The evolution of trans-generational altruism: kin selection meets niche construction.

A cornerstone result of sociobiology states that limited dispersal can induce kin competition to offset the kin selected benefits of altruism. Several mechanisms have been proposed to circumvent this dilemma but all assume that actors and recipients of altruism interact during the same time period. Here, this assumption is relaxed and a model is developed where individuals express an altruistic act, which results in posthumously helping relatives living in the future. The analysis of this model suggests that kin selected benefits can then feedback on the evolution of the trait in a way that promotes altruistic helping at high rates under limited dispersal. The decoupling of kin competition and kin selected benefits results from the fact that by helping relatives living in the future, an actor is helping individuals that are not in direct competition with itself. A direct consequence is that behaviours which actors gain by reducing the common good of present and future generations can be opposed by kin selection. The present model integrates niche-constructing traits with kin selection theory and delineates demographic and ecological conditions under which altruism can be selected for; and conditions where the 'tragedy of the commons' can be reduced.

The genome of the recently domesticated crop plant sugar beet (Beta vulgaris)

Sugar beet (Beta vulgaris ssp. vulgaris) is an important crop of temperate climates which provides nearly 30% of the world's annual sugar production and is a source for bioethanol and animal feed. The species belongs to the order of Caryophylalles, is diploid with 2n = 18 chromosomes, has an estimated genome size of 714-758 megabases and shares an ancient genome triplication with other eudicot plants. Leafy beets have been cultivated since Roman times, but sugar beet is one of the most recently domesticated crops. It arose in the late eighteenth century when lines accumulating sugar in the storage root were selected from crosses made with chard and fodder beet. Here we present a reference genome sequence for sugar beet as the first non-rosid, non-asterid eudicot genome, advancing comparative genomics and phylogenetic reconstructions. The genome sequence comprises 567 megabases, of which 85% could be assigned to chromosomes. The assembly covers a large proportion of the repetitive sequence content that was estimated to be 63%. We predicted 27,421 protein-coding genes supported by transcript data and annotated them on the basis of sequence homology. Phylogenetic analyses provided evidence for the separation of Caryophyllales before the split of asterids and rosids, and revealed lineage-specific gene family expansions and losses. We sequenced spinach (Spinacia oleracea), another Caryophyllales species, and validated features that separate this clade from rosids and asterids. Intraspecific genomic variation was analysed based on the genome sequences of sea beet (Beta vulgaris ssp. maritima; progenitor of all beet crops) and four additional sugar beet accessions. We identified seven million variant positions in the reference genome, and also large regions of low variability, indicating artificial selection. The sugar beet genome sequence enables the identification of genes affecting agronomically relevant traits, supports molecular breeding and maximizes the plant's potential in energy biotechnology.

Evolutionary aspects of population structure for molecular and quantitative traits in the freshwater snail Radix balthica.

Detecting the action of selection in natural populations can be achieved using the QST-FST comparison that relies on the estimation of FST with neutral markers, and QST using quantitative traits potentially under selection. QST higher than FST suggests the action of directional selection and thus potential local adaptation. In this article, we apply the QST-FST comparison to four populations of the hermaphroditic freshwater snail Radix balthica located in a floodplain habitat. In contrast to most studies published so far, we did not detect evidence of directional selection for local optima for any of the traits we measured: QST calculated using three different methods was never higher than FST. A strong inbreeding depression was also detected, indicating that outcrossing is probably predominant over selfing in the studied populations. Our results suggest that in this floodplain habitat, local adaptation of R. balthica populations may be hindered by genetic drift, and possibly altered by uneven gene flow linked to flood frequency.

Characterization and functional identification of a novel plant extradiol 4,5-dioxygenase involved in betalain pigment biosynthesis in Portulaca Grandiflora

RESUME Les bétalaïnes sont des pigments chromo-alcaloïdes violets et jaunes présents dans les plantes appartenant à l'ordre des Caryophyllales et dans les champignons des genres Amanita et Hygrocybe. Leur courte voie de biosynthèse est élucidée chimiquement depuis de nombreuses années, mais les enzymes impliquées dans cette biosynthèse chez les plantes ne sont toujours pas caractérisées. L'enzyme de la DOPA-dioxygénase d' Amanita muscaria a été identifiée (Girod et Zryd, 1991a), mais de nombreuses tentatives d'isolation d'un homologue chez les plantes ont échoué. Afin d'isoler les gènes spécifiques des bétalaïnes chez les plantes, nous avons construit des banques soustraites d'ADNc à partir d'ARN total de pétales immatures de Portulaca grandiflora (Pg) de génotypes jaunes et blancs, respectivement violets et blancs. Les clones couleur- spécifiques ont été détectés en premier par analyse Northem du RNA de pétales blancs et colorés. Les candidats positifs ont alors été soumis à une analyse de transcription au niveau des tiges colorées, vertes et des feuilles, afin d'établir leur expression spécifique. Deux ARNs messagers complets ont une expression corrélée avec l'accumulation des bétalaïnes dans les tissus. Le premier de ces clones, A.16, code pour une oxydase de l'acyl-Coenzyme A (ACX) putative, mais le domaine de liaison du FAD essentiel pour l'activité d'ACX est absent. Toutes nos tentatives pour démontrer sa fonction ont échoué. Le rôle de cette protéine dans la voie de synthèse des bétalaïnes reste inconnu. Le deuxième de ces clones spécifique aux bétalaïnes, L.6 (isolé par Zaiko, 2000), a été renommé DODA en raison de son homologie avec le domaine LigB (pfam02900) d'une 4,5-dioxygénase extradiol bactérienne. DODA a été identifié in silico comme une dioxygénase extradiol en raison de la conservation stricte, au niveau de sa séquence peptidique, des résidus catalytiques de LigB et de ceux liant le cofacteur fer. Une analyse de transfert Southem a montré que ce gène est unique dans Pg. L'expression transitoire de DODA par transformation biolistique dans des pétales blancs de Pg a produit des taches violettes ou jaunes dans des cellules transformées. Une analyse HPLC de ces taches a démontré leur identité avec les bétalaïnes présentes naturellement dans les pétales violets et jaunes de Pg, confirmant ainsi la complémentation par le gène Pg DODA de l'allèle récessif cc présent dans les pétales blancs de Pg. Des homologues de DODA (DOPA-dioxygénase) ont été identifiés dans de nombreuses espèces de plantes, y compris dans celles sans bétalaïne. L'alignement de ces homologues a permis l'identification d'un motif spécifique aux bétalaïnes à côté d'une histidine catalytique conservée. Ce motif [H-P-(S,A)-(N,D)-x-T-P] remplace le motif [H-N-L-R] conservé dans les plantes sans bétalaïne et le motif [H-N-L-x] présent dans tous les homologues bactériens et archaebactériens. Une modélisation tridimensionnelle préliminaire du site actif de Pg DODA et de son homologue dans la mousse Physcomitrella patens a montré l'importance de ce motif spécifique aux bétalaïnes pour l'accessibilité du substrat au site actif. L'analyse phylogénétique de DODA a confirmé l'évolution séparée de cette protéine chez les plantes à bétalaïnes par comparaison avec celle des plantes sans bétalaïne. Nous avons donc conclu que les bétalaïnes sont apparues par modification de l'affinité pour un substrat d'enzymes similaires à DODA, chez un ancêtre unique des Caryophyllales qui a perdu toute capacité de biosynthèse des anthocyanes. Finalement, Pg DODA n'a aucune similarité avec la protéine DODA d' Amanita muscaria, bien que celle-ci complémente aussi la pigmentation des pétales blancs de Pg. La biosynthèse des bétalaïnes est un exemple remarquable de convergence évolutive biochimique indépendante entre espèces de règnes différents. ABSTRACT Betalains are violet and yellow chromo-alkaloid pigments present in plants belonging to the order Caryophyllales and also in the fungal genera Amanita and Hygrocybe. Their short biosynthetic pathway is chemically well understood since many years, but enzymes involved in the plant pathway are still uncharacterized. The DOPA-dioxygenase from Amanita muscaria was identified (Girod and Zryd, 1991a), but numerous attempts to identify a plant homologue to the corresponding gene, failed. In order to isolate betalain-specific genes in plants, subtractive cDNA libraries were built with total RNA from white and yellow and respectively, violet immature petals from Portulaca grandiflora (Pg) genotypes. Colour-specific clones were first detected by Northern blot analysis using RNA from white and coloured petals. Positive candidates were submitted to further transcription analysis in coloured, green stems and leaves in order to assess their specific expression. Two full-length mRNAs showed a correlated expression with betalain accumulation in tissues. One of them, A.16, encodes a putative acyl-Coenzyme A oxidase (ACX), but missing the FAD binding domain essential for the ACX activity. Thus, all attempts to demonstrate its function failed. The role of this protein in the betalain biosynthesis pathway, if any, is still unknown. The second betalain-specific mRNA, L.6 (isolated by Zaiko, 2000) shows a homology with a LigB domain (pfam02900) from a bacterial extradiol 4,5-dioxygenase. It was then renamed DODA (DOPA-dioxygenase). DODA was identified in silico as a highly conserved extradiol dioxygenase due to the strict conservation of its peptidic sequence with LigB catalytic residues and iron-binding cofactor residues. Southern blot analysis showed that this gene is a single copy-gene in Pg. Transient expression of DODA protein through biolistic transformation of Pg white petals produced violet or yellow spots in individual cells. HPLC analysis of these spots showed an identity with betalain pigments present naturally in yellow and violet Pg petals, thus confirming the complementation of the recessive cc allele present in Pg white petals by Pg DODA gene. DODA homologues were identified in numerous plant species including those without betalain. Alignment of these homologues allowed the identification of a betalain-specific pattern beside a highly conserved catalytic histidine. This [H-P-(S,A)-(N,D)-x-T-P] pattern replaces a [H-N-L-R] pattern strictly conserved in non-betalain plants and a [H-N-L-x] pattern present in all bacterial and archaebacterial homologues. Preliminary three-dimensional modeling of the active site of Pg DODA and its Physcomitrella patens moss homologue revealed the importance of this betalain-specific pattern for the substrate accessibility to the DODA active site. DODA phylogenetic analysis confirmed the separate evolution of this protein in betalain-producing plants. We conclude that betalain pigments appeared in a unique ancestor of the Caryophyllales order in which anthocyanin biosynthetic pathway was impaired, by a modification of enzymes of the DODA family for substrate affinity. The Pg DODA protein has no sequence similarity with Amanita muscaria DODA, despite the fact that they both complement Pg white petals for their pigmentation. Betalain biosynthesis is an interesting example of independent biochemical evolutionary convergence between species from different kingdoms.

Geology, correlations, and geodynamic evolution of the Biga Peninsula (NW Turkey)

L?objectif de ce travail de recherche était de décrypter l?évolution géodynamique de la Péninsule de Biga (Turquie du N-O), à travers l?analyse de deux régions géologiques peu connues, le mélange de Çetmi et la zone d?Ezine (i.e. le Groupe d?Ezine et l?ophiolite de Denizgören). Une étude complète et détaillée de terrain (cartographie et échantillonnage) ainsi qu?une approche multidisciplinaire (sédimentologie de faciès, pétrographie sédimentaire et magmatique, micropaléontologie, datations absolues, géochimie sur roche totale, cristallinité de l?illite) ont permis d?obtenir de nouveaux éléments d?information sur la région considérée. ? Le mélange de Çetmi, de type mélange d?accrétion, affleure au nord et au sud de la Péninsule de Biga ; les principaux résultats de son étude peuvent se résumer comme suit: - Son aspect structural actuel (nature des contacts, organisation tectonique) est principalement dû au régime extensif Tertiaire présent dans la région. - Il est constitué de blocs de différentes natures : rares calcaires Scythien-Ladinien dans le faciès Han Bulog, blocs hectométriques de calcaires d?âge Norien-Rhaetien de rampe carbonatée, nombreux blocs décamétriques de radiolarites rouges d?âge Bajocien- Aptien, blocs/écailles de roches magmatiques de type spilites (basaltes à andésite), ayant des signatures géochimiques d?arcs ou intra-plaques. - La matrice du mélange est constituée d?une association greywacke-argilites dont l?âge Albien inférieur à moyen a été déterminé par palynologie. - L?activité du mélange s?est terminée avant le Cénomanien (discordance Cénomanienne au sommet du mélange, pas de bloc plus jeune que la matrice). - Du point de vue de ses corrélations latérales, le mélange de Çetmi partage plus de traits communs avec les mélanges se trouvant dans les nappes allochtones du Rhodope (nord de la Grèce et sud-ouest de la Bulgarie) qu?avec ceux de la suture Izmir-Ankara (Turquie); il apparaît finalement que sa mise en place s?est faite dans une logique balkanique (chevauchements vers le nord d?âge anté-Cénomanien). ? Le Groupe d?Ezine et l?ophiolite sus-jacente de Denizgören affleurent dans la partie ouest de la Péninsule de Biga. Le Groupe d?Ezine est une épaisse séquence sédimentaire continue (3000 m), subdivisée en trois formations, caractérisée chacune par un type de sédimentation spécifique, relatif à un environnement de dépôt particulier. De par ses caractéristiques (grande épaisseur, variations latérales de faciès et d?épaisseur dans les formations, érosion de matériel provenant de l?amont du bassin), le groupe d?Ezine est interprétée comme un dépôt syn-rift d?âge Permien moyen-Trias inférieur. Il pourrait représenter une partie de la future marge passive sud Rhodopienne à la suite de l?ouverture de l?océan Maliac/Méliata. L?ophiolite de Denizgören sus-jacente repose sur le Groupe d?Ezine par l?intermédiaire d?une semelle métamorphique à gradient inverse, du faciès amphibolite à schiste vert. L?âge du faciès amphibolite suggère une initiation de l?obduction au Barrémien (125 Ma, âge Ar/Ar); cet âge est unique dans le domaine égéen, mais il peut là aussi être relié à une logique balkanique, sur la base de comparaison avec le domaine Rhodopien. ? Toutes les unités précédentes (mélange de Çetmi, Groupe d?Ezine et ophiolite de Denizgören) ont passivement subi trois phases extensives pendant le Tertiaire. Dans la région d?Ezine et du mélange nord, les micaschistes HP sous-jacents ont été exhumés avant l?Eocène moyen. Dans le cas du mélange sud, cette exhumation Eocene est en partie enregistrée dans les mylonites séparant le mélange du dôme métamorphique sous-jacent du Kazda?. Le mélange sud est dans tous les cas fortement érodé à la suite de la double surrection du dôme du Kazda?, près de la lim ite Oligocène/Miocene et pendant le Plio- Quaternaire. Dans le premier cas, ce soulèvement est caractérisé par le développement d?une faille de détachement à faible pendage, qui contrôle à la fois l?exhumation du massif, et la formation d?un bassin sédimentaire syntectonique, de type bassin supradétachement; quant à la phase extensive la plus récente, elle est contrôlée par le jeu de failles normales à forts pendages qui remanient l?ensemble des structures héritées, et dictent la géomorphologie actuelle de la région. ? Il est possible de proposer un scénario pour l?évolution géodynamique de la Péninsule de Biga, basé sur l?ensemble des résultats précédents et sur les données de la géologie régionale ; ses points principaux sont: - La Péninsule de Biga fait partie de la marge Rhodopienne. - Le Groupe d?Ezine est un témoin de la marge passive nord Maliac/Méliata. - L?ophiolite de Denizgören et le mélange de Çetmi ont été mis en place tous deux vers le nord sur la marge précédente, respectivement au Barrémien et à l?Albien terminal- Cénomanien inférieur. - Une forte composante décrochante durant l?emplacement est suggérée par la préservation de fragments de la marge passive et l?absence de métamorphisme dans la plaque inférieure. - Tous les évènements précédents ont été largement affectés par le régime d?extension Tertiaire.<br/><br/>The purpose of this study is to unravel the geodynamic evolution of the Biga Peninsula (NW Turkey) through the detailed study of two poorly known areas, the Çetmi mélange and the Ezine zone (i.e. the Ezine Group and the Denizgören ophiolite). The methodology was based on a detailed field work and a multidisciplinary approach. ? The accretion-related Çetmi mélange is mainly cropping out north and south of the Biga Peninsula; the main results of its study can be summarized as follows: -Its present-day structural aspect (type of contacts, tectonic organisation) is largely inherited from the Tertiary extensional regime in the region. -It is made of blocks of various natures: Han Bulog limestones with a Scythian to Ladinian age, common carbonate ramp Norian-Rhaetian limestones (biggest blocks of the mélange), red radolarite with a Bajocian to Aptian age; the most common lithology of the mélange is made by block/slices of spilitic magmatic rocks (basalt to andesite); they have volcanic arc or within plate basalt geochemical signatures. -The matrix of the mélange is made of a greywacke-shale association of Early-Middle Albian age. - The mélange stopped its activity before the Cenomanian (no younger blocks than the matrix, and Cenomanian unconformity). - If compared to the regional geology, the Çetmi mélange shares some characteristics with the Izmir-Ankara mélanges (less), and with the mélanges from allochthonous nappes found in eastern Rhodope (more); it appears finally that its emplacement is related to a Balkanic logic (ante-Cenomanian northward thrusting). ? The Ezine Group and the overlying Denizgören ophiolite are cropping out in the western part of the Biga Peninsula. The Ezine Group is a thick sedimentary sequence interpreted as a syn-rift deposit of Middle Permian-Early Triassic age. It represents a part of the south Rhodopian passive margin, following the opening of the Maliac/Meliata oceanic domain. The Denizgören ophiolite has been emplaced northward on the Ezine Group in the Barremian (125 Ma, age of the amphibolitic sole); this age is unique in the Aegean domain, but here again, it may be related to a Balkan logic. ? All the previous units (Çetmi mélange, Ezine Group and Denizgören ophiolite) have passively suffered two extensional regimes during the Tertiary. In the Ezine and northern Çetmi mélange area, the underlying HP Çamlýca micaschists were exhumed before the Middle Eocene. As for the southern mélange, it was strongly eroded following the Late Oligocene to Quaternary uplift of the underlying Kazda? Massif. This uplift was characterized by the development of a low-angle detachment fault controlling a part of the exhumation, as well as the development of a supra-detachment basin. ? Based on the previous results, and on the data from the regional geology, one can propose a scenario for the geodynamic evolution of the Biga Peninsula. Its key points are:- The Biga Peninsula is belonging to the Rhodope margin. - The Ezine Group is a remnant of the northern Maliac/Meliata passive margin. - Both the Denizgören ophiolite and the Çetmi mélange have been emplaced northward on the previous margin, respectively in the Barremian and in the Late Albian-Early Cenomanian times. - The preservation of the remnants of the Rhodope margin, as well as the absence of metamorphism in the lower plate suggest a strong strike-slip component during the emplacements. - All the previous events are (at least) partly obliterated by the Tertiary extensional regime.<br/><br/>Le géologue est comme un «historien» de la Terre, qui porte un intérêt particulier à l?étude du passé de notre planète; ce dernier, très ancien, se mesure en dizaines ou centaines de millions d?années (Ma). Or le visage de la terre a constamment évolué au cours des ces millions d?années écoulés, car les plaques (continentales et océaniques) qui composent son enveloppe superficielle ne restent pas immobiles, mais se déplacent continuellement à sa surface, à une vitesse de l?ordre du cm/an (théorie de la tectonique des plaques); c?est ainsi, par exemple, que des océans naissent, grandissent, puis finissent par se refermer. On appelle sutures océaniques, les zones, aujourd?hui sur la terre ferme, où l?on retrouve les restes d?océans disparus. Ces sutures sont caractérisées par deux associations distinctes de roches, que l?on appelle les mélanges et les ophiolites; ces mélanges et ophiolites sont donc les témoins de l?activité passée d?un océan aujourd?hui refermé. L?équipe de recherche dans laquelle ce travail à été réalisé s?intéresse à un vaste domaine océanique fossile: l?océan Néotéthys. Cet océan, de plusieurs milliers de kilomètres de large, séparait alors l?Europe et l?Asie au nord, de l?Afrique, l?Inde et l?Australie au sud. De cet océan, il n?en subsiste aujourd?hui qu?une infime partie, qui se confond avec notre mer Méditerranée actuelle. Or, tout comme l?océan Pacifique est bordé de mers plus étroites (Mer de Chine, du Japon, etc?), l?océan Néotéthys était bordé au nord de mers marginales. C?est dans ce cadre que s?est inscrit mon travail de thèse, puisqu?il a consisté en l?étude d?une suture océanique (mélange plus ophiolite), témoin d?une des mers qui bordait l?océan Néotéthys sur sa marge nord. L?objectif était de préciser de quelle suture il s?agissait, puis de déterminer quand et comment elle avait fonctionné (i.e son évolution géologique). Les roches qui composent cette suture affleurent aujourd?hui en Turquie nord occidentale dans la Péninsule de Biga. Au nord et au sud de la péninsule se trouvent les zones géologique du mélange de Çetmi, et à l?ouest, le Groupe d?Ezine et l?ophiolite susjacente, dite ophiolite de Denizgören. Une étude complète et détaillée de terrain (cartographie, échantillonnage), suivie de diverses analyses en laboratoire (détermination de leur âge, de leur condition de formation, etc?), ont permis d?aboutir aux principaux résultats suivants : - Mise en évidence dans le mélange de Çetmi des témoins (1) de l?océan Lycien disparu (ancienne mer marginale de la Néotéthys), et (2) de la marge continentale qui le bordait au nord. - Fin de l?activité du mélange de Çetmi il y a environ 105 Ma (Albien). - Le mélange de Çetmi est difficilement corrélable dans le temps avec les unités semblables affleurant dans la région d?étude (unicité du mélange), ce qui implique des conditions particulière de formation. - L?ophiolite de Denizgören est un morceau d?océan Lycien posé sur un reste préservé de sa marge continentale nord. - Cette dernière est représentée sur le terrain par une succession de roches caractéristiques, le Groupe d?Ezine. Celui-ci est lui-même un témoin de l?ouverture d?un océan marginal de la Néotethys antérieur au Lycien, l?océan Maliac, qui s?est ouvert il y a 245 Ma (Permien-Trias). - La mise en place de l?ophiolite de Denizgören sur le Groupe d?Ezine (125 Ma, Barrémien) est antérieure à la mise en place du mélange de Çetmi. - Il apparaît que ces deux mises en place sont contemporaines de la formation de la chaîne des Balkans, terminée avant le Cénomanien (100 Ma). - L?évolution dans le temps des objets précédents (océans, marges continentales) montre de grands mouvements latéraux est-ouest entre ces objets (translation). Ce qui implique que les roches que l?on retrouve aujourd?hui sur un transect nord-sud ne l?étaient pas nécessairement auparavant. - Enfin, il s?avère que le mélange de Çetmi, l?ophiolite de Denizgören, et le Groupe d?Ezine ont subi par la suite des déformations extensives importantes qui ont considérablement perturbé le schéma post-mise en place.

Idiosyncratic evolution of maternal effects in response to juvenile malnutrition in Drosophila.

Maternal effects often affect fitness traits, but there is little experimental evidence pertaining to their contribution to response to selection imposed by novel environments. We studied the evolution of maternal effects in Drosophila populations selected for tolerance to chronic larval malnutrition. To this end, we performed pairwise reciprocal F1 crosses between six selected (malnutrition tolerant) populations and six unselected control populations and assessed the effect of cross direction on larval growth and developmental rate, adult weight and egg-to-adult viability expressed under the malnutrition regime. Each pair of reciprocal crosses revealed large maternal effects (possibly including cytoplasmic genetic effects) on at least one trait, but the magnitude, sign and which traits were affected varied among populations. Thus, maternal effects contributed significantly to the response to selection imposed by the malnutrition regime, but these changes were idiosyncratic, suggesting a rugged adaptive landscape. Furthermore, although the selected populations evolved both faster growth and higher viability, the maternal effects on growth rate and viability were negatively correlated across populations. Thus, genes mediating maternal effects can evolve to partially counteract the response to selection mediated by the effects of alleles on their own carriers' phenotype, and maternal effects may contribute to evolutionary trade-offs between components of offspring fitness.

Evolution of the mating system in colonizing plants.

Colonization is likely to be more successful for species with an ability to self-fertilize and thus to establish new populations as single individuals. As a result, self-compatibility should be common among colonizing species. This idea, labelled 'Baker's law', has been influential in discussions of sexual-system and mating-system evolution. However, its generality has been questioned, because models of the evolution of dispersal and the mating system predict an association between high dispersal rates and outcrossing rather than selfing, and because of many apparent counter examples to the law. The contrasting predictions made by models invoking Baker's law versus those for the evolution of the mating system and dispersal urges a reassessment of how we should view both these traits. Here, I review the literature on the evolution of mating and dispersal in colonizing species, with a focus on conceptual issues. I argue for the importance of distinguishing between the selfing or outcrossing rate and a simple ability to self-fertilize, as well as for the need for a more nuanced consideration of dispersal. Colonizing species will be characterized by different phases in their life pattern: dispersal to new habitat, implying an ecological sieve on dispersal traits; establishment and a phase of growth following colonization, implying a sieve on reproductive traits; and a phase of demographic stasis at high density, during which new trait associations can evolve through local adaptation. This dynamic means that the sorting of mating-system and dispersal traits should change over time, making simple predictions difficult.

Evolutionary patchwork of an insecticidal toxin shared between plant-associated pseudomonads and the insect pathogens Photorhabdus and Xenorhabdus.

BACKGROUND: Root-colonizing fluorescent pseudomonads are known for their excellent abilities to protect plants against soil-borne fungal pathogens. Some of these bacteria produce an insecticidal toxin (Fit) suggesting that they may exploit insect hosts as a secondary niche. However, the ecological relevance of insect toxicity and the mechanisms driving the evolution of toxin production remain puzzling. RESULTS: Screening a large collection of plant-associated pseudomonads for insecticidal activity and presence of the Fit toxin revealed that Fit is highly indicative of insecticidal activity and predicts that Pseudomonas protegens and P. chlororaphis are exclusive Fit producers. A comparative evolutionary analysis of Fit toxin-producing Pseudomonas including the insect-pathogenic bacteria Photorhabdus and Xenorhadus, which produce the Fit related Mcf toxin, showed that fit genes are part of a dynamic genomic region with substantial presence/absence polymorphism and local variation in GC base composition. The patchy distribution and phylogenetic incongruence of fit genes indicate that the Fit cluster evolved via horizontal transfer, followed by functional integration of vertically transmitted genes, generating a unique Pseudomonas-specific insect toxin cluster. CONCLUSIONS: Our findings suggest that multiple independent evolutionary events led to formation of at least three versions of the Mcf/Fit toxin highlighting the dynamic nature of insect toxin evolution.

Multigene Family Evolution: Perspectives from Insect Chemoreceptors.

Understanding the birth and diversification of multigene families is a fundamental evolutionary problem. I argue for the insect chemoreceptor superfamily as an outstanding model. Although these receptors are currently the preserve of neuroscientists, putative homologous genes exist in diverse animal and plant genomes, implying an ancient origin. Moreover, functional studies suggest that they act as ligand-gated ion channels in both chemosensory and non-chemosensory processes. This family permits synergism of investigations into its structural and regulatory evolution with ecological studies of the selective pressures driving these changes. In addition, sequence divergence in these receptors can be exploited through co-evolutionary and comparative genomics analyses to help to elucidate their 3D structure and signaling mechanisms, and to reveal experimentally-accessible candidate loci to explore the genetic basis of adaptation.

Fifty years after Ehrlich and Raven, is there support for plant-insect coevolution as a major driver of species diversification?

Since Ehrlich & Raven's seminal paper 50 years ago, coevolution has been seen as a major driver of species diversification. Here, we review classical and more recent case studies on the coevolution of plants and associated insects, to examine whether the coevolutionary component holds as an explanation of their current diversity. We discuss the main dogmas in coevolution and argue that coevolutionary processes should not be considered as major drivers of diversification in plants and insects. Instead, we suggest that coevolution essentially occurs through relatively short 'interludes', making the pattern difficult to detect. We also criticize the use of comparative phylogenetics to investigate coevolutionary processes, as coevolution may not necessarily produce congruent phylogenies among interacting lineages and, in turn, other processes may produce patterns of codivergence. Finally, we propose new lines of investigation for future research.

Validation of and comparison between a semidistributed rainfall-runoff hydrological model (PREVAH) and a spatially distributed snow-evolution model (SnowModel) for snow cover prediction in mountain ecosystems

Snow cover is an important control in mountain environments and a shift of the snow-free period triggered by climate warming can strongly impact ecosystem dynamics. Changing snow patterns can have severe effects on alpine plant distribution and diversity. It thus becomes urgent to provide spatially explicit assessments of snow cover changes that can be incorporated into correlative or empirical species distribution models (SDMs). Here, we provide for the first time a with a lower overestimation comparison of two physically based snow distribution models (PREVAH and SnowModel) to produce snow cover maps (SCMs) at a fine spatial resolution in a mountain landscape in Austria. SCMs have been evaluated with SPOT-HRVIR images and predictions of snow water equivalent from the two models with ground measurements. Finally, SCMs of the two models have been compared under a climate warming scenario for the end of the century. The predictive performances of PREVAH and SnowModel were similar when validated with the SPOT images. However, the tendency to overestimate snow cover was slightly lower with SnowModel during the accumulation period, whereas it was lower with PREVAH during the melting period. The rate of true positives during the melting period was two times higher on average with SnowModel with a lower overestimation of snow water equivalent. Our results allow for recommending the use of SnowModel in SDMs because it better captures persisting snow patches at the end of the snow season, which is important when modelling the response of species to long-lasting snow cover and evaluating whether they might survive under climate change.

Molecular basis and regulation of insect pathogenicity in plant-beneficial pseudomonads

Les bactéries du genre Pseudomonas ont la capacité étonnante de s'adapter à différents habitats et d'y survivre, ce qui leur a permis de conquérir un large éventail de niches écologiques et d'interagir avec différents organismes hôte. Les espèces du groupe Pseudomonas fluorescens peuvent être facilement isolées de la rhizosphère et sont communément connues comme des Pseudomonas bénéfiques pour les plantes. Elles sont capables d'induire la résistance systémique des plantes, d'induire leur croissance et de contrer des phytopathogènes du sol. Un sous-groupe de ces Pseudomonas a de plus développé la capacité d'infecter et de tuer certaines espèces d'insectes. Approfondir les connaissances sur l'interaction de ces bactéries avec les insectes pourraient conduire au développement de nouveaux biopesticides pour la protection des cultures. Le but de cette thèse est donc de mieux comprendre la base moléculaire, l'évolution et la régulation de la pathogénicité des Pseudomonas plante-bénéfiques envers les insectes. Plus spécifiquement, ce travail a été orienté sur l'étude de la production de la toxine insecticide appelée Fit et sur l'indentification d'autres facteurs de virulence participant à la toxicité de la bactérie envers les insectes. Dans la première partie de ce travail, la régulation de la production de la toxine Fit a été évaluée par microscopie à épifluorescence en utilisant des souches rapportrices de Pseudomonas protegens CHA0 qui expriment la toxine insecticide fusionnée à une protéine fluorescente rouge, au site natif du gène de la toxine. Celle-ci a été détectée uniquement dans l'hémolymphe des insectes et pas sur les racines des plantes, ni dans les milieux de laboratoire standards, indiquant une production dépendante de l'hôte. L'activation de la production de la toxine est contrôlée par trois protéines régulatrices dont l'histidine kinase FitF, essentielle pour un contrôle précis de l'expression et possédant un domaine "senseur" similaire à celui de la kinase DctB qui régule l'absorption de carbone chez les Protéobactéries. Il est donc probable que, durant l'évolution de FitF, un réarrangement de ce domaine "senseur" largement répandu ait contribué à une production hôte-spécifique de la toxine. Les résultats de cette étude suggèrent aussi que l'expression de la toxine Fit est plutôt réprimée en présence de composés dérivés des plantes qu'induite par la perception d'un signal d'insecte spécifique. Dans la deuxième partie de ce travail, des souches mutantes ciblant des facteurs de virulence importants identifiés dans des pathogènes connus ont été générées, dans le but d'identifier ceux avec une virulence envers les insectes atténuée. Les résultats ont suggéré que l'antigène O du lipopolysaccharide (LPS) et le système régulateur à deux composantes PhoP/PhoQ contribuent significativement à la virulence de P. protegens CHA0. La base génétique de la biosynthèse de l'antigène O dans les Pseudomonas plante-bénéfiques et avec une activité insecticide a été élucidée et a révélé des différences considérables entre les lignées suite à des pertes de gènes ou des acquisitions de gènes par transfert horizontal durant l'évolution de certaines souches. Les chaînes latérales du LPS ont été montrées comme vitales pour une infection des insectes réussie par la souche CHA0, après ingestion ou injection. Les Pseudomonas plante-bénéfiques, avec une activité insecticide sont naturellement résistants à la polymyxine B, un peptide antimicrobien modèle. La protection contre ce composé antimicrobien particulier dépend de la présence de l'antigène O et de la modification du lipide A, une partie du LPS, avec du 4-aminoarabinose. Comme les peptides antimicrobiens cationiques jouent un rôle important dans le système immunitaire des insectes, l'antigène O pourrait être important chez les Pseudomonas insecticides pour surmonter les mécanismes de défense de l'hôte. Le système PhoP/PhoQ, connu pour contrôler les modifications du lipide A chez plusieurs bactéries pathogènes, a été identifié chez Pseudomonas chlororaphis PCL1391 et P. protegens CHA0. Pour l'instant, il n'y a pas d'évidence que des modifications du lipide A contribuent à la pathogénicité de cette bactérie envers les insectes. Cependant, le senseur-kinase PhoQ est requis pour une virulence optimale de la souche CHA0, ce qui suggère qu'il régule aussi l'expression des facteurs de virulence de cette bactérie. Les découvertes de cette thèse démontrent que certains Pseudomonas associés aux plantes sont de véritables pathogènes d'insectes et donnent quelques indices sur l'évolution de ces microbes pour survivre dans l'insecte-hôte et éventuellement le tuer. Les résultats suggèrent également qu'une recherche plus approfondie est nécessaire pour comprendre comment ces bactéries sont capables de contourner ou surmonter la réponse immunitaire de l'hôte et de briser les barrières physiques pour envahir l'insecte lors d'une infection orale. Pour cela, les futures études ne devraient pas uniquement se concentrer sur le côté bactérien de l'interaction hôte-microbe, mais aussi étudier l'infection du point de vue de l'hôte. Les connaissances gagnées sur la pathogénicité envers les insectes des Pseudomonas plante-bénéfiques donnent un espoir pour une future application en agriculture, pour protéger les plantes, non seulement contre les maladies, mais aussi contre les insectes ravageurs. -- Pseudomonas bacteria have the astonishing ability to survive within and adapt to different habitats, which has allowed them to conquer a wide range of ecological niches and to interact with different host organisms. Species of the Pseudomonas fluorescens group can readily be isolated from plant roots and are commonly known as plant-beneficial pseudomonads. They are capable of promoting plant growth, inducing systemic resistance in the plant host and antagonizing soil-borne phytopathogens. A defined subgroup of these pseudomonads evolved in addition the ability to infect and kill certain insect species. Profound knowledge about the interaction of these particular bacteria with insects could lead to the development of novel biopesticides for crop protection. This thesis thus aimed at a better understanding of the molecular basis, evolution and regulation of insect pathogenicity in plant-beneficial pseudomonads. More specifically, it was outlined to investigate the production of an insecticidal toxin termed Fit and to identify additional factors contributing to the entomopathogenicity of the bacteria. In the first part of this work, the regulation of Fit toxin production was probed by epifluorescence microscopy using reporter strains of Pseudomonas protegens CHAO that express a fusion between the insecticidal toxin and a red fluorescent protein in place of the native toxin gene. The bacterium was found to express its insecticidal toxin only in insect hemolymph but not on plant roots or in common laboratory media. The host-dependent activation of Fit toxin production is controlled by three local regulatory proteins. The histidine kinase of this regulatory system, FitF, is essential for the tight control of toxin expression and shares a sensing domain with DctB, a sensor kinase regulating carbon uptake in Proteobacteria. It is therefore likely that shuffling of a ubiquitous sensor domain during the evolution of FitF contributed to host- specific production of the Fit toxin. Findings of this study additionally suggest that host-specific expression of the Fit toxin is mainly achieved by repression in the presence of plant-derived compounds rather than by induction upon perceiving an insect-specific signal molecule. In the second part of this thesis, mutant strains were generated that lack factors previously shown to be important for virulence in prominent pathogens. A screening for attenuation in insect virulence suggested that lipopolysaccharide (LPS) O-antigen and the PhoP-PhoQ two-component regulatory system significantly contribute to virulence of P. protegens CHAO. The genetic basis of O-antigen biosynthesis in plant-beneficial pseudomonads displaying insect pathogenicity was elucidated and revealed extensive differences between lineages due to reduction and horizontal acquisition of gene clusters during the evolution of several strains. Specific 0 side chains of LPS were found to be vital for strain CHAO to successfully infect insects by ingestion or upon injection. Insecticidal pseudomonads with plant-beneficial properties were observed to be naturally resistant to polymyxin B, a model antimicrobial peptide. Protection against this particular antimicrobial compound was dependent on the presence of O-antigen and modification of the lipid A portion of LPS with 4-aminoarabinose. Since cationic antimicrobial peptides play a major role in the immune system of insects, O-antigenic polysaccharides could be important for insecticidal pseudomonads to overcome host defense mechanisms. The PhoP-PhoQ system, which is well-known to control lipid A modifications in several pathogenic bacteria, was identified in Pseudomonas chlororaphis PCL1391 and P. protegens CHAO. No evidence was found so far that lipid A modifications contribute to insect pathogenicity in this bacterium. However, the sensor kinase PhoQ was required for full virulence of strain CHAO suggesting that it additionally regulates the expression of virulence factors in this bacterium. The findings of this thesis demonstrate that certain plant-associated pseudomonads are true insect pathogens and give some insights into how these microbes evolved to survive within and eventually kill the insect host. Results however also point out that more in-depth research is needed to know how exactly these fascinating bacteria manage to bypass or overcome host immune responses and to breach physical barriers to invade insects upon oral infection. To achieve this, future studies should not only focus on the bacterial side of the microbe-host interactions but also investigate the infection from a host-oriented view. The knowledge gained about the entomopathogenicity of plant-beneficial pseudomonads gives hope for their future application in agriculture to protect plants not only against plant diseases but also against insect pests.

A macro-ecological perspective on crassulacean acid metabolism (CAM) photosynthesis evolution in Afro-Madagascan drylands: Eulophiinae orchids as a case study.

Crassulacean acid metabolism (CAM) photosynthesis is an adaptation to water and atmospheric CO2 deficits that has been linked to diversification in dry-adapted plants. We investigated whether CAM evolution can be associated with the availability of new or alternative niches, using Eulophiinae orchids as a case study. Carbon isotope ratios, geographical and climate data, fossil records and DNA sequences were used to: assess the prevalence of CAM in Eulophiinae orchids; characterize the ecological niche of extant taxa; infer divergence times; and estimate whether CAM is associated with niche shifts. CAM evolved in four terrestrial lineages during the late Miocene/Pliocene, which have uneven diversification patterns. These lineages originated in humid habitats and colonized dry/seasonally dry environments in Africa and Madagascar. Additional key features (variegation, heterophylly) evolved in the most species-rich CAM lineages. Dry habitats were also colonized by a lineage that includes putative mycoheterotrophic taxa. These findings indicate that the switch to CAM is associated with environmental change. With its suite of adaptive traits, this group of orchids represents a unique opportunity to study the adaptations to dry environments, especially in the face of projected global aridification.

Pleiotropy and the low cost of individual traits promote cooperation.

The evolution of cooperation is thought to be promoted by pleiotropy, whereby cooperative traits are coregulated with traits that are important for personal fitness. However, this hypothesis faces a key challenge: what happens if mutation targets a cooperative trait specifically rather than the pleiotropic regulator? Here, we explore this question with the bacterium Pseudomonas aeruginosa, which cooperatively digests complex proteins using elastase. We empirically measure and theoretically model the fate of two mutants-one missing the whole regulatory circuit behind elastase production and the other with only the elastase gene mutated-relative to the wild-type (WT). We first show that, when elastase is needed, neither of the mutants can grow if the WT is absent. And, consistent with previous findings, we show that regulatory gene mutants can grow faster than the WT when there are no pleiotropic costs. However, we find that mutants only lacking elastase production do not outcompete the WT, because the individual cooperative trait has a low cost. We argue that the intrinsic architecture of molecular networks makes pleiotropy an effective way to stabilize cooperative evolution. Although individual cooperative traits experience loss-of-function mutations, these mutations may result in weak benefits, and need not undermine the protection from pleiotropy.

Importance of amoebae as a tool to isolate amoeba-resisting microorganisms and for their ecology and evolution: the Chlamydia paradigm.

Free-living amoebae are distributed worldwide and are frequently in contact with humans and animals. As cysts, they can survive in very harsh conditions and resist biocides and most disinfection procedures. Several microorganisms, called amoeba-resisting microorganisms (ARMs), have evolved to survive and multiply within these protozoa. Among them are many important pathogens, such as Legionella and Mycobacteria, and also several newly discovered Chlamydia-related bacteria, such as Parachlamydia acanthamoebae, Estrella lausannensis, Simkania negevensis or Waddlia chondrophila whose pathogenic role towards human or animal is strongly suspected. Amoebae represent an evolutionary crib for their resistant microorganisms since they can exchange genetic material with other ARMs and develop virulence traits that will be further used to infect other professional phagocytes. Moreover, amoebae constitute an ideal tool to isolate strict intracellular microorganisms from complex microbiota, since they will feed on other fast-growing bacteria, such as coliforms potentially present in the investigated samples. The paradigm that ARMs are likely resistant to macrophages, another phagocytic cell, and that they are likely virulent towards humans and animals is only partially true. Indeed, we provide examples of the Chlamydiales order that challenge this assumption and suggest that the ability to multiply in protozoa does not strictly correlate with pathogenicity and that we should rather use the ability to replicate in multiple and diverse eukaryotic cells as an indirect marker of virulence towards mammals. Thus, cell-culture-based microbial culturomics should be used in the future to try to discover new pathogenic bacterial species.