Biodiversity and molecular evolution of malacostraca

No actual cenário de perda acelerada de biodiversidade, o nosso conhecimento dos ecossistemas marinhos, apesar da sua extensão e complexidade, continua muito inferior ao dos ecossistemas terrestres. A classe Malacostraca (Arthropoda, Crustacea), um grupo dos mais representativos nos ecossistemas marinhos, apresenta um elevado nível de diversidade morfológica e ecológica, mas difícil sua identificação ao nível de espécie requer frequentemente a ajuda de especialistas em taxonomia. A utilização recente do “barcoding” (código de barras do ADN), revelou ser um método rápido e eficaz para a identificação de espécies em diversos grupos de metazoários, incluindo os Malacostraca. No âmbito desta tese foi construída uma base de dados de código de barras de ADN envolvendo 132 espécies de Malacostraca vários locais de amostragem no Atlântico Nordeste e Mediterrâneo. As sequências de ADN mitocondrial provenientes de 601 espécimes formaram, em 95% dos casos, grupos congruentes com as identificações baseadas em características morfológicas. No entanto, foi detectado polimorfismo em seis casos e a divergência intra-específica foi elevada em exemplares pertencentes a duas espécies morfológicas, sugerindo, neste caso, a ocorrência de especiação críptica. Este estudo confirma a utilidade do código de barras de ADN para a identificação de Malacostraca marinhos. Apesar do sucesso obtido, este método apresenta alguns problemas, como por exemplo a possível amplificação de pseudogenes. A ocorrência de pseudogenes e as possíveisabordagens para a detecção e resolução deste tipo de problemas são discutidas com base em casos de estudo: análises dos códigos de barras ADN na espécie Goneplax rhomboides (Crustacea, Decapoda). A análise dos códigos de barras ADN revelou ainda grupos prioritários de decápodes para estudos taxonómicos e sistemáticos, nomeadamente os decápodes dos géneros Plesionika e Pagurus. Neste âmbito são discutidas as relações filogenéticas entre espécies seleccionadas dos géneros Plesionika e Pagurus. Este trabalho aponta para várias questões no âmbito da biodiversidade e evolução molecular da classe Malacostraca que carecem de um maior esclarecimento, podendo ser considerado como a base para estudo futuros. Análises filogenéticas adicionais integrando dados morfológicos e moleculares de um maior número de espécies e de famílias deverão certamente conduzir a uma melhor avaliação da biodiversidade e da evolução dentro da classe.

Mythotextuality and the evolution of ideologies the reuse of the Epic of Gilgamesh in North American texts

When the scribes of ancient Mesopotamia rewrote the Epic of Gilgamesh over a period of over two thousand years, the modifications made reflected the social transformations occurring during the same era. The dethroning of the goddess Inanna-Ishtar and the devaluation of other female characters in the evolving Epic of Gilgamesh coincided with the declining status of women in society. Since the 1960s, translations into modern languages have been readily available. The Mesopotamian myth has been reused in a wide variety of mythic and mythological texts by Quebecois, Canadian and American authors. Our analysis of the first group of mythic texts, written in the 1960s and 1970s, shows a reversal of the tendency of the Mesopotamian texts. Written at a time when the feminist movement was transforming North American society, these retellings feature a goddess with her high status restored and her ancient attributes re-established. Another group of writers, publishing in the 1980s and 1990s, makes a radical shift away from these feminist tendencies while still basically rewriting the Epic. In this group of mythic texts, the goddess and other female characters find their roles reduced while the male gods and characters have expanded and glorified roles. The third group of texts analysed does not rewrite the Epic. The Epic is reused here intertextually to give depth to mythological works set in the twentieth century or later. The dialogue created between the contemporary text and the Epic emphasises the role that the individual has in society. A large-scale comparative mythotextual study of texts that share a common hypotext can, especially when socio-historical factors are considered, provide a window onto the relationship between text and society. A comparative study of how the Epic of Gilgamesh is rewritten and referred to intertextually through time can help us relativize the understanding of our own time and culture.

Population and landscape genetics of the stone marten and red fox in Portugal : implications for conservation management of common carnivores

Tese de doutoramento, Biologia (Biologia da Conservação), Universidade de Lisboa, Faculdade de Ciências, 2015

Critical reappraisal of Late Mesozoic-Cenozoic Central and North Atlantic, Caribbean and Mediterranean evolution

(l) The Pacific basin (Pacific area) may be regarded as moving eastwards like a double zip fastener relative to the continents and their respective plates (Pangaea area): opening in the East and closing in the West. This movement is tracked by a continuous mountain belt, the collision ages of which increase westwards. (2) The relative movements between the Pacific area and the Pangaea area in the W-E/E-W direction are generated by tidal forces (principle of hypocycloid gearing), whereby the lower mantle and the Pacific basin or area (Pacific crust = roof of the lower mantle?) rotate somewhat faster eastwards around the Earth's spin axis relative to the upper mantle/crust system with the continents and their respective plates (Pangaea area) (differential rotation). (3) These relative West to East/East to West displacements produce a perpetually existing sequence of distinct styles of opening and closing ocean basins, exemplified by the present East to West arrangement of ocean basins around the globe (Oceanic or Wilson Cycle: Rift/Red Sea style; Atlantic style; Mediterranean/Caribbean style as eastwards propagating tongue of the Pacific basin; Pacific style; Collision/Himalayas style). This sequence of ocean styles, of which the Pacific ocean is a part, moves eastwards with the lower mantle relative to the continents and the upper-mantle/crust of the Pangaea area. (4) Similarly, the collisional mountain belt extending westwards from the equator to the West of the Pacific and representing a chronological sequence of collision zones (sequential collisions) in the wake of the passing of the Pacific basin double zip fastener, may also be described as recording the history of oceans and their continental margins in the form of successive Wilson Cycles. (5) Every 200 to 250 m.y. the Pacific basin double zip fastener, the sequence of ocean styles of the Wilson Cycle and the eastwards growing collisional mountain belt in their wake complete one lap around the Earth. Two East drift lappings of 400 to 500 m.y. produce a two-lap collisional mountain belt spiral around a supercontinent in one hemisphere (North or South Pangaea). The Earth's history is subdivided into alternating North Pangaea growth/South Pangaea breakup eras and South Pangaea growth/North Pangaea breakup eras. Older North and South Pangaeas and their collisional mountain belt spirals may be reconstructed by rotating back the continents and orogenic fragments of a broken spiral (e.g. South Pangaea, Gondwana) to their previous Pangaea growth era orientations. In the resulting collisional mountain belt spiral, pieced together from orogenic segments and fragments, the collision ages have to increase successively towards the West. (6) With its current western margin orientated in a West-East direction North America must have collided during the Late Cretaceous Laramide orogeny with the northern margin of South America (Caribbean Andes) at the equator to the West of the Late Mesozoic Pacific. During post-Laramide times it must have rotated clockwise into its present orientation. The eastern margin of North America has never been attached to the western margin of North Africa but only to the western margin of Europe. (7) Due to migration eastwards of the sequence of ocean styles of the Wilson Cycle, relative to a distinct plate tectonic setting of an ocean, a continent or continental margin, a future or later evolutionary style at the Earth's surface is always depicted in a setting simultaneously developed further to the West and a past or earlier style in a setting simultaneously occurring further to the East. In consequence, ahigh probability exists that up to the Early Tertiary, Greenland (the ArabiaofSouth America?) occupied a plate tectonic setting which is comparable to the current setting of Arabia (the Greenland of Africa?). The Late Cretaceous/Early Tertiary Eureka collision zone (Eureka orogeny) at the northern margin of the Greenland Plate and on some of the Canadian Arctic Islands is comparable with the Middle to Late Tertiary Taurus-Bitlis-Zagros collision zone at the northern margin of the Arabian Plate.

Population demography and the evolution of helping behaviors.

Limited dispersal may favor the evolution of helping behaviors between relatives as it increases their relatedness, and it may inhibit such evolution as it increases local competition between these relatives. Here, we explore one way out of this dilemma: if the helping behavior allows groups to expand in size, then the kin-competition pressure opposing its evolution can be greatly reduced. We explore the effects of two kinds of stochasticity allowing for such deme expansion. First, we study the evolution of helping under environmental stochasticity that may induce complete patch extinction. Helping evolves if it results in a decrease in the probability of extinction or if it enhances the rate of patch recolonization through propagules formed by fission of nonextinct groups. This mode of dispersal is indeed commonly found in social species. Second, we consider the evolution of helping in the presence of demographic stochasticity. When fecundity is below its value maximizing deme size (undersaturation), helping evolves, but under stringent conditions unless positive density dependence (Allee effect) interferes with demographic stochasticity. When fecundity is above its value maximizing deme size (oversaturation), helping may also evolve, but only if it reduces negative density-dependent competition.

The role of trust and its evolution in distributed teams in a multinational organisation

Tutkimuksen päätavoitteena on ollut selvittää miten kansallinen ja organisaatiokulttuuri, niihin liittyvät normit ja arvot edesauttavat tai vaikeuttavat luottamuksen kehittymistä monikulttuurisissa tiimeissä maailmanlaajuisessa organisaatiossa. Tutkimuksen avulla haluttiin myös selvittää miten luottamus kehittyy hajautetuissa monikansallisissa tiimeissä WorldCom Internationalissa. Empiirinen tutkimusmenetelmä perustuu kvalitatiivisiin teemahaastatteluihin, jotka tehtiin WorldComin työntekijöille. Tutkimuksessa havaittiin, ettei yhteisten sosiaalisten normien merkitys luottamuksen syntymiselle ole niin merkittävä, koska WorldComin yhtenäiset toimintatavat sekä hallitseva amerikkalaisen emoyhtiön "kotikulttuuri" muodostavat yhtenäiset toimintalinjat tiimeissä. Tietokonevälitteisen kommunikoinnin jatkuva käyttö on edesauttanut työntekijöiden ns. sosiaalisen älyn kehittymistä, sillä henkilökohtaisen tapaamisen puuttuminen kehittää vastaavasti taitoja aistia ja tulkita sähköpostien tai puhelinneuvotteluiden aikana välittyviä vastapuolen "näkymättömiä" vihjeitä.

Three rounds (1R/2R/3R) of genome duplications and the evolution of the glycolytic pathway in vertebrates

Affiliation: Henner Brinkmann : Département de biochimie, Faculté de médecine, Université de Montreal

Systematics and floral evolution of the Dialiinae (Caesalpinioideae), a diverse lineage of tropical legumes

Le clade Dialiinae représente l’une des premières lignées de la sous-famille Caesalpinioideae des Leguminosae. Il se compose de 17 genres (environ 90 espèces), avec des taxons qui sont répandus dans toutes les régions tropicales du monde. Morphologiquement, le groupe comprend un assemblage divers de taxons qui peut représenter une «phase expérimentale» dans l’évolution florale des légumineuses. Différents représentants du clade présentent de la poly-, mono-, et asymétrie, et semblent avoir subi un haut degré de perte d’organe, produisant, dans certains cas, des fleurs extrêmement réduites qui sont à peine reconnaissables comme appartenant à la famille des légumineuses. Afin d’obtenir une image plus claire de l’évolution florale du clade Dialiinae, une phylogénie bien résolue et bien soutenue est nécessaire. Dans le but de créer une telle phylogénie, un total de 37 échantillons d’ADN des Dialiinae a été séquencé pour deux régions chloroplastiques, soit rps16 et trnL. De plus, une étude morphologique complète a été réalisée. Un total de 135 caractères végétatifs et reproductifs a été évalué pour 79 espèces de Dialiinae et pour quatre groupes externes. Les analyses phylogénétiques ont d’abord été effectuées sur un groupe restreint de taxons pour lesquels les trois types de données étaient disponibles. Les nœuds fortement soutenus de cette phylogénie ont ensuite été utilisés comme contrainte pour une seconde analyse de parcimonie avec les données morphologiques d’un ensemble plus important de taxons. Les caractères morphologiques ont été optimisés sur l’un des arbres les plus parcimonieux de cette seconde analyse. Un certain nombre de nouvelles relations au niveau de l’espèce ont été résolues, créant une image plus claire quant à l’évolution de la forme florale dans le temps, particulièrement pour les genres Labichea et Dialium. En plus de leur morphologie florale mature diverse, les Dialiinae sont également très variables dans leur ontogénèse florale, affichant à la fois la perte et la suppression des organes, et présentant une variété de modes d’initiation d’organes. Afin de construire une image plus complète du développement floral et de l’évolution dans ce clade, l’ontogénèse florale de plusieurs espèces non documentées à ce jour a été étudiée. La série complète du développement a été compilée pour six espèces de Dialiinae; quatre de Dialium, ainsi que Poeppigia procera et Mendoravia dumaziana. Le mode et le moment de l’initiation des organes étaient pour la plupart uniforme pour toutes les espèces de Dialium étudiés. Tant pour ce qui est des gains ou des pertes d’organes chez Dialium, une tendance est apparente – l’absence d’organe abaxial. Que ce soit pour les sépales ou les étamines, les gains se produisent toujours en position médiane adaxiale, tandis que les étamines et les pétales perdus sont toujours les organes les plus ventraux. Les taxons étudiés ici illustrent le manque apparent de canalisation du développement observé chez les Caesalpinioideae. Cette plasticité ontogénétique est le reflet de la diversité morphologique au niveau des fleurs tel qu’observée dans l’ensemble de la sous-famille. Une des espèces de Dialiinae, Apuleia leiocarpa, produit une inflorescence andromonoïque, une caractéristique qui est unique en son clade et rare dans les légumineuses dans son ensemble. La microscopie optique et électronique ont été utilisées pour entreprendre une étude détaillée de la morphologie florale de ce taxon. On a constaté que tandis que les fleurs hermaphrodites produisent un seul carpelle et deux étamines, les fleurs staminées produisent trois étamines sans toutefois montrer signe de développement du carpelle. Les inflorescences semblent produire près de quatre fois plus de fleurs staminées que de fleurs hermaphrodites, lesquelles occupent toujours la position centrale de l’inflorescence cymeuse. Ce ratio élevé mâle/bisexuel et la détermination précoce du sexe chez Apuleia sont rares chez les Caesalpinioideae, ce qui suggère que l’andromonoecie se développe dans ce genre comme un moyen d’accroître la dispersion du pollen plutôt qu’en réponse à des limitations de ressources.

Temporal and spatial evolution of laser ablated plasma from YBa2Cu3O7

YBa2Cu307 target was laser ablated, and the time-of-flight (TOF) distributions of Y, Y+., and YO in the resultant plasma were investigated as functions of distance from the target and laser energy density using emission spectroscopy. Up to a short distance from the target (-1.5 cm), TOF distributions show twin peaks for Y and YO, while only single-peak distribution is observed for Y+. At greater distances (>1.5 cm) all of them exhibit single-peak distribution. The twin peaks are assigned to species corresponding to those generated directly/m the vicinity of target surface and to those generated from collisional/recombination process.

Temporal and spatial evolution of C2 in laser induced plasma from graphite target

Laser ablation of graphite has been carried out using 1.06mm radiation from a Q-switched Nd:YAG laser and the time of flight distribution of molecular C2 present in the resultant plasma is investigated in terms of distance from the target as well as laser fluences employing time resolved spectroscopic technique. At low laser fluences the intensities of the emission lines from C2 exhibit only single peak structure while beyond a threshold laser fluence, emission from C2 shows a twin peak distribution in time. The occurrence of the faster velocity component at higher laser fluences is explained as due to species generated from recombination processes while the delayed peak is attributed to dissociation of higher carbon clusters resulting in the generation of C2 molecule. Analysis of measured data provides a fairly complete picture of the evolution and dynamics of C2 species in the laser induced plasma from graphite.

Swift heavy ion induced surface and microstructural evolution in metallic glass thin films

Swift heavy ion induced changes in microstructure and surface morphology of vapor deposited Fe–Ni based metallic glass thin films have been investigated by using atomic force microscopy, X-ray diffraction and transmission electron microscopy. Ion beam irradiation was carried out at room temperature with 103 MeV Au9+ beam with fluences ranging from 3 1011 to 3 1013 ions/cm2. The atomic force microscopy images were subjected to power spectral density analysis and roughness analysis using an image analysis software. Clusters were found in the image of as-deposited samples, which indicates that the film growth is dominated by the island growth mode. As-deposited films were amorphous as evidenced from X-ray diffraction; however, high resolution transmission electron microscopy measurements revealed a short range atomic order in the samples with crystallites of size around 3 nm embedded in an amorphous matrix. X-ray diffraction pattern of the as-deposited films after irradiation does not show any appreciable changes, indicating that the passage of swift heavy ions stabilizes the short range atomic ordering, or even creates further amorphization. The crystallinity of the as-deposited Fe–Ni based films was improved by thermal annealing, and diffraction results indicated that ion beam irradiation on annealed samples results in grain fragmentation. On bombarding annealed films, the surface roughness of the films decreased initially, then, at higher fluences it increased. The observed change in surface morphology of the irradiated films is attributed to the interplay between ion induced sputtering, volume diffusion and surface diffusion

Structural, topographical and magnetic evolution of RF-sputtered Fe-Ni alloy based thin films with thermal annealing

Metglas 2826 MB having a nominal composition of Fe40Ni38Mo4B18 is an excellent soft magnetic material and finds application in sensors and memory heads. However, the thin-film forms of Fe40Ni38Mo4B18 are seldom studied, although they are important in micro-electro-mechanical systems/nano-electromechanical systems devices. The stoichiometry of the film plays a vital role in determining the structural and magnetic properties of Fe40Ni38Mo4B18 thin films: retaining the composition in thin films is a challenge. Thin films of 52 nm thickness were fabricated by RF sputtering technique on silicon substrate from a target of nominal composition of Fe40Ni38Mo4B18. The films were annealed at temperatures of 400 °C and 600 °C. The micro-structural studies of films using glancing x-ray diffractometer (GXRD) and transmission electron microscope (TEM) revealed that pristine films are crystalline with (FeNiMo)23B6 phase. Atomic force microscope (AFM) images were subjected to power spectral density analysis to understand the probable surface evolution mechanism during sputtering and annealing. X-ray photoelectron spectroscopy (XPS) was employed to determine the film composition. The sluggish growth of crystallites with annealing is attributed to the presence of molybdenum in the thin film. The observed changes in magnetic properties were correlated with annealing induced structural, compositional and morphological changes