bluuebunny/crossref_metadata_2025_split huggingface dataset:
Duplication and Diversification in the APETALA1/FRUITFULL Floral Homeotic Gene Lineage: Implications for the Evolution of Floral Development
Authors: Litt Amy , Irish Vivian F 
Published: April 2021

Abstract
Phylogenetic analyses of angiosperm MADS-box genes suggest that this gene family has undergone multiple duplication events followed by sequence divergence. To determine when such events have taken place and to understand the relationships of particular MADS-box gene lineages, we have identified APETALA1/FRUITFULL-like MADS-box genes from a variety of angiosperm species. Our phylogenetic analyses show two gene clades within the core eudicots, euAP1 (including Arabidopsis APETALA1 and Antirrhinum SQUAMOSA) and euFUL (including Arabidopsis FRUITFULL). Non-core eudicot species have only sequences similar to euFUL genes (FUL-like). The predicted protein products of euFUL and FUL-like genes share a conserved C-terminal motif. In contrast, predicted products of members of the euAP1 gene clade contain a different C terminus that includes an acidic transcription activation domain and a farnesylation signal. Sequence analyses indicate that the euAP1 amino acid motifs may have arisen via a translational frameshift from the euFUL/FUL-like motif. The euAP1 gene clade includes key regulators of floral development that have been implicated in the specification of perianth identity. However, the presence of euAP1 genes only in core eudicots suggests that there may have been changes in mechanisms of floral development that are correlated with the fixation of floral structure seen in this clade.
Fixed Contributions Designs vs. Minimization of Global Coancestry to Control Inbreeding in Small Populations
Authors: Fernández J , Toro M A , Caballero A 
Published: April 2021

Abstract
Populations with small census sizes are at risk because of the loss of genetic variability and the increase of inbreeding and its harmful consequences. For situations with different numbers of males and females, several hierarchical designs have been proposed to control inbreeding through the fixation of individuals' contributions. An alternative method, based on the minimization of global coancestry, has been proposed to determine contributions as to yield of the lowest levels of inbreeding in the population. We use computer simulations to assess the relative efficiency of the different methods. The results show that minimizing the global coancestry leads to equal or lower levels of inbreeding in the short and medium term, although one of the hierarchical designs provides lower asymptotic inbreeding rates and, thus, less net inbreeding in the long term. We also investigate the performance of the alternative methods against departures from the ideal conditions, such as inbred or differentially related base individuals and random failures in the expected contributions. The method of minimization of global coancestry turns out to be more flexible and robust under these realistic situations.
The N-Terminal DNA-Binding Domain of Rad52 Promotes RAD51-Independent Recombination in Saccharomyces cerevisiae
Authors: Tsukamoto Mariko , Yamashita Kentaro , Miyazaki Toshiko , Shinohara Miki , Shinohara Akira 
Published: April 2021

Abstract
In Saccharomyces cerevisiae, the Rad52 protein plays a role in both RAD51-dependent and RAD51-independent recombination pathways. We characterized a rad52 mutant, rad52-329, which lacks the C-terminal Rad51-interacting domain, and studied its role in RAD51-independent recombination. The rad52-329 mutant is completely defective in mating-type switching, but partially proficient in recombination between inverted repeats. We also analyzed the effect of the rad52-329 mutant on telomere recombination. Yeast cells lacking telomerase maintain telomere length by recombination. The rad52-329 mutant is deficient in RAD51-dependent telomere recombination, but is proficient in RAD51-independent telomere recombination. In addition, we examined the roles of other recombination genes in the telomere recombination. The RAD51-independent recombination in the rad52-329 mutant is promoted by a paralogue of Rad52, Rad59. All components of the Rad50-Mre11-Xrs2 complex are also important, but not essential, for RAD51-independent telomere recombination. Interestingly, RAD51 inhibits the RAD51-independent, RAD52-dependent telomere recombination. These findings indicate that Rad52 itself, and more precisely its N-terminal DNA-binding domain, promote an essential reaction in recombination in the absence of RAD51.
Functions of Saccharomyces cerevisiae 14-3-3 Proteins in Response to DNA Damage and to DNA Replication Stress
Authors: Lottersberger Francisca , Rubert Fabio , Baldo Veronica , Lucchini Giovanna , Longhese Maria Pia 
Published: April 2021

Abstract
Two members of the 14-3-3 protein family, involved in key biological processes in different eukaryotes, are encoded by the functionally redundant Saccharomyces cerevisiae BMH1 and BMH2 genes. We produced and characterized 12 independent bmh1 mutant alleles, whose presence in the cell as the sole 14-3-3 source causes hypersensitivity to genotoxic agents, indicating that Bmh proteins are required for proper response to DNA damage. In particular, the bmh1-103 and bmh1-266 mutant alleles cause defects in G1/S and G2/M DNA damage checkpoints, whereas only the G2/M checkpoint is altered by the bmh1-169 and bmh1-221 alleles. Impaired checkpoint responses correlate with the inability to maintain phosphorylated forms of Rad53 and/or Chk1, suggesting that Bmh proteins might regulate phosphorylation/dephosphorylation of these checkpoint kinases. Moreover, several bmh1 bmh2Δ mutants are defective in resuming DNA replication after transient deoxynucleotide depletion, and all display synthetic effects when also carrying mutations affecting the polα-primase and RPA DNA replication complexes, suggesting a role for Bmh proteins in DNA replication stress response. Finally, the bmh1-169 bmh2Δ and bmh1-170 bmh2Δ mutants show increased rates of spontaneous gross chromosomal rearrangements, indicating that Bmh proteins are required to suppress genome instability.
The Homologous Chromosome Is an Effective Template for the Repair of Mitotic DNA Double-Strand Breaks in Drosophila
Authors: Rong Yikang S , Golic Kent G 
Published: April 2021

Abstract
In recombinational DNA double-strand break repair a homologous template for gene conversion may be located at several different genomic positions: on the homologous chromosome in diploid organisms, on the sister chromatid after DNA replication, or at an ectopic position. The use of the homologous chromosome in mitotic gene conversion is thought to be limited in the yeast Saccharomyces cerevisiae and mammalian cells. In contrast, by studying the repair of double-strand breaks generated by the I-SceI rare-cutting endonuclease, we find that the homologous chromosome is frequently used in Drosophila melanogaster, which we suggest is attributable to somatic pairing of homologous chromosomes in mitotic cells of Drosophila. We also find that Drosophila mitotic cells of the germ line, like yeast, employ the homologous recombinational repair pathway more often than imperfect nonhomologous end joining.
Patterns of Inbreeding Depression and Architecture of the Load in Subdivided Populations
Authors: Glémin Sylvain , Ronfort Joëlle , Bataillon Thomas 
Published: April 2021

Abstract
Inbreeding depression is a general phenomenon that is due mainly to recessive deleterious mutations, the so-called mutation load. It has been much studied theoretically. However, until very recently, population structure has not been taken into account, even though it can be an important factor in the evolution of populations. Population subdivision modifies the dynamics of deleterious mutations because the outcome of selection depends on processes both within populations (selection and drift) and between populations (migration). Here, we present a general model that permits us to gain insight into patterns of inbreeding depression, heterosis, and the load in subdivided populations. We show that they can be interpreted with reference to single-population theory, using an appropriate local effective population size that integrates the effects of drift, selection, and migration. We term this the “effective population size of selection” (NeS). For the infinite island model, for example, it is equal to NeS=N(1+m∕hs), where N is the local population size, m the migration rate, and h and s the dominance and selection coefficients of deleterious mutation. Our results have implications for the estimation and interpretation of inbreeding depression in subdivided populations, especially regarding conservation issues. We also discuss the possible effects of migration and subdivision on the evolution of mating systems.
Constructing Large-Scale Genetic Maps Using an Evolutionary Strategy Algorithm
Authors: Mester D , Ronin Y , Minkov D , Nevo E , Korol A 
Published: April 2021

Abstract
This article is devoted to the problem of ordering in linkage groups with many dozens or even hundreds of markers. The ordering problem belongs to the field of discrete optimization on a set of all possible orders, amounting to n!/2 for n loci; hence it is considered an NP-hard problem. Several authors attempted to employ the methods developed in the well-known traveling salesman problem (TSP) for multilocus ordering, using the assumption that for a set of linked loci the true order will be the one that minimizes the total length of the linkage group. A novel, fast, and reliable algorithm developed for the TSP and based on evolution-strategy discrete optimization was applied in this study for multilocus ordering on the basis of pairwise recombination frequencies. The quality of derived maps under various complications (dominant vs. codominant markers, marker misclassification, negative and positive interference, and missing data) was analyzed using simulated data with ∼50-400 markers. High performance of the employed algorithm allows systematic treatment of the problem of verification of the obtained multilocus orders on the basis of computing-intensive bootstrap and/or jackknife approaches for detecting and removing questionable marker scores, thereby stabilizing the resulting maps. Parallel calculation technology can easily be adopted for further acceleration of the proposed algorithm. Real data analysis (on maize chromosome 1 with 230 markers) is provided to illustrate the proposed methodology.
Modes of Reproduction and the Accumulation of Deleterious Mutations With Multiplicative Fitness Effects
Authors: Haccou Patsy , Schneider Maria Victoria 
Published: April 2021

Abstract
Mutational load depends not only on the number and nature of mutations but also on the reproductive mode. Traditionally, only a few specific reproductive modes are considered in the search of explanations for the maintenance of sex. There are, however, many alternatives. Including these may give radically different conclusions. The theory on deterministic deleterious mutations states that in large populations segregation and recombination may lead to a lower load of deleterious mutations, provided that there are synergistic interactions. Empirical research suggests that effects of deleterious mutations are often multiplicative. Such situations have largely been ignored in the literature, since recombination and segregation have no effect on mutation load in the absence of epistasis. However, this is true only when clonal reproduction and sexual reproduction with equal male and female ploidy are considered. We consider several alternative reproductive modes that are all known to occur in insects: arrhenotoky, paternal genome elimination, apomictic thelytoky, and automictic thelytoky with different cytological mechanisms to restore diploidy. We give a method that is based on probability-generating functions, which provides analytical and numerical results on the distributions of deleterious mutations. Using this, we show that segregation and recombination do make a difference. Furthermore, we prove that a modified form of Haldane’s principle holds more generally for thelytokous reproduction. We discuss the implications of our results for evolutionary transitions between different reproductive modes in insects. Since the strength of Muller’s ratchet is reduced considerably for several forms of automictic thelytoky, many of our results are expected to be also valid for initially small populations.
The Effect of Selection on Genealogies
Authors: Barton N H , Etheridge A M 
Published: April 2021

AbstractThe coalescent process can describe the effects of selection at linked loci only if selection is so strong that genotype frequencies evolve deterministically. Here, we develop methods proposed by Kaplan, Darden, and Hudson to find the effects of weak selection. We show that the overall effect is given by an extension to Price’s equation: the change in properties such as moments of coalescence times is equal to the covariance between those properties and the fitness of the sample of genes. The distribution of coalescence times differs substantially between allelic classes, even in the absence of selection. However, the average coalescence time between randomly chosen genes is insensitive to the current allele frequency and is affected significantly by purifying selection only if deleterious mutations are common and selection is strong (i.e., the product of population size and selection coefficient, Ns &gt; 3). Balancing selection increases mean coalescence times, but the effect becomes large only when mutation rates between allelic classes are low and when selection is extremely strong. Our analysis supports previous simulations that show that selection has surprisingly little effect on genealogies. Moreover, small fluctuations in allele frequency due to random drift can greatly reduce any such effects. This will make it difficult to detect the action of selection from neutral variation alone.
Developing a Genetic System in Deinococcus radiodurans for Analyzing Mutations
Authors: Kim Mandy , Wolff Erika , Huang Tiffany , Garibyan Lilit , Earl Ashlee M , Battista John R , Miller, Jeffrey H 
Published: April 2021

Abstract
We have applied a genetic system for analyzing mutations in Escherichia coli to Deinococcus radiodurans, an extremeophile with an astonishingly high resistance to UV- and ionizing-radiation-induced mutagenesis. Taking advantage of the conservation of the β-subunit of RNA polymerase among most prokaryotes, we derived again in D. radiodurans the rpoB/Rif r system that we developed in E. coli to monitor base substitutions, defining 33 base change substitutions at 22 different base pairs. We sequenced &gt;250 mutations leading to Rif r in D. radiodurans derived spontaneously in wild-type and uvrD (mismatch-repair-deficient) backgrounds and after treatment with N-methyl-N′-nitro-N-nitrosoguanidine (NTG) and 5-azacytidine (5AZ). The specificities of NTG and 5AZ in D. radiodurans are the same as those found for E. coli and other organisms. There are prominent base substitution hotspots in rpoB in both D. radiodurans and E. coli. In several cases these are at different points in each organism, even though the DNA sequences surrounding the hotspots and their corresponding sites are very similar in both D. radiodurans and E. coli. In one case the hotspots occur at the same site in both organisms.
General Stress Response Regulator RpoS in Adaptive Mutation and Amplification in Escherichia coli
Authors: Lombardo Mary-Jane , Aponyi Ildiko , Rosenberg Susan M 
Published: April 2021

Abstract
Microbial cells under growth-limiting stress can generate mutations by mechanisms distinct from those in rapidly growing cells. These mechanisms might be specific stress responses that increase mutation rates, potentially altering rates of evolution, or might reflect non-stress-specific processes in rare growing cells. In an Escherichia coli model system, both frameshift reversion mutations and gene amplifications occur as apparent starvation-induced mutations. Whereas frameshift reversion (“point mutation”) requires recombination proteins, the SOS response, and error-prone DNA polymerase IV (DinB), amplification requires neither SOS nor pol IV. We report that both point mutation and amplification require the stationary-phase and general stress response transcription factor RpoS (σS). Growth-dependent mutation does not. Alternative interpretations are excluded. The results imply, first, that point mutation and amplification are stress responses that occur in differentiated stationary-phase (not rare growing) cells and, second, that transient genetic instability, producing both point mutation and genome rearrangement, may be a previously unrecognized component of the RpoS-dependent general stress response.
Nucleotide Variation and Recombination Along the Fourth Chromosome inDrosophila simulans
Authors: Wang Wen , Thornton Kevin , Emerson J J , Long Manyuan 
Published: April 2021

AbstractThe fourth chromosome of Drosophila melanogaster and its sister species are believed to be nonrecombining and have been a model system for testing predictions of the effects of selection on linked, neutral variation. We recently examined nucleotide variation along the chromosome of D. melanogaster and revealed that a low average level of recombination could be associated with considerably high levels of nucleotide variation. In this report, we further investigate the variation along the fourth chromosome of D. simulans. We sequenced 12 gene regions evenly distributed along the fourth chromosome for a worldwide collection of 11 isofemale lines and 5 gene regions in a local population of 10 isofemale lines from South America. In contrast to predictions for regions of very low recombination, these data reveal that the variation levels in many gene regions, including an intron region of the ci gene, vary considerably along the fourth chromosome. Nucleotide diversity ranged from 0.0010 to 0.0074 in 9 gene regions interspersed with several regions of greatly reduced variation. Tests of recombination indicate that the recombination level is not as low as previously thought, likely an order of magnitude higher than that in D. melanogaster. Finally, estimates of the recombination parameters are shown to support a crossover-plus-conversion model.
Isolation and Cytogenetic Characterization of Male Meiotic Mutants ofDrosophila melanogaster
Authors: Hirai Kazuyuki , Toyohira Satomi , Ohsako Takashi , Yamamoto Masa-Toshi 
Published: April 2021

AbstractProper segregation of homologous chromosomes in meiosis I is ensured by pairing of homologs and maintenance of sister chromatid cohesion. In male Drosophila melanogaster, meiosis is achiasmatic and homologs pair at limited chromosome regions called pairing sites. We screened for male meiotic mutants to identify genes required for normal pairing and disjunction of homologs. Nondisjunction of the sex and the fourth chromosomes in male meiosis was scored as a mutant phenotype. We screened 2306 mutagenized and 226 natural population-derived second and third chromosomes and obtained seven mutants representing different loci on the second chromosome and one on the third. Five mutants showed relatively mild effects (&lt;10% nondisjunction). mei(2)yh149 and mei(2)yoh7134 affected both the sex and the fourth chromosomes, mei(2)yh217 produced possible sex chromosome-specific nondisjunction, and mei(2)yh15 and mei(2)yh137 produced fourth chromosome-specific nondisjunction. mei(2)yh137 was allelic to the teflon gene required for autosomal pairing. Three mutants exhibited severe defects, producing &gt;10% nondisjunction of the sex and/or the fourth chromosomes. mei(2)ys91 (a new allele of the orientation disruptor gene) and mei(3)M20 induced precocious separation of sister chromatids as early as prometaphase I. mei(2)yh92 predominantly induced nondisjunction at meiosis I that appeared to be the consequence of failure of the separation of paired homologous chromosomes.
Molecular Organization of Large Fragments in the Maize B Chromosome: Indication of a Novel Repeat
Authors: Cheng Ya-Ming , Lin Bor-Yaw 
Published: April 2021

Abstract
The supernumerary B chromosome has no apparent effects on plant growth, and its molecular makeup is difficult to unravel, due to its high homology to the normal complement, which prevents conventional cloning. This difficulty was overcome previously by microdissecting the B chromosome under the microscope to result in 19 B clones, one of which is B specific and highly repetitive, dispersing over one-third of the B long arm and most regions of the centromeric knob. To gain insights into the molecular structure of the B chromosome, this sequence was used to screen a genomic library constructed from W22 carrying 16 B’s. Five clones (&gt;10 kb each) were isolated, and all were repetitive, showing homology with A chromosomes in Southern and FISH analyses. Two of them were further characterized and sequenced. Each is composed of several restriction fragments with variable degrees of repetitiveness. Some of these are B specific and others have variable degrees of homology with the A chromosomes. The order of each characteristic group is not contiguous; they intersperse within those of other groups. Sequence analysis reveals that their sequences (∼26 kb) have no homology with any published gene other than sequences of transposable elements (retrotransposons and MITEs) and the B as well as the A centromeres. We uncovered a 1.6-kb CL-repeat sequence, seven units of which were present in the two clones in defective forms. Those repeats mostly arrange in tandem array in the B chromosome. Moreover, we detected transposition of a retrotransposon and a MITE element involved in the genesis of these two sequences.
Sibship Reconstruction From Genetic Data With Typing Errors
Authors: Wang Jinliang 
Published: April 2021

Abstract
Likelihood methods have been developed to partition individuals in a sample into full-sib and half-sib families using genetic marker data without parental information. They invariably make the critical assumption that marker data are free of genotyping errors and mutations and are thus completely reliable in inferring sibships. Unfortunately, however, this assumption is rarely tenable for virtually all kinds of genetic markers in practical use and, if violated, can severely bias sibship estimates as shown by simulations in this article. I propose a new likelihood method with simple and robust models of typing error incorporated into it. Simulations show that the new method can be used to infer full- and half-sibships accurately from marker data with a high error rate and to identify typing errors at each locus in each reconstructed sib family. The new method also improves previous ones by adopting a fresh iterative procedure for updating allele frequencies with reconstructed sibships taken into account, by allowing for the use of parental information, and by using efficient algorithms for calculating the likelihood function and searching for the maximum-likelihood configuration. It is tested extensively on simulated data with a varying number of marker loci, different rates of typing errors, and various sample sizes and family structures and applied to two empirical data sets to demonstrate its usefulness.
Recovering Frequencies of Known Haplotype Blocks From Single-Nucleotide Polymorphism Allele Frequencies
Authors: Pe’er Itsik , Beckmann Jacques S 
Published: April 2021

Abstract
Prospects for large-scale association studies rely on economical methods and powerful analysis. Representing available SNPs by small subsets and measuring allele frequencies on pooled DNA samples each improve genotyping cost effectiveness, while haplotype analysis may highlight associations in otherwise underpowered studies. This manuscript provides the mathematical framework to integrate these methodologies.