bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single and Double Infections with Wolbachia in the Parasitic Wasp Nasonia vitripennis Effects on Compatibility
Authors: Perrot-Minnot Marie-Jeanne , Guo Li Rong , Werren John H 
Published: January 2021

Abstract
Wolbachia are cytoplasmically inherited bacteria responsible for reproductive incompatibility in a wide range of insects. There has been little exploration, however, of within species Wolbachia polymorphisms and their effects on compatibility. Here we show that some strains of the parasitic wasp Nasonia vitripennis are infected with two distinct bacterial strains (A and B) whereas others are singly infected (A or B). Double and single infections are confirmed by both PCR amplification and Southern analysis of genomic DNA. Furthermore, it is shown that prolonged larval diapause (the overwintering stage of the wasp) of a double-infected strain can lead to stochastic loss of one or both bacterial strains. After diapause of a double-infected line, sublines were produced with AB, A only, B only or no Wolbachia. A and B sublines are bidirectionally incompatible, whereas males from AB lines are unidirectionally incompatible with females of A and B sublines. Results therefore show rapid development of bidirectional incompatibility within a species due to segregation of associated symbiotic bacteria.
Inversion Monophyly in African Anopheline Malaria Vectors
Authors: García Beatriz A , Caccone Adalgisa , Mathiopoulos Kostas D , Powell Jeffrey R 
Published: January 2021

Abstract
The African Anopheles gambzae complex of six sibling species has many polymorphic and fixed paracentric inversions detectable in polytene chromosomes. These have been used to infer phylogenetic relationships as classically done with Drosophila. Two species, A. gambiae and A. merus, were thought to be sister taxa based on a shared X inversion designated Xag. Recent DNA data have conflicted with this phylogenetic inference as they have supported a sister taxa relationship of A. gambiaeand A. arabiensis. A possible explanation is that the Xag is not monophyletic. Here we present data from a gene (soluble guanylate cyclase) within the Xag that strongly supports the monophyly of the Xag. We conjecture that introgression may be occurring between the widely sympatric species A. gambiae and A. arabzensis and that the previous DNA phylogenies have been detecting the introgression. Evidently, introgression is not uniform across the genome, and species-specific regions, like the X-chromosome inversions, do not introgress probably due to selective elimination in hybrids and backcrosses.
Mapping Quantitative Trait Loci for Complex Binary Diseases Using Line Crosses
Authors: Xu Shizhong , Atchley William R 
Published: January 2021

Abstract
A composite interval gene mapping procedure for complex binary disease traits is proposed in this paper. The binary trait of interest is assumed to be controlled by an underlying liability that is normally distributed. The liability is treated as a typical quantitative character and thus described by the usual quantitative genetics model. Translation from the liability into a binary (disease) phenotype is through the physiological threshold model. Logistic regression analysis is employed to estimate the effects and locations of putative quantitative trait loci (our terminology for a single quantitative trait locus is QTL while multiple loci are referred to as QTLs). Simulation studies show that properties of this mapping procedure mimic those of the composite interval mapping for normally distributed data. Potential utilization of the QTL mapping procedure for resolving alternative genetic models (e.g., single- or two-trait-locus model) is discussed.
Mutations in the Yeast SRB2 General Transcription Factor Suppress hpr1-Induced Recombination and Show Defects in DNA Repair
Authors: Piruat José I , Aguilera Andrés 
Published: January 2021

Abstract
We have obtained genetic and molecular evidence that the hrs2-1 mutation, isolated as a suppressor of the hyperrecombination phenotype of hpr1Δ, is in the SRB2 gene, which encodes a component of the RNA polII holoenzyme. A newly constructed srb2Δ allele restores the wild-type levels of deletions in hpr1Δ ceils, indicating that the lack of a functional SRB2 transcription factor suppresses recombination between direct repeats. These results suggest a direct connection between transcription and recombination between DNA repeats. On the other hand, the hrs2-I mutation (renamed srb2-101), in which Gly150 has been changed to Asp, makes cells sensitive to long MMS treatments, a phenotype observed for the srb2Δ null allele only in a hpr1Δ background. This indicates that mutations in the basal transcription factor SRB2 impair DNA repair of MMS-induced damage, which adds a new connection between transcription and DNA repair. We discuss the possibility that hpr1-induced deletions occurred as a consequence of a SRB2-dependent stalled or blocked transcription complex.
Selective Loss of Sperm Bearing a Compound Chromosome in the Drosophila Female
Authors: Dernburg Abby F , Daily Douglas R , Yook Karen J , Corbin John A , Sedat John W , Sullivan William 
Published: January 2021

Abstract
The Drosophila compound entire second chromosome, C(2)EN, displays paternal transmission well below Mendelian expectations (Novitski et al. 1981). Because C(2)EN stocks also show higher-than-expected rates of zygotic lethality, it was proposed that this reduced paternal inheritance might be wholly or partially due to postfertilization events. Efforts to investigate this phenomenon have been hampered because the progeny of crosses between C(2)EN-bearing individuals and those with normal karyotypes die during embryogenesis. We have circumvented this obstacle by employing fluorescence in situ hybridization to directly karyotype early embryos from crosses involving C(2)EN-bearing individuals. This analysis reveals that the distortion in paternal transmission is established before fertilization. Moreover, measurement of the sperm ratios within both the male and female reproductive organs demonstrates that C(2)EN-bearing sperm are selectively lost after sperm transfer to the female and before storage of sperm in the seminal receptacles and spermathecae. Our results are consistent with a model of meiotic drive in which aberrations occuring early in meiosis lead ultimately to sperm dysfunction.
Environmental and Genetic Effects on the Asymmetry Phenotype: Diazinon Resistance in the Australian Sheep Blowfly, Lucilia cuprina
Authors: Freebairn Kris , Yen Janet L , McKenzie John A 
Published: January 2021

Abstract
The asymmetry phenotype of diazinon-resistant flies lacking a fitness/asymmetry Modfier (+/+; R/−) was dominant and independent of developmental temperature, larval density and diazinon concentration. Asymmetry score, pooled over three bristle characters, was ~50% greater for these phenotypes than for those of modified genotypes (M/−; −/− ) and unmodified susceptibles (+ /+ ; S/S) reared under standard laboratory conditions. Modified and susceptible phenotypes showed increased asymmetry score for temperatures and larval densities above and below standard rearing conditions; a positive correlation was observed between diazinon concentration and asymmetry score. Single and multiple environmental stresses resulted in similar scores that approached, but never exceeded, those of unmodified resistant phenotypes. Irrespective of the developmental conditions anti-symmetry and fluctuating asymmetry were typically observed for each bristle character of unmodified resistant and the modified and susceptible phenotypes, respectively. Thus while similar asymmetry scores could arise from genetic or environmental effects, asymmetry pattern was genetically based. Population cage analyses at different temperatures and larval densities showed a negative association between mean asymmetry and relative fitness.
Analysis of Meiotic Recombination Pathways in the Yeast Saccharomyces cerevisiae
Authors: Mao-Draayer Yang , Galbraith Anne M , Pittman Douglas L , Cool Marc , Malone Robert E 
Published: January 2021

Abstract
In the yeast, Saccharomyces cerevisiae, several genes appear to act early in meiotic recombination. HOPl and REDl have been classified as such early genes. The data in this paper demonstrate that neither a redl nor a hopl mutation can rescue the inviable spores produced by a rad52 spol3 strain; this phenotype helps to distinguish these two genes from other early meiotic recombination genes such as SPOll, REC104, or A4EI4. In contrast, either a redl or a hopl mutation can rescue a rad50S spol3 strain; this phenotype is similar to that conferred by mutations in the other early recombination genes (e.g., REC104). These two different results can be explained because the data presented here indicate that a rad50S mutation does not diminish meiotic intrachromosomal recombination, similar to the mutant phenotypes conferred by redl or hopl. Of course, REDl and HOPl do act in the normal meiotic interchromosomal recombination pathway; they reduce interchromosomal recombination to ~10% of normal levels. We demonstrate that a mutation in a gene (REC104) required for initiation of exchange is completely epistatic to a mutation in REDl. Finally, mutations in either HOPl or RED1 reduce the number of doublestrand breaks observed at the HIS2 meiotic recombination hotspot.
Vacuole Partitioning During Meiotic Division in Yeast
Authors: Roeder Amy D , Shaw Janet M 
Published: January 2021

Abstract
We have examined the partitioning of the yeast vacuole during meiotic division. In pulse-chase experiments, vacuoles labeled with the lumenal ade2 fluorophore or the membrane-specific dye FM 4-64 were not inherited by haploid spores. Instead, these fluorescent markers were excluded from spores and trapped between the spore cell walls and the ascus. Serial optical sections using a confocal microscope confirmed that spores did not inherit detectable amounts of fluorescently labeled vacuoles. Moreover, indirect immunofluorescence studies established that an endogenous vacuolar membrane protein, alkaline phosphatase, and a soluable vacuolar protease, carboxypeptidase Y, were also detected outside spores after meiotic division. Spores that did not inherit ade2- or FM 4-64-labeled vacuoles did generate an organelle that could be visualized by subsequent staining with vacuole-specific fluorophores. These data contrast with genetic evidence that a soluble vacuolar protease is inherited by spores. When the partitioning of both types of markers was examined in sporulating cultures, the vacuolar protease activity was inherited by spores while fluorescently labeled vacuoles were largely excluded from spores. Our results indicate that the majority of the diploid vacuole, both soluble contents and membrane-bound components, are excluded from spores formed during meiotic division.
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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.
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.