Oak masting drivers vary between populations depending on their climatic environments.

Large interannual variation in seed production, called masting, is very common in wind-pollinated tree populations and has profound implications for the dynamics of forest ecosystems and the epidemiology of certain human diseases.1,2,3,4,5 Comparing the reproductive characteristics of populations established in climatically contrasting environments would provide powerful insight into masting mechanisms, but the required data are extremely scarce. We built a database from an unprecedented fine-scale 8-year survey of 150 sessile oak trees (Quercus petraea) from 15 populations distributed over a broad climatic gradient, including individual recordings of annual flowering effort, fruiting rate, and fruit production. Although oak masting was previously considered to depend mainly on fruiting rate variations,6,7 we show that the female flowering effort is highly variable from year to year and explains most of the fruiting dynamics in two-thirds of the populations. What drives masting was found to differ among populations living under various climates. In soft-climate populations, the fruiting rate increases initially strongly with the flowering effort, and the intensity of masting results mainly from the flowering synchrony level between individuals. By contrast, the fruiting rate of harsh-climate populations depends mainly on spring weather, which ensures intense masting regardless of the flowering synchronization level. Our work highlights the need for jointly measuring flowering effort and fruit production to decipher the diversity of masting mechanisms among populations. Accounting for such diversity will be decisive in proposing accurate, and possibly contrasted, scenarios about future reproductive patterns of perennial plants with ongoing climate change and their numerous cascading effects.

Serotyping of Toxoplasma gondii: striking homogeneous pattern between symptomatic and asymptomatic infections within Europe and South America.

Field isolates of Toxoplasma gondii in Europe and North America have been grouped into three clonal lineages that display different virulence in mice. Whether the genetic structure of the parasite is related to clinical expression in humans has not yet been demonstrated. We developed an enzyme-linked immunosorbent assay which uses lineage-specific, polymorphic polypeptides derived from the dense granule antigens, GRA5 and GRA6. Our goal was to compare serotypical patterns observed in asymptomatic versus symptomatic (ocular disease and severe infection in human immunodeficiency virus (HIV)-positive patients) infections among patients from Europe and South America. Independent of the clinical presentation of the disease, serotypes differed according to geographical origin, with a homogeneous distribution of serotype II in Europe and of serotypes I and III in South America. We conclude that GRA5-GRA6 serotyping is an interesting tool to study serotype prevalence in populations but it is not an accurate marker of pathogenicity of Toxoplasma infection in humans.

Revisiting the directional mutation pressure theory: the analysis of a particular genomic structure in Leishmania major.

This paper reports the existence of a significant negative correlation between GC12 and GC3 in the recently sequenced genome of Leishmania major. This result contradicts the previous evidence that the compositional correlations between codon positions are universal. Moreover, it challenges the interpretation of the GC12 vs. GC3 linear regression slope as the relative neutrality of GC12, within the framework of the directional mutation pressure theory [Sueoka, N., 1988. Directional mutational pressure and neutral molecular evolution. P Natl Acad Sci USA 85, 2653-2657.]. The analysis of the codon usage pattern for L. major shows that codon choice is most likely influenced by both mutation pressure and translational selection. Dinucleotide frequencies were also analysed; our results do not support the existence of an unusual neighbour-dependent mutation bias in this genome. We developed two evolutionary models that could explain the origin of the negative GC12/GC3 correlation. The first model is based on the effect of translational selection on the GC3 the second one is based on a potential mutation bias combined with purifying selection at the amino-acid level. Both models predict a negative GC12/GC3 correlation at the equilibrium. The potential implications of these results for this aspect of the directional mutation pressure theory are discussed. We conclude that the particular case of L. major should lead to a careful reevaluation of several hypotheses of this theory. The origin of the negative GC12/GC3 correlation remains for now an open question.

Serotyping of Toxoplasma gondii in chronically infected pregnant women: predominance of type II in Europe and types I and III in Colombia (South America).

Isolates of Toxoplasma gondii, which is responsible for a wide range of clinical manifestations are grouped into three clonal lineages of different virulence in mice. However, it is not clear whether this genotypic pattern is associated with the clinical profile of the disease in humans nor is the geographical distribution of the genotypes known. This is mainly due to difficulties in obtaining parasitic DNA from patients. The available data are therefore limited and originate from acute or congenital infections or from animals. A non-invasive assay is needed to address issues of strain type, geographical distribution and severity of clinical toxoplasmosis. To serotype T. gondii strains, we have developed an enzyme-linked immunosorbent assay (ELISA) that uses polymorphic polypeptides specific to the three clonal lineages and derived from two dense granule antigens, GRA5 and GRA6. Two hundred and fifty-two sera from chronically infected pregnant women from three different European countries and Colombia were investigated. The analysis of genotype-specific antibody response showed a homogeneous type II distribution in the European samples compared with types I and III but no type II in the Colombian population. Our data concord with those obtained from the genotyping of other isolates from Europe and South America. We demonstrated that, despite some limitation due to antigen and/or antibody specificity, serotyping is a promising assay to investigate the relationship between type of strain and severity of the disease.

Polarisation of prokaryotic chromosomes.

In many prokaryotes, asymmetrical mutational or selective pressures have caused compositional skews between complementary strands of replication arms, especially sensitive in the distribution of guanine and cytosine. In Escherichia coli, most of the guanine/cytosine skew is caused by mutation rates differing on leading and lagging strands, but contribution of skewed functionally important guanine-rich motifs (Chi and Rag sites), which control chromosome repair or positioning, is noticeable. Interference between replication and gene expression plays a minor role. The situation may be different in other bacteria. Studies of chromosome processing and bacterial taxonomy might profit from consideration of chromosome polarisation.

Forcing reversibility in the no-strand-bias substitution model allows for the theoretical and practical identifiability of its 5 parameters from pairwise DNA sequence comparisons.

Because of the base pairing rules in DNA, some mutations experienced by a portion of DNA during its evolution result in the same substitution, as we can only observe differences in coupled nucleotides. Then, in the absence of a bias between the two DNA strands, a model with at most 6 different parameters instead of 12 is sufficient to study the evolutionary relationship between homologous sequences derived from a common ancestor. On the other hand the same symmetry reduces the number of independent observations which can be made. Such a reduction can in some cases invalidate the calculation of the parameters. A compromise between biologically acceptable hypotheses and tractability is introduced and a five-parameter reversible no-strand-bias condition (RNSB) is presented. The identifiability of the parameters under this model is shown by examples.

Internal correspondence analysis of codon and amino-acid usage in thermophilic bacteria.

Starting from two datasets of codon usage in coding sequences from mesophilic and thermophilic bacteria, we used internal correspondence analysis to study the variability of codon usage within and between species, and within and between amino acids. The first dataset included 18,958,458 codons from 58,482 coding sequences from completely sequenced genomes of 25 species, along with 6,793,581 dinucleotides from 21,876 intergenic spaces. The second dataset, with partially sequenced genomes, included 97,095,873 codons from 293 bacterial species. Results were consistent between the two datasets. The trend for the amino-acid composition of thermophilic proteins was found to be under the control of a pressure at the nucleic acid level, not a selection at the protein level. This effect was not present in intergenic spaces, ruling out a pressure at the DNA level. The pattern at the mRNA level was more complex than a simple purine enrichment of the sense strand of coding sequences. Outliers in the partial genome dataset introduced a note of caution about the interpretation of temperature as the direct determinant of the trend observed in thermophiles. The surprising lack of selection on the amino-acid content of thermophilic proteins suggests that the amino-acid repertoire was set up in a hot environment.

Analysis of positive control STR experiments reveals that results obtained for FGA, D3S1358, and D13S317 condition the success rate of the analysis of routine reference samples.

About 120,000 reference samples are analyzed each year in the Forensic Laboratory of Lyon. A total of 1640 positive control experiments used to validate and optimize the analytical method in the routine process were submitted to a multivariate exploratory data analysis approach with the aim of better understanding the underlying sources of variability. The peak heights of the 16 genetic markers targeted by the AmpFℓSTR(®) Identifiler(®) STR kit were used as variables of interest. Six different 3130xl genetic analyzers located in the same controlled environment were involved. Two major sources of variability were found: (i) the DNA load of the sample modulates all peak heights in a similar way so that the 16 markers are highly correlated, (ii) the genetic analyzer used with a locus-specific response for peak height and a better sensitivity for the most recently acquired. Three markers (FGA, D3S1358, and D13S317) were found to be of special interest to predict the success rate observed in the routine process.

Estimating the number of contributors to forensic DNA mixtures: does maximum likelihood perform better than maximum allele count?

Determining the number of contributors to a forensic DNA mixture using maximum allele count is a common practice in many forensic laboratories. In this paper, we compare this method to a maximum likelihood estimator, previously proposed by Egeland et al., that we extend to the cases of multiallelic loci and population subdivision. We compared both methods' efficiency for identifying mixtures of two to five individuals in the case of uncertainty about the population allele frequencies and partial profiles. The proportion of correctly resolved mixtures was >90% for both estimators for two- and three-person mixtures, while likelihood maximization yielded success rates 2- to 15-fold higher for four- and five-person mixtures. Comparable results were obtained in the cases of uncertain allele frequencies and partial profiles. Our results support the use of the maximum likelihood estimator to report the number of contributors when dealing with complex DNA mixtures.

A new method for assessing the effect of replication on DNA base composition asymmetry.

DNA base composition asymmetry is at the basis of numerous in silico methods for the detection of the origin and terminus of replication in prokaryotes. However, most of these methods are unable to identify the evolutionary mechanisms that cause the base composition asymmetry. In prokaryotic chromosomes, due to the tendency for coorientation between replication and transcription, compositional biases that discriminate the leading strand from the lagging strand can be produced by 2 superposing mechanisms: replication-associated mutation bias and coding sequence-associated bias (such as transcription-related mutational processes or selective pressures on codon usage). We propose here a new method for the analysis of nucleotide composition asymmetry that allows the decoupling of replication-related and coding sequence-related mechanisms. This method is inspired by a recent work (Nikolaou and Almirantis 2005) that proposed an artificial chromosomal rearrangement meant to create a perfect gene orientation bias. We show that the study of nucleotide skews on the artificially rearranged chromosomes is a powerful means to assess the contributions of the 2 types of mechanisms in generating the base composition asymmetry. We applied our method to all completely sequenced prokaryotic chromosomes available. Our results confirm that in most species the replication mechanism has an important effect on base composition asymmetry but also that it has different impacts on GC and AT skews. We also analyzed the variability in AT skew direction encountered in prokaryotes. In disagreement with a recent report (Worning et al. 2006), we find that the polymerase-alpha subunits encoded in a genome are not sufficient to predict the sign of the AT skew on its leading strand for replication.

No evidence for tissue-specific adaptation of synonymous codon usage in humans.

It has been proposed that the synonymous codon usage of human tissue-specific genes was under selective pressure to modulate the expression of proteins by codon-mediated translational control (Plotkin, J. B., H. Robins, and A. J. Levine. 2004. Tissue-specific codon usage and the expression of human genes. Proc. Natl. Acad. Sci. USA 101:12588-12591.) To test this model, we analyzed by internal correspondence analysis the codon usage of 2,126 human tissue-specific genes expressed in 18 different tissues. We confirm that synonymous codon usage differs significantly between the tissues. However, the effect is very weak: the variability of synonymous codon usage between tissues represents only 2.3% of the total codon usage variability. Moreover, this variability is directly linked to isochore-scale (>100 kb) variability of GC-content that affect both coding and introns or intergenic regions. This demonstrates that variations of synonymous codon usage between tissue-specific genes expressed in different tissues are due to regional variations of substitution patterns and not to translational selection.

UV-targeted dinucleotides are not depleted in light-exposed prokaryotic genomes.

We have investigated the hypothesis that pyrimidine dinucleotides are avoided in light-exposed genomes as the result of selective pressure due to high ultraviolet (UV) exposure. The main damage to DNA produced by UV radiation is known to be the formation of pyrimidine photoproducts: it is estimated that about 10 dimers per minute are formed in an Escherichia coli chromosome exposed to the UV light in direct overhead sunlight at sea level. It is also known that on an E. coli chromosome exposed to UVb wavelengths (290-320 nm), pyrimidine photoproducts are formed in the following proportions: 59% TpT, 7% CpC, and 34% CpT plus TpC. We have analyzed all available complete prokaryotic genomes and the model organism Prochlorococcus marinus and have found that pyrimidine dinucleotides are not systematically avoided. This suggests that prokaryotes must have sufficiently effective protection and repair systems for UV exposure to not affect their dinucleotide composition.

Asymmetric directional mutation pressures in bacteria.

BACKGROUND: When there are no strand-specific biases in mutation and selection rates (that is, in the substitution rates) between the two strands of DNA, the average nucleotide composition is theoretically expected to be A = T and G = C within each strand. Deviations from these equalities are therefore evidence for an asymmetry in selection and/or mutation between the two strands. By focusing on weakly selected regions that could be oriented with respect to replication in 43 out of 51 completely sequenced bacterial chromosomes, we have been able to detect asymmetric directional mutation pressures. RESULTS: Most of the 43 chromosomes were found to be relatively enriched in G over C and T over A, and slightly depleted in G+C, in their weakly selected positions (intergenic regions and third codon positions) in the leading strand compared with the lagging strand. Deviations from A = T and G = C were highly correlated between third codon positions and intergenic regions, with a lower degree of deviation in intergenic regions, and were not correlated with overall genomic G+C content. CONCLUSIONS: During the course of bacterial chromosome evolution, the effects of asymmetric directional mutation pressures are commonly observed in weakly selected positions. The degree of deviation from equality is highly variable among species, and within species is higher in third codon positions than in intergenic regions. The orientation of these effects is almost universal and is compatible in most cases with the hypothesis of an excess of cytosine deamination in the single-stranded state during DNA replication. However, the variation in G+C content between species is influenced by factors other than asymmetric mutation pressure.