bluuebunny/crossref_metadata_2025 huggingface dataset:
Direct determination of retrotransposon transposition rates inDrosophila melanogaster
Authors: Nuzhdin Sergey V. , Mackay Trudy F. C.
Published: September 2009

Rates of transposition and excision of theDrosophila melanogasterretrotransposon elementsmdg3, 297, Doc, rooandcopiawere estimated directly, byin situhybridization analysis of their cytological insertion sites in 31 replicates of a highly inbred line that had accumulated spontaneous mutations for approximately 160generations. Estimated transposition rates ofDoc, rooandcopiawere, respectively, 4·2 × 10−5, 3·1 × 10−3and 1·3 − 10−3; no transpositions of297normdg3were observed. Rates of transposition ofcopiavaried significantly among sublines. Excisions were only observed forrooelements, at a rate of 9·0 × 10−6per element per generation. Copy number averaged over these element families increased 5·9 %; therefore, in these lines the magnitude of the forces opposing transposable element multiplication were weaker than transposition rates.
Population dynamics of the copia, mdg1, mdg3, gypsy, and P transposable elements in a natural population ofDrosophila melanogaster
Authors: Biémont C. , Lemeunier F. , Guerreiro M. P. Garcia , Brookfield J. F. , Gautier C. , Aulard S. , Pasyukova E. G.
Published: September 2009

The insertion site polymorphism of the copia, mdg1, mdg3, gypsy, and P transposable elements was analysed byin situhybridization to the polytene chromosomes in genomes of males from a natural population ofDrosophila melanogaster. Parameters of various theoretical models of the population biology of transposable elements were estimated from our data, and different hypotheses explaining TE copy number containment were tested. The copia, mdg1 and gypsy elements show evidence for a deficiency of insertions on the X chromosomes, a result consistent with selection against the mutational effects of insertions. On the contrary, mdg3 and P copy numbers fit a neutral model with a balance between regulated transposition and excisions. There is no strong evidence of a systematic accumulation of elements in the distal and proximal regions of the chromosomes where crossing over and ectopic exchanges are reduced. For all chromosome arms but 3L, however, the TE site density increases from the proximal to the distal parts of the chromosomes (the centromeric regions were excluded in this analysis) with sometimes a sharp decrease in density at the extreme tip, following in part the exchange coefficient. The way the copy number of TEs is contained in genomes depends thus on the element considered, and on various forces acting simultaneously, indicating that models of TE dynamics should include details of each element.
Erratum
Authors: West John D. , Flockhart Jean H.
Published: September 2009

Genet. Res., Camb. (1994), 63, pp. 87–99

Genotypically unbalanced diploid ↔ diploidfoetal mouse chimaeras:

possible relevance to human confined mosaicism

John D. West, and Jean H. Flockhart

The sentence starting in the middle of line 16 of the Summary should read

In 20/38 chimaeric conceptuses in the unbalanced
Genetic models for the inheritance of the silver colour mutation of foxes
Authors: Skjøth Flemming , Lohi Outi , Thomas Alun
Published: September 2009

We consider genetic models for the inheritance of the particular colour patterns of silver foxes. The models are evaluated by computation of statistical likelihoods based on observations of related foxes in extended pedigrees. Problems caused by incomplete paternity information are addressed by inferences based on phenotypic observations. The unreliability of subjective evaluations of fur colour also provides difficulty, in particular crossfoxes emerge as being difficult to differentiate. No evidence of linkage between Agouti locus and Extension locus is found in this dataset.
Mini-mouse: phenotypic characterization of a transgenic insertional mutant allelic to pygmy
Authors: Benson Kathleen F. , Chada Kiran
Published: September 2009

A phenotypic analysis was performed on two alleles at the pygmy locus which arose by insertional mutagenesis in transgenic mice. Similar to the spontaneous mutant pygmy, the adult insertional transgenic mutants are 40% of the size of wild-type litter-mates whereas adult heterozygotes are 80% of wild-type litter-mates. An analysis of the various organs revealed that, in general, there was a reduction in weight of each organ commensurate with the overall reduction in body size. However, two organs did not follow this pattern, the brain being disproportionately larger and the adrenals disproportionately smaller in the mutant mice. In addition, mini-mice have less adipose tissue than their wild-type or heterozygous litter-mates. A developmental analysis determined that mutants could first be identified on the basis of reduced body weight at day 15·5 of gestation. The small size is not due to a growth hormone deficiency so these mice differ from other known dwarf mouse mutants. Therefore they should provide insight into the growth hormone-resistant human dwarnsms and help in furthering our knowledge of mammalian growth and development.
Phenotypic effect of substitutions of short chromosomal segments containing different alleles of histone HI genes in garden pea (Pisum sativum L.)
Authors: Bogdanova V. S. , Rozov S. M. , Trusov Y. A. , Berdnikov V. A.
Published: September 2009

A hypothesis has been tested that alterations in the molecule of histone H1 are capable of influencing quantitative traits of an organism. Two pairs of isogenic lines were constructed by selfing of plants kept heterozygous either for allelic variants of histone H1 subtype 1 (His1 gene) or for allelic combinations (haplotypes) of closely linked genes of H1 subtypes 3, 4, 5 and 6 (gene clusterHis(2–6)). After 19 and 15 generations of selfing, respectively, expectation of the length of chromosome which remained heterozygous has comprised 2·6 cM nearHisl and 3·5 cM nearHis(2–6). The third pair of isogenic lines was obtained as a result of two successive intracluster cross-over events bordering the gene of the subtype 5 (His5). In each pair of isogenic lines there have been revealed some statistically significant differences between mean values of a number of quantitative traits.
Estimating the covariance structure of traits during growth and ageing, illustrated with lactation in dairy cattle
Authors: Kirkpatrick Mark , Hill William G. , Thompson Robin
Published: September 2009

Quantitative variation in traits that change with age is important to both evolutionary biologists and breeders. We present three new methods for estimating the phenotypic and additive genetic covariance functions of a trait that changes with age, and illustrate them using data on daily lactation records from British Holstein—Friesian dairy cattle. First, a new technique is developed to fit a continuous covariance function to a covariance matrix. Secondly, this technique is used to estimate and correct for a bias that inflates estimates of phenotypic variances. Thirdly, we offer a numerical method for estimating the eigenvalues and eigenfunctions of covariance functions. Although the algorithms are moderately complex, they have been implemented in a software package that is made freely available.

Analysis of lactation shows the advantages of the new methods over earlier ones. Results suggest that phenotypic variances are inflated by as much as 39 % above the underlying covariance structure by measurement error and short term environmental effects. Analysis of additive genetic variation indicates that about 90 % of the additive genetic variation for lactation during the first 10 months is associated with an eigenfunction that corresponds to increased (or decreased) production at all ages. Genetic tradeoffs between early and late milk yield are seen in the second eigenfunction, but it accounts for less than 8 % of the additive variance. This illustrates that selection is expected to increase production throughout lactation.
TheHermestransposable element from the house fly,Musca domestica, is a short inverted repeat-type element of thehobo, Ac, andTam3(hAT) element family
Authors: Warren William D. , Atkinson Peter W. , O'Brochta David A.
Published: September 2009

The genome of the house fly,Musca domestica, contains an active transposable element system, calledHermes. Using PCR and inverse PCR we amplified and sequenced overlapping segments of severalHermeselements and from these data we have constructed a 2749 bp consensusHermesDNA sequence.Hermestermini are composed of 17 bp imperfect inverted repeats that are almost identical to the inverted terminal repeats of thehoboelement ofDrosophila melanogaster. Full lengthHermeselements contain a single long ORF capable of encoding a protein of 612 amino acids which is 55% identical to the amino acid sequence of thehobotransposase. Comparison of the ends of theHermesandhoboelements to those of theAcelement ofZea mays, and theTam3element ofAntirrhinum majus, as well as several other plant and insect elements, revealed a conserved terminal sequence motif. ThusHermesis clearly a member of thehobo,AcandTam3(hAT) transposable element family, other members of which include theTaglelement fromArabidopsis thalianaand theBgelement fromZea mays. The evolution of this class of transposable elements and the potential utility ofHermesas a genetic tool inM. domesticaand related species are discussed.
At least four genes and sex are associated with susceptibility to urethane-induced pulmonary adenomas in mice
Authors: Festing Michael F. W. , Yang Aili , Malkinson A. M.
Published: September 2009

Susceptibility to urethane-induced lung adenomas in mice has a polygenic mode of inheritance, with no obvious discontinuity in lung tumour counts among 37 AXB recombinant inbred strains. However, mean tumour counts were markedly higher in strains carrying the A/J allele at theKras2andH2complex than in those carrying the C57BL/6 allele. In 162 F2hybrids and small numbers of both backcrosses between strain A/J (susceptible) and C57BL/6 (resistant) mice, five factors influencing susceptibility were identified. Variation due to the ‘major’Kras2locus (chromosome 6) accounted for 60% of the total variation. ‘Minor’ loci linked to microsatellite markersTnfb(in theH2complex),D9Mit11andD19MH16(on chromosomes 17, 9 and 19, respectively) accounted for a further 13% of the variation, and males had more tumours than females with sex differences accounting for 2% of the variation. No significant association with 32 other loci was detected. On a square-root transformed scale, heterozygotes at all marker loci were of intermediate susceptibility compared with homozygotes. Thethree minor loci and sex only affected lung tumour counts when at least one susceptibleKras2allele was present.
The HSR on chromosome 1 of the house mouse, Mus domesticus: distribution and frequency in Switzerland
Authors: Hübner Roland , Maddalena Tiziano , Searle Jeremy B. , Vogel Peter
Published: September 2009

A total of 357 house mice (Mus domesticus) from 83 localities uniformly distributed throughout Switzerland were screened for the presence of a homogenously staining region (HSR) on chromosome 1. Altogether 47 mice from 11 localities were HSR/ + or HSR/HSR. One sample of 11 individuals all had an HSR/HSR karyotype. Almost all mice with the variant were collected from the Rhone valley (HSR frequency: 61%) and Val Bregaglia (HSR frequency: 81%). For samples from most of thearea of Switzerland, the HSR was absent. There was no strong association between the geographic distribution of the HSR and the areas of occurrence of metacentrics. However, at Chiggiogna the HSR was found on Rb (1·3). Possible explanations for the HSR polymorphism are discussed.
The testis-determining gene, SRY, exists in multiple copies in Old World rodents
Authors: Nagamine Claude M.
Published: September 2009

SRY is a unique gene on the Y chromosome in most mammalian species including the laboratory mouse, Mus musculus, and the closely related European wild mouse species M. spicilegus, M. macedonicus, and M. spretus. In contrast, SRY is present in 2–6 copies in the more distantly related Asian mouse species M. caroli, M. cervicolor, and M. cookii and in 2–13 copies in the related murid species Pyromys saxicola, Coelomys pahari, Nannomys minutoides, Mastomys natalensis, and Rattus norvegicus. Copy numbers do not correlate with known phylogenetic relationships suggesting that SRY has undergone a rapid and complex evolution in these species. SRY was recently proposed as a molecular probe for phylogenetic inferences. The presence of multiple SRY genes in a wide range of murid species and genera, and at least one cricetid species, necessitates caution in the use of SRY for phylogenetic studies in the Rodentia unless it is ascertained that multiple SRY genes do not exist.
Sex differences in chiasma distribution along two marked mouse chromosomes: differences in chiasma distribution as a reason for sex differences in recombination frequency
Authors: Gorlov Ivan P. , Zhelezova Antonina I. , Gorlova Olga Yu.
Published: September 2009

Chiasma distributions along bivalents 1 and 14 in female and male mice were studied. It was shown that the average chiasma number in both chromosomes show no sex difference. There are however, significant sex differences in chiasma distribution along 1 and 14 chromosomes. In males there are two terminal chiasma peaks in chromosome 1 and one subtelomeric peak of chiasmata in chromosome 14. In females chiasma distributions are more even. According to genetic data, females produce more recombinants between loci of chromosome 1 than males do. By means of a computer simulation it was demonstrated that the differences in the average recombination frequency result from differences in chiasma distribution.
Spatially regulated expression of retrovirus-like transposons duringDrosophila melanogasterembryogenesis
Authors: Ding Dali , Lipshitz Howard D.
Published: September 2009

Over twenty distinct families of long terminal direct repeat (LTR)-containing retrotransposons have been identified inDrosophila melanogaster. While there have been extensive analyses of retrotransposon transcription in cultured cells, there have been few studies of the spatial expression of retrotransposons during normal development. Here we report a detailed analysis of the spatial expression patterns of fifteen families of retrotransposons duringDrosophila melanogasterembryogenesis (17.6,297,412,1731,3S18,blood,copia,gypsy,HMS Beagle,Kermit/flea,mdg1,mdg3,opus,roo/B104andspringer). In each case, analyses were carried out in from two to four wild-type strains. Since the chromosomal insertion sites of any particular family of retrotransposons vary widely among wild-type strains, a spatial expression pattern that is conserved among strains is likely to have been generated through interaction of host transcription factors withcis-regulatory elements resident in the retrotransposons themselves. All fifteen families of retrotransposons showed conserved patterns of spatially and temporally regulated expression during embryogenesis. These results suggest that all families of retrotransposons carrycis-acting elements that control their spatial and temporal expression patterns. Thus, transposition of a retrotransposon into or near a particular host gene-possibly followed by an excision event leaving behind the retrotransposon'scis-regulatory sequences-might impose novel developmental control on such a host gene. Such a mechanism would serve to confer evolutionarily significant alterations in the spatio-temporal control of gene expression.
The distribution of transposable elements within and between chromosomes in a population ofDrosophila melanogaster. III. Element abundances in heterochromatin
Authors: Charlesworth Brian , Jarne Philippe , Assimacopoulos Stavroula
Published: September 2009

The total genomic copy numbers of ten families of transposable elements ofDrosophila melanogasterin a set of ten isogenic lines derived from a natural population were estimated by slot-blotting. The numbers of euchromatic copies of members of each family were determined for each line byin situhybridization of element probes to polytene chromosomes. Heterochromatic numbers were estimated by subtraction of the euchromatic counts from the total numbers. There was considerable variation between element families and lines in heterochromatic abundances, and the variance between lines for many elements was much greater for the heterochromatin than for the euchromatin. The data are consistent with the view that much of the β-heterochromatin consists of sequences derived from transposable elements. They are also consistent with the hypothesis that similar evolutionary forces control element abundances in both the euchromatin and heterochromatin, although amplification of inert sequences derived from transposable elements may be in part responsible for their accumulation in heterochromatin.
Isolation, characterization and RFLP linkage mapping of a DNA repeat family ofSolanum spegazziniiby which chromosome ends can be localized on the genetic map of potato
Authors: Gebhardt C. , Eberle B. , Leonards-Schippers C. , Walkemeier B. , Salamini F.
Published: September 2009

In a random sample of 2263 cloned genomic DNA fragments of the wild potato speciesSolanum spegazziniisix related, highly repetitive fragments (SPG repeat family) were identified that were present in much higher copy numbers inS. spegazziniiwhen compared with the closely related cultivated potatoS. tuberosum. The SPG repeat family was organized in long arrays of multiple copies. Cross hybridization experiments with 29 wild and cultivatedSolanumspecies and with the related tomato showed specificity of the SPG repeat family for tuber-bearingSolanumspecies. Among tuber bearingSolanumspecies a high degree of variation was observed for restriction fragment length and copy number. The variation in copy number was not correlated with established taxonomic relationships between tuber-bearingSolanumspecies. DNA sequence analysis revealed a subrepeat structure of 120–140 base pairs embedded in longer repeat units of variable length. Length polymorphisms between highly repeated restriction fragments detected by the SPG probes were used for segregation- and linkage analysis in four mapping populations of potato, for which RFLP maps had been constructed. Twelve loci were identified, eleven of which mapped to the distal ends of nine linkage groups. All the evidence suggested that the SPG repeat family represents a satellite repeat members of which are localized in the subtelomeric region of potato chromosomes. The SPG repeat family could be used, therefore, for completing the genetic map of potato.
The inbreeding decline and average dominance of genes affecting male life-history characters inDrosophila melanogaster
Authors: Hughes Kimberly A.
Published: September 2009

This paper describes the results of assays of male life-history characters in a large outbred laboratory population ofD. melanogaster. Lines of flies homozygous for the entire third chromosome and lines of flies carrying two different third chromosomes were assayed for agespecific male mating ability (MMA), age-specific survivorship, male fertility, and body mass. The results of these assays were used to calculate the inbreeding decline associated with each of these traits, the average dominance of deleterious alleles that affect the traits, the genotypic and environmental components of variance for the homozygous lines, and phenotypic and genotypic correlations among the characters. Significant inbreeding decline was found for all characters except the Gompertz intercept and fertility. Early and late MMA show larger effects of inbreeding than any other trait. The inbreeding load for MMA is about the same magnitude as that for egg-to-adult viability, but is substantially less than that associated with total fitness. The estimated inbreeding decline and average dominance of male life-history characters are comparable to estimates for otherDrosophilafitness components.
Thirteen genes (Cebpb, E2f1, Tcf4, Cyp24, Pck1, Acra4, Edn3, Kcnb1, Mc3r, Ntsr, Cd40, Plcg1andRcad) that probably lie in the distal imprinting region of mouse Chromosome 2 are not monoallelically expressed
Authors: Williamson Christine M. , Dutton Elizabeth R. , Abbott Catherine M. , Beechey Colin V. , Ball Simon T. , Peters Josephine
Published: September 2009

Seven imprinted genes are currently known in the mouse but none have been identified yet in the distal imprinting region of mouse Chromosome (Chr) 2, a region which shows striking linkage conservation with human chromosome 20q13. Both maternal duplication/paternal deficiency and its reciprocal for distal Chr 2 lead to mice with abnormal body shapes and behavioural abnormalities. We have tested a number of candidate genes, that are either likely or known to lie within the distal imprinting region, for monoallelic expression. These included 3 genes (Cebpb,E2f1andTcf4) that express transcription factors, 2 genes (Cyp24andPck1) that are involved in growth, 5 genes (Acra4,Edn3,Kcnb1,Mc3randNtsr) where a defect could lead to neurological and probably behavioural problems, and 3 genes (Cd40,Plcg1andRcad) that are less obvious candidates but sequence information was available for designing primers to test their expression. On/off expression of each gene was tested by reverse transcription–polymerase chain reaction (RT–PCR) analysis of RNA extracted from tissues of mice with maternal duplication/paternal deficiency and its reciprocal for the distal region of Chr 2. None of the 13 genes is monoallelically expressed in the appropriate tissues before and shortly after birth which suggests that these genes are not imprinted later in development. This study has narrowed down the search for imprinted genes, and valuable information on which genes have been tested for on/off expression is provided. Since there is considerable evidence of conservation of imprinting between mouse and human, we would predict that the 13 genes are not imprinted in human. Five of the genes:E2f1,Tcf4,Kcnb1,Cd40andRcad, have not yet been mapped in human. However, because of the striking linkage conservation observed between mouse Chr 2 and human chromosome 20, we would expect these genes to map on human chromosome 20q13.
Accumulation of mutations affecting body weight in inbred mouse lines
Authors: Caballero Armando , Keightley Peter D. , Hill William G.
Published: September 2009

The variation from spontaneous mutations for 6-week body weight in the mouse was estimated by selection from a cross of two inbred sublines, C57BL/6 and C57BL/10, separated about 50 years previously from the same inbred line. Selection was practised high and low for 12 generations from theF2, followed by one generation of relaxation. The lines diverged by approximately 1·7 g or 0·7 sd. The additive genetic variance was estimated in theF2by restricted maximum likelihood and from the selection response, and from this variance the mutational heritabilityhM2was estimated using the number of generations since divergence. Estimates ofhM2range from 0·08 to 0·10% depending on the method of analysis. These estimates are similar to those found for other species, but lower than other estimates for the mouse. It is concluded that substantial natural and, perhaps, artificial selection operated during the maintenance of the sublines.
Survey of genomic repeat sequence-PCRs that detect differences between inbred mouse strains
Authors: Wood Philip A. , Hamm Doug A.
Published: September 2009

We have developed molecular markers that distinguish between several inbred and congenic mouse strains using polymerase chain reaction (PCR) amplification of genomic DNA repeat sequences. Mouse genomic DNA, digested with four base recognition site-restriction endonucleases, was amplified by PCR using primers for the following repeat sequences: Bl (Alu homolog), LINE, LLR3, IAP, human Alu and myoglobin. Amplification products analysed by agarose gel electrophoresis and stained with ethidium bromide produced unique DNA fragments, some of which are specific for each of 12 strains tested. This method can be used for molecular analysis of the mouse genome, including genetic monitoring.
Preserving genes: a model of the maintenance of genetic variation in a metapopulation under frequency-dependent selection
Authors: Judson Olivia P.
Published: September 2009

Understanding how genetic variability is maintained in natural populations is of both theoretical and practical interest. In particular, the subdivision of populations into demes linked by low levels of migration has been suggested to play an important role. But the maintenance of genetic variation in populations is also often linked to the maintenance of sexual reproduction: any force that acts to maintain sex should also act to maintain variation. One theory for the maintenance of sex, the Red Queen, states that sex and variation are maintained by antagonistic coevolutionary interactions – especially those between hosts and their harmful parasites – that give rise to negative frequency-dependent selection. In this paper I present a model to examine the relationships between population subdivision, negative frequency-dependent selection due to parasites, the maintenance of sex, and the preservation of alleles from fixation. The results show strong interactions between migration rates, negative frequency-dependent selection, and the maintenance of variability for sexual and asexual populations.
A stochastic model of selection on selfing rates in structured populations
Authors: Ronfort J. , Couvet D.
Published: September 2009

Previous theoretical studies of the evolution of the selfing rate have shown that mixed mating systems are not evolutionary stable states. Such models have, however, not included the effects of population structure and thus biparental inbreeding together with the evolution of selfing rates and inbreeding depression. In order to examine selection on selfing rates in structured populations, a stochastic model simulating a finite population with partial selfing and restricted pollen and seed dispersal has been developed. Selection on the mating system was followed by introducing modifiers affecting the selfing rate. The major result was that, with density dependent recruitment, a process which maintains the population structure necessary for biparental inbreeding to occur, a mixed mating system could be maintained. This result was associated with an increase of the mutation load with high selfing rates, and the selected selfing rate depended on the degree of population structure rather than on the initial selfing rate. With low dominance of deleterious alleles, complete allogamy can be selected for. Further studies showed that the more general condition of spatial heterogeneity of recruitment can lead to similar results, the most important condition being the maintenance of genetic structure within populations. A brief survey of the empirical literature shows that a positive relationship between the magnitude of inbreeding depression and the inbreeding coefficient within populations has been observed, in support of the present model.
Esterase polymorphism in insecticide susceptible populations of the mosquitoCulex pipiens
Authors: Raymond Michel , Qiao Chuan L. , Callaghan Amanda
Published: September 2009

Gene amplification involving a particular haplotype has been found at the esterase B locus of mosquitoes from various countries. This similarity has been explained by a unique amplification event followed by migration and selection by organophosphate (OP) insecticides. This assumes that the polymorphism of non-amplified esterase haplotypes is so large that the chance of independent amplification in two distinct populations is negligible. In order to test this assumption, three susceptible populations from northern Europe were sampled and analysed for esterase and haplotype polymorphism. At the protein level, 18 and 16 alleles were found for esterase A and B respectively in one French population (n= 74), and 16 and 14 in an English one(n= 50). At the DNA level, 24 alleles at the esterase B locus were detected in a sample of 72 mosquitoes from one population, with the use of only one restrictionenzyme (EcoR V). Restriction maps of two nonamplified haplotypes randomly sampled from a single breeding site in Belgium were built with six restriction enzymes. 60% of all restriction sites were different among the two maps. The huge polymorphism found in northern Europe requires specific explanations for its stability, but it considerably strengthens the hypothesis of migration of amplified haplotypes.
Interactions of selection, linkage and drift in the dynamics of polygenic characters
Authors: Hospital Frédéric , Chevalet Claude
Published: September 2009

We study the dynamics under directional truncation selection of the genetic variability of a quantitative character controlled by a finite number of possibly linked loci with additive effects. After the first generation of selection, the build-up of linkage disequilibria (Bulmer effect) is analytically demonstrated from a genetical point of view in an infinite population. In the following generations, the dynamics of the system in a finite population are predicted using analytic recurrences under a multi-normal approximation, and computer simulations. The effects of recombination on the dynamics of linkage disequilibria induced by selection and drift, and the consequences for the additive genetic variance are then analysed and discussed from the simulation results. Compared to the rapid exploitation of genetic variability promoted by high recombination rates, low recombination rates promote an early storage of genetic variability in repulsion associations of alleles and a possible late release of genetic variance in the population, so that the variability of the character may be maintained over a longer period of time. In some cases, favourable recombination events in tightly linked systems induce an increase of the additive variance of the character, which may explain some results observed in long-term selection experiments. Our results emphasize that the joint effects of selection, linkage and drift must notbe neglected in theoretical quantitative genetics, and require further investigation.
Identification of the α-galactosidaseMELgenes in some populations ofSaccharomyces cerevisiae: a new geneMEL11
Authors: Naumov Gennadi I. , Naumova Elena S. , Turakainen Hilkka , Korhola Matti
Published: September 2009

In this report we mapped a newMEL11gene and summarize our population studies of the α-galactosidaseMELgenes ofS. cerevisiae. The unique family of structuralMELgenes has undergone rapid translocations to the telomeres of most chromosomes in some specificSaccharomyces cerevisiaepopulations inhabiting olive oil processing waste (alpechin) and animal intestines. A comparative study ofMELgenes in wine, pathogenic and alpechin populations ofS.cerevisiaewas conducted using genetic hybridization analysis, molecular karyotypingand Southern hybridization with theMEL1probe. Five polymeric genes for the fermentation of melibiose,MEL3, MEL4, MEL6, MEL7, MEL11, were identified in an alpechin strain CBS 3081. The newMEL11gene was mapped by tetrad analysis to the left telomeric region of chromosome I. In contrast, in wine and pathogenic populations ofS. cerevisiae, MELgenes have been apparently eliminated. Their rare Mel+strains carry only one of theMEL1, MEL2, orMEL8genes. One clinical strain YJM273 was heterozygotic on theMEL1gene; itsmell0allele did not have a sequence of the gene.
Genomic incompatibilities in the hybrid zone between house mice in Denmark: evidence from steep and non-coincident chromosomal clines for Robertsonian fusions
Authors: Fel-Clair Fabienne , Lenormand Thomas , Catalan Josette , Grobert Jacqueline , Orth Annie , Boursot Pierre , Viroux Marie-Cecile , Britton-Davidian Janice
Published: September 2009

The pattern of chromosomal variation is investigated in house mice from the Danish hybrid zone between the translocation-proneMus musculus domesticusand the chromosomally conservativeM. m. musculus. The cytogenetic analysis confirmed the non-introgression of three pairs of Robertsonian (Rb) fusions fromM. m. domesticusinto theM. m. musculusgenome. The geographic distribution of two of these Rb fusions was shown to follow staggered chromosomal clines which increased in steepness the closer they were to the centre of the hybrid zone as defined by allozymes. Analysis of alternate hypotheses suggests that chromosomal differentiation of the Danishdomesticusoccurred after contact was established withmusculus. The staggering of the clines would reflect the order of arrival of theRb fusions into the hybrid zone. Several models with different processes of underdominance of the chromosomal heterozygotes are discussed to account for the difference in width between clines. A selective model with increasing levels of genomic underdominance due to interaction with a progressively enrichedmusculusgenome provides the best fit for the observed pattern. Selection against Rb fusions with little effect on the recombination of linked allozyme markers supportsthe view that no reduction in gene flow due to chromosomal heterozygosity is yet apparent through the hybrid zone and that only the centromeric segments of the Rb fusions are incompatible with themusculusgenome.
Estimating gene flow in island populations
Authors: Rannala Bruce , Hartigan J. A.
Published: September 2009

A new method is presented for estimating the rate of gene flow into island populations using the distribution of alleles in samples from a number of islands. The pseudo maximum likelihood estimator (PMLE) that we derive may be applied to species with either discrete or continuous generation times. For Wright's discrete-generation island model, the method provides an estimate of θ = 2NmwhereNis the (haploid) population size on each island andmis the fraction of individuals replaced by immigrants in each generation. For a continuous-generation island model, the corresponding parameter φ is the ratio of the immigration rate φ to the individual birth rate λ. Monte Carlo simulations are used to compare the statistical properties of the PMLE with those of two alternative estimatorsof θ derived from Wright'sF-statistics. The PMLE is shown to have greatest efficiency (least mean square error) in most cases for a wide range of sample sizes and parameter values. The PMLE is applied to estimate θ using mtDNA haplotypes and allozymes for subdivided populations of African elephants and Channel Island foxes.
Models of the spread of non-autonomous selfish transposable elements when transposition and fitness are coupled
Authors: Brookfield J. F. Y.
Published: September 2009

I investigate models of the spread of transposable elements, such as theDrosophila melanogasterP elements, that can exist in autonomous and non-autonomous forms. Elements which have their major impact on host fitness in the process of transposition can, under certain conditions, come to a stable balance between transposition and selection. This stable balance for autonomous elements can be disrupted by the invasion of further elements, which do not produce a transposase enzyme, and may produce a repressor of transposition. I examine this secondary invasion process, and show that a stable equilibrium copy number for intact elements is neither a necessary nor a sufficient condition for non-autonomous elements to invade. Nevertheless, invasion occurs under a broad range of models and conditions. This requires neither that the non-autonomous elements produce atrans-acting repressor of transposition, nor that they titrate transposase. The elimination of autonomous elements follows the increase in non-autonomous elements unless the latter encode powerful repressors of transposition. Approximate solutions for the equilibrium copy number of autonomous elements and rate of invasion of non-autonomous elements can be found under some models for transposition and selection. The predictions of the model are compared with recent empirical studies of theD. melanogasterP system
A study of meiotic pairing, nondisjunction and germ cell death in laboratory mice carrying Robertsonian translocations
Authors: Everett C. A. , Searle J. B. , Wallace B. M. N.
Published: September 2009

Frequencies of anaphase I nondisjunction, germ cell death and pairing abnormalities at pachytene were assessed in male mice singly heterozygous and homozygous for the Robertsonian (Rb) translocations: Rb (1.3)lBnr, Rb(ll. 13)4Bnr and Rb(10. ll)8Bnr. Rb homozygotes showed low frequencies of nondisjunction but substantial germ cell death. This germ cell death could not be attributed to problems at pachytene as Rb homozygotes showed no increase in pairing abnormalities over the (C3H/HeH×1O1/H)F1 controls. Instead genie factors are involved. Rb heterozygotes showed substantial frequencies of nondisjunction and even greater germ cell death than found in the homozygotes. Pachytene pairing abnormalities were observed and it appears that these, together with genie factors, cause physiological perturbation of meiocytes, thereby promoting germ cell death, with nondisjunction of the trivalent as a sublethal response.
Interaction of selection and recombination in the fixation of negative-epistatic genes
Authors: Michalakis Yannis , Slatkin Montgomery
Published: September 2009

We investigated the interaction of recombination and selection on the process of fixation of two linked loci with epistatic interactions in fitness. We consider both the probability of fixation of newly arising mutants (the static model) and the time to fixation under continued mutation (the dynamic model). Our results show that the fixation of a new advantageous combination is facilitated by higher fitness of the advantageous genotype and by weaker selection against the intermediate deleterious genotypes. Fixation occurs more rapidly when the recombination rates are small, except when selection against intermediate genotypes is weak and selection in favour of the double mutant is very strong. In these cases fixation is more rapid when the recombinant rate is large. Mutations of strong effects, deleterious when alone but beneficial when coupled, are fixed more easily than mutations of intermediate effects, at least for large recombination rates. Among the possible pathways the process of fixation might follow, independent substitutions lead to the fixation of the double mutant only when selection is weak. The relative importance of the other pathways depends on the interaction between recombination and selection. The coupled-gamete pathway (i.e. when the population waits until the double mutant appears and then drives it to fixation) is more important as selection intensity increases and the recombination rate is reduced. For all recombination rates, asymmetries in fitness of the intermediate genotypes increase the rate at which fixations occur. Finally, throughout the fixation process, the population will be monomorphic at least at one of the two loci for most of the time, which implies that there would be little opportunity to detect the presence of negative epistasis even if it were important for occasional evolutionary transitions.
Waiting for a compensatory mutation: phase zero of the shifting-balance process
Authors: Phillips Patrick C.
Published: September 2009

In highly integrated genetic systems, changes in any one component may have a deleterious effect on fitness, but coordinated, or compensatory, change in these components could lead to an overall increase in fitness compared with the current state. Wright designed his shifting-balance theory to account for evolutionary change in such systems, since natural selection alone can not lead to the new optimal state. A largely untreated aspect of the shifting-balance theory, that of the limiting impact of waiting for the production of new mutations, is analysed here. It is shown that the average time to double fixation of compensatory mutations is extremely long (of the order of tens or hundreds of thousands of generations), because selection is too effective in large populations, and mutations are too rare in small populations. Further, the probability that a new mutant will arise and undergo fixation quickly is extremely small. Tight linkage can reduce the time to fixation somewhat, but only in models in which the double heterozygote does not have reduced fitness. It is argued that the only reasonable way for compensatory mutations to become fixed in a population is if the new mutants are first allowed to achieve a moderate frequency through the relaxation of selection. Under these conditions, the time required to reach fixation is reasonably low, althoug the probability of being fixed is still small when the initial allele frequencies are low. It is likely that the waiting time for fixation of new mutants, which is here called phase zero, is the major limiting factor for the success of the shifting-balance process
Microsatellite polymorphisms in a wild population of Drosophila melanogaster
Authors: England Phillip R. , Briscoe David A. , Frankham Richard
Published: September 2009

Highly variable DNA polymorphisms called microsatellites are rapidly becoming the marker of choice in population genetic studies. Until now, microsatellites have not been utilized for Drosophila studies. We have identified eight polymorphic microsatellite loci in Drosophila melanogaster and used them to characterize the genetic variation in a wild population from the Tyrrell's winery in Australia. Microsatellites were isolated from a partial genomic DNA library. All microsatellites consist of (AC)n repeats ranging from n = 2 to n = 24. Six loci were assigned to chromosomal location by genetic mapping, with three loci on chromosome II, one locus on chromosome III and two loci on the X chromosome. Up to four microsatellite loci were multiplexed in the same reaction. Microsatellite variation is substantially greater than allozyme variation in the Tyrrell's Drosophila population. 80% of the microsatellite loci examined are polymorphic, compared with 28% of allozymes. The mean number of alleles per polymorphic locus is 5·2 in microsatellites compared with 30 in allozymes. The average observed heterozygosity of polymorphic microsatellites is 47% compared with 26% for allozymes. Microsatellite variation in Drosophila melanogaster is similar to that reported for other insects. Higher variability commends microsatellites over allozymes for genetic studies in Drosophila melanogaster.
Selection against transposable elements inD. simulansandD. melanogaster
Authors: Vieira C. , Biémont C.
Published: September 2009

The insertion site numbers of the transposable elements (TEs) copia, mdgl, 412 and gypsy were determined in various natural populations ofDrosophila melanogasterandD. simulansby in situ hybridization. We showed that, while all elements except gypsy had many insertion sites scattered over the chromosomes inD. melanogaster, only the 412 element inD. simulanspresented a high number of insertions, and this number was lower than inD. melanogaster. This low 412 site number per genome inD. simulanswas associated with a lower proportion of insertions on the X chromosome in comparison withD. melanogaster, as determined in diploid genomes (0·090 forD. simulansagainst 0·137 forD. melanogaster) and in haploid genomes (0·102 against 0·146), each value being, moreover, lower than the value of 0·20 expected on the hypothesis of no selection against insertional mutations. These results suggest that selection is a major mechanism explaining 412 copy number regulation inDrosophila, and is stronger inD. simulansthan inD. melanogaster.
Mapping QTLs for binary traits in backcross and F2populations
Authors: Visscher P. M. , Haley C. S. , Knott S. A.
Published: September 2009

Mapping quantitative trait loci (QTLs) for binary traits in backcross andF2populations was investigated using stochastic stimulation. Data were analysed using either linear regression or a generalized linear model. Parameters which were varied in the simulations were the population size (200 and 500), heritability in the backcross orF2population (0·01, 0·05, 0·10), marker spacing (10 and 20 cM) and the incidence of the trait (0·50, 0·25, 0·10). The methods gave very similar results in terms of estimates of the QTL location and QTL effects and power of QTL detection, and it was concluded that in practice treating the zero-one data as continuous and using standard linear regression was efficient.
High genetic variability under the balance between symmetric mutation and fluctuating stabilizing selection
Authors: Kondrashov Alexey S. , Yampolsky Lev Yu.
Published: September 2009

We have studied variability maintained in a quantitative trait by the balance between symmetric mutation and direct stabilizing selection with a fluctuating optimum. Using a simulational computer model, we have found that wide fluctuations, such that the range of the optimum changes exceeds the width of the fitness curve, increase the trait variance, often by two or three orders of magnitude, over its value under constant selection. This happens because such fluctuations cause frequent allele substitutions at the loci that control the trait. At any particular moment the variance is increased mostly due to one or several loci where more than one allele is currently common. The data on fluctuating selection in nature are reviewed
Insertion of the retroposable element,jockey, near theAdhgene ofDrosophila melanogasteris associated with altered gene expression
Authors: White Lisa D. , Jacobson James W.
Published: September 2009

Thealcohol dehydrogenase(Adh) gene ofDrosophila melanogasteris well suited to be a gene expression reporter system.Adhproduces a measurable phenotype at both the enzyme and mRNA levels. We recovered a spontaneous transposable element (TE) insertion mutation near theAdhgene. The insertion is a truncated retroposable element,jockey, inserted upstream of the adultAdhenhancer region. Comparisons between theAdhjockeyallele and its direct wild-type ancestral allele were made in an isogenic background (i.e. identicalcisandtransfactors). Differences inAdhjockeyexpression compared with the wild-type can be attributed solely to the presence of thejockeyelement. Thisjockeyinsertion results in a decrease in adult mRNA transcript levels in theAdhjockeyhomozygous lines relative to the wild-type counterpart and accounts for a correlated decrease in alcohol dehydrogenase (ADH) enzyme activity. The larval ADH activity levels are not detectably different.
Genetics of sexual isolation in male hybrids ofDrosophila simulansandD. mauritiana
Authors: Coyne Jerry A.
Published: September 2009

Sexual isolation between the sibling speciesD. simulansandD. mauritianais due largely to the rejection ofD. simulansmales byD. mauritianafemales. Genetic analysis shows that genes on the X and third chromosomes contribute to the differences between males causing sexual isolation, while the Y chromosome, second chromosome and cytoplasm have no effect. These chromosome effects differ from those observed in a previous analysis of sexual isolation in hybrid females, implying that different genes cause sexual isolation in the two sexes.
Mixed model approaches for diallel analysis based on a bio-model
Authors: Zhu Jun , Weir Bruce S.
Published: September 2009

A MINQUE(l) procedure, which is minimum norm quadratic unbiased estimation (MINQUE) method with 1 for all the prior values, is suggested for estimating variance and covariance components in a bio-model for diallel crosses. Unbiasedness and efficiency of estimation were compared for MINQUE(l), restricted maximum likelihood (REML) and MINQUE(θ) which has parameter values for the prior values. MINQUE(l) is almost as efficient as MINQUE(θ) for unbiased estimation of genetic variance and covariance components. The bio-model is efficient and robust for estimating variance and covariance components for maternal and paternal effects as well as for nuclear effects. A procedure of adjusted unbiased prediction (AUP) is proposed for predicting random genetic effects in the bio-model. The jack-knife procedure is suggested for estimation of sampling variances of estimated variance and covariance components and of predicted genetic effects. Worked examples are given for estimation of variance and covariance components and for prediction of genetic merits.