Multivariate QST-FST comparisons: a neutrality test for the evolution of the g matrix in structured populations.

Neutrality tests in quantitative genetics provide a statistical framework for the detection of selection on polygenic traits in wild populations. However, the existing method based on comparisons of divergence at neutral markers and quantitative traits (Q(st)-F(st)) suffers from several limitations that hinder a clear interpretation of the results with typical empirical designs. In this article, we propose a multivariate extension of this neutrality test based on empirical estimates of the among-populations (D) and within-populations (G) covariance matrices by MANOVA. A simple pattern is expected under neutrality: D = 2F(st)/(1 - F(st))G, so that neutrality implies both proportionality of the two matrices and a specific value of the proportionality coefficient. This pattern is tested using Flury's framework for matrix comparison [common principal-component (CPC) analysis], a well-known tool in G matrix evolution studies. We show the importance of using a Bartlett adjustment of the test for the small sample sizes typically found in empirical studies. We propose a dual test: (i) that the proportionality coefficient is not different from its neutral expectation [2F(st)/(1 - F(st))] and (ii) that the MANOVA estimates of mean square matrices between and among populations are proportional. These two tests combined provide a more stringent test for neutrality than the classic Q(st)-F(st) comparison and avoid several statistical problems. Extensive simulations of realistic empirical designs suggest that these tests correctly detect the expected pattern under neutrality and have enough power to efficiently detect mild to strong selection (homogeneous, heterogeneous, or mixed) when it is occurring on a set of traits. This method also provides a rigorous and quantitative framework for disentangling the effects of different selection regimes and of drift on the evolution of the G matrix. We discuss practical requirements for the proper application of our test in empirical studies and potential extensions.

Tacrolimus and cyclosporine have differential effects on the risk of development of bronchiolitis obliterans syndrome: results of a prospective, randomized international trial in lung transplantation.

BACKGROUND: Chronic lung allograft dysfunction, which manifests as bronchiolitis obliterans syndrome (BOS), is recognized as the primary cause of morbidity and mortality after lung transplantation. In this study we assessed the efficacy and safety of two de novo immunosuppression protocols to prevent BOS. METHODS: Our study approach was a multicenter, prospective, randomized (1:1) open-label superiority investigation of de novo tacrolimus vs cyclosporine, with both study arms given mycophenolate mofetil and prednisolone after lung transplantation. Cytolytic induction therapy was not employed. Patients were stratified at entry for cystic fibrosis. Primary outcome was incidence of BOS 3 years after transplant (intention-to-treat analysis). Secondary outcomes were survival and incidence of acute rejection, infection and other adverse events. RESULTS: Group demographic data were well matched: 110 of 124 tacrolimus vs 74 of 125 cyclosporine patients were treated per protocol (p < 0.01 by chi-square test). Cumulative incidence of BOS Grade ≥1 at 3 years was 11.6% (tacrolimus) vs 21.3% (cyclosporine) (cumulative incidence curves, p = 0.037 by Gray's test, pooled over strata). Univariate proportional sub-distribution hazards regression confirmed cyclosporine as a risk for BOS (HR 1.97, 95% CI 1.04 to 3.77, p = 0.039). Three-year cumulative incidence of acute rejection was 67.4% (tacrolimus) vs 74.9% (cyclosporine) (p = 0.118 by Gray's test). One- and 3-year survival rates were 84.6% and 78.7% (tacrolimus) vs 88.6% and 82.8% (cyclosporine) (p = 0.382 by log-rank test). Cumulative infection rates were similar (p = 0.91), but there was a trend toward new-onset renal failure with tacrolimus (p = 0.09). CONCLUSIONS: Compared with cyclosporine, de novo tacrolimus use was found to be associated with a significantly reduced risk for BOS Grade ≥1 at 3 years despite a similar rate of acute rejection. However, no survival advantage was detected.

Evolution des transferts interhospitaliers au départ d'un centre hospitalier universitaire suisse [Trends in interhospital transfers from a Swiss university hospital center].

OBJECTIVE: Research on interhospital transfers provides a basis for describing and quantifying patient flow and its evolution over time, offering an insight into hospital organization and management and hospital overcrowding. The purpose of this study was to conduct a qualitative and quantitative analysis of patient flow and to examine trends over an eight-year period. METHODS: A retrospective descriptive study of interhospital transfers was conducted between 2003 and 2011 based on an analysis of demographic, medical and operational characteristics. Ambulance transfers and transfers requiring physician assistance were analyzed separately. RESULTS: The number of interhospital transfers increased significantly over the study period,from 4,026 in 2003 to 6,481 in 2011 (+60.9%). The number of ambulance transfers increased by almost 300% (616 in 2003 compared to 2,460 in 2011). Most of the transfers (98%) were to hospitals located less than 75 km from the university hospital (median: 24 km, 5-44). In 2011, 24% of all transfers were to psychiatric institutions. 26% of all transfer cases were direct transfers from the emergency department. An increasing number of transfers required physician assistance. 18% of these patients required ventilatory support, whole 9.8% required vasoactive drugs. 11.6% of these transfers were due to hospital overcrowding. Conclusion: The study shows that there has been a significant increase in interhospital transfers. This increase is related to hospital overcrowding and to the network-based systems governing patient care strategies.

Biased gene conversion and GC-content evolution in the coding sequences of reptiles and vertebrates.

Mammalian and avian genomes are characterized by a substantial spatial heterogeneity of GC-content, which is often interpreted as reflecting the effect of local GC-biased gene conversion (gBGC), a meiotic repair bias that favors G and C over A and T alleles in high-recombining genomic regions. Surprisingly, the first fully sequenced nonavian sauropsid (i.e., reptile), the green anole Anolis carolinensis, revealed a highly homogeneous genomic GC-content landscape, suggesting the possibility that gBGC might not be at work in this lineage. Here, we analyze GC-content evolution at third-codon positions (GC3) in 44 vertebrates species, including eight newly sequenced transcriptomes, with a specific focus on nonavian sauropsids. We report that reptiles, including the green anole, have a genome-wide distribution of GC3 similar to that of mammals and birds, and we infer a strong GC3-heterogeneity to be already present in the tetrapod ancestor. We further show that the dynamic of coding sequence GC-content is largely governed by karyotypic features in vertebrates, notably in the green anole, in agreement with the gBGC hypothesis. The discrepancy between third-codon positions and noncoding DNA regarding GC-content dynamics in the green anole could not be explained by the activity of transposable elements or selection on codon usage. This analysis highlights the unique value of third-codon positions as an insertion/deletion-free marker of nucleotide substitution biases that ultimately affect the evolution of proteins.

Differential gene expression in response to mechanical wounding and insect feeding in Arabidopsis.

Wounding in multicellular eukaryotes results in marked changes in gene expression that contribute to tissue defense and repair. Using a cDNA microarray technique, we analyzed the timing, dynamics, and regulation of the expression of 150 genes in mechanically wounded leaves of Arabidopsis. Temporal accumulation of a group of transcripts was correlated with the appearance of oxylipin signals of the jasmonate family. Analysis of the coronatine-insensitive coi1-1 Arabidopsis mutant that is also insensitive to jasmonate allowed us to identify a large number of COI1-dependent and COI1-independent wound-inducible genes. Water stress was found to contribute to the regulation of an unexpectedly large fraction of these genes. Comparing the results of mechanical wounding with damage by feeding larvae of the cabbage butterfly (Pieris rapae) resulted in very different transcript profiles. One gene was specifically induced by insect feeding but not by wounding; moreover, there was a relative lack of water stress-induced gene expression during insect feeding. These results help reveal a feeding strategy of P. rapae that may minimize the activation of a subset of water stress-inducible, defense-related genes.

Evolution de l'intensité moyenne et de la fréquence des précipitations en Suisse de 1900 à 2009

Les précipitations moyennes et les nombres de jours de pluie par saison et par an ont été analysés pour 151 séries de mesures pluviométriques en Suisse de 1900 à 2009. Ces analyses révèlent que les précipitations moyennes ont augmenté durant le 20ème siècle pour toutes les saisons, sauf en été. Cette hausse est la plus marquée en hiver, surtout dans le Nord des Alpes et en Valais. Les nombres de jours de pluie ont également augmenté en hiver, mais moins fortement que les précipitations moyennes, alors qu'ils tendent à diminuer très légèrement durant les autres saisons. On en déduit que l'intensité moyenne des précipitations s'est accrue en Suisse durant le 20ème siècle en toutes saisons.

Melanism, body condition and elevational distribution in the asp viper

Alternative morphotypes can confer important selective advantages in different habitats, whereas they can be penalized in other circumstances. In ectotherms, such as reptiles, the body colour can have direct effects on numerous aspects of their existence, such as thermoregulation or prey-predator interactions. Darker melanic individuals show lower skin reflectance and consequently heat up more rapidly and maintain optimal body temperatures more easily than lighter coloured individuals. As a consequence, melanistic individuals of diurnal species in cool areas may exhibit higher body condition, growth rate, survival and fecundity than lighter coloured individuals. Such advantages of dark coloration may be counterbalanced by a lower crypsis to predators and a decreased foraging efficiency. We investigated, in two montane populations of asp vipers Vipera aspis, the relationship between (1) colour polymorphism and body condition and length and (2) the coloration of individuals and their elevational distribution. We showed significant relationships between (1) the coloration, body condition and sex of individuals; (2) sexes and reproductive state and morph frequency; and (3) colour morphs that were distributed following an elevational gradient. Hence, colour polymorphism plays an important role in the ecology and evolution of the asp viper and is maintained through differential selective pressures.

Developmental and Anatomical Constraints on Vertebrate Genome Evolution

Pendant ma thèse de doctorat, j'ai utilisé des espèces modèles, comme la souris et le poisson-zèbre, pour étudier les facteurs qui affectent l'évolution des gènes et leur expression. Plus précisément, j'ai montré que l'anatomie et le développement sont des facteurs clés à prendre en compte, car ils influencent la vitesse d'évolution de la séquence des gènes, l'impact sur eux de mutations (i.e. la délétion du gène est-elle létale ?), et leur tendance à se dupliquer. Où et quand il est exprimé impose à un gène certaines contraintes ou au contraire lui donne des opportunités d'évoluer. J'ai pu comparer ces tendances aux modèles classiques d'évolution de la morphologie, que l'on pensait auparavant refléter directement les contraintes s'appliquant sur le génome. Nous avons montré que les contraintes entre ces deux niveaux d'organisation ne peuvent pas être transférées simplement : il n'y a pas de lien direct entre la conservation du génotype et celle de phénotypes comme la morphologie. Ce travail a été possible grâce au développement d'outils bioinformatiques. Notamment, j'ai travaillé sur le développement de la base de données Bgee, qui a pour but de comparer l'expression des gènes entre différentes espèces de manière automatique et à large échelle. Cela implique une formalisation de l'anatomie, du développement et de concepts liés à l'homologie grâce à l'utilisation d'ontologies. Une intégration cohérente de données d'expression hétérogènes (puces à ADN, marqueurs de séquence exprimée, hybridations in situ) a aussi été nécessaire. Cette base de données est mise à jour régulièrement et disponible librement. Elle devrait contribuer à étendre les possibilités de comparaison de l'expression des gènes entre espèces pour des études d'évo-devo (évolution du développement) et de génomique. During my PhD, I used model species of vertebrates, such as mouse and zebrafish, to study factors affecting the evolution of genes and their expression. More precisely I have shown that anatomy and development are key factors to take into account, influencing the rate of gene sequence evolution, the impact of mutations (i.e. is the deletion of a gene lethal?), and the propensity of a gene to duplicate. Where and when genes are expressed imposes constraints, or on the contrary leaves them some opportunity to evolve. We analyzed these patterns in relation to classical models of morphological evolution in vertebrates, which were previously thought to directly reflect constraints on the genomes. We showed that the patterns of evolution at these two levels of organization do not translate smoothly: there is no direct link between the conservation of genotype and phenotypes such as morphology. This work was made possible by the development of bioinformatics tools. Notably, I worked on the development of the database Bgee, which aims at comparing gene expression between different species in an automated and large-scale way. This involves the formalization of anatomy, development, and concepts related to homology, through the use of ontologies. A coherent integration of heterogeneous expression data (microarray, expressed sequence tags, in situ hybridizations) is also required. This database is regularly updated and freely available. It should contribute to extend the possibilities for comparison of gene expression between species in evo-devo and genomics studies.

The evolution of sex determination

Sexual reproduction is a fundamental aspect of life. Sex-determination mechanisms are responsible for the sexual fate and development of sexual characteristics in an organism, be it a unicellular alga, a plant, or an animal. Surprisingly, sex-determination mechanisms are not evolutionarily conserved but are bewilderingly diverse and appear to have had rapid turnover rates during evolution. Evolutionary biologists continue to seek a solution to this conundrum. What drives the surprising dynamics of such a fundamental process that always leads to the same outcome: two sex types, male and female? The answer is complex but the ongoing genomic revolution has already greatly increased our knowledge of sex-determination systems and sex chromosomes in recent years. This novel book presents and synthesizes our current understanding, and clearly shows that sex-determination evolution will remain a dynamic field of future research. The Evolution of Sex Determination is an advanced, research level text suitable for graduate students and researchers in genetics, developmental biology, and evolution.

Evolution of vitellogenin genes: comparative analysis of the nucleotide sequences downstream of the transcription initiation site of four Xenopus laevis and one chicken gene.

Electron microscopic analysis of heteroduplexes between the most distantly related Xenopus vitellogenin genes (A genes X B genes) has revealed the distribution of homologous regions that have been preferentially conserved after the duplication events that gave rise to the multigene family in Xenopus laevis. DNA sequence analysis was limited to the region downstream of the transcription initiation site of the Xenopus genes A1, B1 and B2 and a comparison with the Xenopus A2 and the major chicken vitellogenin gene is presented. Within the coding regions of the first three exons, nucleotide substitutions resulting in amino acid changes accumulate at a rate similar to that observed in globin genes. This suggests that the duplication event which led to the formation of the A and B ancestral genes in Xenopus laevis occurred about 150 million years ago. Homologous exons of the A1-A2 and B1-B2 gene pairs, which formed about 30 million years ago, show a quite similar sequence divergence. In contrast, A1-A2 homologous introns seem to have evolved much faster than their B1-B2 counterparts.

Evolution of a cellular immune response in Drosophila: a phenotypic and genomic comparative analysis.

Understanding the genomic basis of evolutionary adaptation requires insight into the molecular basis underlying phenotypic variation. However, even changes in molecular pathways associated with extreme variation, gains and losses of specific phenotypes, remain largely uncharacterized. Here, we investigate the large interspecific differences in the ability to survive infection by parasitoids across 11 Drosophila species and identify genomic changes associated with gains and losses of parasitoid resistance. We show that a cellular immune defense, encapsulation, and the production of a specialized blood cell, lamellocytes, are restricted to a sublineage of Drosophila, but that encapsulation is absent in one species of this sublineage, Drosophila sechellia. Our comparative analyses of hemopoiesis pathway genes and of genes differentially expressed during the encapsulation response revealed that hemopoiesis-associated genes are highly conserved and present in all species independently of their resistance. In contrast, 11 genes that are differentially expressed during the response to parasitoids are novel genes, specific to the Drosophila sublineage capable of lamellocyte-mediated encapsulation. These novel genes, which are predominantly expressed in hemocytes, arose via duplications, whereby five of them also showed signatures of positive selection, as expected if they were recruited for new functions. Three of these novel genes further showed large-scale and presumably loss-of-function sequence changes in D. sechellia, consistent with the loss of resistance in this species. In combination, these convergent lines of evidence suggest that co-option of duplicated genes in existing pathways and subsequent neofunctionalization are likely to have contributed to the evolution of the lamellocyte-mediated encapsulation in Drosophila.

Variation and evolution of herkogamy in Exochaenium (Gentianaceae): implications for the evolution of distyly.

Backgrounds and Aims The spatial separation of stigmas and anthers (herkogamy) in flowering plants functions to reduce self-pollination and avoid interference between pollen dispersal and receipt. Little is known about the evolutionary relationships among the three main forms of herkogamy - approach, reverse and reciprocal herkogamy (distyly) - or about transitions to and from a non-herkogamous condition. This problem was examined in Exochaenium (Gentianaceae), a genus of African herbs that exhibits considerable variation in floral morphology, including the three forms of herkogamy. Methods Using maximum parsimony and maximum likelihood methods, the evolutionary history of herkogamic and non-herkogamic conditions was reconstructed from a molecular phylogeny of 15 species of Exochaenium and four outgroup taxa, based on three chloroplast regions, the nuclear ribosomal internal transcribed spacer (ITS1 and 2) and the 5·8S gene. Ancestral character states were determined and the reconstructions were used to evaluate competing models for the origin of reciprocal herkogamy. Key results Reciprocal herkogamy originated once in Exochaenium from an ancestor with approach herkogamy. Reverse herkogamy and the non-herkogamic condition homostyly were derived from heterostyly. Distylous species possessed pendent, slightly zygomorphic flowers, and the single transition to reverse herkogamy was associated with the hawkmoth pollination syndrome. Reductions in flower size characterized three of four independent transitions from reciprocal herkogamy to homostyly. Conclusions The results support Lloyd and Webb's model in which distyly originated from an ancestor with approach herkogamy. They also demonstrate the lability of sex organ deployment and implicate pollinators, or their absence, as playing an important role in driving transitions among herkogamic and non-herkogamic conditions.