Perpetuation of the hereditary sigma virus in populations of its host,Drosophila melanogaster. Geographical analysis of correlated polymorphisms

In natural populations of Drosophila melanogaster, about 10% of the individuals are infected by a virus, sigma, which is not contagious but is transmitted through gametes. These populations are also regularly polymorphic for two alleles, O and P, of a locus ref(2)P; the P allele interferes with the multiplication of the virus. Two viral Types are found in populations, differing in their sensitivity to the P allele. Many samples of flies have been collected in different parts of the world and for each of them, the P frequency has been measured and the viral Type determined. A clear geographical differentiation appears for both these traits; they present a mutual adaptation leading to relatively low frequencies of infected flies in natural populations. Most viruses are only known from highly selected laboratory strains. The observations reported in this paper give evidence of the self restraint exercised by the sigma virus at the population level; they indicate that the characteristics of wild viral clones are likely to differ from those of laboratory strains and also from one population to another.The sigma virus is comparable to other genetical elements, that can be more efficiently transmitted than a mendelian allele, such as transposable elements. The discussion illustrates some of the factors involved in the perpetuation of such elements in a population and points out the difficulty of taking them all into consideration in theoretical models dealing with their perpetuation.     

A comparison of genetic information from open-pollinated and control-pollinated progeny tests in two eucalypt species

Genetic-parameter estimates and parental breeding-value predictions were compared from open-pollinated and control-pollinated progeny populations of Eucalyptus globulus and two populations of E. nitens. For E. globulus there were two types of open-pollinated populations (native stand open-pollinated and seed orchard open-pollinated) and two types of control-pollinated populations (intra-provenance and interprovenance full-sib families). For E. nitens there were two populations, a seed orchard open-pollinated population and intra-provenance full-sib families. Progeny tests were established across multiple sites and 2-year height and diameter were measured and volume calculated. Genetic parameters from native stand open-pollinated E. globulus were unlike the parameters from the other three E. globulus populations; heritability estimates were severely inflated, presumably due to high levels, and possibly differential levels, of inbreeding depression relative to the other populations. Estimates of dominance variance in the E. globulus full-sib populations were high, but were zero in the E. nitens population. Correlations among parental breeding values, predicted using data from the different populations, were generally low and non-significant, with two exceptions: predictions from the two E. globulus full-sib populations were significantly correlated (r=0.54, P = 0.001), as were predictions from the E. nitens seed orchard OP and full-sib population (r = 0.61, P = 0.08). There was some indication that superior parents of E. globulus native stand open-pollinated families also tended to have above-average breeding values based on the performance of intra-provenance full-sib offspring. The consequences of these results for exploitation of base-population collections from native stands are discussed.     

Effects of landscape and demographic history on genetic variation in <Emphasis Type="Italic">Picea glehnii</Emphasis> at the regional scale

To evaluate the effects of landscape and demographic history on genetic variation in Picea glehnii at a regional scale we have investigated the genetic diversity and genetic differentiation of P. glehnii populations in the Furano region, central Hokkaido, Japan, using seven simple sequence repeat (SSR) markers. We found significant correlations between elevation and genetic diversity parameters. The value of A _[46] increased and the value of F _IS decreased with increasing elevation, while F _IS values were not significantly different from 0 in any of the populations. Significant recent bottlenecks were detected for isolated populations at low-elevation sites and for relatively large populations at moderate- and high-elevation sites. Evolutionary events pre-dating the Holocene should be taken into consideration, as elevational gradients should be with respect to locally adapted traits such as flowering phenology, However, the palynological data from the Holocene in this region suggest that the distribution pattern of genetic diversity of P. glehnii detected here may have been influenced by past demographic history related to the elevation shifts in this species’ distribution associated with climate change during this period. Population differentiation was low, with F _ST and G′_ST values of 0.022 and 0.065, respectively. However, genetic boundaries were detected around one swamp population (C13). Therefore, significant isolation by distance (IBD) was not detected when all populations were considered, but there was significant IBD when the C13 population was excluded. Information on genetic diversity and genetic differentiation at the regional scale may be useful for selecting seed sources for afforestation programs for P. glehnii.     

Exploring the effects of different immersion environments on the growth of gold nanostructures

Even though Au crystallizes only as a simple FCC structure in bulk there have been many different and fascinating structures discovered experimentally for Au on the nanoscale. Unfortunately, for Au a direct ab-initio approach in studying dynamic growth mechanisms of nanostructures is prohibitively expensive from a computational perspective, so here we use methods based on accurate semi-empirical, many-body potentials whose parameters are obtained from a combination of empirical and ab-initio data as a viable alternative. We show that this method when combined with molecular dynamics may be used to simulate the growth of Au particles in a bath of solvent atoms (either in a gaseous or liquid state) which results in structures of a range of different morphologies. An analysis of the results indicates what characteristics of the solvent and its interactions are important in determining these different morphologies.     

Evolution of natural populations in the Drosophila melanogaster sigma system II. Northern and Central France

A survey of French natural populations of Drosophila melanogaster has been systematically performed, concerning their status of infection by the sigma virus and the characteristics of viral clones. These investigations, which were not as extensive as those performed in the Languedoc region (Fleuriet et al., 1990) nevertheless give a good representation of the evolution of this system because of the long period involved (almost 20 years). Some trends were observed in all French populations such as (1) a decrease in the high efficiency of transmission by males (which is an important parameter for the viral invading ability); (2) high frequency of a best adapted viral Type. These high frequencies might be due to a recent invasion which is expected to spread to other European populations. However, the frequency of infected flies remained low in northern and central France, unlike in Languedoc. The complexity of this, apparently simple, system of two well-known coevolving organisms should once again be stressed. It is impossible with the known parameters to arrive at a general interpretation of observations made in Languedoc and the rest of France. These data may also throw some light on the structure of French wild populations of D. melanogaster which appear to be subdivided into local populations between which gene flow might be low.     

Evolution of natural populations in the Drosophila melanogaster sigma virus system I. Languedoc (Southern France)

In natural populations of Drosophila melanogaster, sigma virus is usually present in a minority of individuals. The virus is transmitted transovarially but is not contagious from fly to fly. Two viral Types (I and II) are found in populations. One of them (Type II) is better adapted to an allele for resistance to the virus, present as a polymorphism in fly populations. Previous observations have led to the hypothesis that a viral Type II originating in central France might be invading populations. The study of Languedoc populations was undertaken to examine this hypothesis. Two striking phenomena were observed. The strong increase in Type II clones frequency (from 0.53 to 0.91) confirmed that there was invasion in this region. The frequency of infected flies also increased dramatically, at levels never observed elsewhere yet, which indicates that Languedoc should present some unusual characteristics. The epidemiological consequences of such a burst, in the case of a pathogenic virus would have to be taken into consideration. Significant changes in other viral characteristics, from 1983 to 1987, in Languedoc populations have also been documented.     

Alpine dandelions originated in the native and introduced range differ in their responses to environmental constraints

Few studies have compared the response of native and invasive populations under stressful conditions. Furthermore, there is little consensus as to whether a plastic response is related to invasiveness in stressful environments. Exotic species have recently been reported in the high Andes of central Chile, where individuals have to cope with drought and poor soils, in addition to extreme temperatures. We explored if the exotic species Taraxacum officinale (dandelion) has plastic responses to soil moisture and nutrient availability, and whether two sets of alpine populations derived from native and introduced populations can converge to similar plastic responses to environmental constraints. Using a common garden approach, we compared plants grown from seeds collected in alpine populations of its native range (Alps, France) and in alpine populations of its introduced range (Andes, Chile) under a drought experiment, a potassium gradient, and a nitrogen gradient. Plasticity was only found as a response to drought. Moreover, different responses were found between both origins. Andean individuals are drought-resistant, while individuals from the Alps were drought-sensitive. According to the nutrient experiments, Andean dandelions behave as a nitrogen demanding-potassium avoiding species, whereas individuals from the Alps did not show any particular dependency or repulsion tendency to either of these two nutrients. Results suggest that differences in life history traits of both derived sets of populations may have an important role in determining the response of dandelions under the evaluated conditions. However, the relative importance of genetic adaptation in these responses is still unclear. Although T. officinale is a cosmopolite weed, this is the first study that compares individuals coming from its native and invaded range under stressful conditions.     

Contrasting levels of genotype by environment interaction for life history and morphological traits in invasive populations of Zaprionus indianus (Diptera: Drosophilidae)

It has been demonstrated that phenotypic plasticity and genotype by environment interaction are important for coping with new and heterogeneous environments during invasions. Zaprionus indianus Gupta (Diptera: Drosophilidae) is an Afrotropical invasive fly species introduced to the South American continent in 1999. This species is generalist and polyphagous, since it develops and feeds in several different fruit species. These characteristics of Z. indianus suggest that phenotypic plasticity and genotype by environment interaction may be important in this species invasion process. In this sense, our aim was to investigate the role of genetic variation for phenotypic plasticity (genotype by environment interaction) in Z. indianus invasion of the South American continent. Specifically, we quantified quantitative genetic variation and genotype by environment interactions of morphological and life history traits in different developmental environments, that is, host fruits. This was done in different populations in the invasive range of Z. indianus in Argentina. Results showed that Z. indianus populations have considerable amounts of quantitative genetic variation. Also, genotype by environment interactions was detected for the different traits analyzed in response to the different developmental environments. Interestingly, the amounts and patterns of these parameters differed between populations. We interpreted these results as the existence of differences in evolutionary potential between populations that have an important role in the short‐ and long‐term success of the Z. indianus invasion process.     

Adaptive genetic differentiation in life-history traits between populations of <Emphasis Type="Italic">Mimulus guttatus</Emphasis> with annual and perennial life-cycles

The optimal allocation to sexual and vegetative reproduction as well as the optimal values of other life-history characteristics such as phenology, growth and mating system are likely to depend on the life-cycle of the organism. I tested whether plants of Mimulus guttatus originating from temporarily wet populations where the species has an enforced annual life-cycle have higher allocation to sexual reproduction, lower allocation to vegetative reproduction, more rapid phenology, faster growth, and floral traits associated with a self-fertilizing mating system than plants from permanently wet populations where the species has a perennial life-cycle. I grew a total of 1377 plants originating from three populations with an annual life-cycle and 11 populations with a perennial life-cycle in a greenhouse under permanently and temporarily wet conditions. Plants of M. guttatus in permanently wet conditions had significantly more vegetative reproduction and tended to have a faster growth than plants in the temporarily wet conditions, indicating plasticity in these life-history traits. Plants from populations with an annual life-cycle invested significantly more in sexual reproduction and significantly less in vegetative reproduction than the ones from populations with a perennial life-cycle. Moreover, this study showed that plants originating from populations with an annual life-cycle have a significantly faster development and floral traits associated with autonomous self-fertilization. In conclusion, this study suggests that there has been adaptive evolution of life history traits of M. guttatus in response to natural watering conditions that determine the life span of the species.     

THE GENETIC STRUCTURE OF LARGE-LAKE DAPHNIA POPULATIONS

Cyclical parthenogenesis allows study of the genetic and evolutionary characteristics of groups exhibiting both asexual and sexual reproduction. The cladoceran genus Daphnia contains species which vary with respect to the relative incidence of sexual reproduction; pond species tend to undergo sexual reproduction more regularly than species found in large lakes. Previous genetic studies have focused on pond populations, generating expectations about large-lake populations that have not been fully met by recent studies. The present study of the Palearctic species Daphnia galeata further examines the genetic structure of large-lake populations. Nine local populations, from lakes in northern Germany, are examined for genetic variation at seven enzyme loci. Populations exhibit similar allelic arrays and often similar allele frequencies at the five polymorphic loci; values of Nei's genetic distance (D) ranged from 0.002 to 0.239, with a mean of 0.084. F_ST values range from 0.012 to 0.257, and spatial autocorrelation coefficients range from -0.533 to 0.551, for the eight alleles analyzed. With few exceptions, within-population genotypic frequencies were in Hardy-Weinberg equilibrium. There was, however, significant heterogeneity in genotypic frequencies among populations. The number of coexisting clonal groups, as determined by three locus genotypes, is high within populations. Clonal groups are widely distributed among localities. The amount of genetic divergence observed among these large-lake populations is smaller than that previously observed among pond populations and suggests that different processes may be important in determining the genetic structure and subsequent phenotypic divergence of lake versus pond populations.     

Modelling the spread of pollen from Lolium perenne. The implications for the release of wind-pollinated transgenics

The dispersal of pollen from a Lolium perenne source has previously been described using various Gaussian plume models which take distance and wind direction into account. One of these models is used here to calculate, using integration, possible pollen deposition onto small conspecific populations a kilometer from the source. The percentage of immigrant pollen is compared for six different sets of parameter values previously estimated from pollen-dispersal experiments. The source size is then scaled up to simulate what might happen if transgenic ryegrass was grown on a large scale. In this case it is seen that small conspecific populations might, in some conditions, be swamped by immigrant pollen, even if they are not directly downwind of the source. The implications of this are discussed in terms of assessing and managing the risks of releasing wind-pollinated transgenic crops. Received: 10 July 1999 / Accepted: 27 August 1999     

Growth of newly established alien populations: comparison of North American gypsy moth colonies with invasion theory

A common characteristic observed in many biological invasions is the existence of a lag between the time of arrival by the alien population and the time when established populations are noticed. Considerable advances have been made in modeling the expansion of invading species, and there is often remarkable congruence between the behavior of these models with spread of actual populations. While these models have been used to characterize expansion of very newly founded colonies, there have been few attempts to compare the behavior predicted from theory with spread in actual newly founded populations, largely due to the difficulty of sampling sparse populations. Models predict that time lags in the radial expansion of newly invaded populations may be due to time requirements for the population to grow from founding to detectable levels. Models also indicate that these time lags can be predicted based upon population parameters such as the intrinsic rate of population growth and diffusion coefficient. In this paper, we compared the behavior of these models with historical data on gypsy moth, Lymantria dispar, establishment and spread to show similarities between model predictions and observed population spread, both of which exhibited temporal lags of expansion. However, actual populations exhibited certain behaviors that were not predicted, and this could be due, in part, to the existence of Allee effects and stochasticity. Further work that incorporates these effects is needed to more fully understand the growth of incipient colonies of invading species. Ultimately, this information can be of critical importance in the selection of effective strategies for their detection and eradication.     

THE INFLUENCE OF SELF-FERTILIZATION AND POPULATION DYNAMICS ON THE GENETIC STRUCTURE OF SUBDIVIDED POPULATIONS: A CASE STUDY USING MICROSATELLITE MARKERS IN THE FRESHWATER SNAIL BULINUS TRUNCATUS

The distribution of neutral genetic variability within and among sets of populations results from the combined actions of genetic drift, migration, extinction and recolonization processes, mutation, and the mating system. We here analyzed these factors in 38 populations of the hermaphroditic snail Bulinus truncatus. The sampling area covered a large part of the species range. The variability was analyzed using four polymorphic microsatellite loci. A very large number of alleles (up to 55) was found at the level of the whole study. Observed heterozygote deficiencies within populations are consistent with very high selfing rates, generally above 0.80, in all populations. These should depress the variability within populations, because of low effective size, genetic hitchhiking, and background selection, whatever the model of mutation assumed. However, that some populations exhibit much more variability than others suggests that historical demographic processes (e.g., population size variation, bottlenecks, or founding events) may play a significant role. A hierarchical analysis of the distribution of the variability across populations indicates a strong pattern of isolation by distance, whatever the geographical scale considered. Our analysis also illustrates how the mutation rate may affect population differentiation, as different mutation rates result in different levels of homoplasy at microsatellite loci. The effects of both genetic drift and gene flow vary with the temporal and spatial scales considered in B. truncatus populations.     

Regression Trees for Survival Data — an Approach to Select Discontinuous Split Points by Rank Statistics

Regression trees allow to search for meaningful explanatory variables that have a non linear impact on the dependent variable. Often they are used when there are many covariates and one does not want to restrict attention to only few of them. To grow a tree at each stage one has to select a cut point for splitting a group into two subgroups. The basis for this are the maxima of the test statistics related to the possible splits due to every covariate. They or the resulting P-values are compared as measure of importance. If covariates have different numbers of missing values, ties, or even different measurement scales the covariates lead to different numbers of tests. Those with a higher number of tests have a greater chance to achieve a smaller P-value if they are not adjusted. This can lead to erroneous splits even if the P-values are looked at informally. There is some theoretical work by Miller and Siegmund (1982) and Lausen and Schumacher (1992) to give an adjustment rule. But the asymptotic is based on a continuum of split points and may not lead to a fair splitting rule when applied to smaller data sets or to covariates with only few different values. Here we develop an approach that allows determination of P-values for any number of splits. The only approximation that is used is the normal approximation of the test statistics. The starting point for this investigation has been a prospective study on the development of AIDS. This is presented here as the main application.     

The falcifolia syndrome of Oenothera: IV. Loss of falcifolia-determining factors

Summary Inheritance of the falcifolia syndrome is explained by the hypothesis that this developmental disturbance is caused by the interaction of a non-chromosomal determinant (sigma) of Oenothera suaveolens with a complementary determinant (lambda) of O. lamarckiana when these two species are crossed. Localization of the determinants in the cell, the mechanism of their expression, and their molecular nature have not been established. Somatic segregation within the hybrids may lead to a separation of the two components, as suggested by the different reactions of sister plants in backcross tests and on selfing. The present paper presents results showing that in rare cases the fal determinants may be eliminated from the hybrid's cytoplasm. Thus, plants are produced that are phenotypically identical with the original parental strains but in crosses react like species that lack such determinants.     

The root of the phylogenetic tree of human populations

Although African populations have been shown to be most divergent from any other human populations, it has been difficult to establish the root of the phylogenetic tree of human populations since the rate of evolutionary change may vary from population to population owing to the fluctuation of population size and other factors. However, the root can be determined by using the chimpanzee as an outgroup and by employing proper statistical methods. Using this strategy, we constructed phylogenetic trees of human populations for five different sets of gene frequency data. The data sets used were two sets of microsatellite loci data (25 and 8 loci, respectively), restriction fragment length polymorphism (RFLP) data (79 loci), protein polymorphism data (15 loci), and Alu insertion frequency data (4 loci). All these data sets showed that the root is located in the branch connecting African and non-African populations, and in the four data sets the root was established at a significant level. These results indicate that Africans are the first group of people that split from the rest of the human populations.      

Multiple losses of self‐incompatibility in North‐American Arabidopsis lyrata?: Phylogeographic context and population genetic consequences

Arabidopsis lyrata is mostly outcrossing due to a sporophytic self‐incompatibility (SI) system but around the Great Lakes of North America some populations have experienced a loss of SI. We researched the loss of SI in a phylogeographic context. We used cpDNA and microsatellite markers to test if populations of North‐American A. lyrata around the Great Lakes have experienced different (recent) histories, and linked this with individually established selfing phenotype and population level realized outcrossing rates calculated based on variation in progeny arrays at multi‐locus microsatellite markers. We found three chloroplast haplotypes, in two of which the loss of self‐incompatibility had occurred independently. Shifts to high rates of inbreeding were most apparent in one of these lineages but individuals showing loss of SI occurred in all three. Self‐compatible individuals usually showed a reduction of observed heterozygosity (H_O) compared to outcrossing individuals. In the lineage that included the populations with the highest levels of inbreeding, this reduction was more substantial. This may indicate that the loss of SI in this lineage did not occur as recently as in the other lineage. The geographic distribution of the haplotypes suggested that there had been at least two independent colonization routes to the north of the Great Lakes following the last glaciation. This is consistent with postglacial migration patterns that have been suggested for other organisms with limited dispersal, such as reptiles and amphibians.     

On the maintenance of the polymorphism at the ref(2)P locus in populations of Drosophila melanogaster

Polymorphism for two alleles of the ref(2)P locus is a very constant feature of French natural populations of Drosophila melanogaster. One of these alleles interferes with the multiplication of the hereditary sigma virus in the fly. An equilibrium, quite similar to the natural one, has been observed previously in experimental populations, whether the sigma virus is present or not. Evidence is given that one of the selection components involved in the maintenance of this equilibrium affects adult stages when flies have not suffered severe larval competition. In conditions of severe larval competition, a maternal effect seems to be involved in the differential egg-to-adult viability of heterozygotes.     

Heterozygosity and phylogenetic relationship of Japanese threespine stickleback (<Emphasis Type="Italic">Gasterosteus aculeatus</Emphasis>) populations revealed by microsatellite analysis

Heterozygosity and phylogenetic relationships were analyzed using eight microsatellite loci for nine freshwater and one anadromous populations of threespine stickleback Gasterosteus aculeatus from northern Japan. Fis values and Hardy–Weinberg tests indicated that nine of the populations were in heterozygote deficit. Furthermore, on-going isolation of most of the populations by artificial destruction of population connection and habitat deterioration suggested that nearly all of the populations are likely to be in a threatened condition. Phylogenetic analysis revealed that there were two distinctive phylogenetic groups, each of which was composed of two and three freshwater populations. These populations included in the groups except ones recently established were located in inland waters and isolated from anadromous populations, so that they may have been able to keep unique genetic features. Therefore, it is necessary to protect as many populations as possible within the local population network including these inland populations. On the other hand, for freshwater populations located near the river mouth but recently isolated from anadromous populations by weir construction, it is important to remove or ameliorate the barrier and recover the gene flow. Microsatellite markers are important tools to monitor the population network and gene flow.     

Geographic variation in otolith morphology among freshwater populations of Aphanius dispar (Teleostei,Cyprinodontiformes) from the southeastern Arabian Peninsula

Aphanius Nardo is a large genus of teleost fishes in the Old World, with 19 described species. Several of these species have only recently been recognized and additional species can be expected from isolated populations in remote areas. We show here that otolith morphology and statistical analyses of otolith variables can contribute to the detection of genetic differentiation in Aphanius. We studied samples of eight Aphanius dispar populations from the southeastern part of the Arabian Peninsula. Two populations originate from freshwater habitats far inland and probably have been isolated since the late Holocene some 4,000 years ago, three populations come from freshwater habitats with occasional connections to the sea, one population originates from a coastal site, and two were artificially introduced populations. The coastal population is interpreted as possessing the basic otolith type of A. dispar. The basic otolith type also occurs in fishes from the freshwater habitat which is located closest to the coast. Otoliths from the two other freshwater populations with occasional connections to the coast differ slightly from the basic type. However, the two populations from the long‐term isolated freshwater habitats far inland show distinct morphological changes. Our results are consistent with the hypotheses that i) otolith morphology is primarily genetically determined and is little influenced by physical parameters of the habitat, and ii) isolated A. dispar populations may be capable of evolving into new species within short periods of time. J. Morphol., 2009. © 2008 Wiley‐Liss, Inc.