bluuebunny/crossref_metadata_2025_split huggingface dataset:
Allele-Specific Population Structure of Drosophila melanogaster Alcohol Dehydrogenase at the Molecular Level
Authors: Veuille Michel , Bénassi Véronique , Aulard Sylvie , Depaulis Frantz 
Published: April 2021

Abstract
The history of the Drosophila melanogaster alcohol dehydrogenase (ADH) Fast/Slow polymorphism was studied by recording molecular variation and inversion polymorphism in 233 chromosomes from European and African populations. Silent molecular variation in the Slow allele was very different between standard chromosomes and chromosomes bearing the In(2L)t inversion. Within populations, inverted Slow haplotypes were more variable than standard Slow haplotypes. Between populations, geographical structure was almost nonexistent for inverted Slow haplotypes and highly significant for standard Slow. All Fast haplotypes occurred on standard chromosomes. They showed little variation within and between populations. They were highly significantly closer to standard Slow haplotypes from Europe. These results suggest that the current range of Fast and In(2L)t Slow haplotypes is recent and that an older genetic differentiation between populations was followed by allele-specific gene flow.
Effects of DNA Double-Strand and Single-Strand Breaks on Intrachromosomal Recombination Events in Cell-Cycle-Arrested Yeast Cells
Authors: Galli Alvaro , Schiestl Robert H 
Published: April 2021

Abstract
Intrachromosomal recombination between repeated elements can result in deletion (DEL recombination) events. We investigated the inducibility of such intrachromosomal recombination events at different stages of the cell cycle and the nature of the primary DNA lesions capable of initiating these events. Two genetic systems were constructed in Saccharomyces cerevisiae that select for DEL recombination events between duplicated alleles of CDC28 and TUB2. We determined effects of double-strand breaks (DSBs) and single-strand breaks (SSBs) between the duplicated alleles on DEL recombination when induced in dividing cells or cells arrested in G1 or G2. Site-specific DSBs and SSBs were produced by overexpression of the I-Sce I endonuclease and the gene II protein (gIIp), respectively. I-Sce I-induced DSBs caused an increase in DEL recombination frequencies in both dividing and cell-cycle-arrested cells, indicating that G1- and G2-arrested cells are capable of completing DSB repair. In contrast, gIIp-induced SSBs caused an increase in DEL recombination frequency only in dividing cells. To further examine these phenomena we used both γ-irradiation, inducing DSBs as its most relevant lesion, and UV, inducing other forms of DNA damage. UV irradiation did not increase DEL recombination frequencies in G1 or G2, whereas γ-rays increased DEL recombination frequencies in both phases. Both forms of radiation, however, induced DEL recombination in dividing cells. The results suggest that DSBs but not SSBs induce DEL recombination, probably via the single-strand annealing pathway. Further, DSBs in dividing cells may result from the replication of a UV or SSB-damaged template. Alternatively, UV induced events may occur by replication slippage after DNA polymerase pausing in front of the damage.
Identification of Heterochronic Mutants in Caenorhabditis elegans: Temporal Misexpression of a Collagen::Green Fluorescent Protein Fusion Gene
Authors: Abrahante Juan E , Miller Eric A , Rougvie Ann E 
Published: April 2021

Abstract
The heterochronic genes lin-4, lin-14, lin-28, and lin-29 specify the timing of lateral hypodermal seam cell terminal differentiation in Caenorhabditis elegans. We devised a screen to identify additional genes involved in this developmental timing mechanism based on identification of mutants that exhibit temporal misexpression from the col-19 promoter, a downstream target of the heterochronic gene pathway. We fused the col-19 promoter to the green fluorescent protein gene (gfp) and demonstrated that hypodermal expression of the fusion gene is adult-specific in wild-type animals and temporally regulated by the heterochronic gene pathway. We generated a transgenic strain in which the col-19::gfp fusion construct is not expressed because of mutation of lin-4, which prevents seam cell terminal differentiation. We have identified and characterized 26 mutations that restore col-19::gfp expression in the lin-4 mutant background. Most of the mutations also restore other aspects of the seam cell terminal differentiation program that are defective in lin-4 mutant animals. Twelve mutations are alleles of three previously identified genes known to be required for proper timing of hypodermal terminal differentiation. Among these are four new alleles of lin-42, a heterochronic gene for which a single allele had been described previously. Two mutations define a new gene, lin-58. When separated from lin-4, the lin-58 mutations cause precocious seam cell terminal differentiation and thus define a new member of the heterochronic gene pathway.
Mitochondrial DNA Haplotype Frequencies in Natural and Experimental Populations of Drosophila subobscura
Authors: García-Martínez José , Castro José Aurelio , Ramón Misericordia , Latorre Amparo , Moya Andrés 
Published: April 2021

Abstract
The evolution of Drosophila subobscura mitochondrial DNA has been studied in experimental populations, founded with flies from a natural population from Esporles (Majorca, Balearic Islands, Spain). This population, like other European ones, is characterized by the presence of two very common (&gt;96%) mitochondrial haplotypes (called I and II) and rare and endemic haplotypes that appear at very low frequencies. There is no statistical evidence of positive Darwinian selection acting on the mitochondrial DNA variants according to Tajima's neutrality test. Two experimental populations, with one replicate each, were established with flies having a heterogeneous nuclear genetic background, which was representative of the composition of the natural population. Both populations were started with the two most frequent mitochondrial haplotypes, but at different initial frequencies. After 13 to 16 generations, haplotype II reached fixation in three cages and its frequency was 0.89 by generation 25 in the fourth cage. Random drift can be rejected as the force responsible for the observed changes in haplotype frequencies. There is not only statistical evidence of a linear trend favoring a mtDNA (haploid) fitness effect, but also of a significant nonlinear deviation that could be due to a nuclear component.
Correlation Between the Substitution Rate and Rate Variation Among Sites in Protein Evolution
Authors: Zhang Jianzhi , Gu Xun 
Published: April 2021

Abstract
It is well known that the rate of amino acid substitution varies among different proteins and among different sites of a protein. It is, however, unclear whether the extent of rate variation among sites of a protein and the mean substitution rate of the protein are correlated. We used two approaches to analyze orthologous protein sequences of 51 nuclear genes of vertebrates and 13 mitochondrial genes of mammals. In the first approach, no assumptions of the distribution of the rate variation among sites were made, and in the second approach, the gamma distribution was assumed. Through both approaches, we found a negative correlation between the extent of among-site rate variation and the average substitution rate of a protein. That is, slowly evolving proteins tend to have a high level of rate variation among sites, and vice versa. We found this observation consistent with a simple model of the neutral theory where most sites are either invariable or neutral. We conclude that the correlation is a general feature of protein evolution and discuss its implications in statistical tests of positive Darwinian selection and molecular time estimation of deep divergences.
Analysis of a Drosophila cyclin E Hypomorphic Mutation Suggests a Novel Role for Cyclin E in Cell Proliferation Control During Eye Imaginal Disc Development
Authors: Secombe Julie , Pispa Johanna , Saint Robert , Richardson Helena 
Published: April 2021

Abstract
We have generated and characterized a Drosophila cyclin E hypomorphic mutation, DmcycEJP, that is homozygous viable and fertile, but results in adults with rough eyes. The mutation arose from an internal deletion of an existing P[w+lacZ] element inserted 14 kb upstream of the transcription start site of the DmcycE zygotic mRNA. The presence of this deleted P element, but not the P[w+lacZ] element from which it was derived, leads to a decreased level of DmcycE expression during eye imaginal disc development. Eye imaginal discs from DmcycEJP larvae contain fewer S phase cells, both anterior and posterior to the morphogenetic furrow. This results in adults with small rough eyes, largely due to insufficient numbers of pigment cells. Altering the dosage of the Drosophila cdk2 homolog, cdc2c, retinoblastoma, or p21CIP1 homolog dacapo, which encode proteins known to physically interact with Cyclin E, modified the DmcycEJP rough eye phenotype as expected. Decreasing the dosage of the S phase transcription factor gene, dE2F, enhanced the DmcycEJP rough eye phenotype. Surprisingly, mutations in G2/M phase regulators cyclin A and string (cdc25), but not cyclin B1, B3, or cdc2, enhanced the DmcycE JP phenotype without affecting the number of cells entering S phase, but by decreasing the number of cells entering mitosis. Our analysis establishes the DmcycE JP allele as an excellent resource for searching for novel cyclin E genetic interactors. In addition, this analysis has identified cyclin A and string as DmcycEJP interactors, suggesting a novel role for cyclin E in the regulation of Cyclin A and String function during eye development.
Identification and Mapping of Two Divergent, Unlinked Major Histocompatibility Complex Class II B Genes in Xiphophorus Fishes
Authors: McConnell Thomas J , Godwin Ulla B , Norton Stephen F , Nairn Rodney S , Kazianis Steven , Morizot Donald C 
Published: April 2021

AbstractWe have isolated two major histocompatibility complex (MHC) class II B genes from the inbred fish strain Xiphophorus maculatus Jp 163 A. We mapped one of these genes, designated here as DXB, to linkage group III, linked to a malic enzyme locus, also syntenic with human and mouse MHC. Comparison of genomic and cDNA clones shows the gene consists of six exons and five introns. The encoded β1 domain has three amino acids deleted and a cytoplasmic tail nine amino acids longer than in other teleost class II β chains, more similar to HLA-DRB, clawed frog Xela-F3, and nurse shark Gici-B. Key residues for disulfide bonds, glycosylation, and interaction with α chains are conserved. These same features are also present in a swordtail (Xiphophorus helleri) genomic DXB PCR clone. A second type of class II B clone was amplified by PCR from X. maculatus and found to be orthologous to class II genes identified in other fishes. This DAB-like gene is 63% identical to the X. maculatus DXB sequence in the conserved β2-encoding exon and was mapped to new unassigned linkage group LG U24. The DXB gene, then, represents an unlinked duplicated locus not previously identified in teleosts.
Analysis of Genetic Structure and Dispersal Patterns in a Population of Sea Beet
Authors: Tufto Jarle , Raybould Alan F , Hindar Kjetil , Engen Steinar 
Published: April 2021

Abstract
A model of the migration pattern in a metapopulation of sea beet (Beta vulgaris L. ssp. maritima), based on the continuous distributions of seed and pollen movements, is fitted to gene frequency data at 12 isozyme and RFLP loci by maximum likelihood by using an approximation of the simultaneous equilibrium distribution of the gene frequencies generated by the underlying multivariate stochastic process of genetic drift in the population. Several alternative restrictions of the general model are fitted to the data, including the island model, a model of complete isolation, and a model in which the seed and pollen dispersal variances are equal. Several likelihood ratio tests between these alternatives are performed, and median bias in the estimated parameters is corrected by using parametric bootstrapping. To assess the fit of the selected model, the predicted covariances are compared with covariances computed from the data directly. The dependency of estimated parameters on the ratio between effective and absolute subpopulation sizes, which is treated as a known parameter in the analysis, is also examined. Finally, we note that the data also appear to contain some information about this ratio.
A Microsatellite Map of Wheat
Authors: Röder Marion S , Korzun Victor , Wendehake Katja , Plaschke Jens , Tixier Marie-Hélène , Leroy Philippe , Ganal Martin W 
Published: April 2021

Abstract
Hexaploid bread wheat (Triticum aestivum L. em. Thell) is one of the world's most important crop plants and displays a very low level of intraspecific polymorphism. We report the development of highly polymorphic microsatellite markers using procedures optimized for the large wheat genome. The isolation of microsatellite-containing clones from hypomethylated regions of the wheat genome increased the proportion of useful markers almost twofold. The majority (80%) of primer sets developed are genome-specific and detect only a single locus in one of the three genomes of bread wheat (A, B, or D). Only 20% of the markers detect more than one locus. A total of 279 loci amplified by 230 primer sets were placed onto a genetic framework map composed of RFLPs previously mapped in the reference population of the International Triticeae Mapping Initiative (ITMI) Opata 85 × W7984. Sixty-five microsatellites were mapped at a LOD &gt;2.5, and 214 microsatellites were assigned to the most likely intervals. Ninety-three loci were mapped to the A genome, 115 to the B genome, and 71 to the D genome. The markers are randomly distributed along the linkage map, with clustering in several centromeric regions.
An AFLP-Based Procedure for the Efficient Mapping of Mutations and DNA Probes in Barley
Authors: Castiglioni P , Pozzi C , Heun M , Terzi V , Müller K J , Rohde W , Salamini F 
Published: April 2021

Abstract
A strategy based upon AFLP markers for high-efficiency mapping of morphological mutations and DNA probes to linkage groups in barley is presented. First, 511 AFLP markers were placed on the linkage map derived from the cross Proctor × Nudinka. Second, loci controlling phenotypic traits were assigned to linkage groups by AFLP analysis, using F2 populations consisting of 30–50 mutant plants derived from crosses of the type “mutant × Proctor” and “mutant × Nudinka.” To map DNA probes, 67 different wild-type barley lines were selected to generate F2 populations by crossing with Proctor and Nudinka. F2 plants that were polymorphic for a given RFLP fragment were classified into genotypic classes. Linkage of the RFLP polymorphism to 1 of the 511 AFLP loci was indicated by cosegregation. The use of the strategy is exemplified by the mapping of the mutation branched-5 to chromosome 2 and of the DNA probes Bkn2 and BM-7 to chromosomes 5 and 1, respectively. Map expansion and marker order in map regions with dense clustering of markers represented a particular problem. A discussion considering the effect of noncanonical recombinant products on these two parameters is provided.
Canalization, Genetic Assimilation and Preadaptation: A Quantitative Genetic Model
Authors: Eshel Ilan , Matessi Carlo 
Published: April 2021

Abstract
We propose a mathematical model to analyze the evolution of canalization for a trait under stabilizing selection, where each individual in the population is randomly exposed to different environmental conditions, independently of its genotype. Without canalization, our trait (primary phenotype) is affected by both genetic variation and environmental perturbations (morphogenic environment). Selection of the trait depends on individually varying environmental conditions (selecting environment). Assuming no plasticity initially, morphogenic effects are not correlated with the direction of selection in individual environments. Under quite plausible assumptions we show that natural selection favors a system of canalization that tends to repress deviations from the phenotype that is optimal in the most common selecting environment. However, many experimental results, dating back to Waddington and others, indicate that natural canalization systems may fail under extreme environments. While this can be explained as an impossibility of the system to cope with extreme morphogenic pressure, we show that a canalization system that tends to be inactivated in extreme environments is even more advantageous than rigid canalization. Moreover, once this adaptive canalization is established, the resulting evolution of primary phenotype enables substantial preadaptation to permanent environmental changes resembling extreme niches of the previous environment.
Two Pleiotropic Classes of daf-2 Mutation Affect Larval Arrest, Adult Behavior, Reproduction and Longevity in Caenorhabditis elegans
Authors: Gems David , Sutton Amy J , Sundermeyer Mark L , Albert Patrice S , King Kevin V , Edgley Mark L , Larsen Pamela L , Riddle Donald L 
Published: April 2021

Abstract
The nematode Caenorhabditis elegans responds to overcrowding and scarcity of food by arresting development as a dauer larva, a nonfeeding, long-lived, stress-resistant, alternative third-larval stage. Previous work has shown that mutations in the genes daf-2 (encoding a member of the insulin receptor family) and age-1 (encoding a PI 3-kinase) result in constitutive formation of dauer larvae (Daf-c), increased adult longevity (Age), and increased intrinsic thermotolerance (Itt). Some daf-2 mutants have additional developmental, behavioral, and reproductive defects. We have characterized in detail 15 temperature-sensitive and 1 nonconditional daf-2 allele to investigate the extent of daf-2 mutant defects and to examine whether specific mutant traits correlate with each other. The greatest longevity seen in daf-2 mutant adults was approximately three times that of wild type. The temperature-sensitive daf-2 mutants fell into two overlapping classes, including eight class 1 mutants, which are Daf-c, Age, and Itt, and exhibit low levels of L1 arrest at 25.5°. Seven class 2 mutants also exhibit the class 1 defects as well as some or all of the following: reduced adult motility, abnormal adult body and gonad morphology, high levels of embryonic and L1 arrest, production of progeny late in life, and reduced brood size. The strengths of the Daf-c, Age, and Itt phenotypes largely correlated with each other but not with the strength of class 2-specific defects. This suggests that the DAF-2 receptor is bifunctional. Examination of the null phenotype revealed a maternally rescued egg, L1 lethal component, and a nonconditional Daf-c component. With respect to the Daf-c phenotype, the dauer-defective (Daf-d) mutation daf-12(m20) was epistatic to daf-2 class 1 alleles but not the severe class 2 alleles tested. All daf-2 mutant defects were suppressed by the daf-d mutation daf-16(m26). Our findings suggest a new model for daf-2, age-1, daf-12, and daf-16 interactions.
Induced Chromosomal Exchange Directs the Segregation of Recombinant Chromatids in Mitosis of Drosophila
Authors: Beumer Kelly J , Pimpinelli Sergio , Golic Kent G 
Published: April 2021

Abstract
In meiosis, the segregation of chromosomes at the reductional division is accomplished by first linking homologs together. Genetic exchange generates the bivalents that direct regular chromosome segregation. We show that genetic exchange in mitosis also generates bivalents and that these bivalents direct mitotic chromosome segregation. After FLP-mediated homologous recombination in G2 of the cell cycle, recombinant chromatids consistently segregate away from each other (x segregation). This pattern of segregation also applies to exchange between heterologs. Most, or all, cases of non-x segregation are the result of exchange in G1. Cytological evidence is presented that confirms the existence of the bivalents that direct this pattern of segregation. Our results implicate sister chromatid cohesion in maintenance of the bivalent. The pattern of chromatid segregation can be altered by providing an additional FRT at a more proximal site on one chromosome. We propose that sister chromatid exchange occurs at the more proximal site, allowing the recombinant chromatids to segregate together. This also allowed the recovery of reciprocal translocations following FLP-mediated heterologous recombination. The observation that exchange can generate a bivalent in mitotic divisions provides support for a simple evolutionary relationship between mitosis and meiosis.
Detection of the Ongoing Sorting of Ancestrally Polymorphic SINEs Toward Fixation or Loss in Populations of Two Species of Charr During Speciation
Authors: Hamada Mitsuhiro , Takasaki Nobuyoshi , Reist James D , DeCicco Alfred L , Goto Akira , Okada Norihiro 
Published: April 2021

Abstract
The FokI family of short interspersed repetitive elements (SINEs) has been found only in the genomes of charr fishes (genus Salvelinus). In an analysis of the insertion of FokI SINEs using PCR, we characterized six loci at which FokI SINEs have been inserted into the genomes of Salvelinus alpinus (Arctic charr) and/or S. malma (Dolly Varden). An analysis of one locus (Fok-223) suggested that a sister relationship exists between S. alpinus and S. malma and the SINE at this locus might have been inserted in a common ancestor of these two species, being fixed in all extant populations examined. By contrast, SINEs at two other loci (Fok-211 and Fok-206) were present specifically in the genome of S. alpinus, with polymorphism among populations of this species. Moreover, the presence or absence of the SINEs of the other three loci (Fok-214, Fok-217, and Fok-600) varied among populations of these two species. The most plausible interpretation of this result is that SINEs, which were ancestrally polymorphic in the genome of a common ancestor of these two species, are involved in an ongoing process of differential sorting and subsequent fixation in the various populations of each species.
A Subset of Conserved tRNA Genes in Plastid DNA of Nongreen Plants
Authors: Lohan Amanda J , Wolfe Kenneth H 
Published: April 2021

Abstract
The plastid genome of the nonphotosynthetic parasitic plant Epifagus virginiana contains only 17 of the 30 tRNA genes normally found in angiosperm plastid DNA. Although this is insufficient for translation, the genome is functional, so import of cytosolic tRNAs into plastids has been suggested. This raises the question of whether the tRNA genes that remain in E. virginiana plastid DNA are active or have just fortuitously escaped deletion. We report the sequences of 20 plastid tRNA loci from Orobanche minor, which shares a nonphotosynthetic ancestor with E. virginiana. The two species have 9 intact tRNA genes in common, the others being defunct in one or both species. The intron-containing trnLUAA gene is absent from E. virginiana, but it is intact, transcribed, and spliced in O. minor. The shared intact genes are better conserved than intergenic sequences, which indicates that these genes are being maintained by natural selection and, therefore, must be functional. For the most part, the tRNA species conserved in nonphotosynthetic plastids are also those that have never been found to be imported in plant mitochondria, which suggests that the same rules may govern tRNA import in the two organelles. A small photosynthesis gene, psbI, is still intact in O. minor, and computer simulations show that some small nonessential genes have an appreciable chance of escaping deletion.