Assessment of genotoxicity in oral epithelial cells of health professionals occupationally exposed to ionizing radiations

Dissertação de Mestrado em Ambiente, Saúde e Segurança.

Geometric morphometric analyses provide evidence for the adaptive character of the Tanganyikan cichlid fish radiations.

The cichlids of East Africa are renowned as one of the most spectacular examples of adaptive radiation. They provide a unique opportunity to investigate the relationships between ecology, morphological diversity, and phylogeny in producing such remarkable diversity. Nevertheless, the parameters of the adaptive radiations of these fish have not been satisfactorily quantified yet. Lake Tanganyika possesses all of the major lineages of East African cichlid fish, so by using geometric morphometrics and comparative analyses of ecology and morphology, in an explicitly phylogenetic context, we quantify the role of ecology in driving adaptive speciation. We used geometric morphometric methods to describe the body shape of over 1000 specimens of East African cichlid fish, with a focus on the Lake Tanganyika species assemblage, which is composed of more than 200 endemic species. The main differences in shape concern the length of the whole body and the relative sizes of the head and caudal peduncle. We investigated the influence of phylogeny on similarity of shape using both distance-based and variance partitioning methods, finding that phylogenetic inertia exerts little influence on overall body shape. Therefore, we quantified the relative effect of major ecological traits on shape using phylogenetic generalized least squares and disparity analyses. These analyses conclude that body shape is most strongly predicted by feeding preferences (i.e., trophic niches) and the water depths at which species occur. Furthermore, the morphological disparity within tribes indicates that even though the morphological diversification associated with explosive speciation has happened in only a few tribes of the Tanganyikan assemblage, the potential to evolve diverse morphologies exists in all tribes. Quantitative data support the existence of extensive parallelism in several independent adaptive radiations in Lake Tanganyika. Notably, Tanganyikan mouthbrooders belonging to the C-lineage and the substrate spawning Lamprologini have evolved a multitude of different shapes from elongated and Lamprologus-like hypothetical ancestors. Together, these data demonstrate strong support for the adaptive character of East African cichlid radiations.

Effects of a fire response trait on diversification in replicated radiations.

Fire has been proposed as a factor explaining the exceptional plant species richness found in Mediterranean regions. A fire response trait that allows plants to cope with frequent fire by either reseeding or resprouting could differentially affect rates of species diversification. However, little is known about the generality of the effects of differing fire response on species evolution. We study this question in the Restionaceae, a family that radiated in Southern Africa and Australia. These radiations occurred independently and represent evolutionary replicates. We apply Bayesian approaches to estimate trait-specific diversification rates and patterns of climatic niche evolution. We also compare the climatic heterogeneity of South Africa and Australia. Reseeders diversify faster than resprouters in South Africa, but not in Australia. We show that climatic preferences evolve more rapidly in reseeder lineages than in resprouters and that the optima of these climatic preferences differ between the two strategies. We find that South Africa is more climatically heterogeneous than Australia, independent of the spatial scale we consider. We propose that rapid shifts between states of the fire response trait promote speciation by separating species ecologically, but this only happens when the landscape is sufficiently heterogeneous.

Molluscan radiations and landscape evolution in Miocene Amazonia

This PhD study aims to exploit the rich archive provided by the Miocene mollusc fauna of the Pebas Formation and other inland Miocene Amazonian formations to reconstruct landscape evolution and biotic development in lowland Amazonia during the Neogene. Over 160 samples from more than 70 Pebas Formation outcrops mostly collected by the author were processed for this study. Additional samples were collected in Andean areas of Colombia and Venezuela and further material from other northwestern South American basins was studied in museums. Pebas Formation samples and well log data made available by Occidental Peru from three wells in the Marañon Basin in Peru were also investigated. During this study four genera and 74 species from the Pebas Formation have been described and a further 13 species have been introduced in open nomenclature, and several species were reported for the first time. The number of mollusc species attributed to the Pebas fauna has increased from around 50 to 156. The Pebas fauna is characterised as aquatic, endemic and extinct, and is a typical representative of a long-lived lake fauna. Fluvial taxa are not common, (marginal) marine taxa are rare. An additional molluscan fauna from the Miocene Solimões Formation of Brazil, containing 13 fresh water species was also described. The newly documented fauna was used to improve biostratigraphic framework of Miocene Amazonian deposits. Twelve mollusc zones were introduced, the upper eleven of which cover a time interval of approximately seven million years covered previously by only three pollen zones. An age model calculated for the borehole data indicates that the Pebas Formation was deposited between c. 24 and 11 Ma. The areal distribution of the outcropping mollusc zones uncovered a broad dome structure, termed here the Iquitos-Araracuara anteclise in the study area. The structure appears to have influenced river courses and also contributed to edaphic heterogeneity that may have been in part responsible for the current high biodiversity in the study area. The Pebas system was a huge system (> one million km2) dominated by relatively shallow lakes, but also containing swamps and rivers. The system was fed by rivers draining the emergent Andes in the west and lowlands and cratons to the east. The Pebas system was located at sea level and was open to marine settings through a northern portal running through the Llanos Basin and East Venezuela Basin towards the Caribbean. Cyclical baselevel changes possibly related to Mylankhovitch cycles, have been documented in depositional sequences of the Pebas Formation. The composition of the Pebasian mollusc fauna implies that the system was mostly a fresh water system. Such an interpretation is matched by strontium isotope ratios as well as very negative δ18O ratios found in the shells, but is at odds with oligohaline and mesohaline ichnofacies found in the same strata. The mollusc fauna of the Pebas Formation diversified through most of the existence of the lake system. The diversification was mostly the result of in-situ cladogenesis. The success of some of the Pebasian endemic clades is explained by adaptation to fresh water, low oxygen, common unconsolidated lake bottoms (soup grounds) as well as high predation intensity. Maximum diversity was reached at the base of the late Middle to early Late Miocene Grimsdalea pollen zone, some 13 Ma. At the time some 85 species co-occurred, 67 of which are considered as Pebasian endemics. A subsequent drop in species richness coincides with indications of elevated salinities, although a causal relation still needs to be established. Apparently the Pebas fauna went (almost) entirely extinct with the replacement of the lake system into a fluvio-tidal system during the Early Late Miocene, some 11 Ma.

Induction of Mitotic Chromosomal Aberrations by Lasers in Comparison to Gamma Radiations

Laser irradiation at wavelength 514 nm was used to study the effect, of lasers in inducing chromosomal aberrations at mitosis. This study offers a new radiation system which could be used for the induction of mutations. Results are compared with those obtained from studies using y-rays as irradiation source.

Genotypic sex determination enabled adaptive radiations of extinct marine reptiles

Adaptive radiations often follow the evolution of key traits, such as the origin of the amniotic egg and the subsequent radiation of terrestrial vertebrates. The mechanism by which a species determines the sex of its offspring has been linked to critical ecological and life-history traits(1-3) but not to major adaptive radiations, in part because sex-determining mechanisms do not fossilize. Here we establish a previously unknown coevolutionary relationship in 94 amniote species between sex-determining mechanism and whether a species bears live young or lays eggs. We use that relationship to predict the sex-determining mechanism in three independent lineages of extinct Mesozoic marine reptiles (mosasaurs, sauropterygians and ichthyosaurs), each of which is known from fossils to have evolved live birth(4-7). Our results indicate that each lineage evolved genotypic sex determination before acquiring live birth. This enabled their pelagic radiations, where the relatively stable temperatures of the open ocean constrain temperature-dependent sex determination in amniote species. Freed from the need to move and nest on land(4,5,8), extreme physical adaptations to a pelagic lifestyle evolved in each group, such as the fluked tails, dorsal fins and wing-shaped limbs of ichthyosaurs. With the inclusion of ichthyosaurs, mosasaurs and sauropterygians, genotypic sex determination is present in all known fully pelagic amniote groups (sea snakes, sirenians and cetaceans), suggesting that this mode of sex determination and the subsequent evolution of live birth are key traits required for marine adaptive radiations in amniote lineages.

DNA barcode discovers two cryptic species and two geographical radiations in the invasive drosophilid Zaprionus indianus

Comparing introduced to ancestral populations within a phylogeographical context is crucial in any study aiming to understand the ecological genetics of an invasive species. Zaprionus indianus is a cosmopolitan drosophilid that has recently succeeded to expand its geographical range upon three continents (Africa, Asia and the Americas). We studied the distribution of mitochondrial DNA (mtDNA) haplotypes for two genes (CO-I and CO-II) among 23 geographical populations. mtDNA revealed the presence of two well-supported phylogenetic lineages (phylads), with bootstrap value of 100%. Phylad I included three African populations, reinforcing the African-origin hypothesis of the species. Within phylad II, a distinct phylogeographical pattern was discovered: Atlantic populations (from the Americas and Madeira) were closer to the ancestral African populations than to Eastern ones (from Madagascar, Middle East and India). This means that during its passage from endemism to cosmopolitanism, Z. indianus exhibited two independent radiations, the older (the Eastern) to the East, and the younger (the Atlantic) to the West. Discriminant function analysis using 13 morphometrical characters was also able to discriminate between the two molecular phylads (93.34 +/- 1.67%), although detailed morphological analysis of male genitalia using scanning electron microscopy showed no significant differences. Finally, crossing experiments revealed the presence of reproductive barrier between populations from the two phylads, and further between populations within phylad I. Hence, a bona species status was assigned to two new, cryptic species: Zaprionus africanus and Zaprionus gabonicus, and both were encompassed along with Z. indianus and Zaprionus megalorchis into the indianus complex. The ecology of these two species reveals that they are forest dwellers, which explains their restricted endemic distribution, in contrast to their relative cosmopolitan Z. indianus, known to be a human-commensal. Our results reconfirm the great utility of mtDNA at both inter- and intraspecific analyses within the frame of an integrated taxonomical project.

Analysis of hourly global, direct and diffuse solar radiations attenuation as a function of optical air mass

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

A molecular phylogeny of bivalve mollusks: ancient radiations and divergences as revealed by mitochondrial genes

The main scope of my PhD is the reconstruction of the large-scale bivalve phylogeny on the basis of four mitochondrial genes, with samples taken from all major groups of the class. To my knowledge, it is the first attempt of such a breadth in Bivalvia. I decided to focus on both ribosomal and protein coding DNA sequences (two ribosomal encoding genes -12s and 16s -, and two protein coding ones - cytochrome c oxidase I and cytochrome b), since either bibliography and my preliminary results confirmed the importance of combined gene signals in improving evolutionary pathways of the group. Moreover, I wanted to propose a methodological pipeline that proved to be useful to obtain robust results in bivalves phylogeny. Actually, best-performing taxon sampling and alignment strategies were tested, and several data partitioning and molecular evolution models were analyzed, thus demonstrating the importance of molding and implementing non-trivial evolutionary models. In the line of a more rigorous approach to data analysis, I also proposed a new method to assess taxon sampling, by developing Clarke and Warwick statistics: taxon sampling is a major concern in phylogenetic studies, and incomplete, biased, or improper taxon assemblies can lead to misleading results in reconstructing evolutionary trees. Theoretical methods are already available to optimize taxon choice in phylogenetic analyses, but most involve some knowledge about genetic relationships of the group of interest, or even a well-established phylogeny itself; these data are not always available in general phylogenetic applications. The method I proposed measures the "phylogenetic representativeness" of a given sample or set of samples and it is based entirely on the pre-existing available taxonomy of the ingroup, which is commonly known to investigators. Moreover, it also accounts for instability and discordance in taxonomies. A Python-based script suite, called PhyRe, has been developed to implement all analyses.

Rapid parallel adaptive radiations from a single hybridogenic ancestral population

The Alpine lake whitefish (Coregonus lavaretus) species complex is a classic example of a recent radiation, associated with colonization of the Alpine lakes following the glacial retreat (less than 15 kyr BP). They have formed a unique array of endemic lake flocks, each with one to six described sympatric species differing in morphology, diet and reproductive ecology. Here, we present a genomic investigation of the relationships between and within the lake flocks. Comparing the signal between over 1000 AFLP loci and mitochondrial control region sequence data, we use phylogenetic tree-based and population genetic methods to reconstruct the phylogenetic history of the group and to delineate the principal centres of genetic diversity within the radiation. We find significant cytonuclear discordance showing that the genomically monophyletic Alpine whitefish clade arose from a hybrid swarm of at least two glacial refugial lineages. Within this radiation, we find seven extant genetic clusters centred on seven lake systems. Most interestingly, we find evidence of sympatric speciation within and parallel evolution of equivalent phenotypes among these lake systems. However, we also find the genetic signature of human-mediated gene flow and diversity loss within many lakes, highlighting the fragility of recent radiations.

Eutrophication causes speciation reversal in whitefish adaptive radiations

Species diversity can be lost through two different but potentially interacting extinction processes: demographic decline and speciation reversal through introgressive hybridization. To investigate the relative contribution of these processes, we analysed historical and contemporary data of replicate whitefish radiations from 17 pre-alpine European lakes and reconstructed changes in genetic species differentiation through time using historical samples. Here we provide evidence that species diversity evolved in response to ecological opportunity, and that eutrophication, by diminishing this opportunity, has driven extinctions through speciation reversal and demographic decline. Across the radiations, the magnitude of eutrophication explains the pattern of species loss and levels of genetic and functional distinctiveness among remaining species. We argue that extinction by speciation reversal may be more widespread than currently appreciated. Preventing such extinctions will require that conservation efforts not only target existing species but identify and protect the ecological and evolutionary processes that generate and maintain species.