bluuebunny/crossref_metadata_2025 huggingface dataset:
A Bayesian Approach to Detect Quantitative Trait Loci Using Markov Chain Monte Carlo
Authors: Satagopan Jaya M , Yandell Brian S , Newton Michael A , Osborn Thomas C
Published: January 2021

Markov chain Monte Carlo (MCMC) techniques are applied to simultaneously identify multiple quantitative trait loci (QTL) and the magnitude of their effects. Using a Bayesian approach a multi-locus model is fit to quantitative trait and molecular marker data, instead of fitting one locus at a time. The phenotypic trait is modeled as a linear function of the additive and dominance effects of the unknown QTL genotypes. Inference summaries for the locations of the QTL and their effects are derived from the corresponding marginal posterior densities obtained by integrating the likelihood, rather than by optimizing the joint likelihood surface. This is done using MCMC by treating the unknown QTL genotypes, and any missing marker genotypes, as augmented data and then by including these unknowns in the Markov chain cycle along with the unknown parameters. Parameter estimates are obtained as means of the corresponding marginal posterior densities. High posterior density regions of the marginal densities are obtained as confidence regions. We examine flowering time data from double haploid progeny of Brassica napus to illustrate the proposed method.
Estimating the Age of the Common Ancestor of a DNA Sample Using the Number of Segregating Sites
Authors: Fu Yun-Xin
Published: January 2021

The number of segregating sites in a sample of DNA sequences and the age of the most recent common ancestor (MRCA) of the sequences in the sample are positively correlated. The value of the former can be used to estimate the value of the latter. Using the coalescent approach, we derive in this paper the joint probability distribution of the number of segregating sites and the age of the MRCA of a sample under the neutral Wright-Fisher model. From this distribution, we are able to compute the likelihood function of the number of segregating sites and the posterior probability of the age of the MRCA of a sample. Three point estimators and one interval estimator of the age of the MRCA are developed; their relationships and properties are investigated. The estimation of the age of the MRCA of human Y chromosomes from a sample of no variation is discussed.
An Evaluation of Evolutionary Constraints on Microsatellite Loci Using Null Alleles
Authors: Lehmann Tovi , Hawley William A , Collins Frank H
Published: January 2021

A test to evaluate constraints on the evolution of single microsatellite loci is described. The test assumes that microsatellite alleles that share the same flanking sequence constitute a series of alleles with a common descent that is distinct from alleles with a mutation in the flanking sequence. Thus two or more different series of alleles at a given locus represent the outcomes of different evolutionary processes. The higher rate of mutations within the repeat region (10−3 or 10−4) compared with that of insertion/deletion or point mutations in adjacent flanking regions (10−9) or with that of recombination between the repeat and the point mutation (10−6 for sequences 100 bp long) provides the rationale for this assumption. Using a two-phase, stepwise mutation model we simulated the evolution of a number of independent series of alleles and constructed the distributions of two similarity indices between pairs of these allele series. Applying this approach to empirical data from locus AG2H46 of Anopheles gambiae resulted in a significant excess of similarity between the main and the null series, indicating that constraints affect allele distribution in this locus. Practical considerations of the test are discussed.
Compensatory Aspects of Allele Diversity at Immunoglobulin Loci: Gene Correlations in Rabbit Populations Devoid of Light Chain Diversity (oryctolagus cuniculus L.; Kerguelen Islands)
Authors: van der Loo Wessel , Boussès Patrick , Arthur Christian P , Chapuis Jean-Louis
Published: January 2021

Is there a selective advantage of increased diversity at one immunoglobulin locus when diversity at another locus is low? A previous paper demonstrated excess heterozygosity at the rabbit light chain b locus when heterozygosity was low at the heavy chain constant region e locus. Here we consider the reverse situation by analyzing allele distributions at heavy chain loci in populations fixed for the light chain b locus. We analyzed the a locus that encodes the predominantly expressed heavy chain variable region, and the d and e loci that control different parts of the Ig gamma class constant region. While there was excess heterozygosity, genetic differentiation between localities was extensive and was most pronounced for females. This was in marked contrast with observations in areas where b-locus diversity was important and confirms a negative correlation between e- and b-locus heterozygosity. Trigenic disequilibria corresponded to a significant negative correlation between e- and a-locus heterozygosity due mainly to strong variation among localities within the context of pronounced (digenic) linkage disequilibria. Although substantial, the average increase in a/e-locus single heterozygosity implemented by higher order disequilibria within localities was not significant.
Optimal Sequencing Strategies for Surveying Molecular Genetic Diversity
Authors: Pluzhnikov Anna , Donnelly Peter
Published: January 2021

Two commonly used measures of genetic diversity for intraspecies DNA sequence data are based, respectively, on the number of segregating sites, and on the average number of pairwise nucleotide differences. Expressions are derived for their variance in the presence of intragenic recombination for a panmictic population of fixed size that is at neutral equilibrium at the region sequenced. We show that, in contrast to the slow decrease in variance with increasing sample size, if the recombination rate is nonzero, the asymptotic rate of decrease of variance with increasing sequence length, for fixed sample size, is quite rapid. In particular, it is close to that which would be obtained by sequencing independent chromosome regions. The correlation between measures of diversity from linked regions is also examined. For a given total number of bases sequenced in a particular region, optimal sequencing strategies are derived. These typically involve sequencing relatively few (three to 10) long copies of the region. Under optimal strategies, the variances of the two measures are very similar for most parameter values considered. Results concerning optimal sequencing strategies will be sensitive to gross departures from the underlying assumptions, such as population bottlenecks, selective sweeps, and substantial population substructure.
Contingency Tests of Neutrality Using Intra/Interspecific Gene Trees: The Rejection of Neutrality for the Evolution of the Mitochondrial Cytochrome Oxidase II Gene in the Hominoid Primates
Authors: Templeton Alan R
Published: January 2021

Contingency tests of neutrality are performed using mitochondrial cytochrome oxidase II (COII) DNA sequences from hominoid primates, including humans. An intra-/interspecific haplotype tree is estimated, including a statistical assessment of ambiguities in tree topology and branch lengths. Four functional mutational categories are considered: silent and replacement substitutions in the transmembrane portion of the COII molecule, and silent and replacement substitutions in the cytosolic portion. Three tree topological mutational categories are used: intraspecific tips, intraspecific interiors, and interspecific fixed mutations. A full contingency analysis is performed, followed by nested contingency analyses. The analyses indicate that replacement mutations in the cytosolic portion are deleterious, and replacement mutations in the transmembrane portion and silent mutations throughout tend to be neutral. These conclusions are robust to ambiguities in tree topology and branch lengths. These inferences would have been impossible with an analysis that only contrasts silent and replacement vs. polymorphic and fixed. Also, intraspecific interior mutations have similar evolutionary dynamics to fixed mutations, so pooling tip and interior mutations into a single “polymorphic” class reduces power. Finally, the detected deleterious selection causes lowered inbreeding effective sizes, so arguments for small effective sizes in recent human evolutionary history based upon mitochondrial DNA may be invalid.
Molecular Evolution Between Drosophila melanogaster and D. simulans Reduced Codon Bias, Faster Rates of Amino Acid Substitution, and Larger Proteins in D. melanogaster
Authors: Akashi Hiroshi
Published: January 2021

Both natural selection and mutational biases contribute to variation in codon usage bias within Drosophila species. This study addresses the cause of codon bias differences between the sibling species, Drosophila melanogaster and D. simulans. Under a model of mutation-selection-drift, variation in mutational processes between species predicts greater base composition differences in neutrally evolving regions than in highly biased genes. Variation in selection intensity, however, predicts larger base composition differences in highly biased loci. Greater differences in the G+C content of 34 coding regions than 46 intron sequences between D. melanogaster and D. simulans suggest that D. melanogaster has undergone a reduction in selection intensity for codon bias. Computer simulations suggest at least a fivefold reduction in Nes at silent sites in this lineage. Other classes of molecular change show lineage effects between these species. Rates of amino acid substitution are higher in the D. melanogaster lineage than in D. simulans in 14 genes for which outgroup sequences are available. Surprisingly, protein sizes are larger in D. melanogaster than in D. simulans in the 34 genes compared between the two species. A substantial fraction of silent, replacement, and insertion/deletion mutations in coding regions may be weakly selected in Drosophila.
Identification and Characterization of FAR3, a Gene Required for Pheromone-Mediated G1 Arrest in Saccharomyces cerevisiae
Authors: Horecka Joe , Sprague George F
Published: January 2021

In haploid Saccharomyces cerevisiae cells, mating pheromones activate a signal transduction pathway that leads to cell cycle arrest in the G1 phase and to transcription induction of genes that promote conjugation. To identify genes that link the signal transduction pathway and the cell cycle machinery, we developed a selection strategy to isolate yeast mutants specifically defective for G1 arrest. Several of these mutants identified previously known genes, including CLN3, FUS3, and FAR1. In addition, a new gene, FAR3, was identified and characterized. FAR3 encodes a novel protein of 204 amino acid residues that is dispensable for viability. Northern blot experiments indicated that FAR3 expression is constitutive with respect to cell type, pheromone treatment, and cell cycle position. As a first step toward elucidating the mechanism by which Far3 promotes pheromone-mediated G1 arrest, we performed genetic and molecular experiments to test the possibility that Far3 participates in one of the heretofore characterized mechanisms, namely Fus3/Farl-mediated inhibition of Cdc28-Cln kinase activity, G1 cyclin gene repression, and G1, cyclin protein turnover. Our data indicate that Far3 effects G1 arrest by a mechanism distinct from those previously known.
Yeast Mutants Deficient in ER-Associated Degradation of the Z Variant of Alpha-1-Protease Inhibitor
Authors: McCracken Ardythe A , Karpichev Igor V , Ernaga James E , Werner Eric D , Dillin Andrew G , Courchesne William E
Published: January 2021

Saccharomyces cerevisiae mutants deficient in degradation of alpha-1-proteinase inhibitor Z (A1PiZ) have been isolated and genetically characterized. Wild-type yeast expressing A1PiZ synthesize an ER form of this protein that is rapidly degraded by an intracellular proteolytic process known as ER-associated protein degradation (ERAD). The mutant strains were identified after treatment with EMS using a colony blot immunoassay to detect colonies that accumulated high levels of A1PiZ. A total of 120,000 colonies were screened and 30 putative mutants were identified. The level of A1PiZ accumulation in these mutants, measured by ELISA, ranged from two to 11 times that of A1PiZ in the parent strain. Further studies demonstrated that the increased levels of A1PiZ in most of the mutant strains was not the result of defective secretion or elevated A1PiZ mRNA. Pulse chase experiments indicated that A1PiZ was stabilized in several strains, evidence that these mutants are defective in ER-associated protein degradation. Genetic analyses revealed that most of the mutations were recessive, ∼30% of the mutants characterized conformed to simple Mendelian inheritance, and at least seven complementation groups were identified.
Identification of Residues in Fission Yeast and Human p34cdc2 Required for S-M Checkpoint Control
Authors: Basi Gabriele , Enoch Tamar
Published: January 2021

In fission yeast, regulation of p34cdc2 plays an important role in the checkpoint coupling mitosis to completion of DNA replication. The cdc2 mutations cdc2-3w (C67Y) and cdc2-4w (C67F) abolish checkpoint control without seriously affecting normal cell proliferation. However the molecular basis of this phenotype is not known. To better understand the role of p34cdc2 in checkpoint control, we have screened for more mutations in Schizosaccharomyces pombe cdc2 with this phenotype. We have isolated cdc2-3w and cdc2-4w, as well as three new cdc2 alleles: cdc2-6w (N66I), cdc2-7w (E8V) and cdc2-8w (K9E). The altered residues map to two different regions on opposite faces of the protein, suggesting that the interaction between p34cdc2 and components of the checkpoint pathway may be complex. In contrast to cdc2-3w and cdc2-4w, the new mutations alter residues that are conserved between the fission yeast cdc  + and other cdks, including the human CDC2 protein. Expression of the equivalent human CDC2 mutants in fission yeast abolishes checkpoint control, suggesting that these residues could be involved in checkpoint-dependent regulation of other eukaryotic cdks.
Genomic Libraries and a Host Strain Designed for Highly Efficient Two-Hybrid Selection in Yeast
Authors: James Philip , Halladay John , Craig Elizabeth A
Published: January 2021

The two-hybrid system is a powerful technique for detecting protein-protein interactions that utilizes the well-developed molecular genetics of the yeast Saccharomyces cerevisiae. However, the full potential of this technique has not been realized due to limitations imposed by the components available for use in the system. These limitations include unwieldy plasmid vectors, incomplete or poorly designed two-hybrid libraries, and host strains that result in the selection of large numbers of false positives. We have used a novel multienzyme approach to generate a set of highly representative genomic libraries from S. cerevisiae. In addition, a unique host strain was created that contains three easily assayed reporter genes, each under the control of a different inducible promoter. This host strain is extremely sensitive to weak interactions and eliminates nearly all false positives using simple plate assays. Improved vectors were also constructed that simplify the construction of the gene fusions necessary for the two-hybrid system. Our analysis indicates that the libraries and host strain provide significant improvements in both the number of interacting clones identified and the efficiency of two-hybrid selections.
Deletion of the Schizophyllum commune Aα Locus: The Roles of Aα Y and Z Mating-Type Genes
Authors: Robertson C Ian , Bartholomew Kirk A , Novotny Charles P , Ullrich Robert C
Published: January 2021

The Aα locus is one of four master regulatory loci that determine mating type and regulate sexual development in Schizophyllum commune. We have made a plasmid containing a URA1 gene disruption of the Aα Y1 gene. Y1 is the sole Aα gene in Aα1 strains. We used the plasmid construction to produce an Aα null (i.e., AαΔ) strain by replacing the genomic Y1 gene with URA1 in an Aα1 strain. To characterize the role of the Aα genes in the regulation of sexual development, we transformed various Aα Y and Z alleles into AαΔ strains and examined the acquired mating types and mating abilities of the transformants. These experiments demonstrate that the Aα Y gene is not essential for fungal viability and growth, that a solitary Z Aα mating-type gene does not itself activate development, that Aβ proteins are sufficient to activate the A developmental pathway in the absence of Aα proteins and confirm that Y and Z genes are the sole determinants of Aα mating type. The data from these experiments support and refine our model of the regulation of A-pathway events by Y and Z proteins.
Repression of Hybrid Dysgenesis in Drosophila melanogaster by Heat-Shock-Inducible Sense and Antisense P-Element Constructs
Authors: Simmons Michael J , Raymond John D , Grimes Craig D , Belinco Carina , Haake Bret C , Jordan Maureen , Lund Chad , Ojala Todd A , Papermaster David
Published: January 2021

Sets of sense and antisense P-element constructs controlled by a heat-shock-inducible promoter were tested for their ability to repress manifestations of P-element activity in vivo. As a group, the antisense constructs repressed pupal lethality, a somatic manifestation of P activity, and this repression was significantly enhanced by heat shock. Three of the 11 antisense constructs also repressed gonadal dysgenesis, a manifestation of P activity in the female germ line; however, none had any effect on P-element-mediated mutability in the male germ line. Among the 13 different heat-shock-inducible sense constructs that were tested, those containing the KP and DP elements were strong repressors of pupal lethality, gonadal dysgenesis and P-element-mediated mutability; however, individual lines carrying these constructs varied in their ability to repress each of these traits, presumably because of genomic position effects. With the exception of the sense construct that contained a complete P element, none of the sense or antisense constructs repressed a lacZ reporter gene driven by the P-element promoter. Overall, the experimental results suggest that in nature, P-element activity could be regulated by P-encoded polypeptides and by antisense P RNAs.
P-Element-Induced Male Recombination and Gene Conversion in Drosophila
Authors: Preston Christine R , Engels William R
Published: January 2021

A P-element insertion flanked by 13 restriction fragment length polymorphism (RFLP) marker sites was used to examine male recombination and gene conversion at an autosomal site. The great majority of crossovers on chromosome arm 2R occurred within the 4-kb region containing the P element and RFLP sites. Of the 128 recombinants analyzed, approximately two-thirds carried duplications or deletions flanking the P element. These rearrangements are described in more detail in the accompanying report. In a parallel experiment, we examined 91 gene conversion tracts resulting from excision of the same autosomal P element. We found the average tract length was 1463 bp, which is essentially the same as found previously at the white locus. The distribution of conversion tract endpoints was indistinguishable from the distribution of crossover points among the nonrearranged male recombinants. Most recombination events can be explained by the “hybrid element insertion” model, but, for those lacking a duplication or deletion, a second step involving double-strand gap repair must be postulated to explain the distribution of crossover points.
Flanking Duplications and Deletions Associated With P-Induced Male Recombination in Drosophila
Authors: Preston Christine R , Sved John A , Engels William R
Published: January 2021

We studied P element-induced recombination in germline mitotic cells by examining the structure of the recombinant chromosomes. We found that most recombinants retain a mobile P element at the site of the recombination, usually with either a deletion or a duplication immediately adjacent to the P end at which the crossover occurred. The sizes of these deletions and duplications ranged from a few base pairs to well over 100 kb. These structures fit the “hybrid element insertion” (HEI) model of male recombination in which the two P-element copies on sister chromatids combine to form a “hybrid element” whose termini insert into a nearby position on the homologue. The data suggest that P-induced recombination can be used as an efficient means of generating flanking deletions in the vicinity of existing P elements. These deletions are easily screened using distant flanking markers, and they can be chosen to extend in a given direction depending on which reciprocal recombinant type is selected. Furthermore, the retention of a mobile P element allows one to extend the deletion or generate additional variability at the site by subsequent rounds of recombination.
Effects of Character Weighting and Species Sampling on Phylogeny Reconstruction: A Case Study Based on DNA Sequence Data in Cetaceans
Authors: Milinkovitch Michel C , LeDuc Richard G , Adachi Jun , Farnir Frederic , Georges Michel , Hasegawa Masami
Published: January 2021

Different phylogenetic analyses of the same genetic data set can yield conflicting results, depending on the choice of parameter settings and included taxa. This is particularly true in studies involving data sets where levels of homoplasy are high and likely to obscure the phylogenetic signal. Filtering of this phylogenetic noise can be attempted, with varying degrees of success, by using different weighting schemes and ingroup/outgroup choices, but it can be difficult to decide objectively which approach is best. Using a cytochrome b data set from cetaceans and artiodactyls, we examined the effects of a suite of parameter settings on the outcome of phylogenetic analyses. We tested 2968 combinations among the seven parameters that most often vary among phylogenetic studies. It is our contention that this sensitivity analysis identifies portions of the multidimensional parameter space where phylogenetic signal is most reliably recovered, and simple rules are given to guide the choice of settings. Portions of this data set have been used in previous studies with conflicting results, namely the monophyly vs. paraphyly of one of the two major recognized cetacean suborders, the toothed whales. This analysis strongly supports the sister relationship between sperm whales and baleen whales.
Classification of European mtDNAs From an Analysis of Three European Populations
Authors: Torroni Antonio , Huoponen Kirsi , Francalacci Paolo , Petrozzi Maurizio , Morelli Laura , Scozzari Rosaria , Obinu Domenica , Savontaus Marja-Liisa , Wallace Douglas C
Published: January 2021

Mitochondrial DNA (mtDNA) sequence variation was examined in Finns, Swedes and Tuscans by PCR amplification and restriction analysis. About 99% of the mtDNAs were subsumed within 10 mtDNA haplogroups (H, I, J, K, M, T, U, V, W, and X) suggesting that the identified haplogroups could encompass virtually all European mtDNAs. Because both hypervariable segments of the mtDNA control region were previously sequenced in the Tuscan samples, the mtDNA haplogroups and control region sequences could be compared. Using a combination of haplogroup-specific restriction site changes and control region nucleotide substitutions, the distribution of the haplogroups was surveyed through the published restriction site polymorphism and control region sequence data of Caucasoids. This supported the conclusion that most haplogroups observed in Europe are Caucasoid-specific, and that at least some of them occur at varying frequencies in different Caucasoid populations. The classification of almost all European mtDNA variation in a number of well defined haplogroups could provide additional insights about the origin and relationships of Caucasoid populations and the process of human colonization of Europe, and is valuable for the definition of the role played by mtDNA backgrounds in the expression of pathological mtDNA mutations
A Statistical Test of a Neutral Model Using the Dynamics of Cytonuclear Disequilibria
Authors: Dutta Susmita , Kiparsky Mike , Rand David M , Arnold Jonathan
Published: January 2021

In this paper we use cytonuclear disequilibria to test the neutrality of mtDNA markers. The data considered here involve sample frequencies of cytonuclear genotypes subject to both statistical sampling variation as well as genetic sampling variation. First, we obtain the dynamics of the sample cytonuclear disequilibria assuming random drift alone as the source of genetic sampling variation. Next, we develop a test statistic using cytonuclear disequilibria via the theory of generalized least squares to test the random drift model. The null distribution of the test statistic is shown to be approximately chi-squared using an asymptotic argument as well as computer simulation. Power of the test statistic is investigated under an alternative model with drift and selection. The method is illustrated using data from cage experiments utilizing different cytonuclear genotypes of Drosophila melanogaster. A program for implementing the neutrality test is available upon request.
apd1
+, a Gene Required for Red Pigment Formation in ade6 Mutants of Schizosaccharomyces pombe, Encodes an Enzyme Required for Glutathione Biosynthesis: A Role for Glutathione and a Glutathione-Conjugate Pump
Authors: Chaudhuri Biswendu , Ingavale Susham , Bachhawat Anand K
Published: January 2021

Mutants in the adenine biosynthetic pathway of yeasts (ade1 and ade2 of Saccharomyces cerevisiae, ade6 and ade7 of Schizosaccharomyces pombe) accumulate an intense red pigment in their vacuoles when grown under adenine-limiting conditions. The precise events that determine the formation of the pigment are however, still unknown. We have begun a genetic investigation into the nature and cause of pigmentation of ade6 mutants of S. pombe and have discovered that one of these pigmentation defective mutants, apd1 (adenine pigmentation defective), is a strict glutathione auxotroph. The gene apd1  + was found to encode the first enzyme in glutathione biosynthesis, γ-glutamylcysteine synthetase, gcs1  +. This gene when expressed in the mutant could confer both glutathione prototrophy and the characteristic red pigmentation, and disruption of the gene led to a loss in both phenotypes. Supplementation of glutathione in the medium, however, could only restore growth but not the pigmentation because the cells were unable to achieve sufficient intracellular levels of glutathione. Disruption of the second enzyme in glutathione biosynthesis, glutathione synthetase, gsh2  +, also led to glutathione auxotrophy, but only a partial defect in pigment formation. A reevaluation of the major amino acids previously reported to be present in the pigment indicated that the pigment is probably a glutathione conjugate. The ability of vanadate to inhibit pigment formation indicated that the conjugate was transported into the vacuole through a glutathione-conjugate pump. This was further confirmed using strains of S. cerevisiae bearing disruptions in the recently identified glutathione-conjugate pump, YCF1, where a significant reduction in pigment formation was observed. The pump of S. pombe is distinct from the previously identified vacuolar pump, hmt1p, for transporting cadystin peptides into vacuoles of S. pombe.
The Specificity Determinant of the Y Mating-Type Proteins of Schizophyllum commune Is Also Essential for Y-Z Protein Binding
Authors: Yue Changli , Osier Michael , Novotny Charles P , Ullrich Robert C
Published: January 2021

This paper concerns the manner in which combinatorial mating proteins of the fungus, Schizophyllum commune, recognize one another to form complexes that regulate target gene expression. In Schizophyllum, tightly linked Y and Z mating-type genes do not promote development in the combinations present in haploid strains (i.e., self combinations). When the Y and Z genes from two different mating types are brought together by the fusion of two haploid cells, the Y and Z proteins from different mating types recognize one another as nonself; form a complex and activate development. Several Y and Z alleles are present in the population and all nonself combinations of Y and Z alleles are equally functional. We have made chimeric genes among Y1, Y3, Y4 and Y5 and examined their mating-type specificities by transformation and mating tests. These studies show that the specificity of Y protein recognized by Z protein is encoded within a short region of N-terminal amino acids. The critical region is not precisely the same in each Y protein and in each Y-Z protein interaction. For Y3 protein compared with Y4 protein, the critical residues are in an N-terminal region of 56 amino acids (residues 17–72), with 40% identity and 65% similarity. Two-hybrid studies show that: the first 144 amino acids of Y4 protein are sufficient to bind Z3 and Z5 proteins, but not Z4 protein, and proteins deleted of the Y4 specificity region do not bind Z3, Z4 or Z5 protein. Thus the specificity determinant of the Y protein is essential for protein-protein recognition, Y-Z protein binding and mating activity.
Mitochondrial Genotype Segregation in a Mouse Heteroplasmic Lineage Produced by Embryonic Karyoplast Transplantation
Authors: Meirelles Flávio V , Smith Lawrence C
Published: January 2021

Mitochondrial genotypes have been shown to segregate both rapidly and slowly when transmitted to consecutive generations in mammals. Our objective was to develop an animal model to analyze the patterns of mammalian mitochondrial DNA (mtDNA) segregation and transmission in an intraspecific heteroplasmic maternal lineage to investigate the mechanisms controlling these phenomena. Heteroplasmic progeny were obtained from reconstructed blastocysts derived by transplantation of pronuclear-stage karyoplasts to enucleated zygotes with different mtDNA. Although the reconstructed zygotes contained on average 19% mtDNA of karyoplast origin, most progeny contained fewer mtDNA of karyoplast origin and produced exclusively homoplasmic first generation progeny. However, one founder heteroplasmic adult female had elevated tissue heteroplasmy levels, varying from 6% (lung) to 69% (heart), indicating that stringent replicative segregation had occurred during mitotic divisions. First generation progeny from the above female were all heteroplasmic, indicating that, despite a meiotic segregation, they were derived from heteroplasmic founder oocytes. Some second and third generation progeny contained exclusively New Zealand Black/BINJ mtDNA, suggesting, but not confirming, an origin from an homoplasmic oocyte. Moreover, several third to fifth generation individuals maintained mtDNA from both mouse strains, indicating a slow or persistent segregation pattern characterized by diminished tissue and litter variability beyond second generation progeny. Therefore, although some initial lineages appear to segregate rapidly to homoplasmy, within two generations other lineages transmit stable amounts of both mtDNA molecules, supporting a mechanism where mitochondria of different origin may fuse, leading to persistent intraorganellar heteroplasmy.
Inferring Coalescence Times From DNA Sequence Data
Authors: Tavaré Simon , Balding David J , Griffiths R C , Donnelly Peter
Published: January 2021

The paper is concerned with methods for the estimation of the coalescence time (time since the most recent common ancestor) of a sample of intraspecies DNA sequences. The methods take advantage of prior knowledge of population demography, in addition to the molecular data. While some theoretical results are presented, a central focus is on computational methods. These methods are easy to implement, and, since explicit formulae tend to be either unavailable or unilluminating, they are also more useful and more informative in most applications. Extensions are presented that allow for the effects of uncertainty in our knowledge of population size and mutation rates, for variability in population sizes, for regions of different mutation rate, and for inference concerning the coalescence time of the entire population. The methods are illustrated using recent data from the human Y chromosome.
Competition Between Adjacent Meiotic Recombination Hotspots in the Yeast Saccharomyces cerevisiae
Authors: Fan Qing-Qing , Xu Fei , White Michael A , Petes Thomas D
Published: January 2021

In a wild-type strain of Saccharomyces cerevisiae, a hotspot for meiotic recombination is located upstream of the HIS4 gene. An insertion of a 49-bp telomeric sequence into the coding region of HIS4 strongly stimulates meiotic recombination and the local formation of meiosis-specific double-strand DNA breaks (DSBs). When strains are constructed in which both hotspots are heterozygous, hotspot activity is substantially less when the hotspots are on the same chromosome than when they are on opposite chromosomes.
Two Neuronal G Proteins are Involved in Chemosensation of the Caenorhabditis elegans Dauer-Inducing Pheromone
Authors: Zwaal Richard R , Mendel Jane E , Sternberg Paul W , Plasterk Ronald H A
Published: January 2021

Caenorhabditis elegans uses chemosensation to determine its course of development. Young larvae can arrest as dauer larvae in response to increasing population density, which they measure by a nematode-excreted pheromone, and decreasing food supply. Dauer larvae can resume development in response to a decrease in pheromone and increase in food concentration. We show here that two novel G protein alpha subunits (GPA-2 and GPA-3) show promoter activity in subsets of chemosensory neurons and are involved in the decision to form dauer larvae primarily through the response to dauer pheromone. Dominant activating mutations in these G proteins result in constitutive, pheromone-independent dauer formation, whereas inactivation results in reduced sensitivity to pheromone, and, under certain conditions, an alteration in the response to food. Interactions between gpa-2, gpa-3 and other genes controlling dauer formation suggest that these G proteins may act in parallel to regulate the neuronal decision making that precedes dauer formation.
Male-Dependent Doubly Uniparental Inheritance of Mitochondrial DNA and Female-Dependent Sex-Ratio in the Mussel Mytilus galloprovincialis
Authors: Saavedra Carlos , Reyero María-Isabel , Zouros Eleftherios
Published: January 2021

We have investigated sex ratio and mitochondrial DNA inheritance in pair-matings involving five female and five male individuals of the Mediterranean mussel Mytilus galloprovincialis. The percentage of male progeny varied widely among families and was found to be a characteristic of the female parent and independent of the male to which it was mated. Thus sex-ratio in Mytilus appears to be independent of the nuclear genotype of the sperm. With a few exceptions, doubly uniparental inheritance (DUI) of mtDNA was observed in all families fathered by four of the five males: female and male progeny contained the mother's mtDNA (the F genome), but males contained also the father's paternal mtDNA (the M genome). Two hermaphrodite individuals found among the progeny of these crosses contained the F mitochondrial genome in the female gonad and both the F and M genomes in the male gonad. All four families fathered by the fifth male showed the standard maternal inheritance (SMI) of animal mtDNA: both female and male progeny contained only the maternal mtDNA. These observations illustrate the intimate linkage between sex and mtDNA inheritance in species with DUI and suggest different major roles for each gender. We propose a model according to which development of a male gonad requires the presence in the early germ cells of an agent associated with sperm-derived mitochondria, these mitochondria are endowed with a paternally encoded replicative advantage through which they overcome their original minority in the fertilized egg and this advantage (and, therefore, the chance of an early entrance into the germ line) is countered by a maternally encoded egg factor.
Genetics of Hybrid Sterility and Hybrid Breakdown in an Intersubspecific Rice (Oryza sativa L.) Population
Authors: Li Zhikang , Pinson Shannon R M , Paterson Andrew H , Park William D , Stansel James W
Published: January 2021

F1 hybrid sterility and “hybrid breakdown” of F2 and later generations in rice (Oryza sativa L.) are common and genetically complicated. We used a restriction fragment length polymorphism linkage map and F4 progeny testing to investigate hybrid sterility and hybrid breakdown in a cross between “widely compatible” O. sativa ssp. japonica cultivar Lemont from the Southern U.S. and ssp. indica cultivar Teqing from China. Our results implicate different genetic mechanisms in hybrid sterility and hybrid breakdown, respectively. Hybrid sterility appeared to be due to recombination within a number of putative differentiated “supergenes” in the rice genome, which may reflect cryptic structural rearrangements. The cytoplasmic genome had a large effect on fertility of both male and female gametes in the F1 hybrids. There appeared to be a pair of complementary genes that behaved like “wide compatibility” genes. This pair of genes and the “gamete eliminator” (S1) or “egg killer” (S-5) may influence the phenotypic effects of presumed supergenes in hybrids. Hybrid breakdown appeared to be largely due to incompatibilities between indica and japonica alleles at many unlinked epistatic loci in the genome. These proposed mechanisms may partly account for the complicated nature of postreproductive barriers in rice.
The Development and Meiotic Behavior of Asymmetrical Isochromosomes in Wheat
Authors: Lukaszewski Adam J
Published: January 2021

To determine which segments of a chromosome arm are responsible for the initiation of chiasmate pairing in meiosis, a series of novel isochromosomes was developed in hexaploid wheat (Triticum aestivum L.). These isochromosomes are deficient for different terminal segments in the two arms. It is proposed to call them “asymmetrical.” Meiotic metaphase I pairing of these asymmetrical isochromosomes was observed in plants with various doses of normal and deficient arms. The two arms of an asymmetrical isochromosome were bound by a chiasma in only two of the 1134 pollen mother cells analyzed. Pairing was between arms of identical length whenever such were available; otherwise, there was no pairing. However, two arms deficient for the same segment paired with a frequency similar to that of normal arms, indicating that the deficient arms retained normal capacity for pairing. Pairing of arms of different length was prevented not by the deficiency itself, but rather, by the heterozygosity for the deficiency. Whether two arms were connected via a centromere in an isochromosome or were present in two different chromosomes had no effect on pairing. This demonstrates that in the absence of homology in the distal regions of chromosome arms, even if relatively short, very long homologous segments may remain unrecognized in meiosis and will not be involved in chiasmate pairing.
Circularized Ac/Ds Transposons: Formation, Structure and Fate
Authors: Gorbunova Vera , Levy Avraham A
Published: January 2021

The maize Ac/Ds transposable elements are thought to transpose via a cut-and-paste mechanism, but the intermediates formed during transposition are still unknown. In this work we present evidence that circular Ac molecules are formed in plants containing actively transposing elements. In these circles, transposon ends are joined head-to-head. The sequence at the ends' junction is variable, containing small deletions or insertions. Circles containing deleted Ac ends are probably unable to successfully reintegrate. To test the ability of circles with intact transposon ends to integrate into the genome, an artificial Ds circle was constructed by cloning the joined ends of Ac into a plasmid carrying a plant selectable marker. When such a circular Ds was introduced into tobacco protoplasts in the presence of Ac-transposase, no efficient transposase-mediated integration was observed. Although a circular transposition intermediate cannot be ruled out, the findings of circles with deleted transposon ends and the absence of transposase-mediated integration of the circular Ds suggest that some of the joined-ends-carrying elements are not transposition intermediates, but rather abortive excision products. The formation of Ac circles might account for the previously described phenomenon of Ac-loss. The origin of Ac circles and the implications for models of Ac transposition are discussed.
stand still, a Drosophila Gene Involved in the Female Germline for Proper Survival, Sex Determination and Differentiation
Authors: Pennetta Giuseppa , Pauli Daniel
Published: January 2021

We identified a new gene, stand still (stil), required in the female germline for proper survival, sex determination and differentiation. Three strong loss-of-function alleles were isolated. The strongest phenotype exhibited by ovaries dissected from adult females is the complete absence of germ cells. In other ovaries, the few surviving germ cells frequently show a morphology typical of primary spermatocytes. stil is not required either for fly viability or for male germline development. The gene was cloned and found to encode a novel protein. stil is strongly expressed in the female germ cells. Using P[stil  +] transgenes, we show that stil and a closely localized gene are involved in the modification of the ovarian phenotypes of the dominant alleles of ovo caused by heterozygosity of region 49 A-D. The similarity of the mutant phenotypes of stil to that of otu and ovo suggests that the three genes function in a common or in parallel pathways necessary in the female germline for its survival, sex determination and differentiation.
Germline and Somatic Transformation of Mating Tetrahymena thermophila by Particle Bombardment
Authors: Cassidy-Hanley Donna , Bowen Josephine , Lee John H , Cole Eric , VerPlank Lynn A , Gaertig Jacek , Gorovsky Martin A , Bruns Peter J
Published: January 2021

Mating Tetrahymena thermophila were bombarded with ribosomal DNA-coated particles at various times in development. Both macronuclear and micronuclear transformants were recovered. Optimal developmental stages for transformation occurred during meiosis for the micronucleus and during anlagen formation for the macronucleus. Evidence is given for transient retention of the introduced plasmid. Genetic and molecular tests confirmed that sexually heritable transformation was associated with integration at the homologous site in the recipient micronuclear chromosome.
Natural Selection and the Frequency Distributions of “Silent” DNA Polymorphism in Drosophila
Authors: Akashi Hiroshi , Schaeffer Stephen W
Published: January 2021

In Escherichia coli, Saccharomyces cerevisiae, and Drosophila melanogaster, codon bias may be maintained by a balance among mutation pressure, genetic drift, and natural selection favoring translationally superior codons. Under such an evolutionary model, silent mutations fall into two fitness categories: preferred mutations that increase codon bias and unpreferred changes in the opposite direction. This prediction can be tested by comparing the frequency spectra of synonymous changes segregating within populations; natural selection will elevate the frequencies of advantageous mutations relative to that of deleterious changes. The frequency distributions of preferred and unpreferred mutations differ in the predicted direction among 99 alleles of two D. pseudoobscura genes and five alleles of eight D. simulans genes. This result confirms the existence of fitness classes of silent mutations. Maximum likelihood estimates suggest that selection intensity at silent sites is, on average, very weak in both D. pseudoobscura and D. simulans (|Nes| ≈ 1). Inference of evolutionary processes from within-species sequence variation is often hindered by the assumption of a stationary frequency distribution. This assumption can be avoided when identifying the action of selection and tested when estimating selection intensity.
Phytoalexin-Deficient Mutants of Arabidopsis Reveal That PAD4 Encodes a Regulatory Factor and That Four PAD Genes Contribute to Downy Mildew Resistance
Authors: Glazebrook Jane , Zook Michael , Mert Figen , Kagan Isabelle , Rogers Elizabeth E , Crute Ian R , Holub Eric B , Hammerschmidt Raymond , Ausubel Frederick M
Published: January 2021

We are working to determine the role of the Arabidopsis phytoalexin, camalexin, in protecting the plant from pathogen attack by isolating phytoalexin-deficient (pad) mutants in the accession Columbia (Col-0) and examining their response to pathogens. Mutations in PAD1, PAD2, and PAD4 caused enhanced susceptibility to the bacterial pathogen Pseudomonas syringae pv. maculicola strain ES4326 (PsmES4326), while mutations in PAD3 or PAD5 did not. Camalexin was not detected in any of the double mutants pad1-1 pad2-1, pad1-1 pad3-1 or pad2-1 pad3-1. Growth of PsmES4326 in pad1-1 pad2-1 was greater than that in pad1-1 or pad2-1 plants, while growth in pad1-1 pad3-1 and pad2-1 pad3-1 plants was similar to that in pad1-1 and pad2-1 plants, respectively. The pad4-1 mutation caused reduced camalexin synthesis in response to PsmES4326 infection, but not in response to Cochliobolus carbonum infection, indicating that PAD4 has a regulatory function. PAD1, PAD2, PAD3 and PAD4 are all required for resistance to the eukaryotic biotroph Peronospora parasitica. The pad4-1 mutation caused the most dramatic change, exhibiting full susceptibility to four of six Col-incompatible parasite isolates. Interestingly, each combination of double mutants between pad1-1, pad2-1 and pad3-1 exhibited additive shifts to moderate or full susceptibility to most of the isolates.
Comparing Patterns of Nucleotide Substitution Rates Among Chloroplast Loci Using the Relative Ratio Test
Authors: Muse Spencer V , Gaut Brandon S
Published: January 2021

Even when several genetic loci are used in molecular evolutionary studies, each locus is typically analyzed independently of the others. This type of approach makes it difficult to study mechanisms and processes that affect multiple genes. In this work we develop a statistical approach for the joint analysis of two or more loci. The tests we propose examine whether or not nucleotide substitution rates across evolutionary lineages have the same relative proportions at two loci. Theses procedures are applied to 33 genes from the chloroplast genomes of rice, tobacco, pine, and liverwort. With the exception of five clearly distinct loci, we find that synonymous substitution rates tend to change proportionally across genes. We interpret these results to be consistent with a “lineage effect” acting on the entire chloroplast genome. In contrast, nonsynonymous rates do not change proportionally across genes, suggesting that locus-specific evolutionary effects dominate patterns of nonsynonymous substitution.
Mutants of Arabidopsis thaliana Hypersensitive to DNA-Damaging Treatments
Authors: Masson Jean E , King Patrick J , Paszkowski Jerzy
Published: January 2021

A simple screening method was developed for the isolation of Arabidopsis thaliana mutants hypersensitive to X-ray irradiation. The root meristem was used as the target for irradiation with sublethal doses of X rays, while protection of the shoot meristem by a lead cover allowed the rescue of hypersensitive individuals. We isolated nine independent X-ray-hypersensitive mutants from 7000 M2 seedlings. Analysis of three chosen mutants (xrs4, xrs9 and xrs11) showed that alterations in single recessive alleles are responsible for their phenotypes. The mutations are not allelic but linked and map to chromosome 4, suggesting mutations in novel genes as compared to previously mapped mutant alleles. Importantly, hypersensitivity to X rays was found to correlate with hypersensitivity to the DNA-alkylating agent mitomycin C, which provokes interstrand crosslinks, and/or to methyl methanesulfonate, which is known as a radiomimetic chemical. These novel phenotypes suggest that the mutants described here are altered in the repair of DNA damage, most probably by recombinational repair.