Origin and evolution of coastal talus-platforms (fajãs) with pond systems in oceanic volcanic islands

Dissertação de Mestrado, Geologia do Ambiente e Sociedade, 15 de Fevereiro de 2016, Universidade dos Açores.

Origin and evolution of Upper Triassic to Miocene clay-mineral associations from the eastern Algarve of Portugal

XRD-analyses of pelitic deposits of Upper Jurassic to Miocene age occuring in the eastern Algarve (Portugal), give evidence of the occurrence of detrital clay minerals of continental origin as well as of conspicuous neoformations of marine provenance. The vertical succession of clay-mineral associations indicates the existence of three distinctive evolutionary cycles which are thought to reflect tectonically controlled transgressive-regressive events.

Origen y evolución del magma granítico en el Batolito de Achala: Fundamentos petrológicos, geoquímicos y estructurales para la preconcentración uranífera en el área de Cañada del Puerto. Origin and evolution of the granitic magma in the Achala Batholith: petrological, geochemical and structural constraint for the uranium preconcentration in the Cañada del Puerto area.

El batolito de Achala es uno de los macizos graníticos más grandes de las Sierras Pampeanas, el cual se localiza en las Sierras Grandes de Córdoba. Si bien el batolito de Achala ha sido objeto de diversos estudios geológicos, principalmente debido a sus yacimientos de uranio, el mismo todavía no posee un inequívoco modelo petrogéntico. Tampoco existe, en la actualidad, un inequívoco modelo que explique la preconcentración de uranio en las rocas graníticas portadores de este elemento. Este Proyecto tiene como objetivo general realizar estudios petrológicos y geoquímicos en la región conocida como CAÑADA del PUERTO, un lugar estratégicamente definido debido a la abundancia de granitos equigranulares de grano fino y/o grano medio biotíticos, emplazados durante el desarrollo de cizallas magmáticas tardías, y que constituirían las rocas fuentes de uranio. El objetivo específico requiere estudios detallados de las diferentes facies del batolito de Achala en el área seleccionada, incluyendo investigaciones petrológicas, geoquímicas de roca total, geoquímica de isótopos radiactivos y química mineral, con el fin de definir un MODELO PETROGENÉTICO que permita explicar: (a) el origen del magma padre y el subsiguiente proceso de cristalización de las diferentes facies graníticas aflorantes en el área de estudio, (b) identificar el proceso principal que condujo a la PRECONCENTRACIÓN uranífera de los magmas graníticos canalizados en las cizallas magmáticas tardías. Ambos objetivos se complementan y no son compartimentos estancos, ya que el logro combinado de estos objetivos permitirá comprender de mejor manera el proceso geoquímico que gobernó la distribución y concentración del U. De esta manera, se intentará definir un MODELO de PRECONCENTRACIÓN URANÍFERA EXTRAPOLABLE a otras áreas graníticas enriquecidas en uranio, constituyendo una poderosa herramienta de investigación aplicada a la exploración uranífera. En particular, el conocimiento de los recursos uraníferos es parte de una estrategia nacional con vistas a triplicar antes del 2025 la disponibilidad energética actual, en cuyo caso, el uranio constituye la materia prima de las centrales nucleares que se están planificando y en construcción. Por otro lado, la Argentina adhirió al Protocolo de Kioto y, junto a los países adherentes, deben disminuir de manera progresiva el uso de combustibles fósiles (que producen gases de efecto invernadero), reemplazándola por otras fuentes de energía, entre ellas, la ENERGÍA NUCLEAR. Este Proyecto, si bien NO es un Proyecto de exploración y/o prospección minera, es totalmente consistente con la política energética nacional promocionada desde el Ministerio de Planificación Federal, Inversión Pública y Servicios (v. sitio WEB CNEA), que ha invertido, desde 2006, importantes sumas de dinero, en el marco del Programa de Reactivación de la Actividad Nuclear.Los estudios referidos serán conducidos por los Drs. Dahlquist (CONICET-UNC) y Zarco (CNEA) quienes integrarán sus experiencias desarrolladas en el campo de las Ciencias Básicas con aquel logrado en el campo de las Ciencias Aplicadas, respectivamente. Se pretende, por tanto, aplicar conocimientos académicos-científicos a un problema de geología con potencial significado económico-energético, vinculando las instituciones referidas, esto es, CONICET-UNC y CNEA, con el fin de contribuir a la actividad socioeconómica de la provincia de Córdoba en particular y de Argentina en general.Finalmente, convencidos de que el progreso de la Ciencia y el Desarrollo Tecnológico está íntimamente vinculada con la sólida Formación de Recursos Humanos se pretende que este Proyecto contribuya SIGNIFICATIVAMENTE a las investigaciones de Doctorado que iniciará la Geóloga Carina Bello, actual Becaria de la CNEA.

Speculations on the origin and evolution of the genus Leishmania

Recently two hypotheses have been proposed for the evolution of Leishmania involving respectively a Neotropical or Paleartic origin for the species. Here an alternative proposal on the phylogeny of Leishmania based on the major divisions within the genus is presented. In this hypothesis a Neotropic origin is retained for L. (Viannia) and Paraleishmania, a recently desribed section within the genus Leishmania, while an African origin is proposed for L. (Leishmania) and possibly Sauroleishmania. The current distribution of Leishmania in the Neotropics is explained as the product of multiple introductions of Leishmania parasites into the New World. Problems with organismal identity in Sauroleishmania and the use of molecular sequence data in inferring phylogenies are also discussed.

The role of gene duplication in the origin and evolution of new biological functions

Abstract : Gene duplication is an essential source of material for the origin of genetic novelty and the evolution of lineage- or species-specific phenotypic traits. The reverse transcription of source gene mRNA followed by the genomic insertion of the resulting cDNA - retroposition - has provided the human genome with a significant number of gene copies during the last ~63 million years (MYA) of primate evolution. We estimated that at least 1 new functional gene (retrogene) per MYA emerged by retroposition in the primate lineage leading to humans. Using a combination of comparative sequencing and evolutionary simulations, we obtained strong evidence of functionality for 7 primate specific retrogenes. Most of these genes are specifically expressed in testis suggesting that retroposition has contributed with genetic raw material necessary for the evolution ofmale-specific functions in primates. We characterized CDC14Bretro (identified in the previous survey) that originated from the retroposition of a cell cycle gene - CDC14B - in the common ancestor of humans and apes. We demonstrate that CDC14Bretro experienced a period of intense positive selection in the African ape ancestor. By virtue of the amino acid substitutions that occurred during this period CDC 14Bretro adapted to a new subcellular compartment in African apes. Further analyses indicate that this subcellular shift reflects the evolution of anew functional role of CDC 14Bretro. Prompted by this result, we used yeast (Saccharomyces cerevisiae) to investigate on a global scale the extent of functional diversification of duplicate genes through the subcellular adaptation of their encoded proteins. We found that duplicate proteins frequently evolved new cellular localization patterns, either by partitioning of ancestral localizations ("sublocalization"), or more frequently by relocalization to previously unoccupied compartments ("neolocalization"). Interestingly, proteins involved in processes with a wider subcellular distribution more frequently evolved new localization patterns suggesting that subcellular localization changes are dependent on progenitor gene functions. Relocated proteins adapted to their new subcellular environments and evolved new functional roles through changes of their physio-chemical properties, expression levels, and interaction partners. Our work suggests an important role of subcellular adaptation for the emergence of new gene functions.

Origin and evolution of homologous repeated sequences in the mitochondrial DNA control region of shrews.

The complete mitochondrial DNA (mtDNA) control region was amplified and directly sequenced in two species of shrew, Crocidura russula and Sorex araneus (Insectivora, Mammalia). The general organization is similar to that found in other mammals: a central conserved region surrounded by two more variable domains. However, we have found in shrews the simultaneous presence of arrays of tandem repeats in potential locations where repeats tend to occur separately in other mammalian species. These locations correspond to regions which are associated with a possible interruption of the replication processes, either at the end of the three-stranded D-loop structure or toward the end of the heavy-strand replication. In the left domain the repeated sequences (R1 repeats) are 78 bp long, whereas in the right domain the repeats are 12 bp long in C. russula and 14 bp long in S. araneus (R2 repeats). Variation in the copy number of these repeated sequences results in mtDNA control region length differences. Southern blot analysis indicates that level of heteroplasmy (more than one mtDNA form within an individual) differs between species. A comparative study of the R2 repeats in 12 additional species representing three shrew subfamilies provides useful indications for the understanding of the origin and the evolution of these homologous tandemly repeated sequences. An asymmetry in the distribution of variants within the arrays, as well as the constant occurrence of shorter repeated sequences flanking only one side of the R2 arrays, could be related to asymmetry in the replication of each strand of the mtDNA molecule. The pattern of sequence and length variation within and between species, together with the capability of the arrays to form stable secondary structures, suggests that the dominant mechanism involved in the evolution of these arrays in unidirectional replication slippage.

Origin and evolution of 3'UTR of flaviviruses: long direct repeats as a basis for the formation of secondary structures and their significance for virus transmission

The 3' untranslated regions (3'UTRs) of flaviviruses are reviewed and analyzed in relation to short sequences conserved as direct repeats (DRs). Previously, alignments of the 3'UTRs have been constructed for three of the four recognized flavivirus groups, namely mosquito-borne, tick-borne, and nonclassified flaviviruses (MBFV, TBFV, and NCFV, respectively). This revealed (1) six long repeat sequences (LRSs) in the 3'UTR and open-reading frame (ORF) of the TBFV, (2) duplication of the 3'UTR of the NCFV by intramolecular recombination, and (3) the possibility of a common origin for all DRs within the MBFV. We have now extended this analysis and review it in the context of all previous published analyses. This has been achieved by constructing a robust alignment between all flaviviruses using the published DRs and secondary RNA structures as "anchors" to reveal additional homologies along the 3'UTR. This approach identified nucleotide regions within the MBFV, NKV (no-known vector viruses), and NCFV 3'UTRs that are homologous to different LRSs in the TBFV 3'UTR and ORF. The analysis revealed that some of the DRs and secondary RNA structures described individually within each flavivirus group share common evolutionary origins. The 3'UTR of flaviviruses, and possibly the ORF, therefore probably evolved through multiple duplication of an RNA domain, homologous to the LRS previously identified only in the TBFV. The short DRs in all virus groups appear to represent the evolutionary remnants of these domains rather than resulting from new duplications. The relevance of these flavivirus DRs to evolution, diversity, 3'UTR enhancer function, and virus transmission is reviewed.

Origin and evolution of flavivirus 5'UTRs and panhandles: trans-terminal duplications?

Flavivirus replication is mediated by interactions between complementary ssRNA sequences of the 5'- and 3'-termini that form dsRNA cyclisation stems or panhandles, varying in length, sequence and specific location in the mosquito-borne, tick-borne, non-vectored and non-classified flaviviruses. In this manuscript we manually aligned the flavivirus 5'UTRs and adjacent capsid genes and revealed significantly more homology than has hitherto been identified. Analysis of the alignments revealed that the panhandles represent evolutionary remnants of a long cyclisation domain that probably emerged through duplication of one of the UTR termini.

Origin and evolution of a myxozoan worm

Buddenbrockia pluinatellae is an active, muscular, worm-shaped parasite of freshwater bryozoans. This rare and enigmatic animal has been assigned to the Myxozoa on the basis of 18S ribosomal DNA sequences and the presence of malacosporean spores. Here we report cloning of four homologous protein-coding genes from Buddenbrockia worms, the putatively conspecific sac-shaped parasite originally described as Tetracapsula bryozoides and the related sac-shaped parasite Tetracapsuloides bryosalmonae, the causative agent of proliferative kidney disease in salmonid fish. Analyses are consistent with the hypothesis that Buddenbrockia is indeed a malacosporean myxozoan, but do not provide support for conspecificity with either T. bryozoides or T. bryosalmonae. Implications for the evolution of worm-like body plans in the Myxozoa are discussed.

ORIGIN and EVOLUTION of DOMESTIC CATTLE

The origin and evolution of domestic cattle have recently moved to the forefront of the scientific literature in consideration of their links to human history and to decisions on Genetic Resources conservation strategies. DNA from modern and ancient Bos samples is being analysed to reconstruct, in cooperation with archaezoology, the main events and forces that shaped nowadays cattle genetic diversity. Still, a number of open questions remain, that hopefully will be answered with the help of new technologies and the combined analysis of worldwide data.

RFLP and cytogenetic evidence on the origin and evolution of allotetraploid domesticated peanut, Arachis hypogaea (Leguminosae)

Nuclear restriction fragment length polymorphism (RFLP) analysis was used to determine the wild diploid Arachis species that hybridized to form tetraploid domesticated peanut. Results using 20 previously mapped cDNA clones strongly indicated A. duranensis as the progenitor of the A genome of domesticated peanut and A. ipaensis as the B genome parent. A large amount of RFLP variability was found among the various accessions of A. duranensis, and accessions most similar to the A genome of cultivated peanut were identified. Chloroplast DNA RFLP analysis determined that A. duranensis was the female parent of the original hybridization event. Domesticated peanut is known to have one genome with a distinctly smaller pair of chromosomes ('A'), and one genome that lacks this pair. Cytogenetic analysis demonstrated that A. duranensis has a pair of 'A' chromosomes, and A. ipaensis does not. The cytogenetic evidence is thus consistent with the RFLP evidence concerning the identify of the progenitors. RFLP and cytogenetic evidence indicate a single origin for domesticated peanut in Northern Argentina or Southern Bolivia, followed by diversification under the influence of cultivation.

Origin and Evolution of B Chromosomes in the Cichlid Fish Astatotilapia latifasciata Based on Integrated Genomic Analyses

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Origin and evolution of reactive and noble gases dissolved in matrix pore water

Reactive and noble gases dissolved in matrix pore water of low permeable crystalline bedrock were successfully extracted and characterized for the fist time based on drillcore samples from the Olkiluoto investigation site (SW Finland). Interaction between matrix pore water and fracture groundwater occurs predominately by diffusion. Changes in the chemical and isotopic composition of gases dissolved in fracture groundwater are transmitted and preserved in the pore water. Absolute concentrations, their ratios and the stable carbon isotope signature of hydrocarbon gases dissolved in pore water give valuable indications about the evolution of these gases in the nearby-flowing fracture groundwaters. Inert noble gases dissolved in matrix pore water and their isotopes combined with their in-situ production and accumulation rates deliver information about the residence time of pore water.

Origin and evolution of Cycladophora davisiana (Radiolaria) in DSDP Hole 19-192, Northwest Pacific

This paper documents the evolutionary history of Cycladophora davisiana Ehrenberg from an uppermost Miocene to Pleistocene sedimentary record in the high-latitude Northwest Pacific. It apparently evolved from C. sakaii Motoyama through a series of intermediates. C. sakaii has a relatively large shell with an external spongy layer. The evolutionary transition is characterized by a relatively rapid decrease in thorax size with a reduction of the spongy appendage. This change occurred during about 0.4 m.y. from 2.8 to 2.4 Ma without cladogenesis. Following this interval, a decrease in thorax size continued gradually up to the Recent, resulting in a very small morphology. Although the population of C. davisiana first appeared at about 2.5 Ma, some morphotypic specimens may occur in earlier periods as indistinguishable very small endmembers in the C. sakaii populations. Timing of the first appearance events both of morphotypic specimens and of a population of C. davisiana in Site 192 and previously reported cores does not disprove the idea that C. davisiana evolved first in the Northwest Pacific region, and later migrated into other regions of the world ocean. Biometrics clearly indicate no direct phylogenetic relationships between C. davisiana and C. cornutoides Kling in the studied core. Thus, the latter species, which was originally described as a variation and later elevated to a subspecies of the former species, is separated from the former species and raised to the species rank.