Characterization of the rice PHO1 gene family reveals a key role for OsPHO1;2 in phosphate homeostasis and the evolution of a distinct clade in dicotyledons.

Phosphate homeostasis was studied in a monocotyledonous model plant through the characterization of the PHO1 gene family in rice (Oryza sativa). Bioinformatics and phylogenetic analysis showed that the rice genome has three PHO1 homologs, which cluster with the Arabidopsis (Arabidopsis thaliana) AtPHO1 and AtPHO1;H1, the only two genes known to be involved in root-to-shoot transfer of phosphate. In contrast to the Arabidopsis PHO1 gene family, all three rice PHO1 genes have a cis-natural antisense transcript located at the 5 ' end of the genes. Strand-specific quantitative reverse transcription-PCR analyses revealed distinct patterns of expression for sense and antisense transcripts for all three genes, both at the level of tissue expression and in response to nutrient stress. The most abundantly expressed gene was OsPHO1;2 in the roots, for both sense and antisense transcripts. However, while the OsPHO1;2 sense transcript was relatively stable under various nutrient deficiencies, the antisense transcript was highly induced by inorganic phosphate (Pi) deficiency. Characterization of Ospho1;1 and Ospho1;2 insertion mutants revealed that only Ospho1;2 mutants had defects in Pi homeostasis, namely strong reduction in Pi transfer from root to shoot, which was accompanied by low-shoot and high-root Pi. Our data identify OsPHO1;2 as playing a key role in the transfer of Pi from roots to shoots in rice, and indicate that this gene could be regulated by its cis-natural antisense transcripts. Furthermore, phylogenetic analysis of PHO1 homologs in monocotyledons and dicotyledons revealed the emergence of a distinct clade of PHO1 genes in dicotyledons, which include members having roles other than long-distance Pi transport.

Estimation of reference curves for the urinary steroid metabolome in the first year of life in healthy children : Tracing the complexity of human postnatal steroidogenesis.

CONTEXT: Complex steroid disorders such as P450 oxidoreductase deficiency or apparent cortisone reductase deficiency may be recognized by steroid profiling using chromatographic mass spectrometric methods. These methods are highly specific and sensitive, and provide a complete spectrum of steroid metabolites in a single measurement of one sample which makes them superior to immunoassays. The steroid metabolome during the fetal-neonatal transition is characterized by (a) the metabolites of the fetal-placental unit at birth, (b) the fetal adrenal androgens until its involution 3-6 months postnatally, and (c) the steroid metabolites produced by the developing endocrine organs. All these developmental events change the steroid metabolome in an age- and sex-dependent manner during the first year of life. OBJECTIVE: The aim of this study was to provide normative values for the urinary steroid metabolome of healthy newborns at short time intervals in the first year of life. METHODS: We conducted a prospective, longitudinal study to measure 67 urinary steroid metabolites in 21 male and 22 female term healthy newborn infants at 13 time-points from week 1 to week 49 of life. Urine samples were collected from newborn infants before discharge from hospital and from healthy infants at home. Steroid metabolites were measured by gas chromatography-mass spectrometry (GC-MS) and steroid concentrations corrected for urinary creatinine excretion were calculated. RESULTS: 61 steroids showed age and 15 steroids sex specificity. Highest urinary steroid concentrations were found in both sexes for progesterone derivatives, in particular 20α-DH-5α-DH-progesterone, and for highly polar 6α-hydroxylated glucocorticoids. The steroids peaked at week 3 and decreased by ∼80% at week 25 in both sexes. The decline of progestins, androgens and estrogens was more pronounced than of glucocorticoids whereas the excretion of corticosterone and its metabolites and of mineralocorticoids remained constant during the first year of life. CONCLUSION: The urinary steroid profile changes dramatically during the first year of life and correlates with the physiologic developmental changes during the fetal-neonatal transition. Thus detailed normative data during this time period permit the use of steroid profiling as a powerful diagnostic tool.

The evolution of punishment through reputation.

Punishment of non-cooperators has been observed to promote cooperation. Such punishment is an evolutionary puzzle because it is costly to the punisher while beneficial to others, for example, through increased social cohesion. Recent studies have concluded that punishing strategies usually pay less than some non-punishing strategies. These findings suggest that punishment could not have directly evolved to promote cooperation. However, while it is well established that reputation plays a key role in human cooperation, the simple threat from a reputation of being a punisher may not have been sufficiently explored yet in order to explain the evolution of costly punishment. Here, we first show analytically that punishment can lead to long-term benefits if it influences one's reputation and thereby makes the punisher more likely to receive help in future interactions. Then, in computer simulations, we incorporate up to 40 more complex strategies that use different kinds of reputations (e.g. from generous actions), or strategies that not only include punitive behaviours directed towards defectors but also towards cooperators for example. Our findings demonstrate that punishment can directly evolve through a simple reputation system. We conclude that reputation is crucial for the evolution of punishment by making a punisher more likely to receive help in future interactions, and that experiments investigating the beneficial effects of punishment in humans should include reputation as an explicit feature.

Evidence for the evolution of multiple genomes in arbuscular mycorrhizal fungi.

Ancient asexuals directly contradict the evolutionary theories that explain why organisms should evolve a sexual life history. The mutualistic, arbuscular mycorrhizal fungi are thought to have been asexual for approximately 400 million years. In the absence of sex, highly divergent descendants of formerly allelic nucleotide sequences are thought to evolve in a genome. In mycorrhizal fungi, where individual offspring receive hundreds of nuclei from the parent, it has been hypothesized that a population of genetically different nuclei should evolve within one individual. Here we use DNA-DNA fluorescent in situ hybridization to show that genetically different nuclei co-exist in individual arbuscular mycorrhizal fungi. We also show that the population genetics techniques used in other organisms are unsuitable for detecting recombination because the assumptions and underlying processes do not fit the fungal genomic structure shown here. Instead we used a phylogenetic approach to show that the within-individual genetic variation that occurs in arbuscular mycorrhizal fungi probably evolved through accumulation of mutations in an essentially clonal genome, with some infrequent recombination events. We conclude that mycorrhizal fungi have evolved to be multi-genomic.

The evolution of gene expression levels in mammalian organs.

Changes in gene expression are thought to underlie many of the phenotypic differences between species. However, large-scale analyses of gene expression evolution were until recently prevented by technological limitations. Here we report the sequencing of polyadenylated RNA from six organs across ten species that represent all major mammalian lineages (placentals, marsupials and monotremes) and birds (the evolutionary outgroup), with the goal of understanding the dynamics of mammalian transcriptome evolution. We show that the rate of gene expression evolution varies among organs, lineages and chromosomes, owing to differences in selective pressures: transcriptome change was slow in nervous tissues and rapid in testes, slower in rodents than in apes and monotremes, and rapid for the X chromosome right after its formation. Although gene expression evolution in mammals was strongly shaped by purifying selection, we identify numerous potentially selectively driven expression switches, which occurred at different rates across lineages and tissues and which probably contributed to the specific organ biology of various mammals.

The evolution of inbred social systems in spiders and other organisms: from short-term gains to long-term evolutionary dead-ends?

The question of why some social systems have evolved close inbreeding is particularly intriguing given expected short- and long-term negative effects of this breeding system. Using social spiders as a case study, we quantitatively show that the potential costs of avoiding inbreeding through dispersal and solitary living could have outweighed the costs of inbreeding depression in the origin of inbred spider sociality. We further review the evidence that despite being favored in the short term, inbred spider sociality may constitute in the long run an evolutionary dead end. We also review other cases, such as the naked mole rats and some bark and ambrosia beetles, mites, psocids, thrips, parasitic ants, and termites, in which inbreeding and sociality are associated and the evidence for and against this breeding system being, in general, an evolutionary dead end.

A cohort-based analysis of the evolution of lifetime prevalence of recourse to prostitution by men in the general population of Switzerland, 1987-2000

Background: Despite their relevance to the prevention of sexually transmitted infections, there are few data on the frequency of recourse to prostitution in the male population in Switzerland. Using data gathered for the evaluation of the Swiss AIDS prevention strategy, we analysed net aggregate change and cohort-based change in lifetime prevalence of recourse to prostitution. Methods: Seven repeated cross-sectional telephone surveys of the general population aged 17-45 years (17-30 years only for the 1987 and 1988 surveys) were undertaken from 1987 to 2000 providing information on sexual behaviour including men's recourse to prostitution (total n¼9318). Age categories were: 17-20, 21-25, 26-30, 31-35, 36-40 and 41-45 years. Prevalence at 17-30 years was available in all surveys and prevalence at 41-45 was available for 1989-2000, though not for the same cohorts. Intra-cohort increase in prevalence over 10 years was analysed using truncated information for cohorts aged 21-25 and 26-30 years in 1987 and 1990. Population estimates were computed with 95% confidence intervals (CI). Results: No net change occurred in the 17-45 years male population prevalence between 1989 (17.6%, CI ¼ 15.4; 20.0) and 2000 (17.7%, CI ¼ 15.6; 20.0). The median starting prevalence of recourse to prostitution at age 17-20 was 4.8% (in 1989, CI ¼ 2.0; 9.7) and the range was from 1.8 (in 1994) to 10.4% (in 1990). The median ending prevalence at age 41-45 was 21.9% (in 1994, CI 16.7; 27.9) and the range was from 17.9 (in 2000) to 26.1% (in 1992). No clear trend was observed in either starting or ending prevalence. Intra-cohort evolution of the 1997 and 1990 cohorts was very similar. Conclusions: Based on available data, there was no net (aggregate) change in the prevalence of recourse to prostitution by males in Switzerland between 1989 and 2000. Within the time frame available, intra-cohort evolution was also very similar.

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.

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.

U-Pb and Ar-Ar geochronological data from the Pelagonian basement in Evia (Greece): geodynamic implications for the evolution of Paleotethys

High precision U-Pb zircon and Ar-40/Ar-39 mica geochronological data on metagranodiorites, metagranites and mica schists from north and central Evia island (Greece) are presented in this study. U-Pb zircon ages range from 308 to 1912 Ma, and indicate a prolonged magmatic activity in Late Carboniferous. Proterozoic ages represent inherited cores within younger crystals. Muscovite Ar-40/Ar-39 plateau ages of 288 to 297 Ma are interpreted as cooling ages of the magmatic bodies and metamorphic host rocks in upper greenschist to epidote-amphibolite metamorphic conditions. The multistage magmatism had a duration between 308 and 319 hla but some older intrusions, as well as metamorphic events, cannot be excluded. Geochemical analyses and zircon typology indicate calc-alkaline affinities for the granites of central Evia and alkaline to calc-alkaline characteristics for the metagranodiorites from the northern part of the island. The new data point towards the SE continuation, in Evia and the Cyclades, of a Variscan continental crust already recognised in northern Greece (Pelagonian basement). The Late Carboniferous magmatism is viewed as a result of northward subduction of the Paleotethys under the Eurasian margin.

Multiple causes of the evolution of dispersal in metapopulations

Abstract This work investigates the outcome of the interaction of the multiple causes of selection acting on dispersal in metapopulations. Dispersal, defined here as the ability of individuals to move out of their natal population to reproduce in an other one, has three main causes. First, population variability, as caused by random population extinctions, induces high incentives to disperse through the probability to recolonize an empty population and thus to escape competition for space. This adds to the second cause, kin competition avoidance where individuals in a crowded patch will benefit from the release of competition with relatives caused by dispersal. Dispersal may thus be viewed as an altruistic act. Third, dispersal might evolve as a strategy of avoiding inbred matings which are expected to bear fitness costs due to the presence of a mutation load. The interaction of inbreeding avoidance and kin competition is explored in chapter 2. Conditions conducive to the establishment of a high relatedness within population are expected to induce high dispersal through both kin competition avoidance and inbreeding avoidance. However, the dynamics of inbreeding depression is bound to depend on the level of gene flow as well as on the deleterious mutation parameters. Mutations more prone to settle a high level of inbreeding depression will select for increased dispersal. Chapter 3 investigates the effect of the mating system on the joint dynamics of dispersal and inbreeding depression. Higher inbreeding rates as those found in various mating systems lead to a more efficient purge of the deleterious mutations. However, this decrease in the costs of inbreeding are usually accompanied by a higher within deme relatedness which balances the decreased effect of inbreeding avoidance on the evolution of dispersal. Finally, population turnover, as found in most natural populations has a dual effect on dispersal. Indeed, it increases dispersal by the increased probability of winning a breeding slot in extinct demes it creates but, on the other hand, it counter-selects for dispersal through the slow establishment of unsaturated demic conditions which contribute to lower the local competition for space. Résumé Ce travail se propose d'étudier les effets conjoints des multiples causes de l'évolution de la dispersion en métapopulation. La dispersion, définie ici comme étant la capacité de quitter sa population d'origine pour se reproduire dans une antre population, possède trois principales causes. Premièrement, l'extinction aléatoire de populations sélectionne pour plus de dispersion car elle augmente la Probabilité de recoloniser un patch éteint et donc d'échapper à la compétition locale. La seconde cause, l'évitement de la compétition de parentèle, sélectionne pour plus de dispersion par les bénéfices qu'elle apporte par diminution de la compétition entre individus apparentés. Troisièmement, la dispersion évolue "comme stratégie d'évitement de la dépression de consanguinité présente dans des petites populations isolées. L'interaction entre l'évitement de la consanguinité et de la compétition de parentèle est étudiée dans le chapitre 2. Les conditions conduisant à l'établissement d'un fort apparentement à l'intérieur des populations sont celles qui génèrent le plus de sélection pour la dispersion. Cependant, la dynamique de la dépression de consanguinité est dépendante de la dispersion entre populations ainsi que des paramètres des mutations délétères. Les mutations créant le plus de dépression de consanguinité sont celles qui sélectionneront le plus pour de la dispersion. Le chapitre 3 s'intéresse aux effets du système de reproduction sur la dynamique conjointe du fardeau de mutation et de la dispersion. La purge des mutations délétère étant plus sévère dans des conditions de forte consanguinité, elle diminue les coûts de la consanguinité mais est habituellement accompagné par une augmentation de l'apparentement et donc l'effet peut être neutre sur la dispersion. Finalement, le turnover de populations a un effet dual sur la dispersion. La dispersion est sélectionnée par l'augmentation de la probabilité de gagner une place de reproduction dans des patchs éteints mais elle est également contre sélectionnée par la désaturation des patchs causée par l'extinction et la diminution de la compétition pour l'espace qui intervient dans ce cas.

The evolution of information suppression in communicating robots with conflicting interests.

Reliable information is a crucial factor influencing decision-making and, thus, fitness in all animals. A common source of information comes from inadvertent cues produced by the behavior of conspecifics. Here we use a system of experimental evolution with robots foraging in an arena containing a food source to study how communication strategies can evolve to regulate information provided by such cues. The robots could produce information by emitting blue light, which the other robots could perceive with their cameras. Over the first few generations, the robots quickly evolved to successfully locate the food, while emitting light randomly. This behavior resulted in a high intensity of light near food, which provided social information allowing other robots to more rapidly find the food. Because robots were competing for food, they were quickly selected to conceal this information. However, they never completely ceased to produce information. Detailed analyses revealed that this somewhat surprising result was due to the strength of selection on suppressing information declining concomitantly with the reduction in information content. Accordingly, a stable equilibrium with low information and considerable variation in communicative behaviors was attained by mutation selection. Because a similar coevolutionary process should be common in natural systems, this may explain why communicative strategies are so variable in many animal species.

Stochastic stability and the evolution of coordination in spatially structured populations.

Animals can often coordinate their actions to achieve mutually beneficial outcomes. However, this can result in a social dilemma when uncertainty about the behavior of partners creates multiple fitness peaks. Strategies that minimize risk ("risk dominant") instead of maximizing reward ("payoff dominant") are favored in economic models when individuals learn behaviors that increase their payoffs. Specifically, such strategies are shown to be "stochastically stable" (a refinement of evolutionary stability). Here, we extend the notion of stochastic stability to biological models of continuous phenotypes at a mutation-selection-drift balance. This allows us to make a unique prediction for long-term evolution in games with multiple equilibria. We show how genetic relatedness due to limited dispersal and scaled to account for local competition can crucially affect the stochastically-stable outcome of coordination games. We find that positive relatedness (weak local competition) increases the chance the payoff dominant strategy is stochastically stable, even when it is not risk dominant. Conversely, negative relatedness (strong local competition) increases the chance that strategies evolve that are neither payoff nor risk dominant. Extending our results to large multiplayer coordination games we find that negative relatedness can create competition so extreme that the game effectively changes to a hawk-dove game and a stochastically stable polymorphism between the alternative strategies evolves. These results demonstrate the usefulness of stochastic stability in characterizing long-term evolution of continuous phenotypes: the outcomes of multiplayer games can be reduced to the generic equilibria of two-player games and the effect of spatial structure can be analyzed readily.