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Spatial structure of genetic variation and primary succession in the pioneer tree species Antirhea borbonica on La Réunion.

In habitats where colonization and extinction are recurrent, the distribution of gene frequencies among patches of suitable habitat may reflect the age structure of different populations. In this study, we quantify population genetic structure for a pioneer tree species, Antirhea borbonica, in a chrono-sequence of primary succession on the lava flows of the Piton de La Fournaise volcano (La Réunion). Using microsatellite loci and amplified fragment length polymorphism (AFLP) markers, we quantified genetic variation within and among populations for early- and late-succession populations in a landscape where extinction and recolonization are recurrent (the 'Grand Brûlé') and for late-succession populations in a more stable landscape. This study produced three main results. First, we detected no evidence that founder events increase genetic differentiation among colonizing populations; F(ST) values among early- and among late-succession populations were similar. Second, we found no evidence for isolation by distance; genetic distance was not correlated with spatial distance within and among populations. Third, F(IS) values are consistently high in all populations, despite the fact that A. borbonica populations are functionally close to dioecy and thus expected to have an outcrossing mating system. Multiple colonization events from different sources may limit differentiation among young populations and spatial isolation may enhance differentiation among late-succession populations. Ecological processes acting during colonization may create the conditions for spatial aggregation within pioneer populations, and thus contribute to the high F(IS) values.

DNA Primers↗

Female guppies agree to differ: phenotypic and genetic variation in mate-choice behavior and the consequences for sexual selection.

Variation among females in mate choice may influence evolution by sexual selection. The genetic basis of this variation is of interest because the elaboration of mating preferences requires additive genetic variation in these traits. Here we measure the repeatability and heritability of two components of female choosiness (responsiveness and discrimination) and of female preference functions for the multiple ornaments borne by male guppies (Poecilia reticulata). We show that there is significant repeatable variation in both components of choosiness and in some preference functions but not in others. There appear to be several male ornaments that females find uniformly attractive and others for which females differ in preference. One consequence is that there is no universally attractive male phenotype. Only responsiveness shows significant additive genetic variation. Variation in responsiveness appears to mask variation in discrimination and some preference functions and may be the most biologically relevant source of phenotypic and genetic variation in mate-choice behavior. To test the potential evolutionary importance of the phenotypic variation in mate choice that we report, we estimated the opportunity for and the intensity of sexual selection under models of mate choice that excluded and that incorporated individual female variation. We then compared these estimates with estimates based on measured mating success. Incorporating individual variation in mate choice generally did not predict the outcome of sexual selection any better than models that ignored such variation.

Animals↗

RAPD analysis of genetic variation in the Australian fan flower, Scaevola.

The use of randomly amplified polymorphic DNA (RAPD) to study genetic variability in Scaevola (family Goodeniaceae), a native Australian species used in ornamental horticulture, is demonstrated. Plants of the genus Scaevola are commonly known as "fan flowers," due to the fan-like shape of the flowers. Nineteen accessions of Scaevola (12 cultivated and 7 wild) were studied using 20 random decamer arbitrary primers. Eight primers gave a distinct reproducible amplification profile of 90 scorable polymorphic fragments, enabling the differentiation of the Scaevola accessions. RAPD amplification of genomic DNA revealed a high genetic variability among the different species of Scaevola studied. Molecular markers were used to calculate the similarity coefficients, which were then used for determining genetic distances between each of the accessions. Based on genetic distances, a dendrogram was constructed. Though the dendrogram is in general agreement with the taxonomy, it also highlights discrepancies in the classification. The RAPD data showed that Scaevola aemula (series Pogogynae) is closer to Scaevola glandulifera of series Globuliferae than to the rest of members of series Pogogynae. In addition, the RAPD banding pattern of white flower S. aemula, one of the commercial cultivars, was identical to that of Scaevola albida, indicating their genetic similarity. Our study showed that there is a large genetic distance between commercial cultivars of Scaevola (Purple Fanfare, Pink Perfection, and Mauve Cluster), indicating considerable genetic variation among them. The use of RAPDs in intra- and inter-specific breeding of Scaevola is also explored.

DNA, Plant↗

Superimposing two-dimensional gels to study genetic variation in malaria parasites.

Two-dimensional polyacrylamide gel electrophoresis is a valuable tool for studying genetic variation in the human malaria parasite, Plasmodium falciparum. It involves examining the position of protein spots in gel produced from different isolates. Some spots have been seen to vary, while others have had a constant position in all isolates so far examined. These invariant spots provide a reference frame to compare variations in other spots. This paper discusses the usefulness of digital image handling, warping and superimposition in a personal computer environment. Rather than produce a fully automatic interpretation system, we show how the computer may be used as a tool for manipulating gel images, although interpretation of the gels' features remains with the human expert. Autoradiographs are scanned on a desktop scanner, and the images in digital form can be displayed on a monitor attached to a personal computer. The coordinates of the invariant spots on each of several gels are identified by the user. Each of the gels is then warped so that the invariant spots of all the gels coincide as closely as possible. The variable spots are then examined. We have used both affine warping transformations, which match the invariant spots as closely as possible, and thin plate spline transformations, which match them exactly. Colour superimposition proved a useful way of examining the gels.

Animals↗

[Genetic variations of hepatitis C virus circulating in the Ural region].

A study of distributions of different genetic variations (subtypes) of hepatitis C virus (HCV), circulating in the territories of Yekaterinburg and Chelyabinsk among infected population categories of different social statuses and age, is reported in the paper. The predominance of 1b subtype was shown in the HCV-infected patients at the hemodialysis center (HDC) and at the pediatric oncohematology center (OHC), 83.3% and 84.6% respectively. The summarized results of examinations of patients conducted at HCV-infection departments (97 persons) did not reveal any essential differences between the data, obtained for Moscow and Saint-Petersburg, concerning the distributions of HCV subtypes. However, according to an analysis made in cities of the Urals region, the prevalence of 1b subtype in Chelyabinsk was 2-fold higher than that of 3a subtype, whereas in Yekaterinburg there was an equal ratio (1:1) between the above subtypes. Besides, unequal distributions of HCV subtypes were registered in different age groups. 3a subtype was found to be predominant in patients aged 15 to 27, and prevalence of 1b subtype persisted in persons aged below 15 and above 27. The conclusion is that the redistributed occurrence rates of separate HCV subtypes, with their spectrum in mentioned territories being preserved, is associated with a growing number of young drug-addicts who are more often get infected with 3a subtype.

Adolescent↗

Heritable genetic variation via mutation-selection balance: Lerch's zeta meets the abdominal bristle.

Most quantitative traits in most populations exhibit heritable genetic variation. Lande proposed that high levels of heritable variation may be maintained by mutation in the face of stabilizing selection. Several analyses have appeared of two distinct models with n additive polygenic loci subject to mutation and stabilizing selection. Each is reviewed and a new analysis and model are presented. Lande and Fleming analyzed extensions of a model originally treated by Kimura which assumes a continuum of possible allelic effects at each locus. Latter and Bulmer analyzed a model with diallelic loci. The published analyses of these models lead to qualitatively different predictions concerning the dependence of the equilibrium genetic variance on the underlying biological parameters. A new asymptotic analysis of the Kimura model shows that the different predictions are not consequences of the number of alleles assumed but rather are attributable to assumptions concerning the relative magnitudes of per locus mutation rates, the phenotypic effects of mutation, and the intensity of selection. This conclusion is reinforced by analysis of a model with triallelic loci. None of the approximate analyses presented are mathematically rigorous. To quantify their accuracy and display the domains of validity for alternative approximations, numerically determined equilibria are presented. In addition, empirical estimates of mutation rates and selection intensity are reviewed, revealing weaknesses in both the data and its connection to the models. Although the mathematical results and underlying biological requirements of my analyses are quite different from those of Lande , the results do not refute his hypothesis that considerable additive genetic variance may be maintained by mutation-selection balance. However, I argue that the validity of this hypothesis can only be determined with additional data and mathematics.

Alleles↗

Naturally occurring genetic variation affecting the expression of sn-glycerol-3-phosphate dehydrogenase in Drosophila melanogaster.

Genetic variation among second and third chromosomes from natural populations of Drosophila melanogaster affects the activity level of sn-glycerol-3-phosphate dehydrogenase (EC 1.1.1.8; GPDH) at both the larval and the adult stages. The genetic effects, represented by differences among chromosome substitution lines with coisogenic backgrounds, are very repeatable over time and are generally substantially larger than environmental and measurement error effects. Neither the GPDH allozyme, the geographic origin, nor the karyotype of the chromosome contributes significantly to GPDH activity variation. The strong relationship between GPDH activity level and GPDH-specific CRM level, as well as our failure to find any thermostability variation among the lines, indicates that most, if not all, of the activity variation is due to variation in the steady-state quantity of enzyme rather than in its catalytic properties. The lack of a strong relationship between adult and larval activity levels suggests the importance of stage- or isozyme-specific effects.

Animals↗

Genetic variation in the recruitment and activation of chicken peritoneal macrophages.

Genetic variation in the ability to recruit and activate peritoneal macrophages was examined in seven partially developed 15I5-B congenic White Leghorn chicken lines. While the ability to generate peritoneal exudate cells (PECs) was similar in all lines, major differences were observed in the numbers, composition, and functional activity of harvestable peritoneal adherent cell populations. In response to a general stimulant, Sephadex, lines .7-2 and .6-2 produced the greatest numbers of adherent peritoneal cells while lines .C-12 and .15I-5 were among the poorest responders. Macrophage percentage of adherent PECs varied between lines. 15I5 chickens produced a consistently high percentage of adherent macrophages while .6-2 birds exhibited the lowest macrophage percentage at all ages examined. Phagocytosis was used as one measure of the level of macrophage activation and similar results were obtained using both opsonized and unopsonized sheep erythrocytes; adherent peritoneal cells from lines .6-2, .7-2, and .P-13 exhibited the highest activity and .C-12, .15I-5, and background 15I5(B15) lines produced cells with the lowest phagocytic activity. In a second functional assay, the killing of Salmonella typhimurium, macrophage-rich cells from line .P-13 exhibited the lowest activity which was significantly lower than that obtained with cells from lines .6-2 and .15I-5. Antigen-specific stimulation of peritoneal adherent cells by ferritin also showed that .C-12 was a low responder in contrast with other lines. The results indicate that these genetic lines differ in peritoneal macrophage function and suggest that the chicken major histocompatibility complex may influence certain properties of chicken macrophage function.

Animals↗

Patterns of genetic variation in native grape phylloxera on two sympatric host species.

Random amplified polymorphic DNA (RAPD) markers were used to examine population genetic structure in populations of native grape phylloxera. This research asked: (i) do RAPD markers distinguish two groups corresponding to the two host plant species; and (ii) do RAPD markers distinguish groups according to spatial location, independent of host plant association? Forty-nine phylloxera clones were collected from five pairs of adjacent individuals of two sympatric grape species in five sites along a 145 km transect in Missouri, USA. A high level of polymorphism was observed, with some evidence for structuring between host plant species and no evidence for spatial structuring. An analysis of molecular variance (AMOVA) found that 6.52% of the variance in RAPD banding patterns was attributable to host species and 7.96% of the variance was attributable to spatial location. A cluster analysis did not result in two groups corresponding to the two hosts, or to five groups corresponding to the geographical sites sampled. A Mantel test showed a low correlation between genetic similarity and spatial location. Two of the 93 RAPD markers were nonrandomly associated between the hosts. It is suggested that there may be a small host-mediated effect on genetic variation but stochastic dispersal and a highly heterogeneous environment may be the primary influences on the observed polymorphism.

Animals↗

Identifying genes and genetic variation underlying human diseases and complex phenotypes via recombination mapping.

Understanding the mechanisms by which DNA and DNA variation influence diseases, naturally occurring phenotypic variation, and complex biological systems, has been one of the major tasks associated with contemporary human genetics research. The identification and characterization of specific genetic variations that influence particular human diseases and phenotypes is complicated by the fact that most diseases and phenotypes are influenced by many genetic and environmental factors. Thus, the identification of any particular phenotypically relevant factor might be hampered as other relevant factors may obscure its individual effect. Over the years numerous methods and study designs have been described to identify disease causing genes and mutations. One in particular - meiotic or recombination mapping - has received considerable attention over the last 50 years, and has been used widely with varying degrees of success. This review describes the motivation behind, and problems associated with, recombination mapping, in terms of both linkage mapping and linkage disequilibrium mapping.

Chromosome Mapping↗

Genetic variation in the incidence of pipped eggs in turkeys selected for low and high semen ejaculate volume.

Genetic variation in embryonic mortality, expressed as embryos that pip their eggshell but do not hatch, was investigated in turkeys selected for low and high semen ejaculate volume (SEV). Through five generations (Generations 10 to 14, inclusive) mean heritability estimates for pipped eggs were .21 and .08 in the low- and high-SEV lines, respectively. Estimates of sire, dam, and within-hatch components of variance suggest greater environmental and maternal effects than genetic influences on the incidence of pipped eggs in turkeys.

Animals↗

Genetic variation in EEG activity during sleep in inbred mice.

The genetic variation in spontaneous rhythmic electroencephalographic (EEG) activity was assessed by the quantitative analysis of the EEG in six inbred mice strains. Mean spectral EEG profiles (0-25 Hz) over 24 h were obtained for paradoxical sleep (PS), slow-wave sleep (SWS), and wakefulness. A highly significant genotype-specific variation was found for theta peak frequency during both PS and SWS, which strongly suggests the presence of a gene with a major effect. The strain distribution of theta peak frequency during exploratory behavior differed from that during sleep. In SWS, the relative contributions of delta (1-4 Hz) and sigma (11-15) power to the EEG varied with genotype and power in both frequency bands was negatively correlated. In addition, the EEG dynamics at state transitions were analyzed with a 4-s resolution. The onset of PS, but not that of wakefulness, was preceded by a pronounced peak in high-frequency (>11 Hz) power. These findings are discussed in terms of the neurophysiological mechanisms underlying rhythm generation and their control and modulation by the brain stem reticular-activating system.

Animals↗

[Genetic variation of six breeds of pigs by RAPD analysis].

The genetic variation of Meishan, Huainan, Tongcheng, Bamei, Hezuo and Largewhite pigs were analyzed by RAPD markers. Twenty-four single polymorphic primers were selected out of 276 primers by amplifying six pool DNA. The index of Shannon were 0.178672, 0.17781,0.15995, 0.14549,0.16949, 0.14159 respectively; Hpop was 0.16216, Hsp was 0.2534. The phylogenetic tree was constructed using NJ and UPGMA. The results indicated that the phenylogenetic relationship of the six pig breeds was consistent with their distribution.

English Abstract↗

Genetic variation of Marchalina hellenica (Hemiptera: Margarodidae) sampled from different hosts and localities in Greece.

Random amplified polymorphic DNA (RAPD) analysis was applied to 120 individuals of Marchalina hellenica (Gennadius) representing six populations collected in northern, central and southern mainland Greece. One population was sampled on one species of fir tree and the others on two species of pine trees. Four random decamer primers were used to evaluate genetic variation among the populations examined. The results revealed intra- and interpopulation polymorphism both related to host type and region of origin. Phylogenetic analysis based on genetic distances estimated by the RAPD frequencies revealed an important genetic differentiation in samples collected on fir trees in southern Greece and to a lesser extent in samples from pine trees in central and northern Greece. Furthermore, considerable subdivision and restricted gene flow among the populations examined were observed. The results are discussed in relation to the biology and geographical distribution of M. hellenica in Greece.

Animals↗

Genetic variation in alkaline phosphatase of the house mouse (Mus musculus) with emphasis on a manganese-requiring isozyme.

Genetic variation among inbred strains is described for electrophoretic migration of alkaline phosphatase from intestine, kidney, blood plasma, and three isozymes of liver. A manganese-requiring isozyme of liver and kidney unaffected by neuraminidase is described, and the locus controlling variation in this isozyme is designated Akp-1. Data from recombinant inbred strains place the locus on chromosome 1 at a distance of 3.6 +/- 2.9 cM from the M1s locus on the side distal to the centromere. Test-cross data show the following gene order and recombination percentages: Dip-1 19.0 +/- 3.8% Lp 7.4 +/- 2.2% Akp-1.

Alkaline Phosphatase↗

Genetic variation in the tumor necrosis factor-alpha promoter region and in the stress protein hsp70-2: susceptibility and prognostic implications in breast carcinoma.

BACKGROUND: Tumor necrosis factor-alpha (TNF-alpha) and stress proteins (heat shock proteins) are determining factors in the immune response to tumor cells. The authors designated a large study to investigate the susceptibility and prognostic implications of the genetic variation in TNF-alpha and hsp70-2 in breast carcinoma. METHODS: The authors used the polymerase chain reaction and restriction enzyme digestion to characterize the variation of the TNF-alpha promoter region and that of the hsp70-2 gene in 243 unrelated Tunisian patients with breast carcinoma and 174 healthy control subjects. Associations of the clinicopathologic parameters and the genetic markers with the rates of the breast carcinoma specific overall survival and the disease free survival (DFS) were assessed using univariate and multivariate analyses. RESULTS: A highly significant association was found between TNF2 homozygous genotype and breast carcinoma (relative risk [RR], 4.44; P = 0.006). A high relative risk of breast carcinoma was found to be associated with one hsp70-2 homozygous genotype (P2/P2; RR, 7.12; P = 0.0001). The TNF2 homozygous genotype showed a significant association with reduced DFS and/or overall survival by univariate test. Conversely, P2-hsp70-2 homozygous genotype associated with increased overall survival but not with DFS. Multivariate analysis retained significance for TNF2 homozygous genotype as an independent prognostic indicator for both DFS (RR, 2.75; P = 0.01) and overall survival (RR, 4.08; P = 0.01). CONCLUSIONS: Genetic variation in TNF-alpha and hsp70-2 may represent not only markers for the increased risk of breast carcinoma but also may predict the clinical outcome.

Adult↗

The effects of habitat fragmentation on demography and on the loss of genetic variation in the red squirrel.

A major problem in conservation biology is the extent to which the loss of genetic variability in isolated populations reduces their chance of survival. We present data in which the loss of genetic diversity in small and isolated populations can be directly related to population dynamics. Genetic similarity in red squirrels is inversely correlated with population size. The loss of genetic variation and the lower population densities in isolated populations are both the result of reduced immigration. Our data suggest that population processes rather than genetic problems are the real threat to small squirrel populations.

Animals↗

Epistasis and the release of genetic variation during long-term selection.

It is an enigma how long-term selection in model organisms and agricultural species can lead to marked phenotypic changes without exhausting genetic variation for the selected trait. Here, we show that the genetic architecture of an apparently major locus for growth in chicken dissects into a genetic network of four interacting loci. The interactions in this radial network mediate a considerably larger selection response than predicted by a single-locus model.

Animals↗