Maternal heterozygosity and progeny fitness association in an inbred Scots pine population.

Associations between heterozygosity and fitness traits have typically been investigated in populations characterized by low levels of inbreeding. We investigated the associations between standardized multilocus heterozygosity (stMLH) in mother trees (obtained from12 nuclear microsatellite markers) and five fitness traits measured in progenies from an inbred Scots pine population. The traits studied were proportion of sound seed, mean seed weight, germination rate, mean family height of one-year old seedlings under greenhouse conditions (GH) and mean family height of three-year old seedlings under field conditions (FH). The relatively high average inbreeding coefficient (F) in the population under study corresponds to a mixture of trees with different levels of co-ancestry, potentially resulting from a recent bottleneck. We used both frequentist and Bayesian methods of polynomial regression to investigate the presence of linear and non-linear relations between stMLH and each of the fitness traits. No significant associations were found for any of the traits except for GH, which displayed negative linear effect with stMLH. Negative HFC for GH could potentially be explained by the effect of heterosis caused by mating of two inbred mother trees (Lippman and Zamir 2006), or outbreeding depression at the most heterozygote trees and its negative impact on the fitness of the progeny, while their simultaneous action is also possible (Lynch. 1991). However,since this effect wasn't detected for FH, we cannot either rule out that the greenhouse conditions introduce artificial effects that disappear under more realistic field conditions.

Simultaneous estimation of multiple quantitative trait loci and growth curve parameters through hierarchical Bayesian modeling.

A novel hierarchical quantitative trait locus (QTL) mapping method using a polynomial growth function and a multiple-QTL model (with no dependence in time) in a multitrait framework is presented. The method considers a population-based sample where individuals have been phenotyped (over time) with respect to some dynamic trait and genotyped at a given set of loci. A specific feature of the proposed approach is that, instead of an average functional curve, each individual has its own functional curve. Moreover, each QTL can modify the dynamic characteristics of the trait value of an individual through its influence on one or more growth curve parameters. Apparent advantages of the approach include: (1) assumption of time-independent QTL and environmental effects, (2) alleviating the necessity for an autoregressive covariance structure for residuals and (3) the flexibility to use variable selection methods. As a by-product of the method, heritabilities and genetic correlations can also be estimated for individual growth curve parameters, which are considered as latent traits. For selecting trait-associated loci in the model, we use a modified version of the well-known Bayesian adaptive shrinkage technique. We illustrate our approach by analysing a sub sample of 500 individuals from the simulated QTLMAS 2009 data set, as well as simulation replicates and a real Scots pine (Pinus sylvestris) data set, using temporal measurements of height as dynamic trait of interest.

Joint analysis of spatial genetic structure and inbreeding in a managed population of Scots pine.

We have investigated the fine-scale spatial genetic structure in a managed Scots pine forest. For this purpose, we perform a Bayesian genetic-cluster analysis of 96 geographically mapped individual seed trees of Swedish Scots pine based on 14 microsatellite loci. The analysis was carried out with the recently developed program GENECLUST (François et al., 2006), which provides the facility to jointly incorporate both spatial information from a geographical neighborhood structure through a Potts-Dirichlet model and account for variable degrees of inbreeding within the clusters. To evaluate whether inbreeding and spatial interaction should be included in the best-fitting statistical model for our data, we used the deviance information criterion (DIC), a weighted measure of model fit that accounts for an effective number of free parameters in a model. Analysis shows that a model with a single estimated cluster, with high levels of inbreeding (0.25) and with a moderate amount of spatial dependency within the unique cluster (Psi=0.2-0.4), best explains the data. We also carried out Bayesian parentage analysis, which enabled us to exclude the possibility that the sample constitutes one single full-sib family.

An ecotoxicological view on neurotoxicity assessment.

The numbers of potential neurotoxicants in the environment are raising and pose a great risk for humans and the environment. Currently neurotoxicity assessment is mostly performed to predict and prevent harm to human populations. Despite all the efforts invested in the last years in developing novel in vitro or in silico test systems, in vivo tests with rodents are still the only accepted test for neurotoxicity risk assessment in Europe. Despite an increasing number of reports of species showing altered behaviour, neurotoxicity assessment for species in the environment is not required and therefore mostly not performed. Considering the increasing numbers of environmental contaminants with potential neurotoxic potential, eco-neurotoxicity should be also considered in risk assessment. In order to do so novel test systems are needed that can cope with species differences within ecosystems. In the field, online-biomonitoring systems using behavioural information could be used to detect neurotoxic effects and effect-directed analyses could be applied to identify the neurotoxicants causing the effect. Additionally, toxic pressure calculations in combination with mixture modelling could use environmental chemical monitoring data to predict adverse effects and prioritize pollutants for laboratory testing. Cheminformatics based on computational toxicological data from in vitro and in vivo studies could help to identify potential neurotoxicants. An array of in vitro assays covering different modes of action could be applied to screen compounds for neurotoxicity. The selection of in vitro assays could be guided by AOPs relevant for eco-neurotoxicity. In order to be able to perform risk assessment for eco-neurotoxicity, methods need to focus on the most sensitive species in an ecosystem. A test battery using species from different trophic levels might be the best approach. To implement eco-neurotoxicity assessment into European risk assessment, cheminformatics and in vitro screening tests could be used as first approach to identify eco-neurotoxic pollutants. In a second step, a small species test battery could be applied to assess the risks of ecosystems.

DNA damage susceptibility and repair in correlation to calendric age and longevity.

In two mouse strains, SAM P (senescence acceleration prone) and SAM R (senescence acceleration resistant), of different longevities, with a ratio of P/R=1:2), the DNA status in the course of aging has been investigated using the DNA Alkaline Filter Elution (AFE) technique. Six different organs (brain, liver, heart, lung, intestine, and muscle) have been used in each of the four animals of a given age. Earlier it had been shown, that DNA is damaged the more the higher the age of the animal. DNA damage susceptibility, measured after exposure of organ pieces to nitroquinoline-N-oxide (NQO), is also significantly increased at higher ages, while repair, measured of NQO damaged tissue after 3 h incubation in full medium is significantly reduced. In the strain with shorter longevity the damage increments and the repair deficiencies are drastically deviating from those with higher longevity. These findings of strong coupling of the DNA status to aging as well as longevity suggest causative relations.

The effect of inbreeding and population hybridization on developmental instability in petals and leaves of the rare plant silene diclinis (Caryophyllaceae)

Studies of fluctuating asymmetry (FA), a measure of developmental instability (DI), may provide insights into the importance of genetic factors in the long-term survival of small and isolated populations. In the present study of the rare, endemic plant Silene diclinis, I tested how moderate inbreeding within populations (full-sib crosses) and hybridization between populations influenced levels of developmental instability of petals and leaves, using plants derived from controlled crosses and raised under uniform growth conditions. The area and length of petals and leaves were digitized and measured with an image analysis system, but only bifid petals could be tested for true fluctuating asymmetry (normally distributed left-minus-right values with a mean of zero). Based on a bootstrap procedure, I found little evidence for directional asymmetry and antisymmetry in the area and length of the two lobes of the petals. Only the length measurements showed a significant leptokurtic distribution, which may reflect limited resolution (too few classes) in the image analysis system. Randomization tests were performed to test for differences between crossing treatments. Levels of FA of petal area and petal length were significantly higher for both the inbred and the interpopulation hybrid progenies relative to offspring from crosses between unrelated plants from the same population (control). There was no significant treatment effect on DI of leaves. Comparison of plants in the control group revealed that DI of leaf area was significantly higher than FA of petal area, and that these parameters were uncorrelated. This study demonstrates that FA of petals in Silene diclinis is sensitive to moderate levels of inbreeding and outbreeding, and therefore might serve as an indicator of genetic stress.

Genotoxicity of dental materials.

This study was performed to characterize the (possible) DNA-damaging properties of dental materials and to identify specific compounds that contribute to this genotoxicity. For screening, three tests that assay for different aspects of genotoxicity (i) the bacterial umu-test; (ii) the eucaryotic DNA synthesis inhibition test; and (iii) the in vivo alkaline filter elution technique were chosen. This investigation gives several lines of evidence that most dental materials tested (14 chemical monosubstances present in dental devices and 7 extracts of dental materials) yield 'positive' results in at least one of the genotoxicity tests, however, with effects ranging from 'borderline' to 'strong positive'. The extracts of the widely used dental materials Vitrebond and AH26 elicited clear concentration-related genotoxic responses in all test systems. On the basis of these data and public concern, more attention has to be given to local or systemic complications which may be associated with the use of dental materials.

Increased genotoxicity of acetylaminofluorene by modulators of multixenobiotic resistance mechanism: studies with the fresh water clam Corbicula fluminea.

The presence of a 'multixenobiotic resistance' [MXR] mechanism in gills of the freshwater clam Corbicula fluminea was investigated. Western blot analyses of membrane vesicles from gills, applying antibodies to vertebrate P170 multidrug resistance (MDR) protein, revealed a 135 kDa immunoreactive protein. Verapamil caused a reduction of 3H-vincristine (3H-VCR) binding onto vesicles from clam. Exposure of clams to 3H-VCR in the presence of verapamil or staurosporine (STP) enhanced the accumulation of 3H-VCR over control values. Furthermore, clams were exposed instead to VCR, to a model carcinogen, 2-acetylaminofluorene (AAF), to determine the verapamil- and STP-dependent increase of single-strand breaks (SSBs) in DNA from gills of this organism. Verapamil caused no or little increase of SSBs induced by exposure to 0.01 or 0.10 microM AAF, respectively, as measured by the alkaline elution technique. In contrast, in the presence of STP a highly significant and dose-dependent enhancement of AAF-mediated SSBs was measured already at exposure to 0.01 microM AAF. These data indicate (i) that the clam C. fluminea is provided with a P-glycoprotein-like element of the MDR-mechanism, (ii) that this system can be poisoned by chemosensitizers such as verapamil and STP, (iii) the role of protein kinase C in the regulation of MXR function and (iv) the importance of the MXR modulators for the assessment of ecotoxicological effects of pollutants.

Genotoxicity and cytotoxicity of the epoxy resin-based root canal sealer AH plus.

Previous studies with four rapid in vitro and in vivo test systems have shown that the epoxy resin-based root canal sealer AH26 may be genotoxic and cytotoxic (9). The purpose of this study was to determine the cytotoxic and genotoxic effects of the new resinous root canal sealer AH Plus by means of the growth inhibition test with primary human periodontal ligament fibroblasts and permanent 3T3 monolayers, the procaryotic umu test, the eucaryotic DNA synthesis inhibition test, and the in vivo alkaline filter elution test. In addition, Ames tests were performed with extracts from AH Plus. AH Plus caused only slight or no cellular injuries. Furthermore, no genotoxicity and mutagenicity were revealed by AH Plus. These data should be taken into consideration when deciding about a root canal sealer.

The effect of non-additive genetic interactions on selection in multi-locus genetic models.

Additive genetic variance might usually be expected to decrease in a finite population because of genetic drift. However, both theoretical and empirical studies have shown that the additive genetic variance of a population could, in some cases, actually increase owing to the action of genetic drift in presence of non-additive effects. We used Monte-Carlo simulations to address a less-well-studied issue: the effects of directional truncation selection on a trait affected by non-additive genetic variation. We investigated the effects on genetic variance and the response to selection. We compared two different genetic models, representing various numbers of loci. We found that the additive genetic variance could also increase in the case of truncation selection, when dominance and epistasis was present. Additive-by-additive epistatic effects generally gave a higher increase in additive variance compared to dominance. However, the magnitude of the increase differed depending on the particular model and on the number of loci.

Comparing Bayesian estimates of genetic differentiation of molecular markers and quantitative traits: an application to Pinus sylvestris.

Comparison of the level of differentiation at neutral molecular markers (estimated as F(ST) or G(ST)) with the level of differentiation at quantitative traits (estimated as Q(ST)) has become a standard tool for inferring that there is differential selection between populations. We estimated Q(ST) of timing of bud set from a latitudinal cline of Pinus sylvestris with a Bayesian hierarchical variance component method utilizing the information on the pre-estimated population structure from neutral molecular markers. Unfortunately, the between-family variances differed substantially between populations that resulted in a bimodal posterior of Q(ST) that could not be compared in any sensible way with the unimodal posterior of the microsatellite F(ST). In order to avoid publishing studies with flawed Q(ST) estimates, we recommend that future studies should present heritability estimates for each trait and population. Moreover, to detect variance heterogeneity in frequentist methods (ANOVA and REML), it is of essential importance to check also that the residuals are normally distributed and do not follow any systematically deviating trends.

Additive and non-additive genetic architecture of two different-sized populations of Scabiosa canescens.

Future adaptation to changes in the environment depends on the existence of additive genetic variances within populations. Recently, considerable attention has also been given to the non-additive component, which plays an important role in inbreeding depression and bottleneck situations. In this study, I used data from a North Carolina II crossing experiment, analysed with restricted maximum-likelihood methods, to estimate the additive and dominance genetic (co)variances for eight quantitative characters in two different-sized populations of Scabiosa canescens, a rare and threatened plant in Sweden. There was no evidence for genetic erosion in the small Hällestad population ( approximately 25 individuals) relative to the large Ahus population ( approximately 5000 individuals). In fact, slightly higher heritabilities were found in the Hällestad population. The additive genetic variance was statistically significant for all traits in both populations, but only a few additive covariances reached significance. The Hällestad population also had higher mean levels and more traits with significant dominance variance than the Ahus population. The variance attributable to maternal effects was too low to be considered significant. There was only a weak correspondence between heritabilities for each trait in the present study and previous estimates based on open-pollinated families of the same populations, but the mean heritability (over characters) was consistent between the studies.