Inbreeding and relatedness coefficients: what do they measure?

This paper reviews and discusses what is known about the relationship between identity in state, allele frequency, inbreeding coefficients, and identity by descent in various uses of these terms. Generic definitions of inbreeding coefficients are given, as ratios of differences of probabilities of identity in state. Then some of their properties are derived from an assumption in terms of differences between distributions of coalescence times of different genes. These inbreeding coefficients give an approximate measurement of how much higher the probability of recent coalescence is for some pair of genes relative to another pair. Such a measure is in general not equivalent to identity by descent; rather, it approximates a ratio of differences of probabilities of identity by descent. These results are contrasted with some other formulas relating identity, allele frequency, and inbreeding coefficients. Additional assumptions are necessary to obtain most of them, and some of these assumptions are not always correct, for example when there is localized dispersal. Therefore, definitions based on such formulas are not always well-formulated. By contrast, the generic definitions are both well-formulated and more broadly applicable.

Heterosis, marker mutational processes and population inbreeding history

Genotype-fitness correlations (GFC) have previously been studied using allozyme markers and have often focused on short-term processes such as recent inbreeding. Thus, models of GFC usually neglect marker mutation and only use heterozygosity as a genotypic index. Recently, GFC have also been reported (i) with DNA markers such as microsatellites, characterized by high mutation rates and specific mutational processes and (ii) using new individual genotypic indices assumed to be more precise than heterozygosity. The aim of this article is to evaluate the theoretical impact of marker mutation on GFC. We model GFC due to short-term processes generated by the current breeding system (partial selfing) and to long-term processes generated by past population history (hybridization). Various mutation rates and mutation models corresponding to different kinds of molecular markers are considered. Heterozygosity is compared to other genotypic indices designed for specific marker types. Highly mutable markers (such as microsatellites) are particularly suitable for the detection of GFC that evolve in relation to short-term processes, whereas GFC due to long-term processes are best observed with intermediate mutation rates. Irrespective of the marker type and population scenario, heterozygosity usually provides higher correlations than other genotypic indices under most biologically plausible conditions.

Are partial mantel tests adequate?

Partial Mantel tests were designed to test for correlation among three matrices of pairwise distances. We show through an example that these tests may be inadequate, because the associated P-value is not indicative of the type I error.

"Neighbourhood" size, dispersal and density estimates in the prickly forest skink (Gnypetoscincus queenslandiae) using individual genetic and demographic methods

Dispersal, or the amount of dispersion between an individual's birthplace and that of its offspring, is of great importance in population biology, behavioural ecology and conservation, however, obtaining direct estimates from field data on natural populations can be problematic. The prickly forest skink, Gnypetoscincus queenslandiae, is a rainforest endemic skink from the wet tropics of Australia. Because of its log-dwelling habits and lack of definite nesting sites, a demographic estimate of dispersal distance is difficult to obtain. Neighbourhood size, defined as 4piDsigma2 (where D is the population density and sigma2 the mean axial squared parent-offspring dispersal rate), dispersal and density were estimated directly and indirectly for this species using mark-recapture and microsatellite data, respectively, on lizards captured at a local geographical scale of 3 ha. Mark-recapture data gave a dispersal rate of 843 m2/generation (assuming a generation time of 6.5 years), a time-scaled density of 13 635 individuals * generation/km2 and, hence, a neighbourhood size of 144 individuals. A genetic method based on the multilocus (10 loci) microsatellite genotypes of individuals and their geographical location indicated that there is a significant isolation by distance pattern, and gave a neighbourhood size of 69 individuals, with a 95% confidence interval between 48 and 184. This translates into a dispersal rate of 404 m2/generation when using the mark-recapture density estimation, or an estimate of time-scaled population density of 6520 individuals * generation/km2 when using the mark-recapture dispersal rate estimate. The relationship between the two categories of neighbourhood size, dispersal and density estimates and reasons for any disparities are discussed.

Contact sensitizers specifically increase MHC class II expression on murine immature dendritic cells

Contact sensitivity is a T-cell-mediated immune disease that can occur when low-molecular-weight chemicals penetrate the skin. In vivo topical application of chemical sensitizers results in morphological modification of Langerhans cells (LC). Moreover, within 18 h, LC increase their major histocompatibility complex (MHC) class II antigens expression and migrate to lymph nodes where they present the sensitizer to T lymphocytes. We wanted to determine if such an effect could also be observed in vitro. However, because of the high genetic diversity encountered in humans, assays were performed with dendritic cells (DC) obtained from a Balb/c mouse strain. The capacity of a strong sensitizer, DNBS (2,4-dinitrobenzene sulfonic acid), to modulate the phenotype of bone marrow-derived DC in vitro, was investigated. A specific and marked increase of MHC class II molecules expression was observed within 18 h. To eliminate the use of animals in sensitization studies, the XS52 DC line was tested at an immature stage. A 30-min contact with the strong sensitizers DNBS and oxazolone, or the moderate mercaptobenzothiazole, resulted in upregulation of MHC class II molecules expression, analyzed after 18-h incubation. This effect was not observed with irritants (dimethyl sulfoxide and sodium lauryl sulfate) nor with a neutral molecule (sodium chloride). These data suggested the possibility of developing an in vitro model for the identification of the sensitizing potential of chemicals, using a constant and non animal-consuming material.

Upregulation of the Netrin Receptor (DCC) Gene during Activation of B Lymphocytes and Modulation by Interleukins

The DCC (deleted in colon cancer) gene has a brain restricted high expression pattern. It encodes a transmembrane protein of the immunoglobulin superfamily identified as the netrin-1 receptor. It might be a member of the so called "brain-lymphoid" molecules, which control key cell surface events. To test this hypothesis we have assessed the DCC mRNA level in human normal and malignant myeloid and lymphoid cells. A high mRNA content has been observed only in mature B cells at the secreting or presecreting stage. Expression of DCC was also assessed in the anti-CD40 model of immunopoiesis. Activation of purified tonsillar B cells by anti-CD 40 antibody strongly increased the DCC mRNA level and this effect was dramatically enhanced by the association of IL-2 + IL-10, which is a potent and selective in vitro inducer of the B cell memory phenotype. In contrast no effect has been detected after activation of T cells by anti-CD3. These data suggest that the DCC encoded netrin receptor is involved in B cell immunopoiesis.

Population genetics and dynamics of the black truffle in a man-made truffle field

The colonization dynamics of the black truffle in an artificial field were assessed through analyses of microsatellite and RAPD markers. The truffle field was composed of three tree species and mycelial inoculum of three different origins, and was monitored for the first three years of truffle production. We found very low levels of genetic diversity. Isolation by distance was detected only at the between-tree level. This could be interpreted as local colonization around each tree facilitated by the presence of the tree root system. At the larger spatial scale of the European range, the absence of isolation by distance corroborates the hypothesis of an impact of glaciation on genetic variation, followed by rapid postglaciation demographic expansion. In addition, genetic variation of harvested truffles was explained by neither inoculation origin, nor tree species. Our study questions the real impact of man-made inoculation of tree root systems with fungal mycelia.

A critical role for p38 mitogen-activated protein kinase in the maturation of human blood-derived dendritic cells induced by lipopolysaccharide, TNF-alpha, and contact sensitizers

We investigated the involvement of mitogen-activated protein kinases (MAPKs) in the maturation of CD83(-) dendritic cells (DC) derived from human blood monocytes. Maturating agents such as LPS and TNF-alpha induced the phosphorylation of members of the three families of MAPK (extracellular signal-regulated kinase l/2, p46/54 c-Jun N-terminal kinase, and p38 MAPK). SB203580, an inhibitor of the p38 MAPK, but not the extracellular signal-regulated kinase l/2 pathway blocker PD98059, inhibited the up-regulation of CD1a, CD40, CD80, CD86, HLA-DR, and the DC maturation marker CD83 induced by LPS and TNF-alpha. In addition, SB203580 inhibited the enhancement of the allostimulatory capacity and partially prevented the down-regulation of FITC-dextran uptake induced by LPS and TNF-alpha. Likewise, SB203580 partially prevented the up-regulation of IL-1alpha, IL-1beta, IL-lRa, and TNF-alpha mRNA upon stimulation with LPS and TNF-alpha, as well as the release of bioactive TNF-alpha induced by LPS. DC maturation induced by the contact sensitizers 2,4-dinitrofluorobenzene and NiSO(4), as seen by the up-regulation of CD80, CD86, and CD83, was also coupled to the phosphorylation of p38 MAPK, and was inhibited by SB203580. The irritants SDS and benzalkonium chloride that do not induce DC maturation did not trigger p38 MAPK phosphorylation. Together, these data indicate that phosphorylation of p38 MAPK is critical for the maturation of immature DC. These results also suggest that p38 MAPK phosphorylation in DC may become useful for the identification of potential skin contact sensitizers.

In vitro human T cell sensitization to haptens by monocyte-derived dendritic cells

We previously reported that in vitro primary sensitization of hapten-specific T cells by cultured human epidermal Langerhans cells (LC) provides an alternative approach to discriminate strong contact sensitizers from irritants (Krasteva et al., 1996; Moulon et al., 1993). However, this LC-based immunoassay was limited by the availability of human skin samples. In the present study, we used monocyte-derived dendritic cells (DC) to analyse the autologous proliferative T cell response to several allergens. Monocytes were purified from the peripheral blood of healthy donors and cultured for 6-8 days in the presence of GM/CSF and IL-4 and then for 2 days in the presence of GM/CSF and TNFalpha. The resulting cells exhibited the phenotype of mature DC, as assessed by the strong expression of HLA-DR, CD80, CD83 and CD86 antigens. We showed that trinitrophenyl (TNP)-treated mature DC induced a significant T cell proliferative response in all experiments, while fluorescein isothiocyanate (FITC) gave positive results in about half of them. The prohaptens eugenol and isoeugenol induced significant proliferation in one out of eight and in four out of 12 experiments, respectively. Interestingly, in 16 assays T cells never proliferated in the presence of sodium lauryl sulfate (SLS)-treated DC. Thus, this in vitro model allows discrimination between strong contact sensitizers and irritants. It might be very useful, therefore, for restriction of animal experimentation.

Absence of evidence for isolation by distance in an expanding cane toad (Bufo marinus) population: an individual-based analysis of microsatellite genotypes

The cane toad (Bufo marinus) was introduced in 1935 in Australia, where it spread rapidly. We have tested for isolation by distance by analysing at a local geographical scale a continuous population using seven microsatellite markers and an individual-based method. The matrix of pairwise individual differentiation was not significantly correlated with that of geographical distance. Regression analyses gave a low positive slope of 0.00072 (all individuals) or a negative slope of 0.0017 (individuals with a distance higher than the previously estimated mean dispersal distance). The absence of evidence for isolation by distance favours the hypothesis that the substantial differentiation and autocorrelation previously observed at enzyme loci, mainly results from discontinuities in the colonization process with founder effects occurring at the time of the establishment of new populations.

Kin selection and natal dispersal in an age-structured population

We examine the effect of iteroparity on the evolution of dispersal for a species living in a stable but fragmented habitat. We use a kin selection model that incorporates the effects of demographic stochasticity on the local age structure and age-specific genetic identities. We consider two cases: when the juvenile dispersal rate is allowed to change with maternal age and when it is not. In the latter case, we find that the unconditional evolutionarily stable dispersal rate increases when the adult survival rate increases. Two antagonistic forces act upon the evolution of age-specific dispersal rates. First, when the local age structure varies between patches of habitat, the intensity of competition between adults and juveniles in the natal patch is, on average, lower for offspring born to older senescent mothers. This selects for decreasing dispersal with maternal age. Second, offspring born to older parents are on average more related to other juveniles in the same patch and they experience a higher intensity of kin competition, which selects for increasing dispersal with maternal age. We show that the evolutionary outcome results from a balance between these two opposing forces, which depends on the amount of variance in age structure among sub-populations.

Interleukin-10 in Epstein-Barr virus-associated post-transplant lymphomas

We used enzyme-linked immunosorbent assays (ELISA) to investigate the presence of interleukin-10 (IL-10) in the serum of patients developing post-transplant lymphomas. Serum IL-10 was detected in 14 out of 19 cases with a lymphoma or Hodgkin's disease, with higher values being observed in patients who had developed a lymphoma within the first few months post-transplantation, and who had an aggressive form of the disease. Eleven out of the 14 patients in whom IL-10 was detected had Epstein Barr virus-positive tumors. And 11 out of 14 patients died of lymphomas. In most of the patients who had detectable IL-10 at the time of diagnosis of the lymphoma, the IL-10 had not been present previously, but it was found in the serum of 7 out of 9 dialysis patients, and in 8 out of 17 stable transplant patients. We conclude that IL-10 plays a role in the development of the more severe forms of post-transplant lymphomas, and may be secreted by tumor cells. However. data from patients with chronic renal failure or patients undergoing immunosuppressive therapy must be treated with caution.

Genetic differentiation in populations with different classes of individuals

I formulate and analyse a model of population structure with different classes of individuals. These different classes may be age classes, other demographic classes, or different types of habitats homogeneously distributed over a geographical area. The value of population differentiation under an island model of dispersal and the increase of differentiation with geographical distance in one- and two-dimensional "isolation by distance" models are then obtained for a generalization of the FST measure of population structure, as a function of "effective" mutation, migration, and population size parameters. The relevant effective subpopulation size is related to the "mutation effective population size" of a single isolated subpopulation and, in models of age-structured populations, to the inbreeding effective population size.

A stable triple Wolbachia infection in Drosophila with nearly additive incompatibility effects

Drosophila simulans strains infected with three different Wolbachia strains were generated by experimental injection of a third symbiont into a naturally double-infected strain. This transfer led to a substantial increase in total Wolbachia density in the host strain. Each of the three symbionts was stably transmitted in the presence of the other two. Triple-infected males were incompatible with double-infected females. No evidence was obtained for interference between modification effects of the different Wolbachia strains in males. Some incompatibility was observed between triple-infected males and females. However, this incompatibility reaction is not a specific property of triple-infected flies, because it was also observed in double-infected strains.

Contact sensitizers decrease 33D1 expression on mature Langerhans cells

Langerhans cells play a critical role in allergic contact hypersensitivity. In vivo, these cells capture xenobiotics that penetrate the skin and transport them through the lymphatic vessels into regional lymph nodes for presentation to T cells. During this migration step, Langerhans cells become mature dendritic cells according to their phenotype and their high immunostimulatory capacity. In vitro, when isolated from the skin and cultured for 3 days, Langerhans cells undergo similar phenotypic and functional maturation. In this study, the capacity of sensitizers, irritants and neutral chemicals to modulate the surface marker expression and morphology of pure mature murine Langerhans cells in vitro was examined. Contact with 4 sensitizers (2,4-dinitrobenzenesulfate, 4-ethoxymethylene-2-phenyl-2-oxazolin-5-one, p-phenylenediamine, mercaptobenzo-thiazole) resulted in a rapid, specific, marked fall in 33D1 expression, a murine specific dendritic cell marker. No effect was observed with 2 neutral chemicals (sodium chloride, methyl nicotinate) or 2 irritants (dimethyl sulfoxide, benzalkonium chloride). Nevertheless, sodium lauryl sulfate, a very irritant detergent, altered morphology and down-regulated all membrane markers. These preliminary data suggest that in vitro modulation of 33D1 expression by strong sensitizers may be an approach to the development of an in vitro model for the identification of chemicals that have the potential to cause skin sensitization and to distinguish them as far as possible from irritants.

Wolbachia infections are distributed throughout insect somatic and germ line tissues

Wolbachia are intracellular microorganisms that form maternally-inherited infections within numerous arthropod species. These bacteria have drawn much attention, due in part to the reproductive alterations that they induce in their hosts including cytoplasmic incompatibility (CI), feminization and parthenogenesis. Although Wolbachia's presence within insect reproductive tissues has been well described, relatively few studies have examined the extent to which Wolbachia infects other tissues. We have examined Wolbachia tissue tropism in a number of representative insect hosts by western blot, dot blot hybridization and diagnostic PCR. Results from these studies indicate that Wolbachia are much more widely distributed in host tissues than previously appreciated. Furthermore, the distribution of Wolbachia in somatic tissues varied between different Wolbachia/host associations. Some associations showed Wolbachia disseminated throughout most tissues while others appeared to be much more restricted, being predominantly limited to the reproductive tissues. We discuss the relevance of these infection patterns to the evolution of Wolbachia/host symbioses and to potential applied uses of Wolbachia.

Genetic differentiation within and between two habitats

We investigate the usefulness of analyses of population differentiation between different ecological types, such as host races of parasites or sources and sink habitats. To that aim, we formulate a model of population structure involving two classes of subpopulations found in sympatry. Extensions of previous results for Wright's F-statistics in island and isolation-by-distance models of dispersal are given. It is then shown that source and sinks cannot in general be distinguished by F-statistics nor by their gene diversities. The excess differentiation between two partially isolated classes with respect to differentiation within classes is shown to decrease with distance, and for a wide range of parameter values it should be difficult to detect. In the same circumstances little differentiation will be observed in "hierarchical" analyses between pools of samples from each habitat, and differences between levels of differentiation within each habitat will only reflect differences between levels of gene diversity within each habitat. Exceptions will indicate strong isolation between the different classes or habitat-related divergent selection.

Analysis of population structure in autotetraploid species

Population structure parameters commonly used for diploid species are reexamined for the particular case of tetrasomic inheritance (autotetraploid species). Recurrence equations that describe the evolution of identity probabilities for neutral genes in an "island model" of population structure are derived assuming tetrasomic inheritance. The expected equilibrium value of FST is computed. In contrast to diploids, the correlation of genes between individuals within populations with respect to genes between populations (FST) may vary among loci due to the particular segregation patterns expected under tetrasomic inheritance and is consequently inappropriate for estimating demographic parameters in such populations. We thus define a new parameter (rho) and derive its relationship with Nm. This relationship is shown to be independent from both the selfing rate and the proportion of double reduction. Finally, the statistical procedure required to evaluate these parameters using data on gene frequencies distribution among autotetraploid populations is developed.

Phylogeny and PCR-based classification of Wolbachia strains using wsp gene sequences

Wolbachia are a group of intracellular inherited bacteria that infect a wide range of arthropods. They are associated with a number of different reproductive phenotypes in their hosts, such as cytoplasmic incompatibility, parthenogenesis and feminization. While it is known that the bacterial strains responsible for these different host phenotypes form a single clade within the alpha-Proteobacteria, until now it has not been possible to resolve the evolutionary relationships between different Wolbachia strains. To address this issue we have cloned and sequenced a gene encoding a surface protein of Wolbachia (wsp) from a representative sample of 28 Wolbachia strains. The sequences from this gene were highly variable and could be used to resolve the phylogenetic relationships of different Wolbachia strains. Based on the sequence of the wsp gene from different Wolbachia isolates we propose that the Wolbachia pipientis clade be initially divided into 12 groups. As more sequence information becomes available we expect the number of such groups to increase. In addition, we present a method of Wolbachia classification based on the use of group-specific wsp polymerase chain reaction (PGR) primers which will allow Wolbachia isolates to be typed without the need to clone and sequence individual Wolbachia genes. This system should facilitate future studies investigating the distribution and biology of Wolbachia strains from large samples of different host species.

Comparative analysis of microsatellite and allozyme markers: a case study investigating microgeographic differentiation in brown trout (Salmo trutta)

A comparative study between microsatellite and allozyme markers was conducted on natural populations of resident brown trout (Salmo trutta) sampled over a reduced geographical scale and on hatchery strains. The higher level of polymorphism observed at microsatellite loci resulted in higher power of statistical tests for differentiation among population samples and for genotypic linkage disequilibrium. Genetic distances of Cavalli-Sforza and Edwards were on average two times larger for microsatellites than for allozymes but multilocus FST estimates computed over the entire set of populations were not significantly different for both categories of markers. Assignment tests of individual fish to the set of sampled populations demonstrated a much higher efficiency of microsatellites compared to allozymes. Pairwise multilocus FST estimates were significantly correlated to waterway distances and there was a significant tendency for the incorrectly classified individuals to be assigned to one of the nearest populations, indicating that isolation-by-distance acted significantly on brown trout populations. This increase of differentiation with distance was higher for allozymes than for microsatellites. Traditional measures of genetic differentiation (Cavalli-Sforza and Edwards' chord distance and FST) were compared for microsatellites to recently proposed statistics taking into account allele size differences (Goldstein's distance and PST). Using Goldstein's distance for neighbour-joining analysis did not improve the tree structure resolution. Multilocus estimates of PST and FST were not significantly different when computed over the entire set of populations but no significant correlation was detected between matrices of pairwise multilocus PST estimates and waterway distances.

Pleiotropy of adaptive changes in populations: comparisons among insecticide resistance genes in Culex pipiens

Resistance to toxicants is a convenient model for investigating whether adaptive changes are associated with pleiotropic fitness costs. Despite the voluminous literature devoted to this subject, intraspecific comparisons among toxicant resistance genes are rare. We report here results on the pleiotropic effect on adult survival of Culex pipiens mutants involved in the same adaptation: the resistance to organophosphorus insecticides. This field study was performed in southern France where four resistance genes sequentially appeared and increased in frequency in response to intense insecticide control. By repeated sampling of overwintering females through winter, we analysed the impact of each of three resistance genes on adult survival. We showed that (i) the most recent gene seems to be of no disadvantage during winter, (ii) the oldest affects survival in some environmental conditions, and (iii) the third induces a constant, severe and dominant survival cost. Such variability is discussed in relation to the physiological changes involved in resistance.