The pattern of health care use of older prisoners in Switzerland.

Introduction: Population ageing is a worldwide phenomenon that forces us to make radical changes on multiple levels of society. So far, studies have concluded that the health, both physical and mental, of prisoners in general and older prisoners in particular is worse than that of the general population. Prisoners are reported to age faster as compared to adults in the community. However, to date, very little is known about the actual healthcare conditions of older prisoners and almost no substantial knowledge is available concerning their patterns of healthcare use. Method: A quantitative study was conducted in four prisons for male prisoners in Switzerland, including two open and two closed prisons situated in different cantons. In this study, medical records of older prisoners (50+) were obtained from the respective authority upon consent and total anonymity was ensured. Data gathered from all available medical records included basic demographic information, education and prison sentencing. Healthcare data obtained were extensive in nature encompassing data related to illness types, number of visits to different health care providers and hospitals. The corresponding reasons for visits and outcomes of these visits were extracted. All data are analysed using statistical software SPSS 20.0. Results: Data were extracted for a total of 50 older prisoners living in Switzerland. The chosen prisons are located in German-speaking cantons. Preliminary results show that the age average was 56 years. For more than half, this was their first imprisonment. Nevertheless, a third of them were sentenced to measures (Art. 64 Swiss Criminal Code) which means that the length of the detention is indefinite and while release is possible it is in most cases not very likely. This entails that these prisoners will grow old in prison and some will even spend their remaining years there. Concerning their health, a third of the sample reported respiratory and cardiovascular illnesses and half reported suffering from some form of musculoskeletal related pain. Older prisoners were prescribed on average only 3.5 medications, which is significantly fewer than the number of medication prescribed to younger prisoners, whose data were also sampled. Conclusion: Access to healthcare is a right given to all prisoners through the principle of equivalence which is generally exercised in Switzerland. Prisoners growing old in prison will represent a challenge for prison health care services.

Evolutionary games on complex networks : the emergence and maintenance of cooperation

Abstract The object of game theory lies in the analysis of situations where different social actors have conflicting requirements and where their individual decisions will all influence the global outcome. In this framework, several games have been invented to capture the essence of various dilemmas encountered in many common important socio-economic situations. Even though these games often succeed in helping us understand human or animal behavior in interactive settings, some experiments have shown that people tend to cooperate with each other in situations for which classical game theory strongly recommends them to do the exact opposite. Several mechanisms have been invoked to try to explain the emergence of this unexpected cooperative attitude. Among them, repeated interaction, reputation, and belonging to a recognizable group have often been mentioned. However, the work of Nowak and May (1992) showed that the simple fact of arranging the players according to a spatial structure and only allowing them to interact with their immediate neighbors is sufficient to sustain a certain amount of cooperation even when the game is played anonymously and without repetition. Nowak and May's study and much of the following work was based on regular structures such as two-dimensional grids. Axelrod et al. (2002) showed that by randomizing the choice of neighbors, i.e. by actually giving up a strictly local geographical structure, cooperation can still emerge, provided that the interaction patterns remain stable in time. This is a first step towards a social network structure. However, following pioneering work by sociologists in the sixties such as that of Milgram (1967), in the last few years it has become apparent that many social and biological interaction networks, and even some technological networks, have particular, and partly unexpected, properties that set them apart from regular or random graphs. Among other things, they usually display broad degree distributions, and show small-world topological structure. Roughly speaking, a small-world graph is a network where any individual is relatively close, in terms of social ties, to any other individual, a property also found in random graphs but not in regular lattices. However, in contrast with random graphs, small-world networks also have a certain amount of local structure, as measured, for instance, by a quantity called the clustering coefficient. In the same vein, many real conflicting situations in economy and sociology are not well described neither by a fixed geographical position of the individuals in a regular lattice, nor by a random graph. Furthermore, it is a known fact that network structure can highly influence dynamical phenomena such as the way diseases spread across a population and ideas or information get transmitted. Therefore, in the last decade, research attention has naturally shifted from random and regular graphs towards better models of social interaction structures. The primary goal of this work is to discover whether or not the underlying graph structure of real social networks could give explanations as to why one finds higher levels of cooperation in populations of human beings or animals than what is prescribed by classical game theory. To meet this objective, I start by thoroughly studying a real scientific coauthorship network and showing how it differs from biological or technological networks using divers statistical measurements. Furthermore, I extract and describe its community structure taking into account the intensity of a collaboration. Finally, I investigate the temporal evolution of the network, from its inception to its state at the time of the study in 2006, suggesting also an effective view of it as opposed to a historical one. Thereafter, I combine evolutionary game theory with several network models along with the studied coauthorship network in order to highlight which specific network properties foster cooperation and shed some light on the various mechanisms responsible for the maintenance of this same cooperation. I point out the fact that, to resist defection, cooperators take advantage, whenever possible, of the degree-heterogeneity of social networks and their underlying community structure. Finally, I show that cooperation level and stability depend not only on the game played, but also on the evolutionary dynamic rules used and the individual payoff calculations. Synopsis Le but de la théorie des jeux réside dans l'analyse de situations dans lesquelles différents acteurs sociaux, avec des objectifs souvent conflictuels, doivent individuellement prendre des décisions qui influenceront toutes le résultat global. Dans ce cadre, plusieurs jeux ont été inventés afin de saisir l'essence de divers dilemmes rencontrés dans d'importantes situations socio-économiques. Bien que ces jeux nous permettent souvent de comprendre le comportement d'êtres humains ou d'animaux en interactions, des expériences ont montré que les individus ont parfois tendance à coopérer dans des situations pour lesquelles la théorie classique des jeux prescrit de faire le contraire. Plusieurs mécanismes ont été invoqués pour tenter d'expliquer l'émergence de ce comportement coopératif inattendu. Parmi ceux-ci, la répétition des interactions, la réputation ou encore l'appartenance à des groupes reconnaissables ont souvent été mentionnés. Toutefois, les travaux de Nowak et May (1992) ont montré que le simple fait de disposer les joueurs selon une structure spatiale en leur permettant d'interagir uniquement avec leurs voisins directs est suffisant pour maintenir un certain niveau de coopération même si le jeu est joué de manière anonyme et sans répétitions. L'étude de Nowak et May, ainsi qu'un nombre substantiel de travaux qui ont suivi, étaient basés sur des structures régulières telles que des grilles à deux dimensions. Axelrod et al. (2002) ont montré qu'en randomisant le choix des voisins, i.e. en abandonnant une localisation géographique stricte, la coopération peut malgré tout émerger, pour autant que les schémas d'interactions restent stables au cours du temps. Ceci est un premier pas en direction d'une structure de réseau social. Toutefois, suite aux travaux précurseurs de sociologues des années soixante, tels que ceux de Milgram (1967), il est devenu clair ces dernières années qu'une grande partie des réseaux d'interactions sociaux et biologiques, et même quelques réseaux technologiques, possèdent des propriétés particulières, et partiellement inattendues, qui les distinguent de graphes réguliers ou aléatoires. Entre autres, ils affichent en général une distribution du degré relativement large ainsi qu'une structure de "petit-monde". Grossièrement parlant, un graphe "petit-monde" est un réseau où tout individu se trouve relativement près de tout autre individu en termes de distance sociale, une propriété également présente dans les graphes aléatoires mais absente des grilles régulières. Par contre, les réseaux "petit-monde" ont, contrairement aux graphes aléatoires, une certaine structure de localité, mesurée par exemple par une quantité appelée le "coefficient de clustering". Dans le même esprit, plusieurs situations réelles de conflit en économie et sociologie ne sont pas bien décrites ni par des positions géographiquement fixes des individus en grilles régulières, ni par des graphes aléatoires. De plus, il est bien connu que la structure même d'un réseau peut passablement influencer des phénomènes dynamiques tels que la manière qu'a une maladie de se répandre à travers une population, ou encore la façon dont des idées ou une information s'y propagent. Ainsi, durant cette dernière décennie, l'attention de la recherche s'est tout naturellement déplacée des graphes aléatoires et réguliers vers de meilleurs modèles de structure d'interactions sociales. L'objectif principal de ce travail est de découvrir si la structure sous-jacente de graphe de vrais réseaux sociaux peut fournir des explications quant aux raisons pour lesquelles on trouve, chez certains groupes d'êtres humains ou d'animaux, des niveaux de coopération supérieurs à ce qui est prescrit par la théorie classique des jeux. Dans l'optique d'atteindre ce but, je commence par étudier un véritable réseau de collaborations scientifiques et, en utilisant diverses mesures statistiques, je mets en évidence la manière dont il diffère de réseaux biologiques ou technologiques. De plus, j'extrais et je décris sa structure de communautés en tenant compte de l'intensité d'une collaboration. Finalement, j'examine l'évolution temporelle du réseau depuis son origine jusqu'à son état en 2006, date à laquelle l'étude a été effectuée, en suggérant également une vue effective du réseau par opposition à une vue historique. Par la suite, je combine la théorie évolutionnaire des jeux avec des réseaux comprenant plusieurs modèles et le réseau de collaboration susmentionné, afin de déterminer les propriétés structurelles utiles à la promotion de la coopération et les mécanismes responsables du maintien de celle-ci. Je mets en évidence le fait que, pour ne pas succomber à la défection, les coopérateurs exploitent dans la mesure du possible l'hétérogénéité des réseaux sociaux en termes de degré ainsi que la structure de communautés sous-jacente de ces mêmes réseaux. Finalement, je montre que le niveau de coopération et sa stabilité dépendent non seulement du jeu joué, mais aussi des règles de la dynamique évolutionnaire utilisées et du calcul du bénéfice d'un individu.

Trait decoupling promotes evolutionary diversification of the trophic and acoustic system of damselfishes.

Trait decoupling, wherein evolutionary release of constraints permits specialization of formerly integrated structures, represents a major conceptual framework for interpreting patterns of organismal diversity. However, few empirical tests of this hypothesis exist. A central prediction, that the tempo of morphological evolution and ecological diversification should increase following decoupling events, remains inadequately tested. In damselfishes (Pomacentridae), a ceratomandibular ligament links the hyoid bar and lower jaws, coupling two main morphofunctional units directly involved in both feeding and sound production. Here, we test the decoupling hypothesis by examining the evolutionary consequences of the loss of the ceratomandibular ligament in multiple damselfish lineages. As predicted, we find that rates of morphological evolution of trophic structures increased following the loss of the ligament. However, this increase in evolutionary rate is not associated with an increase in trophic breadth, but rather with morphofunctional specialization for the capture of zooplanktonic prey. Lineages lacking the ceratomandibular ligament also shows different acoustic signals (i.e. higher variation of pulse periods) from others, resulting in an increase of the acoustic diversity across the family. Our results support the idea that trait decoupling can increase morphological and behavioural diversity through increased specialization rather than the generation of novel ecotypes.

Evolution of Y chromosomes : lessons from mammals and amphibians

RÉSUMÉ : Le sexe des individus peut être déterminé par l'environnement ou la génétique. Lorsque la détermination du sexe est génétique, il y a dans le génome, la présence de chromosomes spécifiques qui détermineront le sexe. Dans cette thèse, j'ai étudié l'évolution des chromosomes sexuels et dans quel contexte des marqueurs sur ces chromosomes peuvent être utilisés. Pour explorer la formation du chromosome Y, nous avons étudié les caractéristiques des chromosomes sexuels chez la rainette verte, Hyla arborea. Dans un premier temps, nous avons utilisé un marqueur situé sur les chromosomes sexuels X et Y chez plusieurs espèces appartenant au groupe de la rainette verte. Cela nous a permis de révéler chez toutes ces espèces une hétérogamétie mâle. Dans un deuxième temps, nous avons tiré profit de deux autres marqueurs situés sur les chromosomes sexuels pour montrer que la recombinaison est supprimée chez les mâles mais pas chez les femelles. Pour expliquer la réduction de la variabilité sur le chromosome Y, il n'est pas nécessaire d'invoquer le balayage sélectif ou la sélection d'arrière-plan : le nombre de copies plus petit du chromosome Y dans le génome et l'absence de recombinaison suffisent à l'expliquer. Nous avons également analysé plus en détail la suppression de la recombinaison chez les mâles de H. arborea. Les modèles classiques de l'évolution des chromosomes sexuels supposent que la taille de la région non-recombinante augmente progressivement pendant l'évolution du chromosome Y, due à l'accumulation de changements structuraux. Dans cette étude, nous montrons un modèle différent, à savoir que la recombinaison est supprimée ou diminuée non seulement sur les chromosomes sexuels mais aussi sur les autosomes chez les mâles, dû à l'action de modificateurs généraux. En utilisant des marqueurs localisés sur le chromosome Y, ainsi que sur l'ADN mitochondrial et le chromosome X, nous avons étudié l'histoire évolutive de la musaraigne musette, Crocidura russula. Cette étude illustre que les analyses génétiques avec plusieurs types de marqueurs génétiques peuvent faciliter l'interprétation de l'histoire évolutive des espèces, mais que l'utilisation des marqueurs sur les chromosomes X et Y pour des études phylogéographiques est limitée par le peu de polymorphisme observé sur ces deux types de marqueurs. Le même jeu de données combiné avec des simulations a été employé pour comprendre les facteurs responsables de la faible variabilité sur le chromosome Y qui peut être expliqué, dans notre étude, par la démographie et les traits d'histoire de vie de C. russula. SUMMARY The sex of an individual is determined either by its environment or its genetics. Genetic sex determination relies on the presence of specific chromosomes that will determine the sex of their bearer. In this thesis, I studied the evolution of the sex chromosomes and the context in which markers on this type of chromosomes can be used. To explore the evolution of a Y chromosome, we studied the nascent sex chromosomes in the European tree frog Hyla arborea. First; we amplified a sex specific marker in several related species of European tree frog and found a homogeneous pattern of male heterogamety. Secondly, we used two additional sex-specific markers to show that recombination is suppressed in males but not in females. There is, therefore, no need to invoke background selection or selective sweeps to explain the reduced genetic variability on the Y chromosome, because the lower number of copies of the Y chromosomes per breeding pair and the absence of recombination are sufficient. To further analyze the suppression of recombination in male European. tree frogs, we constructed a microsatellite linkage map for this species. Classical models of sex-chromosome evolution assume that the non-recombining region expands progressively during the long-term evolution of the Y chromosome, owing to the accumulation of structural changes. Here we show a strikingly different pattern: recombination is suppressed or depressed both on sex chromosomes and autosomes in the heterogametic sex, presumably due to the action of general modifiers. We investigated the evolutionary history of the greater white-toothed shrew, Crocidura russula, using markers on both sex chromosomes and mtDNA. This study illustrates that multilocus genetic analyses facilitates the interpretation of a species' evolutionary history. It also demonstrates that phylogeographic inferences from X and Y chromosomal markers are restricted by the low levels of observed polymorphism. Combining this genetic study with simulations, we determined that the demography and the life-history traits of this species can alone be responsible for the low Y diversity. In conclusion, this thesis shows that sex chromosomes, in combination with autosomes or mtDNA, are necessary to understand the evolution of sex chromosomes and to precisely infer the population history of a species.

Large-scale evolutionary trends of Acrochordiceratidae Arthaber, 1911 (Ammonoidea, Middle Triassic) and Cope's rule

Directed evolution of life through millions of years, such as increasing adult body size, is one of the most intriguing patterns displayed by fossil lineages. Processes and causes of such evolutionary trends are still poorly understood. Ammonoids (externally shelled marine cephalopods) are well known to have experienced repetitive morphological evolutionary trends of their adult size, shell geometry and ornamentation. This study analyses the evolutionary trends of the family Acrochordiceratidae Arthaber, 1911 from the Early to Middle Triassic (251228 Ma). Exceptionally large and bed-rock-controlled collections of this ammonoid family were obtained from strata of Anisian age (Middle Triassic) in north-west Nevada and north-east British Columbia. They enable quantitative and statistical analyses of its morphological evolutionary trends. This study demonstrates that the monophyletic clade Acrochordiceratidae underwent the classical evolute to involute evolutionary trend (i.e. increasing coiling of the shell), an increase in its shell adult size (conch diameter) and an increase in the indentation of its shell suture shape. These evolutionary trends are statistically robust and seem more or less gradual. Furthermore, they are nonrandom with the sustained shift in the mean, the minimum and the maximum of studied shell characters. These results can be classically interpreted as being constrained by the persistence and common selection pressure on this mostly anagenetic lineage characterized by relatively moderate evolutionary rates. Increasing involution of ammonites is traditionally interpreted by increasing adaptation mostly in terms of improved hydrodynamics. However, this trend in ammonoid geometry can also be explained as a case of Copes rule (increasing adult body size) instead of functional explanation of coiling, because both shell diameter and shell involution are two possible paths for ammonoids to accommodate size increase.

Predation drives interpopulation differences in parental care expression.

Expressing parental care after oviposition or parturition is usually an obligate (evolved) trait within a species, despite evolutionary theory predicting that widespread species should vary in whether or not they express parental care according to local selection pressures. The lizard Eutropis longicaudata expresses maternal care only in a single population throughout its large geographical range, but why this pattern occurs is unknown. We used reciprocal translocation and predator exclusion experiments to test whether this intraspecific variation is a fixed trait within populations and whether predator abundance explains this perplexing pattern. Wild-caught female lizards that were reciprocally translocated consistently guarded or abandoned eggs in line with their population of origin. By contrast, most lizards raised in a common garden environment and subsequently released as adults adopted the maternal care strategy of the recipient population, even when the parents originated from a population lacking maternal care. Egg predation represents a significant fitness cost in the populations where females display egg-guarding behaviour, but guarding eggs outweighs this potential cost by increasing hatching success. These results imply that predators can be a driving force in the expression of parental care in instances where it is normally absent and that local selection pressure is sufficient to cause behavioural divergence in whether or not parental care is expressed.

Spatial pattern of floral morphology: a possible insight into the effects of pollinators on plant distribution

Pollination syndromes involve convergent evolution towards phenotypes composed of specific scents, colours or floral morphologies that attract or restrict pollinator access to reward. How these traits might influence the distributions of plant species in interaction with pollinators has rarely been investigated. We sampled 870 vegetation plots in the western Swiss Alps and classified the plant species into seven blossom types according to their floral morphology (wind, disk, funnel, tube, bilabiate, head or brush). We investigated the environmental features of plots with functional diversity (FD) lower than expected by chance alone to detect potential pollination filtering and related the proportions of the seven blossom types to a combination of environmental descriptors. From these results, we inferred the potential effect of the pollinator on the spatial distribution of plant species. The vegetation plots with significantly lower FD of blossom types than expected by chance were found at higher altitudes, and the proportions of blossom types were strongly patterned along the same gradient. These results support a biotic filtering effect on plant species assemblages through pollination: disk blossoms became dominant at higher altitudes, resulting in a lower FD. In harsh conditions at high altitudes, pollinators usually decrease in activity, and the openness of the disk blossom grants access to any available pollinator. Inversely, bilabiate blossoms, which are mostly pollinated by bees, were more abundant at lower elevations, which are characterised by greater abundance and diversity of bees. Generalisation through openness of the blossom could be advantageous at high elevations, while specialisation could be a successful alternative strategy at lower elevations. The approach used in this study is purely correlative, and further investigations should be conducted to infer the nature of the causal relationship between plant and pollinator distributions.

Learning ability and longevity: a symmetrical evolutionary trade-off in Drosophila.

Learning ability can be substantially improved by artificial selection in animals ranging from Drosophila to rats. Thus these species have not used their evolutionary potential with respect to learning ability, despite intuitively expected and experimentally demonstrated adaptive advantages of learning. This suggests that learning is costly, but this notion has rarely been tested. Here we report correlated responses of life-history traits to selection for improved learning in Drosophila melanogaster. Replicate populations selected for improved learning lived on average 15% shorter than the corresponding unselected control populations. They also showed a minor reduction in fecundity late in life and possibly a minor increase in dry adult mass. Selection for improved learning had no effect on egg-to-adult viability, development rate, or desiccation resistance. Because shortened longevity was the strongest correlated response to selection for improved learning, we also measured learning ability in another set of replicate populations that had been selected for extended longevity. In a classical olfactory conditioning assay, these long-lived flies showed an almost 40% reduction in learning ability early in life. This effect disappeared with age. Our results suggest a symmetrical evolutionary trade-off between learning ability and longevity in Drosophila.

Mutualism with sea anemones triggered the adaptive radiation of clownfishes.

ABSTRACT: BACKGROUND: Adaptive radiation is the process by which a single ancestral species diversifies into many descendants adapted to exploit a wide range of habitats. The appearance of ecological opportunities, or the colonisation or adaptation to novel ecological resources, has been documented to promote adaptive radiation in many classic examples. Mutualistic interactions allow species to access resources untapped by competitors, but evidence shows that the effect of mutualism on species diversification can greatly vary among mutualistic systems. Here, we test whether the development of obligate mutualism with sea anemones allowed the clownfishes to radiate adaptively across the Indian and western Pacific oceans reef habitats. RESULTS: We show that clownfishes morphological characters are linked with ecological niches associated with the sea anemones. This pattern is consistent with the ecological speciation hypothesis. Furthermore, the clownfishes show an increase in the rate of species diversification as well as rate of morphological evolution compared to their closest relatives without anemone mutualistic associations. CONCLUSIONS: The effect of mutualism on species diversification has only been studied in a limited number of groups. We present a case of adaptive radiation where mutualistic interaction is the likely key innovation, providing new insights into the mechanisms involved in the buildup of biodiversity. Due to a lack of barriers to dispersal, ecological speciation is rare in marine environments. Particular life-history characteristics of clownfishes likely reinforced reproductive isolation between populations, allowing rapid species diversification.

Evolutionary genetics of arbuscular mycorrhizal fungi - causes and consequences of multiple genomes in Glomus intraradices

Résumé Les champignons endomycorhiziens arbusculaires (CEA) forment des symbioses avec la plupart des plantes terrestres. Les CEA influencent la croissance des plantes et la biodiversité. Ils sont supposés avoir évolué de manière asexuée pendant au moins 400 millions d'années et aucune diversification morphologique majeure n'a été constatée. Pour ces raisons, les CEA sont considérés comme d'anciens asexués. Très peu d'espèces sont connues actuellement. Les individus de ces champignons contiennent des noyaux génétiquement différents dans un cytoplasme continu. La signification évolutive, la variabilité et la maintenance des génomes multiples au sein des individus sont inconnues. Ce travail a démontré qu'une population du CEA Glomus intraradices est génétiquement très variable. Nous avons conclu que les plantes hôtes plutôt que la différenciation géographique devraient être responsables de cette grande diversité. Puis nous avons cherché l'existence de recombinaison entre génotypes dans une population. Nous avons détecté un groupe recombinant au sein de la population, ce qui met en doute l'état d'anciens asexués des CEA. Nous avons également détecté l'occurrence de fusions d'hyphes et l'échange de noyaux entre isolats génétiquement différents. La descendance hybride issue de cet échange était viable et distincte phénotypiquement des isolats parentaux. En résumé, ce travail identifie des événements cruciaux dans le cycle de vie des CEA qui ont le potentiel d'influencer l'évolution de génomes multiples. L'étude des conséquences de ces événements sur les interactions avec les plantes hôtes pourrait éclaircir significativement la compréhension de la symbiose entre plantes et CEA. Abstract Arbuscular mycorrhizal fungi (AMF) are important symbionts of most land plants. AMF influence plant growth and biodiversity. Very few extant species are described. AMF are thought to have evolved asexually for at least 400 million years and no major morphological diversification has occurred. Due to these reasons, they were termed `ancient asexuals'. Fungal individuals harbour genetically different nuclei in a continuous cytoplasm. The variability, maintenance and evolutionary significance of multiple genomes within individuals are unknown. This work showed that a population of the AMF Glomus intraradices harbours very high genetic diversity. We concluded that host plants rather than geographic differentiation were responsible for this diversity. Furthermore, we investigated whether recombination occurred among genotypes of a G. intraradices population. The identification of a core group of recombining genotypes in the population refutes the assumption of ancient asexuality in AMF. We found that genetically different isolates can form hyphal fusions and exchange nuclei. The hybrid progeny produced by the exchange was viable and phenotypically distinct from the parental isolates. Taken together, this work provided evidence for key events in the AMF life cycle, that influence the evolution of multiple genomes. Studying the consequences of these events on the interaction with host plants may significantly further the understanding of the AMF-plant symbiosis.

Phenetic, biogeographical, and evolutionary study ofOrnithogalum subg.Heliocharmos (Hyacinthaceae) in the western Mediterranean basin

A macromorphological study is made on taxa of the genusOrnithogalum subg.Heliocharmos in North Africa, Spain, and France. The results obtained are consistent with data from cytogenetics, reproductive biology and strategies of reproduction. They allow the retention of two species:O. algeriense and O. umbellatum. A biogeographical and phylogenetic interpretation of the subgenus is proposed for the western Mediterranean. Theoretical views on phenetics are discussed.

Evolutionary rates of Jurassic ammonites in relation to sea-level fluctuations

An analysis is presented of the diversity and faunal turnover of Jurassic ammonites related to transgressive /regressive events. The data set contained 400 genera and 1548 species belonging to 67 ammonite zones covering the entire Jurassic System. These data were used in the construction of faunal turnover curves and ammonite diversities, that correlate with sea-level fluctuation curves. Twenty-four events of ammonite faunal turnover are analyzed throughout the Jurassic. The most important took place at the Sinemurian-Carixian boundary, latest Carixian-Middle Domerian, Domerian-Toarcian boundary, latest Middle Toarcian-Late Toarcian, Toarcian-Aalenian boundary, latest Aalenian-earliest Bajocian, latest Early Bajocian-earliest Late Bojocian, Early Bathonian-Middle Bathonian boundary, latest Middle Bathonian-earliest Late Bathonian, latest Bathonian-Early Callovian, earliest Early Oxfordian-Middle Oxfordian, earliest Late Oxfordian-latest Oxfordian, latest Early Kimmeridgian, Late Kimmeridgian, middle Early Tithonian and Early Tithonian-Late Tithonian boundary. More than 75 percent of these turnovers correlate with regressive-transgressive cycles in the Exxon, and /or Hallam's sea-level curves. Inmost cases the extinction events coincide with regressive intervals, whereas origination and radiation events are related to transgressive cycles. The turnovers frequently coincide with major or minor discontinuities in the Subbetic basin (Betic Cordillera).

Generation of the primary hair follicle pattern.

Hair follicles are spaced apart from one another at regular intervals through the skin. Although follicles are predominantly epidermal structures, classical tissue recombination experiments indicated that the underlying dermis defines their location during development. Although many molecules involved in hair follicle formation have been identified, the molecular interactions that determine the emergent property of pattern formation have remained elusive. We have used embryonic skin cultures to dissect signaling responses and patterning outcomes as the skin spatially organizes itself. We find that ectodysplasin receptor (Edar)-bone morphogenetic protein (BMP) signaling and transcriptional interactions are central to generation of the primary hair follicle pattern, with restriction of responsiveness, rather than localization of an inducing ligand, being the key driver in this process. The crux of this patterning mechanism is rapid Edar-positive feedback in the epidermis coupled with induction of dermal BMP4/7. The BMPs in turn repress epidermal Edar and hence follicle fate. Edar activation also induces connective tissue growth factor, an inhibitor of BMP signaling, allowing BMP action only at a distance from their site of synthesis. Consistent with this model, transgenic hyperactivation of Edar signaling leads to widespread overproduction of hair follicles. This Edar-BMP activation-inhibition mechanism appears to operate alongside a labile prepattern, suggesting that Edar-mediated stabilization of beta-catenin active foci is a key event in determining definitive follicle locations.

Phylogenetic analyses of C4 photosynthesis evolution in grasses: genetics of convergence and convergence of genes

Summary : During the evolutionary diversification of organisms, similar ecological constraints led to the recurrent appearances of the same traits (phenotypes) in distant lineages, a phenomenon called convergence. In most cases, the genetic origins of the convergent traits remain unknown, but recent studies traced the convergent phenotypes to recurrent alterations of the same gene or, in a few cases, to identical genetic changes. However, these cases remain anecdotal and there is a need for a study system that evolved several times independently and whose genetic determinism is well resolved and straightforward, such as C4 photosynthesis. This adaptation to warm environments, possibly driven by past atmospheric CO2 decreases, consists in a CO2-concentrating pump, created by numerous morphological and biochemical novelties. All genes encoding C4 enzymes already existed in C3 ancestors, and are supposed to have been recruited through gene duplication followed by neo-functionalization, to acquire the cell specific expression pattern and altered kinetic properties that characterize Ca-specific enzymes. These predictions have so far been tested only in species-poor and ecologically marginal C4 dicots. The monocots, and especially the grass family (Poaceae), the most important C4 family in terms of species number, ecological dominance and economical importance, have been largely under-considered as suitable study systems. This thesis aimed at understanding the evolution of the C4 trait in grasses at a molecular level and to use the genetics of C4 photosynthesis to infer the evolutionary history of the C4 phenotype and its driving selective pressures. A molecular phylogeny of grasses and affiliated monocots identified 17 to 18 independent acquisitions of the C4 pathway in the grass family. A relaxed molecular clock was used to date these events and the first C4 evolution was estimated in the Chloridoideae subfamily, between 32-25 million years ago, at a period when atmospheric CO2 abruptly declined. Likelihood models showed that after the COZ decline the probability of evolving the C4 pathway strongly increased, confirming low CO2 as a likely driver of C4 photosynthesis evolution. In order to depict the genetic changes linked to the numerous C4 origins, genes encoding phopshoenolpyruvate carboxylase (PEPC), the key-enzyme responsible for the initial fixation of atmospheric CO2 in the C4 pathway, were isolated from a large sample of C3 and C4 grasses. Phylogenetic analyses were used to reconstruct the evolutionary history of the PEPC multigene family and showed that the evolution of C4-specific PEPC had been driven by positive selection on 21 codons simultaneously in up to eight C4 lineages. These selective pressures led to numerous convergent genetic changes in many different C4 clades, highlighting the repeatability of some evolutionary processes, even at the molecular level. PEPC C4-adaptive changes were traced and used to show multiple appearances of the C, pathway in clades where species tree inferences were unable to differentiate multiple C4 appearances and a single appearance followed by C4 to C3 reversion. Further investigations of genes involved in some of the C4 subtypes only (genes encoding decarboxylating enzymes NADP-malic enzyme and phosphoenolpyruvate carboxykinase) showed that these C4-enzymes also evolved through strong positive selection and underwent parallel genetic changes during the different Ca origins. The adaptive changes on these subtype-specific C4 genes were used to retrace the history of the C4-subtypes phenotypes, which revealed that the evolution of C4-PEPC and C4-decarboxylating enzymes was in several cases disconnected, emphasizing the multiplicity of the C4 trait and the gradual acquisition of the features that create the CO2-pump. Finally, phylogenetic analyses of a gene encoding the Rubisco (the enzyme responsible for the fixation of CO2 into organic compounds in all photosynthetic organisms) showed that C4 evolution switched the selective pressures on this gene. Five codons were recurrently mutated to adapt the enzyme kinetics to the high CO2 concentrations of C4 photosynthetic cells. This knowledge could be used to introgress C4-like Rubisco in C3 crops, which could lead to an increased yield under predicted future high CO2 atmosphere. Globally, the phylogenetic framework adopted during this thesis demonstrated the widespread occurrence of genetic convergence on C4-related enzymes. The genetic traces of C4 photosynthesis evolution allowed reconstructing events that happened during the last 30 million years and proved the usefulness of studying genes directly responsible for phenotype variations when inferring evolutionary history of a given trait. Résumé Durant la diversification évolutive des organismes, des pressions écologiques similaires ont amené à l'apparition récurrente de certains traits (phénotypes) dans des lignées distantes, un phénomène appelé évolution convergente. Dans la plupart des cas, l'origine génétique des traits convergents reste inconnue mais des études récentes ont montré qu'ils étaient dus dans certains cas à des changements répétés du même gène ou, dans de rares cas, à des changements génétiques identiques. Malgré tout, ces cas restent anecdotiques et il y a un réel besoin d'un système d'étude qui ait évolué indépendamment de nombreuses fois et dont le déterminisme génétique soit clairement identifié. La photosynthèse dite en Ça répond à ces critères. Cette adaptation aux environnements chauds, dont l'évolution a pu être encouragé par des baisses passées de la concentration atmosphérique en CO2, est constituée de nombreuses nouveautés morphologiques et biochimiques qui créent une pompe à CO2. La totalité des gènes codant les enzymes Ç4 étaient déjà présents dans les ancêtres C3. Leur recrutement pour la photosynthèse Ç4 est supposé s'être fait par le biais de duplications géniques suivies par une néo-fonctionnalisation pour leur conférer l'expression cellule-spécifique et les propriétés cinétiques qui caractérisent les enzymes C4. Ces prédictions n'ont jusqu'à présent été testées que dans des familles C4 contenant peu d'espèces et ayant un rôle écologique marginal. Les graminées (Poaceae), qui sont la famille C4 la plus importante, tant en termes de nombre d'espèces que de dominance écologique et d'importance économique, ont toujours été considérés comme un système d'étude peu adapté et ont fait le sujet de peu d'investigations évolutives. Le but de cette thèse était de comprendre l'évolution de la photosynthèse en C4 chez les graminées au niveau génétique et d'utiliser les gènes pour inférer l'évolution du phénotype C4 ainsi que les pressions de sélection responsables de son évolution. Une phylogénie moléculaire de la famille des graminées et des monocotylédones apparentés a identifié 17 à 18 acquisitions indépendantes de la photosynthèse chez les graminées. Grâce à une méthode d'horloge moléculaire relâchée, ces évènements ont été datés et la première apparition C4 a été estimée dans la sous-famille des Chloridoideae, il y a 32 à 25 millions d'années, à une période où les concentrations atmosphériques de CO2 ont décliné abruptement. Des modèles de maximum de vraisemblance ont montré qu'à la suite du déclin de CO2, la probabilité d'évoluer la photosynthèse C4 a fortement augmenté, confirmant ainsi qu'une faible concentration de CO2 est une cause potentielle de l'évolution de la photosynthèse C4. Afin d'identifier les mécanismes génétiques responsables des évolutions répétées de la photosynthèse C4, un segment des gènes codant pour la phosphoénolpyruvate carboxylase (PEPC), l'enzyme responsable de la fixation initiale du CO2 atmosphérique chez les plantes C4, ont été séquencés dans une centaine de graminées C3 et C4. Des analyses phylogénétiques ont permis de reconstituer l'histoire évolutive de la famille multigénique des PEPC et ont montré que l'évolution de PEPC spécifiques à la photosynthèse Ça a été causée par de la sélection positive agissant sur 21 codons, et ce simultanément dans huit lignées C4 différentes. Cette sélection positive a conduit à un grand nombre de changements génétiques convergents dans de nombreux clades différents, ce qui illustre la répétabilité de certains phénomènes évolutifs, et ce même au niveau génétique. Les changements sur la PEPC liés au C4 ont été utilisés pour confirmer des évolutions indépendantes du phénotype C4 dans des clades où l'arbre des espèces était incapable de différencier des apparitions indépendantes d'une seule apparition suivie par une réversion de C4 en C3. En considérant des gènes codant des protéines impliquées uniquement dans certains sous-types C4 (deux décarboxylases, l'enzyme malique à NADP et la phosphoénolpyruvate carboxykinase), des études ultérieures ont montré que ces enzymes C4 avaient elles-aussi évolué sous forte sélection positive et subi des changements génétiques parallèles lors des différentes origines de la photosynthèse C4. Les changements adaptatifs sur ces gènes liés seulement à certains sous-types C4 ont été utilisés pour retracer l'histoire des phénotypes de sous-types C4, ce qui a révélé que les caractères formant le trait C4 ont, dans certains cas, évolué de manière déconnectée. Ceci souligne la multiplicité du trait C4 et l'acquisition graduelle de composants participant à la pompe à CO2 qu'est la photosynthèse C4. Finalement, des analyses phylogénétiques des gènes codant pour la Rubisco (l'enzyme responsable de la fixation du CO2 en carbones organiques dans tous les organismes photosynthétiques) ont montré que l'évolution de la photosynthèse Ça a changé les pressions de sélection sur ce gène. Cinq codons ont été mutés de façon répétée afin d'adapter les propriétés cinétiques de la Rubisco aux fortes concentrations de CO2 présentes dans les cellules photosynthétiques des plantes C4. Globalement, l'approche phylogénétique adoptée durant cette thèse de doctorat a permis de démontré des phénomène fréquents de convergence génétique sur les enzymes liées à la photosynthèse C4. Les traces génétiques de l'évolution de la photosynthèse C4 ont permis de reconstituer des évènements qui se sont produits durant les derniers 30 millions d'années et ont prouvé l'utilité d'étudier des gènes directement responsables des variations phénotypiques pour inférer l'histoire évolutive d'un trait donné.

Reinitialization of evolutionary clocks during sublethal environmental stress in some invertebrates

This paper describes the influence of high environmental stress on evolutionary trends in some selected Mesozoic ammonite lineages and some protists. During extinction periods, many ammonoids are affected by drastic simplifications of their shell geometry, ornamentation and suture line. We observe that relatively tightly coiled ammonites can give rise to highly evolute forms or uncoiled heteromorphs with simple ornamentation and almost ceratitic suture line-a phenomenon called "proteromorphosis". Such simplifications often correspond to a reappearance of ancestral geometries (primitive ornamentation, evolute coiling or uncoiling) which suggest that the evolutionary clock of these organisms can be reinitialized by extreme, sublethal, environmental stress such as giant volcanism (including its consequences on diverse pollutions and on climatic changes) and major regressive events. (c) 2006 Elsevier B.V. All rights reserved.