, but it could not fully complement abx mutations. In the posterior wing disc, the bx-prv allele, and to a much lesser extent the bx34e chromosome from which it arose, led to ectopic expression of Ubx. Unlike other grain-of-function mutations in the BX-C, this phenotype appeared to be partially recessive to wild type. Finally, we asked whether the ppx transformation, which results from early lack of Ubx+ function in the mesothorax and is seen in abx animals, is due to ectopic Scr expression. Some mesothoracic leg and wing discs from abx2 larvae displayed ectopic expression of Scr, which was variable in extent but always confined to the posterior compartment.
Molecular cloning and genetic mapping of the t complex responder candidate gene family.
Authors: Bullard D C , Schimenti J C 
Published: January 2021

Abstract
Male transmission ratio distortion (TRD) is a property of mouse t haplotypes requiring the t complex responder locus (Tcr). Tcr maps to the central region of t haplotypes, and is embedded within a series of large duplicated tracts of DNA known as "T66 elements." In previous work, a family of genes (the "T66" genes) was identified within this region that encodes male germ cell-specific transcripts. Genetic and molecular data indicate that one of these genes represents Tcr. Here, we describe the molecular cloning of the four members of the T66 gene family, the genetic mapping of these genes to three adjacent t haplotype loci, and comparative restriction enzyme analysis of the genes. The results indicate that these genes are highly similar to one another, and were created by recent, complex duplication events. This suggests that a minor alteration(s) could have been responsible for conferring "mutant" responder activity upon Tcr, while the other homologs retained "wild-type" biochemical function. In addition, we have identified and mapped three T66 genes in wild-type t complexes. They reside in two separate loci at the opposite ends of the proximal t complex inversion, and are separated by at least 3 cM.
The organization and expression of the light gene, a heterochromatic gene of Drosophila melanogaster.
Authors: Devlin R H , Bingham B , Wakimoto B T 
Published: January 2021

Abstract
The light (lt) gene is located in the centromeric heterochromatin of chromosome 2 of Drosophila melanogaster. This gene is necessary for normal levels of pigmentation in a number of adult and larval tissues and is required for viability. Hybrid dysgenic and X-ray induced mutations have been used to identify the gene and compare its organization to that of euchromatic genes. Molecular mapping of lt mutations and its major transcripts has shown that the lt gene is at least 17 kb. By injecting cosmid clones that include this region into lt mutant embryos, we have defined a 30-kb region that can transiently rescue the pigmentation defect in the Malpighian tubules. The major transcription unit of this gene is comprised of exons that are single copy. It is unusual in its organization in having a heterogeneous array of middle repetitive DNA sequences within its intronic and flanking regions.
Alternative fitness models with the same allele frequency dynamics.
Authors: Denniston C , Crow J F 
Published: January 2021

Abstract
For any set of one- or two-locus genotypic fitnesses there are alternative sets, usually frequency-dependent and often with quite different biological meanings, that give rise to the same equations for change of allele or haplotype frequencies. Therefore, it is not possible to distinguish among alternative fitness models from allele or haplotype frequency trajectories or equilibrium distributions. For a single locus and for two loci when linkage equilibrium can be assumed, a simple procedure generates some of the alternative fitness sets.
Tissue-specific expression phenotypes of Hawaiian Drosophila Adh genes in Drosophila melanogaster transformants.
Authors: Wu C Y , Mote J , Brennan M D 
Published: January 2021

Abstract
Interspecific differences in the tissue-specific patterns of expression displayed by the alcohol dehydrogenase (Adh) genes within the Hawaiian picture-winged Drosophila represent a rich source of evolutionary variation in gene regulation. Study of the cis-acting elements responsible for regulatory differences between Adh genes from various species is greatly facilitated by analyzing the behavior of the different Adh genes in a homogeneous background. Accordingly, the Adh gene from Drosophila grimshawi was introduced into the germ line of Drosophila melanogaster by means of P element-mediated transformation, and transformants carrying this gene were compared to transformants carrying the Adh genes from Drosophila affinidisjuncta and Drosophila hawaiiensis. The results indicate that the D. affinidisjuncta and D. grimshawi genes have relatively higher levels of expression and broader tissue distribution of expression than the D. hawaiiensis gene in larvae. All three genes are expressed at similar overall levels in adults, with differences in tissue distribution of enzyme activity corresponding to the pattern in the donor species. However, certain systematic differences between Adh gene expression in transformants and in the Hawaiian Drosophila are noted along with tissue-specific position effects in some cases. The implications of these findings for the understanding of evolved regulatory variation are discussed.
Parental analysis of introgressive hybridization between African and European honeybees using nuclear DNA RFLPs.
Authors: Hall H G 
Published: January 2021

Abstract
African honeybees, introduced into Brazil 33 years ago, have spread through most of South and Central America and have largely replaced the extant European bees. Due to a paucity of genetic markers, genetic interactions between European and African bees are not well understood. Three restriction fragment length polymorphisms (RFLPs), detected with random, nuclear DNA probes, are described. The polymorphisms are specific to bees of European descent, possibly specific to certain European races. Each European marker was found present at a high frequency in U.S. colonies but absent in South African bees. Previous mitochondrial DNA studies of neotropical bees have revealed negligible maternal gene flow from managed European apiaries into feral African populations. The findings reported here with nuclear DNA show paternal gene flow between the two but suggest asymmetries in levels of introgressive hybridization. Managed colonies in southern Mexico, derived from European maternal lines, showed diminished levels of the European nuclear markers, reflecting significant hybridization with African drones. The European alleles were present only at low frequencies in feral swarms from the same area. The swarms were of African maternal descent. In Venezuelan colonies, also derived from African maternal lines, the European markers were almost totally absent. The results point to limited paternal introgression from European colonies into the African honeybee populations. These findings dispute other views regarding modes of Africanization.
"Alternative self-diploidization" or "ASD" homothallism in Saccharomyces cerevisiae: isolation of a mutant, nuclear-cytoplasmic interaction and endomitotic diploidization.
Authors: Ono B , Ishino-Arao Y , Takasugi K , Taniguchi M , Fukuda M , Fukui M , Miyakawa I , Sando N 
Published: January 2021

Abstract
A mutant of Saccharomyces cerevisiae representing a novel life cycle, named "alternative self-diploidization" or "ASD" homothallism, was obtained fortuitously. In this life cycle, MAT alpha (or MATa) haplophase and MAT alpha/MAT alpha (or MATa/MATa) diplophase alternate. Germinated cells are haploid and mating. They soon become nonmating and sporogenous as they vegetatively grow. They sooner or later diploidize presumably via endomitosis. The diploid cells haploidize via normal meiosis. A single recessive nuclear mutation, named asd 1-1, is responsible for "ASD" homothallism. In the rho 0 cytoplasm, asd 1-1 cells mate even if at a low efficiency and fail to diploidize. Since pet mutations do not have such effects, we conclude that a certain mitochondrial function other than respiration is required for manifestation of "ASD" homothallism. That is, "ASD" homothallism is the result of some sort of nuclear-cytoplasmic interaction.
Genetic analysis of the enhancer of zeste locus and its role in gene regulation in Drosophila melanogaster.
Authors: Jones R S , Gelbart W M 
Published: January 2021

Abstract
The Enhancer of zeste [E(z)] locus of Drosophila melanogaster is implicated in multiple examples of gene regulation during development. First identified as dominant gain-of-function modifiers of the zeste1-white (z-w) interaction, mutant E(z) alleles also produce homeotic transformations. Reduction of E(z)+ activity leads to both suppression of the z-w interaction and ectopic expression of segment identity genes of the Antennapedia and bithorax gene complexes. This latter effect defines E(z) as a member of the Polycomb-group of genes. Analysis of E(z)S2, a temperature-sensitive E(z) allele, reveals that both maternally and zygotically produced E(z)+ activity is required to correctly regulate the segment identity genes during embryonic and imaginal development. As has been shown for other Polycomb-group genes, E(z)+ is required not to initiate the pattern of these genes, but rather to maintain their repressed state. We propose that the E(z) loss-of-function eye color and homeotic phenotypes may both be due to gene derepression, and that the E(z)+ product may be a general repressing factor required for both examples of negative gene regulation.
Mutations affecting the meiotic and mitotic divisions of the early Caenorhabditis elegans embryo.
Authors: Mains P E , Kemphues K J , Sprunger S A , Sulston I A , Wood W B 
Published: January 2021

Abstract
We describe interactions between maternal-effect lethal mutations in four genes of Caenorhabditis elegans whose products appear to be involved in the meiotic and mitotic divisions of the one-cell embryo. Mitosis is disrupted by two dominant temperature-sensitive gain-of-function maternal-effect lethal mutations, mei-1(ct46) and mel-26(ct61), and by recessive loss-of-function maternal-effect lethal mutations of zyg-9. The phenotypic defects resulting from these mutations are similar. Doubly mutant combinations show a strong enhancement of the maternal-effect lethality under semipermissive conditions, suggesting that the mutant gene products interact. We isolated 15 dominant suppressors of the gain-of-function mutation mei-1(ct46). Thirteen of these suppressors are apparently intragenic, but 11 of them suppress in trans as well as cis. Two extragenic suppressors define a new gene, mei-2. The suppressor mutations in these two genes also result in recessive maternal-effect lethality, but with meiotic rather than mitotic defects. Surprisingly, most of these suppressors are also able to suppress mel-26(ct61) in addition to mei-1(ct46). The products of the four genes mei-1, mei-2, zyg-9 and mel-26 could be responsible for some of the specialized features that distinguish the meiotic from the mitotic divisions in the one-cell embryo.
The exuperantia gene is required for Drosophila spermatogenesis as well as anteroposterior polarity of the developing oocyte, and encodes overlapping sex-specific transcripts.
Authors: Hazelrigg T , Watkins W S , Marcey D , Tu C , Karow M , Lin X R 
Published: January 2021

Abstract
The Drosophila gene exuperantia (exu) is a maternal effect gene which is needed for proper localization of the bcd RNA during the formation of oocytes. We have extended the characterization of the exu phenotype and find that the gene functions in the male as well as the female germline. Six of seven exu alleles are male-sterile; mutant defects in spermatogenesis first appear during meiosis. A genetic analysis presented here shows that the exu gene does not encode a zygotic vital function. The isolation of two overlapping deficiencies that delete exu function localizes the gene cytologically to polytene bands 57A4-B1. We describe the molecular cloning and identification of the gene, and show that it encodes overlapping sex-specific transcripts of 2.9 kb in the male and 2.1 kb in the female. We also show that these two transcripts are limited in expression to the germline. We demonstrate that one allele, exuVL57, is a deletion of about 700 bp which results in a loss of both transcripts.