bluuebunny/crossref_metadata_2025_split huggingface dataset:
The effect of background selection against deleterious mutations on weakly selected, linked variants
Authors: Charlesworth Brian 
Published: September 2009

SummaryThis paper analyses the effects of selection against deleterious alleles maintained by mutation (‘ background selection’) on rates of evolution and levels of genetic diversity at weakly selected, completely linked, loci. General formulae are derived for the expected rates of gene substitution and genetic diversity, relative to the neutral case, as a function of selection and dominance coefficients at the loci in question, and of the frequency of gametes that are free of deleterious mutations with respect to the loci responsible for background selection. As in the neutral case, most effects of background selection can be predicted by considering the effective size of the population to be multiplied by the frequency of mutation-free gametes. Levels of genetic diversity can be sharply reduced by background selection, with the result that values for sites under selection approach those for neutral variants subject to the same regime of background selection. Rates of fixation of slightly deleterious mutations are increased by background selection, and rates of fixation of advantageous mutations are reduced. The properties of sex-linked and autosomal asexual and self-fertilizing populations are considered. The implications of these results for the interpretation of studies of molecular evolution and variation are discussed.
An application of population genetic theory to synonymous gene sequence evolution in the human immunodeficiency virus (HIV)
Authors: Kelly John K. 
Published: September 2009

SummaryA population genetic model is developed and then applied to the synonymous gene sequence variation observed in samples of the Human Immunodeficiency Virus Type 1 (HIV-1). The samples, which were taken from several previous studies, contain sequences of the envelope glycoprotein gene (gp 120) of HIV-1. This analysis suggests that the viral population within an infected patient at any specific time is likely to be composed of close relatives. The viruses in a sample are likely to share a recent common ancestor probably due to consistent positive selection for non-synonymous mutations coupled with low recombination in this region of the genome. There is no substantial difference in synonymous evolutionary rate between samples of sequences obtained from Peripheral Blood Mononucleate Cells (PBMCs) and samples taken from blood plasma. This is likely to be due to the high rate of migration between these 2 HIV sub-populations. The mutation rate for the genetic region examined is estimated at 9·20 × 10−4per site per month. Under the assumptions of the estimation procedure, this estimate can be bounded between 8·50 and 9·91 × 10−4with 95% confidence. When coupled with direct estimates of mutation rate, the rate of synonymous evolution suggests that the mean number of generations per month for HIV-1in vivois between 1 and 4.
Spontaneous sex reversal inPleurodeles waltl(urodele amphibia): analysis of its inheritance
Authors: Collenot Alain , Durand Danielle , Lauthier Michel , Dorazi Robert , Lacroix Jean-Claude , Dournon Christian 
Published: September 2009

SummaryUp to now, no case of spontaneous sex reversal has been described in the urodele amphibianPleurodeles waltlreared at ambient temperature. However in offspring reared under laboratory conditions, males, females but also intersex individuals were obtained. The males, some females and the intersexes had the ZZ male genotype identified through a test performed with a sex-linked enzyme. The other females had the ZW female genotype. Using the animals of this particular strain, an offspring analysis was made on crosses between, respectively, ZZ males and ZW females, ZZ males and ZZ females, and ZZ intersexes and ZZ males or females. All these crosses gave ZZ males, ZZ females and ZZ intersexes. The spontaneous complete or partial sex reversal is inheritable, but the genetic mechanism of this inheritance has not yet been elucidated.
An exact test for neutrality based on the Ewens sampling distribution
Authors: Slatkin Montgomery 
Published: September 2009

SummaryUsing the Ewens sampling distribution of selectively neutral alleles in a finite population, it is possible to develop an exact test of neutrality by finding the probability of each configuration with the same sample size and observed number of allelic classes. The exact test provides the probability of obtaining a configuration with the same or smaller probability as the observed configuration under the null hypothesis. The results from the exact test may be quite different from those from the Ewens—Watterson test based on the homozygosity in the sample. The advantages and disadvantages of using an exact test in this and other population genetic contexts are discussed.
Selection on reaction norms, genetic correlations and constraints
Authors: Van Tienderen Peter H. , Koelewijn Hans P. 
Published: September 2009

SummaryTwo approaches to the evolution of phenotypic plasticity in heterogeneous environments have recently been put forward. The first focuses on selection on the character expression within each environment; plasticity is seen as a by-product of local selection in various habitats. The second approach focuses on selection on the parameters of the response function of genotypes, and selection is thought to change the frequencies of ‘plasticity’ genes that affect the function. This paper discusses the relationship between the two approaches, with emphasis on applications. A method is described that allows switching from one approach to the other. It is argued that character state and reaction norm approaches, while to a large extent interchangeable, usually differ in the response function chosen. This choice, however, may strongly affect the biological interpretation. The methods outlined in this paper permit one to look at the data from different perspectives in order to avoid this danger.
Estimation of inbreeding coefficients from genotypic data on multiple alleles, and application to estimation of clonality in malaria parasites
Authors: Hill William G. , Babiker Hamza A. , Ranford-Cartwright Lisa C. , Walliker David 
Published: September 2009

SummaryMethods for estimating probability of identity by descent (f) are derived for data on numbers of genotypes at single loci and at pairs of loci with many alleles at each locus. The methods are general, but are specifically applied to data on genotype frequencies in zygotes of the malaria parasite sampled from its mosquito host in order to find the extent of outcrossing in the parasite and the degree of clonality in populations. It is assumed that zygotes are the outcome either of gametes of the same clone, in which they are identical at all loci, or are products of two random, unrelated clones. From the estimate offan effective number of clones per human host can also be derived. ForPlasmodium falciparumfrom a Tanzanian village, estimates offare 0·33 from data on zygote frequencies at two multiallelic loci, indicating that two-thirds of zygotes produce recombinant types.
Comparative population structuring of molecular and allozyme variation ofDrosophila melanogaster Adhbetween Europe, West Africa and East Africa
Authors: Bénassi Véronique , Veuille Michel 
Published: September 2009

SummaryRestriction enzyme molecular variation inDrosophila melanogaster Adhwas compared between three natural populations from Europe, West Africa and East Africa. The frequency distribution of silent variation in theslowallele was compatible with the neutral model in all three samples. The number of haplotypes in East Africa was significantly higher than in the other two populations. The largest divergence, as measured byFst, was between the East African population and a group made up from the West African, the European, and previously studied American populations. We suggest that a split first occurred within African populations at least 44000 years ago. European populations separated from West Africa more recently, between the last glacial maximum and the post-glacial optimum, 18000 to 8000 years ago. We suggest that this species was domesticated recently relative to human evolution, possibly with the advent of agriculture. Population differentiation with respect to the two allozymes,fastandslow, does not follow the geographical pattern of silent variation. It opposes European to both African populations, and probably results from selection for adaptation to alcohol in recent temperate populations.
Dynamics of unconditionally deleterious mutations: Gaussian approximation and soft selection
Authors: Kondrashov Alexey S. 
Published: September 2009

SummaryThis paper studies the influence of two opposite forces, unidirectional unconditionally deleterious mutations and directional selection against them, on an amphimictic population. Mutant alleles are assumed to be equally deleterious and rare, so that homozygous mutations can be ignored. Thus, a genotype is completely described by its value with respect to a quantitative traitx, the number of mutations it carries, while a population is described by its distributionp(x) with meanM[p] and varianceV[p] = σ2[p]. When mutations are only slightly deleterious, so thatM» 1, before selectionp(x) is close to Gaussian with any mode of selection. I assume that selection is soft in the sense that the fitness of a genotype depends on the difference between its value ofxandM, in units of σ. This leads to a simple system of equations connecting the values ofMandVin successive generations. This system has a unique and stable equilibrium,whereUis the genomic deleterious mutation rate, δ is the selection differential forxin units of σ, andpis the ratio of variances ofp(x) after and before selection. Both δ and ρ are parameters of the mode of soft selection, and do not depend onMorV. In an equilibrium population, the selection coefficient against a mutant allele is ŝ = δ2[U(2–ρ)]−1. The mutation load can be tolerable only if the genome degradation rate υ =U/σ is below 2. Other features of mutation-selection equilibrium are also discussed.
Partial deletion of the Y chromosome removes the effect of paternal genome imprinting on periovum sensitivity to hyaluronidase in mice
Authors: Styrna Józefa 
Published: September 2009

SummaryCumulus-oocyte complexes from the two consomic strains of mice, B10. BR and BIO.BR-Ydel (with a partial deletion of the Y chromosome) and the BALB/c strain, as well as reciprocal Fl and F2 hybrids, were tested for their susceptibility to attack by hyaluronidase. The cumulus cell dispersal was significantly more rapid in the eggs of B10.BR females and of Fl and F2 hybrid females sired by the B10.BR males than in those of BALB/c females and hybrids sired by BALB/c males. These results confirm the earlier data of Bander et al. (1989) which were interpreted as evidence of paternal imprinting of the C57BL genome. In contrast, cumulus cell dispersal in the eggs of females sired by BIO.BR-Ydel males was significantly slower than in females sired by B10.BR males, and did not differ from that in the BALB/c strain. The results suggest that the partial deletion of the Y chromosome abolished the effect of paternal genome imprinting which is observed in the B10.BR strain.
Mitochondrial inheritance inAspergillus nidulans
Authors: Coenen Alex , Croft Jim H. , Slakhorst Marijke , Debets Fons , Hoekstra Rolf 
Published: September 2009

SummaryMitochondrial chloramphenicol and oligomycin resistance mutations were used to investigate mitochondrial inheritance inA. nidulans. Mitochondrial RFLPs could not be used to distinguish between paternal and maternal mitochondria because none were detected in the 54 isolates investigated. Several thousand ascospores from each of 111 hybrid cleistothecia from 21 different crosses between 7 heterokaryon incompatible isolates were tested for biparental inheritance. All mitochondrial inheritance was strictly uniparental. Not one instance of paternal inheritance of mitochondria was observed. The implications of our results for the theory that uniparental inheritance evolved to avoid cytoplasmic conflictare discussed. Possible explanations for the maintenance of strict uniparental inheritance of mitochondria in an inbreeding homothallic organism are suggested. The chloramphenicol resistance marker was inherited preferentially to the oligomycin resistance marker probably due to the inhibited energy production of mitochondria with the oligomycin resistance mutation. The maternal parent was determined for 93 hybrid cleistothecia from 17 crosses between 7 different strains. Contraryto previous reportsA. nidulansstrains functioned as both maternal and paternal parent in most crosses.
Estimators for pairwise relatedness and individual inbreeding coefficients
Authors: Ritland Kermit 
Published: September 2009

SummaryMethod-of-moments estimators (MMEs) for the two-gene coefficients of relationship and inbreeding, and for thxe four-gene Cotterman coefficients, are described. These estimators, which use co-dominant genetic markers, are most appropriate for estimating pairwise relatedness or individual inbreeding coefficients, as opposed to their mean values in a group. This is because, compared to the maximum likelihood estimate (MLE), they show reduced small-sample bias and lack distributional assumptions. The ‘efficient’ MME is an optimally weighted average of estimates given by each allele at each locus. Generally, weights must be computed numerically, but if true coefficients are assumed zero, simplifiedestimators are obtained whose relative efficiencies are quite high. Population gene frequency is assumed to be assayed ina larger, ‘reference population’ sample, and the biases introduced by small reference samples and/or genetic drift of the reference population are discussed. Individual-level estimates of relatedness or inbreeding, while displaying high variance, are useful in several applications as a covariate in population studies.
Genetic analysis ofDrosophila virilissex pheromone: genetic mapping of the locus producing Z-(ll)-pentacosene
Authors: Doi Motomichi , Tomaru Masatoshi , Matsubayashi Hiroshi , Yamanoi Kiyo , Oguma Yuzuru 
Published: September 2009

SummaryZ-(ll)-pentacosene,Drosophila virilissex pheromone, is predominant among the female cuticular hydrocarbons and can elicit male courtship behaviours. To evaluate the genetic basis of its production, interspecific crosses betweenD. novamexicanaand genetically markedD. viriliswere made and hydrocarbon profiles of their backcross progeny were analysed. The production of Z-(ll)-pentacosene was autosomally controlled and was recessive. Of the sixD. virilischromosomes only the second and the third chromosomes showed significant contributions to sex pheromone production, and acted additively. Analysis of recombinant females indicated that the locus on the second chromosome mapped to the proximity of position 2–218.
Stability and genetic basis of variability of phally polymorphism in natural populations of the self-fertile freshwater snailBulinus truncatus
Authors: Doums Claudie , Labbo Rabiou , Jarne Philippe 
Published: September 2009

SummaryWe investigated the genetic variability for phally polymorphism within and between natural populations of the hermaphrodite self-fertile freshwater snailBulinus truncatus. Phally polymorphism is characterized by the co-occurrence in natural populations of regular hermaphrodite individuals (euphallic) and individuals deprived of the male copulatory organ (aphallic). The two morphs can both self-fertilize and outcross. However, aphallic individuals cannot outcross as males. We examined the variation of the aphally ratio in 22 natural populations from Niger over two successive years. During the second years, populations were sampled three times at 3 week intervals. The aphally ratio was highly variable among populations at a given sampling data and remained relatively stable over time. For 10 of these populations, one population from Corsica and two from Sardinia, we also estimated the between- and within- population variability, analysing the aphally ratio of 346 families under laboratory conditions. The aphally ratio varied significantly among populations and was highly correlated with the aphally ratio of the natural populations. Some within-population variability, associated with a high value of the broad sense heritability, was observed in four populations out of 13. In these populations, aphallic individuals produced significantly more aphallic offspring than euphallic individuals. Our results indicate a strong genetic basis for aphally, with large genetic differences among populations and some genetic variability for aphally within populations. We discuss the adaptive and stochastic factors that may shape the distribution of the genetic variability for aphally.
Pleiotropy as a factor maintaining genetic variation in quantitative characters under stabilizing selection
Authors: Gimelfarb A. 
Published: September 2009

SummaryA model of pleiotropy withNdiallelic loci contributing additively toNquantitative traits and stabilizing selection acting on each of the traits is considered. Every locus has a major contribution to one trait and a minor contribution to the rest of them, while every trait is controlled by one major locus and N−1 minor loci. It is demonstrated that a stable equilibrium with the allelic frequency equal to 0·5 in allNloci can be maintained in such a model for a wide range of parameters. Such a ‘totally polymorphic’ equilibrium is maintained for practically any strength of selection and any recombination, if the relative contribution by a minor locus to a trait is less than 20 % of the contribution by a major locus. The dynamic behaviour of the model is shown to be quite complex with a possibility under sufficiently strong selection of multiple stable equilibria and positive linkage disequilibria between loci. It is also suggested that pleiotropy among loci controlling traits experiencing direct selection can be responsible for apparent selection on neutral traits also controlled by these loci.
Distortion of Mendelian recovery ratio for a mouse HSR is caused by maternal and zygotic effects
Authors: Weichenhan Dieter , Traut Walther , Kunze Bärbel , Winking Heinz 
Published: September 2009

SummaryAn HSR in chromosome 1 which is found in many feral populations ofMus musculus domesticuswas shown in previous studies to consist of a high-copy long-range repeat cluster. One such cluster,MUT, showed distorted transmission ratios when introduced by female parents.MUT/ + offspring were preferentially recovered at the expense of + / + embryos in the progeny of ♀MUT/+ x♂ +/+ but were found at the expected 1:1 ratio in reciprocal crosses. Preferential recovery of maternal MUT was due to lethality of postimplantation + /+ embryos. There was no distortion of the recovery ratio inMUT/+ xMUT/MUTprogeny: maternalMUTand + clusters were present among live implants at a 1:1 ratio. Maternal and zygotic effects therefore contribute to the phenomenon. The mechanism of their interaction is unknown.
Evolution of amphimixis and recombination under fluctuating selection in one and many traits
Authors: Kondrashov Alexey S. , Yampolsky Lev Yu. 
Published: September 2009

SummaryBoth stabilizing and directional selection acting on one or many quantitative traits usually reduce the genetic variance in a polymorphic population. Amphimixis and recombination restore the variance, pushing it closer to its value under linkage equilibrium. They thus increase the response of the population to fluctuating selection and decrease the genetic load when the mean phenotype is far from optimum. Amphimixis can have a short-term advantage over apomixis if selection fluctuates frequently and widely, so that every genotype often has a low fitness. Such selection causes high genetic variance due to frequent allele substitutions, and a high load even with amphimixis. Recombination in an amphimictic population is maintained only if selection is usually strong and effectively directional. A modifier allele causing free recombination can have a significant advantage only if fluctuations of selection are such that the load is substantial. With smaller fluctuations, an intermediate recombination rate can be established, either due to fixation of alleles that cause such a rate or due to the stable coexistence of alleles causing high and low recombination. If many traits simultaneously are under fluctuating selection, amphimixis and recombination can be maintained when selection associated with individual traits is weaker and the changes in their mean values are smaller than with a single trait. Still, the range of changes of the fitness optima in each trait must be at least of the order of the trait's standard deviation, and the total load must be high.
Mapping quantitative trait loci using four-way crosses
Authors: Xu Shizhong 
Published: September 2009

SummaryIn plant species, typical gene mapping strategies use populations initiated from crosses between two inbred lines. However, schemes including more than two parents could be used. In this paper, a new approach is introduced which uses a four-way cross population derived from four inbred lines. The four-way cross design for mapping quantitative trait loci (QTLs) provides tests for QTL segregation in four lines simultaneously in one experiment. Therefore, it is a more economical strategy than oneusing line crosses between only two lines. The new strategy also increases the probability of detecting QTLs if they segregate in one line cross but not in the other. A multiple linear regression analysis is used for QTL detection. It is proven that the expected residual variance from the regression analysis differs from the pure environmental variance. Correction for the bias is proposed and verified by computer simulations.
A 1·5 kb direct repeat sequence flanks thesuppressor of forkedgene at the euchromatin–heterochromatin boundary of theDrosophila melanogasterX chromosome
Authors: Tudor Mark , Mitchelson Andrew , O'hare Kevin 
Published: September 2009

SummaryA 1·5 kilobasepair repeated DNA sequence is duplicated in direct orientation so as to flank thesuppressor of forkedgene in the euchromatin–heterochromatin transition region on the X chromosome ofDrosophila melanogaster. These two copies are almost identical, but DNA blotting, analysis of cloned sequences and database searches show that elsewhere in the genome, homologous sequences are poorly conserved. They are often associated with other repeats, suggesting that they may belong to a scrambled and clustered middle repetitive DNA family. The sequences do not appear to be related to transposable elements and their location in different strains is conserved.In situhybridization to metaphase chromosomes shows that homologous sequences are concentrated in the pericentric regions of the autosomes and the X chromosome. The sequences are not significantly under-represented in DNA from polytene tissue and must lie in the replicated regions of polytene chromosomes. The almost perfect conservation of the two repeats aroundsuppressor of forkedinD. melanogastersuggests they arose by duplication or gene conversion. Suppression of recombination in this chromosomal region presumably allows this unusual organization to be stably maintained. In the X-ray induced allele,suppressor of forked-L26, the sequence between the repeats, including the gene, and one copy of the repeat have been deleted.