The non-LTR retrotransposons in Ciona intestinalis: new insights into the evolution of chordate genomes

Background: Non-long terminal repeat (non-LTR) retrotransposons have contributed to shaping the structure and function of genomes. In silico and experimental approaches have been used to identify the non-LTR elements of the urochordate Ciona intestinalis. Knowledge of the types and abundance of non-LTR elements in urochordates is a key step in understanding their contribution to the structure and function of vertebrate genomes. Results: Consensus elements phylogenetically related to the I, LINE1, LINE2, LOA and R2 elements of the 14 eukaryotic non-LTR clades are described from C. intestinalis. The ascidian elements showed conservation of both the reverse transcriptase coding sequence and the overall structural organization seen in each clade. The apurinic/apyrimidinic endonuclease and nucleic-acid-binding domains encoded upstream of the reverse transcriptase, and the RNase H and the restriction enzyme-like endonuclease motifs encoded downstream of the reverse transcriptase were identified in the corresponding Ciona families. Conclusions: The genome of C. intestinalis harbors representatives of at least five clades of non-LTR retrotransposons. The copy number per haploid genome of each element is low, less than 100, far below the values reported for vertebrate counterparts but within the range for protostomes. Genomic and sequence analysis shows that the ascidian non-LTR elements are unmethylated and flanked by genomic segments with a gene density lower than average for the genome. The analysis provides valuable data for understanding the evolution of early chordate genomes and enlarges the view on the distribution of the non-LTR retrotransposons in eukaryotes.

Comparative genomic analysis of the odorant-binding protein family in 12 Drosophila genomes: purifying selection and birth-and-death evolution

Background: Chemoreception is a widespread mechanism that is involved in critical biologic processes, including individual and social behavior. The insect peripheral olfactory system comprises three major multigene families: the olfactory receptor (Or), the gustatory receptor (Gr), and the odorant-binding protein (OBP) families. Members of the latter family establish the first contact with the odorants, and thus constitute the first step in the chemosensory transduction pathway.Results: Comparative analysis of the OBP family in 12 Drosophila genomes allowed the identification of 595 genes that encode putative functional and nonfunctional members in extant species, with 43 gene gains and 28 gene losses (15 deletions and 13 pseudogenization events). The evolution of this family shows tandem gene duplication events, progressive divergence in DNA and amino acid sequence, and prevalence of pseudogenization events in external branches of the phylogenetic tree. We observed that the OBP arrangement in clusters is maintained across the Drosophila species and that purifying selection governs the evolution of the family; nevertheless, OBP genes differ in their functional constraints levels. Finally, we detect that the OBP repertoire evolves more rapidly in the specialist lineages of the Drosophila melanogaster group (D. sechellia and D. erecta) than in their closest generalists.Conclusion: Overall, the evolution of the OBP multigene family is consistent with the birth-and-death model. We also found that members of this family exhibit different functional constraints, which is indicative of some functional divergence, and that they might be involved in some of the specialization processes that occurred through the diversification of the Drosophila genus.

Ecological-economic optimization of biodiversity conservation under climate change

Substantial investment in climate change research has led to dire predictions of the impacts and risks to biodiversity. The Intergovernmental Panel on Climate Change fourth assessment report(1) cites 28,586 studies demonstrating significant biological changes in terrestrial systems(2). Already high extinction rates, driven primarily by habitat loss, are predicted to increase under climate change(3-6). Yet there is little specific advice or precedent in the literature to guide climate adaptation investment for conserving biodiversity within realistic economic constraints(7). Here we present a systematic ecological and economic analysis of a climate adaptation problem in one of the world's most species-rich and threatened ecosystems: the South African fynbos. We discover a counterintuitive optimal investment strategy that switches twice between options as the available adaptation budget increases. We demonstrate that optimal investment is nonlinearly dependent on available resources, making the choice of how much to invest as important as determining where to invest and what actions to take. Our study emphasizes the importance of a sound analytical framework for prioritizing adaptation investments(4). Integrating ecological predictions in an economic decision framework will help support complex choices between adaptation options under severe uncertainty. Our prioritization method can be applied at any scale to minimize species loss and to evaluate the robustness of decisions to uncertainty about key assumptions.

Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution.

Arising from either retrotransposition or genomic duplication of functional genes, pseudogenes are "genomic fossils" valuable for exploring the dynamics and evolution of genes and genomes. Pseudogene identification is an important problem in computational genomics, and is also critical for obtaining an accurate picture of a genome's structure and function. However, no consensus computational scheme for defining and detecting pseudogenes has been developed thus far. As part of the ENCyclopedia Of DNA Elements (ENCODE) project, we have compared several distinct pseudogene annotation strategies and found that different approaches and parameters often resulted in rather distinct sets of pseudogenes. We subsequently developed a consensus approach for annotating pseudogenes (derived from protein coding genes) in the ENCODE regions, resulting in 201 pseudogenes, two-thirds of which originated from retrotransposition. A survey of orthologs for these pseudogenes in 28 vertebrate genomes showed that a significant fraction ( approximately 80%) of the processed pseudogenes are primate-specific sequences, highlighting the increasing retrotransposition activity in primates. Analysis of sequence conservation and variation also demonstrated that most pseudogenes evolve neutrally, and processed pseudogenes appear to have lost their coding potential immediately or soon after their emergence. In order to explore the functional implication of pseudogene prevalence, we have extensively examined the transcriptional activity of the ENCODE pseudogenes. We performed systematic series of pseudogene-specific RACE analyses. These, together with complementary evidence derived from tiling microarrays and high throughput sequencing, demonstrated that at least a fifth of the 201 pseudogenes are transcribed in one or more cell lines or tissues.

The evolution of lncRNA repertoires and expression patterns in tetrapods.

Only a very small fraction of long noncoding RNAs (lncRNAs) are well characterized. The evolutionary history of lncRNAs can provide insights into their functionality, but the absence of lncRNA annotations in non-model organisms has precluded comparative analyses. Here we present a large-scale evolutionary study of lncRNA repertoires and expression patterns, in 11 tetrapod species. We identify approximately 11,000 primate-specific lncRNAs and 2,500 highly conserved lncRNAs, including approximately 400 genes that are likely to have originated more than 300 million years ago. We find that lncRNAs, in particular ancient ones, are in general actively regulated and may function predominantly in embryonic development. Most lncRNAs evolve rapidly in terms of sequence and expression levels, but tissue specificities are often conserved. We compared expression patterns of homologous lncRNA and protein-coding families across tetrapods to reconstruct an evolutionarily conserved co-expression network. This network suggests potential functions for lncRNAs in fundamental processes such as spermatogenesis and synaptic transmission, but also in more specific mechanisms such as placenta development through microRNA production.

Neutral and selection-driven decay of sexual traits in asexual stick insects.

Environmental shifts and lifestyle changes may result in formerly adaptive traits becoming non-functional or maladaptive. The subsequent decay of such traits highlights the importance of natural selection for adaptations, yet its causes have rarely been investigated. To study the fate of formerly adaptive traits after lifestyle changes, we evaluated sexual traits in five independently derived asexual lineages, including traits that are specific to males and therefore not exposed to selection. At least four of the asexual lineages retained the capacity to produce males that display normal courtship behaviours and are able to fertilize eggs of females from related sexual species. The maintenance of male traits may stem from pleiotropy, or from these traits only regressing via drift, which may require millions of years to generate phenotypic effects. By contrast, we found parallel decay of sexual traits in females. Asexual females produced altered airborne and contact signals, had modified sperm storage organs, and lost the ability to fertilize their eggs, impeding reversals to sexual reproduction. Female sexual traits were decayed even in recently derived asexuals, suggesting that trait changes following the evolution of asexuality, when they occur, proceed rapidly and are driven by selective processes rather than drift.

Comparative modular analysis of gene expression in vertebrate development

The focus of my PhD research was the concept of modularity. In the last 15 years, modularity has become a classic term in different fields of biology. On the conceptual level, a module is a set of interacting elements that remain mostly independent from the elements outside of the module. I used modular analysis techniques to study gene expression evolution in vertebrates. In particular, I identified ``natural'' modules of gene expression in mouse and human, and I showed that expression of organ-specific and system-specific genes tends to be conserved between such distance vertebrates as mammals and fishes. Also with a modular approach, I studied patterns of developmental constraints on transcriptome evolution. I showed that none of the two commonly accepted models of the evolution of embryonic development (``evo-devo'') are exclusively valid. In particular, I found that the conservation of the sequences of regulatory regions is highest during mid-development of zebrafish, and thus it supports the ``hourglass model''. In contrast, events of gene duplication and new gene introduction are most rare in early development, which supports the ``early conservation model''. In addition to the biological insights on transcriptome evolution, I have also discussed in detail the advantages of modular approaches in large-scale data analysis. Moreover, I re-analyzed several studies (published in high-ranking journals), and showed that their conclusions do not hold out under a detailed analysis. This demonstrates that complex analysis of high-throughput data requires a co-operation between biologists, bioinformaticians, and statisticians.

Geochemical evolution of active porphyry copper tailings impoundments : from alkaline deposition towards acidification

J. Smuda: Geochemical evolution of active porphyry copper tailings impoundments Thesis abstract Mine waste is the largest volume of materials handled in the world. The oxidation of sulfidic mine waste may result in the release of acid mine drainage (AMD) rich in heavy metals and arsenic to the environment, one of the major problems the mining industry is facing today. To control and reduce this environmental impact, it is crucial to identify the main geochemical and hydrological processes influencing contaminant liberation, transport, and retention. This thesis presents the results of a geochemical, mineralogical and stable isotope study (δ2H, δ18O, δ34S) from two active porphyry copper tailings impoundments in Mediterranean (Carén tailings impoundment, El Teniente mine, Central Chile) and hyper-arid climate (Talabre tailings impoundment, Chuquicamata, Northern Chile) from the deposition in alkaline environment (pH 10.5) towards acidification after several years of exposure. The major hydrological results were the identification of vertical contaminant and water transport in the uppermost, not water-saturated zone, triggered by capillary rise due to evaporation, and infiltration downwards due to new tailings deposition, and of horizontal transport in the groundwater zone. At the surface of the sedimented tailings, evaporation of pore water led to the precipitation of Na-Ca-Mg sulfates (e.g., gypsum, tenorite), in hyper-arid climate also halite. At the Carén tailings impoundment, renewed deposition in a 4-week interval inhibited a pH decrease below neutral values and the formation of an efflorescent salt crust. At the Talabre tailings impoundment, deposition breaks of several years resulted in the formation of acidic oxidation zones in the timeframe of less than 4 years. This process enabled the transport of liberated Cu, Zn, and Fe via capillary rise to the surface, where these metals precipitated as heavy-metal sulfates (e.g., devilline, krohnkite) and chlorides (eriochalcite, atacamite). Renewed depositing may dissolve efflorescent salts and transport liberated elements towards the groundwater zone. This zone was found to be highly dynamic due to infiltration and mixing with water from different sources, like groundwater, catchment water, and infiltration from superficial waters. There, Cu was found to be partially mobile due to complexation with Cl (in Cl-rich groundwater, Talabre) and dissolved organic matter (in zones with infiltration of catchment water rich in dissolved organic matter, Carén). A laboratory study on the isotopic fractionation of sulfur and oxygen of sulfate in different minerals groups (water-soluble sulfates, low- and high-crystalline Fe(III) oxyhydroxides) contributed to the use of stable isotopes as tracer of geochemical and transport processes for environmental studies. The results highlight that a detailed geochemical, stable isotope and mineralogical study permits the identification of contamination processes and pathways already during the deposition of mine tailings. This knowledge allows the early planning of adequate actions to reduce and control the environmental impact during tailings deposition and after the closing of the impoundment. J. Smuda: Geochemical evolution of active porphyry copper tailings impoundments Résumé de these Les déchets miniers constituent les plus grands volumes de matériel gérés dans le monde. L'oxydation des déchets miniers sulfuriques peut conduire à la libération de drainages miniers acides (DMA) riches en métaux et arsenic dans l'environnement, ce qui est l'un des principaux problèmes de l'industrie minière aujourd'hui. Pour contrôler et réduire ces impacts sur l'environnement, il est crucial d'identifier les principaux processus géochimiques et hydrologiques influençant la libération, le transport et la rétention des contaminants. Cette thèse présente les résultats d'une étude géochimique, minéralogique et des isotopes stables (δ2H, δ18O, δ34S) sur des déchets miniers de 2 sites de dépôt actifs en climat méditerranéen (Dépôt de déchets de Carén, mine de El Teniente, Centre du Chili) et en climat hyper-aride (Dépôt de déchets de Talabre, mine de Chuquicamata, Nord du Chili). L'objectif était d'étudier l'évolution des déchets de la déposition en milieu alcalin (pH = 10.5) vers l'acidification après plusieurs années d'exposition. Le principal résultat hydrologique a été l'identification de 2 types de transport : un transport vertical de l'eau et des contaminants dans la zone non saturée en surface, induit par la montée capillaire due à l'évaporation et par l'infiltration subséquente de la déposition de sédiments frais ; et un transport horizontal dans la zone des eaux souterraines. À la surface des déchets, l'évaporation de l'eau interstitielle conduit à la précipitation de sulfates de Na-Ca-Mg (ex. gypse, ténorite) et halite en climat hyper-aride. Dans le site de Carén, une nouvelle déposition de déchets frais à 4 semaines intervalle a empêché la baise du pH en deçà des valeurs neutres et la formation d'une croûte de sels efflorescentes en surface. Dans le site de Talabre, les fentes de dessiccation des dépôts ont entraîné la formation d'une zone d'oxydation à pH acide en moins de 4 ans. Ce processus a permis la libération et le transport par capillarité de Cu, Zn, Fe vers la surface, où ces éléments précipitent sous forme de sulfates de métaux lourds (ex., dévilline, krohnkite) de chlorures (ex. ériochalcite, atacamite). Une nouvelle déposition de sédiments frais pourrait dissoudre ces sels et les transporter vers la zone des eaux souterraines. Cette dernière zone était très dynamique en raison du mélange d'eaux provenant de différentes sources, comme les eaux souterraines, l'eau de captage et l'infiltration des eaux superficielles. Egalement dans cette zone, le cuivre était partiellement mobile à cause de la formation de complexe avec le chlore (dans les zone riche en Cl, Talabre) et avec la matière organique dissoute (dans les zones où s'infiltre l'eau de captage riche en matière organique, Carén). Une étude en laboratoire sur le fractionnement des isotopes stables de sulfure et d'oxygène des sulfates dans différents groupes de minéraux (sulfates hydrosolubles, sulfures de oxy-hydroxyde de Fe(III) faiblement ou fortement cristallins) a permis d'apporter une contribution à leur utilisation comme traceurs dans l'étude des processus géochimiques et de transport lors d'études environnementales. Les résultats montrent qu'une étude détaillée de la géochimie, des isotopes stables et de la minéralogie permet d'identifier les processus et les voies de contamination déjà pendant la période de dépôt des déchets miniers. Cette connaissance permet de planifier, dès le début de l'exploitation, des mesures adéquates pour réduire et contrôler l'impact sur l'environnement pendant la période de dépôts de déchets miniers et après la fermeture du site.

Late Cretaceous to Eocene geology of the South Central American forearc area (southern Costa Rica and western Panama) : initiation and evolution of an intra-oceanic convergent margin

Résumé : L'arc volcanique du sud de l'Amérique Centrale se situe sur la marge SW de la Plaque Caraïbe, au-dessus des plaques subduites de Cocos et Nazca. Il s'agit de l'un des arcs intra-océaniques les plus étudiés au monde, qui est généralement considéré comme s'étant développé à la fin du Crétacé le long d'un plateau océanique (le Plateau Caraïbe ou CLIP) et se trouvant actuellement dans un régime de subduction érosive. Au cours des dernières décennies, des efforts particuliers ont été faits pour comprendre les processus liés à la subduction sur la base d'études géophysiques et géochimiques. Au sud du Costa Rica et à l'ouest du Panama, des complexes d'accrétions et structures à la base de l'arc volcanique ont été exposés grâce à la subduction de rides asismiques et de failles transformantes. Des affleurements, situés jusqu'à seulement 15 km de la fosse, offrent une possibilité unique de mieux comprendre quelques uns des processus ayant lieu le long de la zone de subduction. Nous présentons de nouvelles contraintes sur l'origine de ces affleurements en alliant une étude de terrain poussée, de nouvelles données géochimiques, sédimentaires et paléontologiques, ainsi que des observations structurales effectuées en télédétection. Une nouvelle stratigraphie tectonique entre le Campanien et l'Éocène est définie pour la région d'avant-arc située entre la Péninsule d'Osa (Costa Rica) et la Péninsule d'Azuero (Panama). Nos résultats montrent que la partie externe de la marge est composée d'un arrangement complexe de roches ignées et de séquences sédimentaires de recouvrement qui comprennent principalement le socle de l'arc, des roches d'arc primitif, des fragments de monts sous-marins accrétés et des mélanges d'accrétion. Des preuves sont données pour le développement de l'arc volcanique du sud de l'Amérique Centrale sur un plateau océanique. Le début de la subduction le long de la marge SW de la Plaque Caraïbe a eu lieu au Campanien et a généré des roches d'arc primitif caractérisées par des affinités géochimiques particulières, globalement intermédiaires entre des affinités de plateau et d'arc insulaire. L'arc était mature au Maastrichtien et formait un isthme essentiellement continu entre l'Amérique du Nord et l'Amérique du Sud. Ceci a permis la migration de faunes terrestres entre les Amériques et pourrait avoir contribué à la crise fin Crétacé -Tertiaire en réduisant les courants océaniques subéquatoriaux entre le Pacifique et l'Atlantique. Plusieurs unités composées de fragments de monts sous-marins accrétés sont définies. La nature et l'arrangement structural de ces unités définissent de nouvelles contraintes sur les modes d'accrétion des monts sous-marins/îles océaniques et sur l'évolution de la marge depuis la formation de la zone de subduction. Entre la fin du Crétacé et l'Éocène moyen, la marge a enregistré plusieurs épisodes ponctuels d'accrétion de monts sous-marins alternant avec de la subduction érosive. A l'Éocène moyen, un événement tectonique régional pourrait avoir causé un fort couplage entre les plaques supérieure et inférieure, menant à des taux plus important d'accrétion de monts sous-marins. Durant cette période, la situation le long de la marge était très semblable à la situation actuelle et caractérisée par la présence de monts sous-marins subductants et l'absence d'accrétion de sédiments. L'enregistrement géologique montre qu'il n'est pas possible d'attribuer une nature érosive ou accrétionnaire à la marge dans le passé ou -par analogie- aujourd'hui, parce que (1) les processus d'accrétion et érosifs varient fortement spatialement et temporellement et (2) il est impossible d'évaluer la quantité exacte de matériel tectoniquement enlevé à la marge depuis le début de la subduction. Au sud du Costa Rica, certains fragments de monts sous-marins accrétés sont représentatifs d'une interaction entre une ride et un point chaud dans le Pacifique au Crétacé terminal/Paléocène. L'existence de ces fragments de monts sous-marins et la morphologie du fond de l'Océan Pacifique indiquent que la formation de la ride de Cocos-Nazca s'est formée au moins ~40 Ma avant l'âge proposé par les modèles tectoniques actuels. Au Panama, nous avons identifié une île océanique d'âge début Éocène qui a été accrétée à l'Éocène moyen. L'accrétion a eu lieu à très faible profondeur par détachement de l'île dans la fosse, et a mené à une exceptionnelle préservation des structures volcaniques. Des affleurement comprenant aussi bien des parties basses et hautes de l'édifice volcanique on été étudiées, depuis la phase sous-marine bouclier jusqu'à la phase subaérienne post-bouclier. La stratigraphie nous a permis de différencier les laves de la phase sous-marine de celles de la phase subaérienne. La composition des laves indique une diminution progressive de l'intensité de la fusion partielle de la source et une diminution de la température des laves produites durant les derniers stades de l'activité volcanique. Nous interprétons ces changements comme étant liés à l'éloignement progressif de l'île océanique de la zone de fusion ou point chaud. Abstract The southern Central American volcanic front lies on the SW edge of the Caribbean Plate, inboard of the subducting Cocos and Nazca Plates. It is one of the most studied intra-oceanic convergent margins around the world, which is generally interpreted to have developed in the late Cretaceous along an oceanic plateau (the Caribbean Large Igneous Province or CLIP) and to be currently undergoing a regime of subduction erosion. In the last decades a particular effort has been made to understand subduction-related processes on the basis of geophysical and geochemical studies. In southern Costa Rica and western Panama accretionary complexes and structures at the base of the volcanic front have been exposed in response to subduction of aseismic ridges and transforms. Onland exposures are located as close as to 15 km from the trench and provide a unique opportunity to better understand some of the processes occurring along the subduction zone. We provide new constraints on the origins of these exposures by integrating a comprehensive field work, new geochemical, sedimentary and paleontological data, as well as structural observations based on remote imaging. A new Campanian to Eocene tectonostratigraphy is defined for the forearc area located between the Osa Peninsula (Costa Rica) and the Azuero Peninsula (Panama). Our results show that the outer margin is composed of a complicated arrangement of igneous complexes and overlapping sedimentary sequences that essentially comprise an arc basement, primitive island-arc rocks, accreted seamount fragments and accretionary mélanges. Evidences are provided for the development of the southern Central American arc on the top an oceanic plateau. The subduction initiation along the SW edge of the Caribbean Plate occurred in the Campanian and led to formation of primitive island-arc rocks characterized by unusual geochemical affinities broadly intermediate between plateau and arc affinities. The arc was mature in the Maastrichtian and was forming a predominantly continuous landbridge between the North and South Americas. This allowed migration of terrestrial fauna between the Americas and may have contributed to the Cretaceous-Tertiary crisis by limiting trans-equatorial oceanic currents between the Pacific and the Atlantic. Several units composed of accreted seamount fragments are defined. The nature of the units and their structural arrangement provide new constraints on the modes of accretion of seamounts/oceanic islands and on the evolution of the margin since subduction initiation. Between the late Cretaceous and the middle Eocene, the margin recorded several local episodes of seamount accretion alternating with tectonic erosion. In the middle Eocene a regional tectonic event may have triggered strong coupling between the overriding and subducting plates, leading to higher rates of seamount accretion. During this period the situation along the margin was very similar to the present and characterized by subducting seamounts and absence of sediment accretion. The geological record shows that it is not possible to ascribe an overall erosive or accretionary nature to the margin in the past and, by analogy, today, because (1) accretionary and erosive processes exhibit significant lateral and temporal variations and (2) it is impossible to estimate the exact amount of material tectonically eroded from the margin since subduction initiation. In southern Costa Rica, accreted seamount fragments point toward a plume-ridge interaction in the Pacific in the late Cretaceous/Paleocene. This occurrence of accreted seamount fragments and morphology of the Pacific Ocean floor is indicative of the formation of the Cocos-Nazca spreading system at least ~40 Ma prior to the age proposed in current tectonic models. In Panama, we identified a remarkably-well preserved early Eocene oceanic island that accreted in the middle Eocene. The accretion probably occurred at very shallow depth by detachment of the island in the trench and led to an exceptional preservation of the volcanic structures. Exposures of both deep and superficial parts of the volcanic edifice have been studied, from the submarine-shield to subaerial-postshield stages. The stratigraphy allowed us to distinguish lavas produced during the submarine and subaerial stages. The lava compositions likely define a progressive diminution of source melting and a decrease in the temperature of erupted melts in the latest stages of volcanic activity. We interpret these changes to primarily reflect the progressive migration of the oceanic island out of the melting region or hotspot.

Evolution of specialization: a phylogenetic study of host range in the red milkweed beetle (Tetraopes tetraophthalmus).

Specialization is common in most lineages of insect herbivores, one of the most diverse groups of organisms on earth. To address how and why specialization is maintained over evolutionary time, we hypothesized that plant defense and other ecological attributes of potential host plants would predict the performance of a specialist root-feeding herbivore (the red milkweed beetle, Tetraopes tetraophthalmus). Using a comparative phylogenetic and functional trait approach, we assessed the determinants of insect host range across 18 species of Asclepias. Larval survivorship decreased with increasing phylogenetic distance from the true host, Asclepias syriaca, suggesting that adaptation to plant traits drives specialization. Among several root traits measured, only cardenolides (toxic defense chemicals) correlated with larval survival, and cardenolides also explained the phylogenetic distance effect in phylogenetically controlled multiple regression analyses. Additionally, milkweed species having a known association with other Tetraopes beetles were better hosts than species lacking Tetraopes herbivores, and milkweeds with specific leaf area values (a trait related to leaf function and habitat affiliation) similar to those of A. syriaca were better hosts than species having divergent values. We thus conclude that phylogenetic distance is an integrated measure of phenotypic and ecological attributes of Asclepias species, especially defensive cardenolides, which can be used to explain specialization and constraints on host shifts over evolutionary time.

On the evolution of harming and recognition in finite panmictic and infinite structured populations.

Natural selection may favor two very different types of social behaviors that have costs in vital rates (fecundity and/or survival) to the actor: helping behaviors, which increase the vital rates of recipients, and harming behaviors, which reduce the vital rates of recipients. Although social evolutionary theory has mainly dealt with helping behaviors, competition for limited resources creates ecological conditions in which an actor may benefit from expressing behaviors that reduce the vital rates of neighbors. This may occur if the reduction in vital rates decreases the intensity of competition experienced by the actor or that experienced by its offspring. Here, we explore the joint evolution of neutral recognition markers and marker-based costly conditional harming whereby actors express harming, conditional on actor and recipient bearing different conspicuous markers. We do so for two complementary demographic scenarios: finite panmictic and infinite structured populations. We find that marker-based conditional harming can evolve under a large range of recombination rates and group sizes under both finite panmictic and infinite structured populations. A direct comparison with results for the evolution of marker-based conditional helping reveals that, if everything else is equal, marker-based conditional harming is often more likely to evolve than marker-based conditional helping.

Structure of the extracellular domains of human and Xenopus Fn14: implications in the evolution of TWEAK and Fn14 interactions.

TWEAK (TNF homologue with weak apoptosis-inducing activity) and Fn14 (fibroblast growth factor-inducible protein 14) are members of the tumor necrosis factor (TNF) ligand and receptor super-families. Having observed that Xenopus Fn14 cross-reacts with human TWEAK, despite its relatively low sequence homology to human Fn14, we examined the conservation in tertiary fold and binding interfaces between the two species. Our results, combining NMR solution structure determination, binding assays, extensive site-directed mutagenesis and molecular modeling, reveal that, in addition to the known and previously characterized β-hairpin motif, the helix-loop-helix motif makes an essential contribution to the receptor/ligand binding interface. We further discuss the insight provided by the structural analyses regarding how the cysteine-rich domains of the TNF receptor super-family may have evolved over time. DATABASE: Structural data are available in the Protein Data Bank/BioMagResBank databases under the accession codes 2KMZ, 2KN0 and 2KN1 and 17237, 17247 and 17252. STRUCTURED DIGITAL ABSTRACT: TWEAK binds to hFn14 by surface plasmon resonance (View interaction) xeFn14 binds to TWEAK by enzyme linked immunosorbent assay (View interaction) TWEAK binds to xeFn14 by surface plasmon resonance (View interaction) hFn14 binds to TWEAK by enzyme linked immunosorbent assay (View interaction).

Construction mechanisms and thermal evolution of upper crustal intrusions : the Saint-Jean-du-Doigt bimodal intrusion (Brittany, France)

Understanding the emplacement and growth of intrusive bodies in terms of mechanism, duration, ther¬mal evolution and rates are fundamental aspects of crustal evolution. Recent studies show that many plutons grow in several Ma by in situ accretion of discrete magma pulses, which constitute small-scale magmatic reservoirs. The residence time of magmas, and hence their capacities to interact and differentiate, are con¬trolled by the local thermal environment. The latter is highly dependant on 1) the emplacement depth, 2) the magmas and country rock composition, 3) the country rock thermal conductivity, 4) the rate of magma injection and 5) the geometry of the intrusion. In shallow level plutons, where magmas solidify quickly, evi¬dence for magma mixing and/or differentiation processes is considered by many authors to be inherited from deeper levels. This work shows however that in-situ differentiation and magma interactions occurred within basaltic and felsic sills at shallow depth (0.3 GPa) in the St-Jean-du-Doigt (SJDD) bimodal intrusion, France. This intrusion emplaced ca. 347 Ma ago (IDTIMS U/Pb on zircon) in the Precambrian crust of the Armori- can massif and preserves remarkable sill-like emplacement processes of bimodal mafic-felsic magmas. Field evidence coupled to high precision zircon U-Pb dating document progressive thermal maturation within the incrementally built ioppolith. Early m-thick mafic sills (eastern part) form the roof of the intrusion and are homogeneous and fine-grained with planar contacts with neighboring felsic sills; within a minimal 0.8 Ma time span, the system gets warmer (western part). Sills are emplaced by under-accretion under the old east¬ern part, interact and mingle. A striking feature of this younger, warmer part is in-situ differentiation of the mafic sills in the top 40 cm of the layer, which suggests liquids survival in the shallow crust. Rheological and thermal models were performed in order to determine the parameters required to allow this observed in- situ differentiation-accumulation processes. Strong constraints such as total emplacement durations (ca. 0.8 Ma, TIMS date) and pluton thickness (1.5 Km, gravity model) allow a quantitative estimation of the various parameters required (injection rates, incubation time,...). The results show that in-situ differentiation may be achieved in less than 10 years at such shallow depth, provided that: (1) The differentiating sills are injected beneath consolidated, yet still warm basalt sills, which act as low conductive insulating screens (eastern part formation in the SJDD intrusion). The latter are emplaced in a very short time (800 years) at high injection rate (0.5 m/y) in order to create a "hot zone" in the shallow crust (incubation time). This implies that nearly 1/3 of the pluton (400m) is emplaced by a subsequent and sustained magmatic activity occurring on a short time scale at the very beginning of the system. (2) Once incubation time is achieved, the calculations show that a small hot zone is created at the base of the sill pile, where new injections stay above their solidus T°C and may interact and differentiate. Extraction of differentiated residual liquids might eventually take place and mix with newly injected magma as documented in active syn-emplacement shear-zones within the "warm" part of the pluton. (3) Finally, the model show that in order to maintain a permanent hot zone at shallow level, injection rate must be of 0.03 m/y with injection of 5m thick basaltic sills eveiy 130yr, imply¬ing formation of a 15 km thick pluton. As this thickness is in contradiction with the one calculated for SJDD (1.5 Km) and exceed much the average thickness observed for many shallow level plutons, I infer that there is no permanent hot zone (or magma chambers) at such shallow level. I rather propose formation of small, ephemeral (10-15yr) reservoirs, which represent only small portions of the final size of the pluton. Thermal calculations show that, in the case of SJDD, 5m thick basaltic sills emplaced every 1500 y, allow formation of such ephemeral reservoirs. The latter are formed by several sills, which are in a mushy state and may interact and differentiate during a short time.The mineralogical, chemical and isotopic data presented in this study suggest a signature intermediate be¬tween E-MORB- and arc-like for the SJDD mafic sills and feeder dykes. The mantle source involved produced hydrated magmas and may be astenosphere modified by "arc-type" components, probably related to a sub¬ducting slab. Combined fluid mobile/immobile trace elements and Sr-Nd isotopes suggest that such subduc¬tion components are mainly fluids derived from altered oceanic crust with minor effect from the subducted sediments. Close match between the SJDD compositions and BABB may point to a continental back-arc setting with little crustal contamination. If so, the SjDD intrusion is a major witness of an extensional tectonic regime during the Early-Carboniferous, linked to the subduction of the Rheno-Hercynian Ocean beneath the Variscan terranes. Also of interest is the unusual association of cogenetic (same isotopic compositions) K-feldspar A- type granite and albite-granite. A-type granites may form by magma mixing between the mafic magma and crustal melts. Alternatively, they might derive from the melting of a biotite-bearing quartz-feldspathic crustal protolith triggered by early mafic injections at low crustal levels. Albite-granite may form by plagioclase cu¬mulate remelting issued from A-type magma differentiation.

The genome and development-dependent transcriptomes of Pyronema confluens: a window into fungal evolution

Fungi are a large group of eukaryotes found in nearly all ecosystems. More than 250 fungal genomes have already been sequenced, greatly improving our understanding of fungal evolution, physiology, and development. However, for the Pezizomycetes, an early-diverging lineage of filamentous ascomycetes, there is so far only one genome available, namely that of the black truffle, Tuber melanosporum, a mycorrhizal species with unusual subterranean fruiting bodies. To help close the sequence gap among basal filamentous ascomycetes, and to allow conclusions about the evolution of fungal development, we sequenced the genome and assayed transcriptomes during development of Pyronema confluens, a saprobic Pezizomycete with a typical apothecium as fruiting body. With a size of 50 Mb and ~13,400 protein-coding genes, the genome is more characteristic of higher filamentous ascomycetes than the large, repeat-rich truffle genome; however, some typical features are different in the P. confluens lineage, e.g. the genomic environment of the mating type genes that is conserved in higher filamentous ascomycetes, but only partly conserved in P. confluens. On the other hand, P. confluens has a full complement of fungal photoreceptors, and expression studies indicate that light perception might be similar to distantly related ascomycetes and, thus, represent a basic feature of filamentous ascomycetes. Analysis of spliced RNA-seq sequence reads allowed the detection of natural antisense transcripts for 281 genes. The P. confluens genome contains an unusually high number of predicted orphan genes, many of which are upregulated during sexual development, consistent with the idea of rapid evolution of sex-associated genes. Comparative transcriptomics identified the transcription factor gene pro44 that is upregulated during development in P. confluens and the Sordariomycete Sordaria macrospora. The P. confluens pro44 gene (PCON_06721) was used to complement the S. macrospora pro44 deletion mutant, showing functional conservation of this developmental regulator.