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A partir da descoberta dos íntrons, muitas questões sobre sua origem vêm sendo discutidas como: porque eles existem em eucariotos e não são encontrados em procariotos, quando e como eles se originaram. Basicamente duas hipóteses existem para explicar a origem dos íntrons: \"introns-early\" e \"introns-late\". A primeira hipótese sugere que íntrons e éxons já existiam nos primeiros genes e os íntrons foram perdidos posteriormente na linhagem de bactérias. A hipótese oponente, introns-late, assume que os íntrons foram adicionados posteriormente durante a evolução, somente em eucariotos. Introns de genes diferentes podem sofrer recombinação durante a divisão celular e assim formar novos genes. Este processo permite e aumenta a freqüência de troca completa de éxons e, conseqüentemente, aumenta a probabilidade de novos genes funcionais serem formados. Este fenômeno é chamado de \"exon-shuffling\" e é um mecanismo importante em relação a origem de muitas proteínas novas em eucariotos. Entretanto, o papel do exon-shuffling na criação das proteínas no ancestral comum dos procariotos e eucariotos é o ponto de discordância entre as hipóteses introns-early e introns-late porque este mecanismo depende da presença dos introns no progenoto. Excesso de éxons simétricos é considerado uma evidência de exon-shuffling, já que a troca de éxons flanqueados por íntrons da mesma fase não muda o quadro de leitura do gene receptor. Nesta tese, apresentamos dois estudos relacionados ao papel do fenômeno de exon-shuffling na evolução das proteínas. No primeiro estudo, observamos que existe uma correlação significativa entre unidades simétricas de shuffling e a idade de domínios protéicos. Domínios antigos, presentes em procariotos e eucariotos, são mais freqüentemente flanqueados por íntrons de fase zero e são preferencialmente localizados nas partes centrais das proteínas. Domínios modernos são mais freqüentemente flanqueados por íntrons de fase um e estão presentes predominantemente nas extremidades das proteínas. Propomos um modelo no qual o shuffling de domínios antigos flanqueados por íntrons de fase zero deve ter sido importante durante a criação das partes centrais das proteínas no ancestral comum de eucariotos e procariotos. Shuffling de domínios modernos, predominantemente flanqueados por íntrons de fase um, deve ter sido importante para a origem das extremidades das proteínas durante a evolução de eucariotos. O segundo estudo trata do possível papel do exon-shuffling na evolução de peptídeos sinal em proteínas humanas. Recentemente, foi mostrado que existe uma predominância de íntrons de fase um próximo ao sítio de clivagem de peptídeos sinal em genes humanos [Tordai, H., Patthy, L. (2004) FEBS lett. 575:109-111]. Os autores sugeriram que tal distribuição é causada pela inserção de íntrons em sítios de inserção preferencial AGG. Apresentamos evidências de que o sinal observado não é tão forte como inicialmente mostrado e que não existe excesso desproporcional de AGG que daria suporte a inserção em sítios preferenciais. Como estas proteínas evoluíram através de exon-shuffling, levantamos a possibilidade de que este fenômeno possa também ter sido amplamente responsável pelo excesso de íntrons de fase um. Acreditamos que os dados presentes nestes dois estudos representam uma contribuição importante para o campo de estudo de evolução de íntrons e do fenômeno de exon-shuffling porque estes apresentam dados importantes e originais acerca do papel do \"exon-shuffling\" antigo e moderno durante a evolução das proteínas. / Since the discovery of introns, many questions about their origin have been raised such as: why they exist in eukaryotic organisms and not in prokaryotes, when and how did they originate. Mainly, there are two hypotheses explaining the origin of introns: ?introns-early? and ?introns-late?. The first hypothesis suggests that introns and exons already existed in the first genes and were lost later in the bacteria lineage. The opposing hypothesis, introns-late, assumes that introns were inserted late in evolution, in eukaryotic organisms only. Introns from different genes may suffer recombination during cell division and this way form new genes. This process allows and increases the frequency of exchanging complete exons and, consequently, increases the probability of forming new functional genes. This phenomenon is called ?exon-shuffling? and is an important mechanism accounting for the origin of many new proteins in eukaryotes. However, the role of exon-shuffling in the creation of proteins in the ancestor of prokaryotes and eukaryotes is the point of disagreement between the hypotheses \"introns-early\" and \"introns-late\" because this mechanism depends of the presence of introns in the progenote. Excess of symmetric exons is thought to represent evidence for exon-shuffling since the exchange of exons flanked by introns of the same phase does not disrupt the reading frame of the host gene. In this thesis, we present two studies concerning the role of the exon-shuffling phenomenon in protein evolution. In the first study, we found that there is a significant correlation between symmetric units of shuffling and the age of protein domains. Ancient domains, present in both prokaryotes and eukaryotes, are more frequently bounded by phase zero introns and their distribution is biased towards the central part of proteins. Modern domains are more frequently bounded by phase one introns and are present predominantly at the ends of proteins. We propose a model in which shuffling of ancient domains mainly flanked by phase zero introns would have been important during the creation of the central part of proteins in the ancestor of eukaryotes and prokaryotes. Shuffling of modern domains, predominantly flanked by phase one introns, would have accounted for the origin of the extremities of proteins during eukaryotic evolution. The second study accounts the possible role of exon-shuffling in the acquisition of signal peptides in human proteins. It was recently shown that there is a predominance of phase one introns near the cleavage site of signal peptides of human genes [Tordai, H., Patthy, L. (2004) FEBS lett. 575:109-111]. The authors suggested that it was due to intron insertion at AGG proto-splice sites. We present evidence that the signal observed is not as strong as initially shown and that there is no disproportional excess of AGG that would support insertion at proto-splice sites. As these proteins evolved by exon-shuffling, we raise the possibility that this phenomenon might also be largely responsible for such excess of phase one introns. We believe the data present in these two studies represent an important contribution to the field of introns and exon-shufling evolution due to their important and original data concerning the role of ancient and modern exon-shuffling during the evolution of the proteins.

The continental margin in the area west of Shetland was subjected to repeated and extensive ice sheet advances during the Late Pleistocene. Seabed imagery, seismic survey and borehole core data show the Late Devensian ice sheets expanded across the continental shelf three times, two of these advances reaching the shelf edge. On the inner shelf, where present-day water depths are generally less than 100m, only thin sediments from the last retreat phase and exposed rock surfaces remain, all other deposits from earlier phases having been removed by the last advance. On the mid to outer shelf elements of all three phases are preserved, including lodgement and deformation tills, melt-out and water-lain till sheets, in-filled hollows left by stagnant ice decaying in situ and a series of large recessional and terminal moraines. In addition, there is evidence of shallow troughs and overdeepend basins which indicate preferential ice-drainage pathways across the shelf which were formerly occupied by ice streams. At the shelf edge, a thick wedge of glacigenic sediment forms a transition from the till sheets and moraines of the shelf to debris flows composed of glacigenic sediments on the upper slope. Shelf-edge moraines show an architecture indicating floating ice in modern water depths over approximately 180m, suggesting the West Shetland ice sheet was no more than about 250m thick. The upper and middle slope is dominated by glacigenic debris flows which are focused in the slope areas below the proposed ice stream discharges at the shelf edge. The mid-to-lower slope has been subjected to contour current activity which has re-worked much of the glacigenic sediment in this position. The lower slope and floor of the Faroe-Shetland Channel are marked by either large debris flow lobes of glacigenic sediment or thin glacimarine muds deposited from suspension. A conceptual model of the glacigenic development of a passive continental margin based upon the West Shetland example shows the deposited sequence for both advance and retreat phases of a glacial cycle, and the actual preserved sequence which might be expected in the rock record. The model also shows that ice sheet buoyancy, thickness, and to a lesser extent, basin subsidence, are the most important factors in the deposition and preservation of a glacially-influenced marine sequence.

A partir da descoberta dos íntrons, muitas questões sobre sua origem vêm sendo discutidas como: porque eles existem em eucariotos e não são encontrados em procariotos, quando e como eles se originaram. Basicamente duas hipóteses existem para explicar a origem dos íntrons: \"introns-early\" e \"introns-late\". A primeira hipótese sugere que íntrons e éxons já existiam nos primeiros genes e os íntrons foram perdidos posteriormente na linhagem de bactérias. A hipótese oponente, introns-late, assume que os íntrons foram adicionados posteriormente durante a evolução, somente em eucariotos. Introns de genes diferentes podem sofrer recombinação durante a divisão celular e assim formar novos genes. Este processo permite e aumenta a freqüência de troca completa de éxons e, conseqüentemente, aumenta a probabilidade de novos genes funcionais serem formados. Este fenômeno é chamado de \"exon-shuffling\" e é um mecanismo importante em relação a origem de muitas proteínas novas em eucariotos. Entretanto, o papel do exon-shuffling na criação das proteínas no ancestral comum dos procariotos e eucariotos é o ponto de discordância entre as hipóteses introns-early e introns-late porque este mecanismo depende da presença dos introns no progenoto. Excesso de éxons simétricos é considerado uma evidência de exon-shuffling, já que a troca de éxons flanqueados por íntrons da mesma fase não muda o quadro de leitura do gene receptor. Nesta tese, apresentamos dois estudos relacionados ao papel do fenômeno de exon-shuffling na evolução das proteínas. No primeiro estudo, observamos que existe uma correlação significativa entre unidades simétricas de shuffling e a idade de domínios protéicos. Domínios antigos, presentes em procariotos e eucariotos, são mais freqüentemente flanqueados por íntrons de fase zero e são preferencialmente localizados nas partes centrais das proteínas. Domínios modernos são mais freqüentemente flanqueados por íntrons de fase um e estão presentes predominantemente nas extremidades das proteínas. Propomos um modelo no qual o shuffling de domínios antigos flanqueados por íntrons de fase zero deve ter sido importante durante a criação das partes centrais das proteínas no ancestral comum de eucariotos e procariotos. Shuffling de domínios modernos, predominantemente flanqueados por íntrons de fase um, deve ter sido importante para a origem das extremidades das proteínas durante a evolução de eucariotos. O segundo estudo trata do possível papel do exon-shuffling na evolução de peptídeos sinal em proteínas humanas. Recentemente, foi mostrado que existe uma predominância de íntrons de fase um próximo ao sítio de clivagem de peptídeos sinal em genes humanos [Tordai, H., Patthy, L. (2004) FEBS lett. 575:109-111]. Os autores sugeriram que tal distribuição é causada pela inserção de íntrons em sítios de inserção preferencial AGG. Apresentamos evidências de que o sinal observado não é tão forte como inicialmente mostrado e que não existe excesso desproporcional de AGG que daria suporte a inserção em sítios preferenciais. Como estas proteínas evoluíram através de exon-shuffling, levantamos a possibilidade de que este fenômeno possa também ter sido amplamente responsável pelo excesso de íntrons de fase um. Acreditamos que os dados presentes nestes dois estudos representam uma contribuição importante para o campo de estudo de evolução de íntrons e do fenômeno de exon-shuffling porque estes apresentam dados importantes e originais acerca do papel do \"exon-shuffling\" antigo e moderno durante a evolução das proteínas. / Since the discovery of introns, many questions about their origin have been raised such as: why they exist in eukaryotic organisms and not in prokaryotes, when and how did they originate. Mainly, there are two hypotheses explaining the origin of introns: ?introns-early? and ?introns-late?. The first hypothesis suggests that introns and exons already existed in the first genes and were lost later in the bacteria lineage. The opposing hypothesis, introns-late, assumes that introns were inserted late in evolution, in eukaryotic organisms only. Introns from different genes may suffer recombination during cell division and this way form new genes. This process allows and increases the frequency of exchanging complete exons and, consequently, increases the probability of forming new functional genes. This phenomenon is called ?exon-shuffling? and is an important mechanism accounting for the origin of many new proteins in eukaryotes. However, the role of exon-shuffling in the creation of proteins in the ancestor of prokaryotes and eukaryotes is the point of disagreement between the hypotheses \"introns-early\" and \"introns-late\" because this mechanism depends of the presence of introns in the progenote. Excess of symmetric exons is thought to represent evidence for exon-shuffling since the exchange of exons flanked by introns of the same phase does not disrupt the reading frame of the host gene. In this thesis, we present two studies concerning the role of the exon-shuffling phenomenon in protein evolution. In the first study, we found that there is a significant correlation between symmetric units of shuffling and the age of protein domains. Ancient domains, present in both prokaryotes and eukaryotes, are more frequently bounded by phase zero introns and their distribution is biased towards the central part of proteins. Modern domains are more frequently bounded by phase one introns and are present predominantly at the ends of proteins. We propose a model in which shuffling of ancient domains mainly flanked by phase zero introns would have been important during the creation of the central part of proteins in the ancestor of eukaryotes and prokaryotes. Shuffling of modern domains, predominantly flanked by phase one introns, would have accounted for the origin of the extremities of proteins during eukaryotic evolution. The second study accounts the possible role of exon-shuffling in the acquisition of signal peptides in human proteins. It was recently shown that there is a predominance of phase one introns near the cleavage site of signal peptides of human genes [Tordai, H., Patthy, L. (2004) FEBS lett. 575:109-111]. The authors suggested that it was due to intron insertion at AGG proto-splice sites. We present evidence that the signal observed is not as strong as initially shown and that there is no disproportional excess of AGG that would support insertion at proto-splice sites. As these proteins evolved by exon-shuffling, we raise the possibility that this phenomenon might also be largely responsible for such excess of phase one introns. We believe the data present in these two studies represent an important contribution to the field of introns and exon-shufling evolution due to their important and original data concerning the role of ancient and modern exon-shuffling during the evolution of the proteins.

Big Bone Lick (BBL) is a late Pleistocene and Holocene fossil locality in the Ohio River valley of Kentucky. This study utilized stable isotopes (δ13C, δ18O, and 87Sr/86Sr) in tooth enamel to reconstruct mobility and diet in Bison, as well as diet in Bootherium bombifrons. Isotopic results from seven Bison and two B. bombifrons are reported. Results suggest Pleistocene Bison and Bootherium occupied different dietary niches. Although both had C3-dominated diets, Bison occupied more open environments than B. bombifrons. Two bison from the late Holocene deposit had diets that consisted of more C3 vegetation than Pleistocene bison, which may indicate these individuals occupied a closed C3 landscape. However, one specimen previously identified as late Holocene had diet and mobility patterns consistent with Pleistocene bison, which could indicate temporal mixing. Pleistocene and Holocene Bison have 87Sr/86Sr values that suggest they spent most of their time in places other than BBL.

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