Shotgun Mitogenomics Provides a Reference Phylogenetic Framework and Timescale for Living Xenarthrans

Xenarthra (armadillos, sloths, and anteaters) constitutes one of the four major clades of placental mammals. Despite their phylogenetic distinctiveness in mammals, a reference phylogeny is still lacking for the 31 described species. Here we used Illumina shotgun sequencing to assemble 33 new complete mitochondrial genomes, establishing Xenarthra as the first major placental clade to be fully sequenced at the species level for mitogenomes. The resulting data set allowed the reconstruction of a robust phylogenetic framework and timescale that are consistent with previous studies conducted at the genus level using nuclear genes. Incorporating the full species diversity of extant xenarthrans points to a number of inconsistencies in xenarthran systematics and species definition. We propose to split armadillos in two distinct families Dasypodidae (dasypodines) and Chlamyphoridae (euphractines, chlamyphorines, and tolypeutines) to better reflect their ancient divergence, estimated around 42 million years ago. Species delimitation within long-nosed armadillos (genus Dasypus) appeared more complex than anticipated, with the discovery of a divergent lineage in French Guiana. Diversification analyses showed Xenarthra to be an ancient clade with a constant diversification rate through time with a species turnover driven by high but constant extinction. We also detected a significant negative correlation between speciation rate and past temperature fluctuations with an increase in speciation rate corresponding to the general cooling observed during the last 15 million years. Biogeographic reconstructions identified the tropical rainforest biome of Amazonia and the Guianan shield as the cradle of xenarthran evolutionary history with subsequent dispersions into more open and dry habitats.Fil: Gibb, Gillian C.. Universite de Montpellier; Francia. Massey Universit; Nueva ZelandaFil: Condamine, Fabien L.. University of Gothenburg; Suecia. Universite de Montpellier; Francia. University of Alberta; CanadáFil: Kuch, Melanie. McMaster University; CanadáFil: Enk, Jacob. McMaster University; CanadáFil: Moraes Barros, Nadia. Universidade Do Porto; Portugal. Universidade de Sao Paulo; BrasilFil: Superina, Mariella. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Medicina y Biología Experimental de Cuyo; ArgentinaFil: Poinar, Hendrik N.. McMaster University; CanadáFil: Delsuc, Frederic. Universite de Montpellier; Franci

Rôle du phlogopite sur la genèse de magmas riches en potassium : approche expérimentale

K2O-rich melts (K2O > 2 wt. %; K2O/Na2O > 1) have been described in all of the major geodynamic settings on Earth. These melts are mainly characterized by their huge K2O content, ranging between 2 – 13 wt. % and K2O/Na 2 O ratios of 1 – 40. The chemical compositions of the different K2O-rich melt groups span a very high variability, from strongly silica undersaturated melts (kamfugites, kimberlites, madupitic lamproites) to silica-rich terms (shoshonites, phlogopite lamproites). These very high K2O contents together with strong K2O/Na2O ratios cannot be derived from partial melting of fertile or depleted peridotites. Partial melting experiments have been conducted in piston cylinder apparatus on phlogopite ± amphibole-peridotite in the spinel and garnet stability fields (1 – 3 GPa) in order to determine the ability of the lithospheric mantle to produce K2O-rich melts. The presence of small amounts of fluorine in the starting material leads to stabilize phlogopite at higher temperatures than previously determined. The first degrees of melting at 1 GPa are silica-rich and their K2O contents are buffered to 4 – 6 wt. % in the presence of residual phlogopite, depending on the source fertility (lherzolite and harzburgite, respectively). In the garnet stability field at 3 GPa, low-degree melts are silica-undersaturated but are enriched in K2O, compared to the garnet stability field: from 6 to 8 wt. % in lherzolite and harzburgite sources, respectively. These results suggest that pressure is a key parameter in the mantle to produce K2O-rich melts. Partition coefficient modelings show that increasing the phlogopite proportion in the mantle source does not modify the K2O content of derived melts, but decreases their K2O/Na2O ratios. Consequently, partial melting of phlogopite-peridotite in this range of pressure cannot accounts for the highest K2O contents observed in natural lamproites and kamafugites. A series of experiments has been realized on pure phlogopite at 1 and 3 GPa, showing that derived melts are strongly enriched in K2O (12 – 14 wt. %) and share chemical affinities with lamproites. Peridotite or pyroxenite melting in the presence of phlogopite, however, do not permit to reproduce the high chemical variability of natural K2O-rich melts requires volatile-rich conditions (H2O, CO2, F) and reduced oxygen fugacities.Des liquides riches en K2O ( K2O > 2 pds. % ; K2O/Na2O > 1) sont observés dans la majeure partie des contextes géodynamiques sur Terre. Ces liquides sont principalement caractérisés par leurs teneurs en K2O variant entre 3 et 13 pds. % et des rapports K2O/Na2O de 1 – 40. Les compositions chimiques des différents groupes de liquides riches en K2O observés sont extrêmement variables, depuis des termes très sous-saturés en silice (kamafugites, kimberlites, lamproïtes madupitiques à olivine) à des termes sur-saturés en silice (shoshonites, lamproïtes à phlogopite). Ces fortes teneurs en K2O et les rapports K2O/ Na2O élevés ne peuvent pas être obtenus par la fusion de péridotites fertiles ou réfractaires. Des expériences de fusion partielle en piston-cylindre ont été réalisées sur des péridotites à phlogopite ± amphibole dans les domaines de stabilité du spinelle et du grenat (1 et 3 GPa) afin de déterminer la capacité du manteau lithosphérique à produire des liquides riches en K2O. La présence de faibles teneurs en fluor dans le matériel de départ stabilise le phlogopite à des températures supérieures aux études antérieures. Les faibles degrés de fusion obtenus à 1 GPa sont sur-saturés en silice et leur teneur en K2O est tamponnée à 4 – 6 pds. % par la présence de phlogopite résiduel pour des péridotites fertile et réfractaire, respectivement. Les expériences réalisées à 3 GPa montrent que les premiers degrés de fusion sont sous-saturés en silice mais plus riches en K2O (6 – 8 pds. % pour la lherzolite et la harzburgite, respectivement) que dans le domaine du spinelle, démontrant l’importance de la pression sur la genèse de liquides riches en K2O. Les modélisations réalisées montrent également que l’augmentation de la proportion de phlogopite dans la source ne modifie pas la teneur en K2O des liquides formés mais diminue leurs rapports K2O/Na2O. Par conséquent, la fusion de péridotite à phlogopite dans la gamme de pression étudiée ne permet pas d’obtenir des liquides aussi riches en K2O que certains lamproïtes et kamafugites. Une série d’expériences réalisée sur du phlogopite pur à 1 et 3 GPa montrent que les liquides dérivés de telles sources sont très riches en K2O (12 – 14 pds. %) et comparables aux lamproïtes. Les différentes lithologies dans le manteau ne permettent cependant pas d’expliquer la grande gamme de composition des liquides riches en K2O et nécessitent des conditions riches en éléments volatils (H2O, CO2, F) et des fugacités d’oxygène réductrices

Organisation anatomique et rôle du couplage astrocytaire dans l’activité rythmique du noyau sensoriel du trijumeau

Plusieurs fonctions cérébrales dépendent de la capacité de générer une activité rythmique dans les circuits neuronaux. L’exemple le plus intuitif est celui des réseaux de neurones, nommés générateurs de patrons centraux (GPCs), encodant des patrons de mouvements répétitifs tels que ceux de la locomotion, de la respiration et de la mastication. Nos travaux ont été réalisés dans le noyau sensoriel principal du trijumeau (NVsnpr) dans lequel une activité rythmique est observée uniquement dans la partie dorsale qui formerait le cœur rythmogénique du GPC de la mastication. Des travaux antérieurs ont démontré le rôle clé des interactions astrocytes-neurones pour la genèse de décharges rythmiques. En effet, l’activité rythmogénique de ces neurones dépend d’un courant sodique persistant (INaP) dont l’activation est favorisée par une baisse du calcium extracellulaire. Les astrocytes activés par les afférences au noyau interviennent dans ce processus en libérant une protéine chélatrice du calcium, le S100β, provoquant une baisse de calcium extracellulaire. Les astrocytes sont généralement couplés par des jonctions communicantes et dans de nombreux cas, la forme des réseaux astrocytaires chevauche parfaitement l’organisation neuronale sous-jacente dans les régions où celle-ci respecte une certaine cartographie. Cependant, il n’existe aucune description de l’organisation des réseaux astrocytaires dans les GPCs. Notre première hypothèse est que le couplage astrocytaire présenterait une organisation spatiale supportant la fonction rythmogénique neuronale située exclusivement dans la partie dorsale du NVsnpr. Pour cela, nous avons développé une méthode d’analyse vectorielle pour étudier l’orientation préférentielle des réseaux astrocytaires dans le noyau. Deuxièmement, ce couplage astrocytaire pourrait jouer un rôle dans la rythmogenèse et sa coordination. Nos résultats démontrent que le couplage astrocytaire est augmenté par les stimuli induisant la rythmogenèse, cette modulation impliquant le S100β. Ces réseaux d’astrocytes présentent une étendue limitée et une organisation spatiale qui épouse les frontières de la partie dorsale du NVsnpr. Enfin, ce couplage astrocytaire est nécessaire à la rythmogenèse. Ces résultats démontrent l’implication des réseaux astrocytaires dans la délimitation d’une frontière fonctionnelle et suggèrent qu’ils pourraient jouer un rôle important dans la coordination et/ou la synchronisation de la décharge des populations. Cette implication des réseaux astrocytaires dans une activité rythmique pourrait être observée dans d’autres circuits neuronaux comme les GPCs de la respiration ou de la locomotion.Several cerebral functions depend on the capacity of neuronal circuit to generate rhythmic activity. The most intuitive example is neuronal circuits referred to as central pattern generators (CPGs), which encode the repetitive movement patterns for locomotion, respiration and mastication. Our work was performed in the trigeminal main sensory nucleus where rhythmic activity observed only in the dorsal part is thought to reflect the rhythmogenic core of the masticatory CPG. Previous studies have shown the key role that astrocytes-neurons interactions play in neuronal rhythmic firing. In these neurons, rhythmogenic activity relies on a sodium persistent current (INaP) which activation is promoted by a decrease of extracellular calcium. Astrocytes activated by afferences to the nucleus take part in this process by releasing S100β, a protein that chelates calcium and promotes INaP activation by decreasing extracellular calcium. Generally, astrocytes are coupled by gap junctions and in many cases where neurons are organized topographically, the shape of astrocytic networks overlap perfectly the underlying neuronal organization. However, the organization of astrocytic networks in CPGs has not been described so far. Our first hypothesis is that the organization of astrocytic coupling supports the rhythmogenic function in the dorsal part of the NVsnpr. We developed a vectorial analysis method to address the preferential orientation of astrocytic networks in the nucleus. Secondly, astrocytic coupling could be implicated in rhythmogenesis. The results presented in this thesis show that rhythmogenic stimuli increase astrocytic coupling and S100β is implicated in this modulation. Astrocytic networks show a limited spread and a spatial organization which follow the boundaries of the dorsal part of NVsnpr. Finally, astrocytic coupling is required for rhythmogenesis. Our results indicate that astrocytic networks define functional boundaries and suggest that they could play an important role in the coordination and/or synchronization of firing of neuronal populations. Astrocytic coupling may also play a similar role in other neural circuits such as locomotion and respiration CPG

RPANDA: an R package for macroevolutionary analyses on phylogenetic trees

A number of approaches for studying macroevolution using phylogenetic trees have been developed in the last few years. Here, we present RPANDA, an R package that implements model‐free and model‐based phylogenetic comparative methods for macroevolutionary analyses. The model‐free approaches implemented in RPANDA are recently developed approaches stemming from graph theory that allow summarizing the information contained in phylogenetic trees, computing distances between trees, and clustering them accordingly. They also allow identifying distinct branching patterns within single trees. RPANDA also implements likelihood‐based models for fitting various diversification models to phylogenetic trees. It includes birth–death models with i) constant, ii) time‐dependent and iii) environmental‐dependent speciation and extinction rates. It also includes models with equilibrium diversity derived from the coalescent process, as well as a likelihood‐based inference framework to fit the individual‐based model of Speciation by Genetic Differentiation, which is an extension of Hubbell's neutral theory of biodiversity. RPANDA can be used to (i) characterize trees by plotting their spectral density profiles (ii) compare trees and cluster them according to their similarities, (iii) identify and plot distinct branching patterns within trees, (iv) compare the fit of alternative diversification models to phylogenetic trees, (v) estimate rates of speciation and extinction, (vi) estimate and plot how these rates have varied with time and environmental variables and (vii) deduce and plot estimates of species richness through geological time. RPANDA provides investigators with a set of tools for exploring patterns in phylogenetic trees and fitting various models to these trees, thereby contributing to the ongoing development of phylogenetics in the life sciences

Amazonia is the primary source of Neotropical biodiversity.

The American tropics (the Neotropics) are the most species-rich realm on Earth, and for centuries, scientists have attempted to understand the origins and evolution of their biodiversity. It is now clear that different regions and taxonomic groups have responded differently to geological and climatic changes. However, we still lack a basic understanding of how Neotropical biodiversity was assembled over evolutionary timescales. Here we infer the timing and origin of the living biota in all major Neotropical regions by performing a cross-taxonomic biogeographic analysis based on 4,450 species from six major clades across the tree of life (angiosperms, birds, ferns, frogs, mammals, and squamates), and integrate >1.3 million species occurrences with large-scale phylogenies. We report an unprecedented level of biotic interchange among all Neotropical regions, totaling 4,525 dispersal events. About half of these events involved transitions between major environmental types, with a predominant directionality from forested to open biomes. For all taxonomic groups surveyed here, Amazonia is the primary source of Neotropical diversity, providing >2,800 lineages to other regions. Most of these dispersal events were to Mesoamerica (∼1,500 lineages), followed by dispersals into open regions of northern South America and the Cerrado and Chaco biomes. Biotic interchange has taken place for >60 million years and generally increased toward the present. The total amount of time lineages spend in a region appears to be the strongest predictor of migration events. These results demonstrate the complex origin of tropical ecosystems and the key role of biotic interchange for the assembly of regional biotas

Integrative taxonomy of New Caledonian beetles: species delimitation and definition of the [i]Uloma isoceroides[/i] species group (Coleoptera, Tenebrionidae, Ulomini), with the description of four new species

New Caledonia is an important biodiversity hotspot with much undocumented biodiversity, especially in many insect groups. Here we used an integrative approach to explore species diversity in the tenebrionid genus Uloma (Coleoptera, Tenebrionidae, Ulomini), which encompasses about 150 species, of which 22 are known from New Caledonia. To do so, we focused on a morphologically homogeneous group by comparing museum specimens with material collected during several recent field trips. We also conducted molecular phylogenetic analyses based on a concatenated matrix of four mitochondrial and three nuclear genes for 46 specimens. The morphological study allowed us to discover and describe four new species that belong to the group of interest, the Uloma isoceroides group. Molecular analyses confirmed the species boundaries of several of the previously described species and established the validity of the four new species. The phylogenetic analyses also provided additional information on the evolutionary history of the group, highlighting that a species that was thought to be unrelated to the group was in fact a member of the same evolutionary lineage. Molecular species delimitation confirmed the status of the sampled species of the group and also suggested some hidden (cryptic) biodiversity for at least two species of the group. Altogether this integrative taxonomic approach has allowed us to better define the boundaries of the Uloma isoceroides species group, which comprises at least 10 species: Uloma isoceroides (Fauvel, 1904), Uloma opacipennis (Fauvel, 1904), Uloma caledonica Kaszab, 1982, Uloma paniei Kaszab, 1982, Uloma monteithi Kaszab, 1986, Uloma robusta Kaszab, 1986, Uloma clamensae sp. n., Uloma condaminei sp. n., Uloma jourdani sp. n., and Uloma kergoati sp. n. We advocate more studies on other New Caledonian groups, as we expect that much undocumented biodiversity can be unveiled through the use of similar approache

Cryptands and bismacrocycles with cyanuric and isocyanuric units: synthesis and structural investigations

Hay synthesis of cryptands and bismacrocycles starting from tripodands with cyanuric and isocyanuric cores is reported. The structure of the compounds is revealed by X-ray diffraction, NMR spectrometry and MS investigations. DNMR experiments carried out with bismacrocycles indicated the flipping of the rings and the free-energy barrier for the conformational process could be determined in one case. (C) 2012 Elsevier Ltd. All rights reserved