This paper is a summary of the methods and key results of my analysis of 7,997 sherds from 14 sites in Beef Basin, Utah. I discuss physical attributes of the collection, the results of mean ceramic dating, the results of neutron activation analysis, and the results of refiring a sample of nips in an oxidizing atmosphere. I briefly summarize the architecture at each site , as well as possible Fremont cultural material found in and near Beef Basin. I conclude that Beef Basin was likely occupied in the early Pueblo III period and that the occupation was sudden and brief. I determined that paste color can be used as a general indicator of clay procurement locale north of the Abajo Mountains, just as it is in the Comb Ridge vicinity (Glowacki et al. 2015), that there was ceramic production in Beef Basin using local materials, and that the people of Beef Basin had similar connections as, or connections with the east of the Comb Ridge area, as evinced by similar sources for light-paste ceramics found in both areas.

Fortifications are a common type of ancient monument found throughout Scandinavia, and while the functions of forts are studied and debated quite heavily, the re-use of these structures is less known. On Gotland, there exist 84 ancient fortifications, of which approximately one-third have burials or registered graves within or in close proximity to their locations. This thesis identifies those locations where empirical evidence can be found to identify burials as a form of secondary use of fortifications. The case study of Gudings slott, in Eke Parish, is examined to exemplify the chronological extent of secondary use of an ancient fortification by continued burial rituals from the Late Iron Age through the early Middle Ages. Ancestral worship, memory theory, burial practices, and spatial analysis are utilized to explain why these sites may have been chosen for re-use as burial grounds during the Late Iron Age. The resulting interpretations reveal a unique combination of topographic location, ancestral connectivity, and social stressors as key factors in the secondary use of the examined sites. In addition, new possibilities for the study of Gotland’s ancient fortification sites and suggestions for future research are put forward. / Fornborgar är en vanlig typ av forntida monument som finns i hela Skandinavien, och även om borgarnas funktioner har studerats och diskuterats tämligen omfattande är återanvändningen av dessa strukturer mindre känd. På Gotland finns 84 fornborgar, varav ungefär en tredjedel har begravningar eller registrerade gravar inom eller i närheten av deras lokalisering. Denna uppsats identifierar de platser där empirska blägg finns för begravningar som en form av sekundär användning av borgar. Fallstudien av Gudings slott i Eke socken används för att exemplifiera den kronologiska omfattningen av sekundär användning av en fornborg som en plats för fostsatta begravningsritualer från yngre järnålder upp i tidig medeltid. Förfädersdyrkan, minnesteori, begravningsmetoder och rumslig analys används för att förklara varför dessa platser kan ha valts för återanvändning som gravplatser under yngre järnålder. De resulterande tolkningarna avslöjar en unik kombination av topografisk lokalisering, koppling till förfäder och sociala stressfaktorer som nyckelfaktor i den sekundära användningen av de undersökta platserna. Dessutom presenteras nya möjligheter för att studera Gotlands fornborgar och förslag till framtida forskning.

This study contributes to the 'unwritten chapter' in migration studies, namely transnational return migration, with specific reference to Tongan migrants who have voluntarily returned to live in Tonga. Return migration of transnational Tongans is not 'permanent' as their mobility pre and post-return is characterised by circulation or repeated return rather than staying at 'home'. In examining the circulation of transnational Tongans, two new forms of return migration are identified -- 'return for career advancement' and 'ancestral return'. These additions to a new typology of return migration represent better the contemporary mobility system of transnational Tongans and suggest a means for addressing 'brain drain' through strengthening the 'Tongan-ness' of the diaspora while simultaneously stimulating economic development in the Kingdom. Despite these positive dimensions of return, re-integration is a 'bumpy' process, and there needs to be a holistic migration strategy if greater numbers in the Tongan diaspora are to return and make their potential contribution to sustainable development in the Island Kingdom.

Vertebrate evolution has resulted in a diversity of feeding mechanisms. Cetaceans are secondarily derived tetrapods that have returned to a marine habitat. As a result, they display feeding modes that have converged with more basal aquatic vertebrates, but display a diversity of new solutions and adaptations. To begin to explore the diversity of feeding adaptations among odontocetes, kinematics of feeding modes and feeding adaptations for belugas (Delphinapterus leucas), Pacific white-sided dolphins (Lagenorhynchus obliquidens), and long-finned pilot whales (Globicephala melas) were characterized. In addition, direct measurements of intraoral pressure were collected to determine maximum suction performance. Characters from these analyses were combined with data for other odontocetes, and were mapped onto a phylogeny of Odontoceti to begin to explore where changes in feeding modes took place. Feeding modes were diverse in belugas, Pacific white-sided dolphins, and pilot whales and included suction, ram, and a combination of both. In general, four phases were observed: (I) preparatory, (II) jaw opening, (III) gular depression, and (IV) jaw closing. Suction was a large component of the prey capture method in belugas and subambient pressures in excess of 100 kPa were generated. Belugas were also capable of lateral lip gape occlusion and anterior lip pursing to form a small anterior aperture. Pacific whitesided dolphins relied on ram to capture prey. However, some degree of pursing and resultant subambient pressure was observed that was likely used to compensate for high ram speeds or for prey manipulation and transport to the esophagus. Pilot whales were more similar to belugas in kinematics, but maintained high approach velocities and did not generate significant suction pressures; suction and ram were used in combination. Belugas and pilot whales appeared to employ hyolingual depression as a primary suction generation mechanism, whereas Pacific white-sided dolphins relied on fast jaw opening. Ancestral state reconstructions indicated that suction feeding capability evolved independently at least six times within Odontoceti. These results indicate the diversity of feeding behaviors in odontocetes and provide directives for future studies on the diversity of feeding in secondarily aquatic mammals.

The plant genus Tolpis (Asteraceae) is a predominantly insular plant lineage. It inhabits four of the five archipelagoes that comprise the Atlantic region of Macaronesia and also occurs in Mediterranean Europe and North Africa. Twelve species are currently recognized in Tolpis, of which ten are insular and two continental. The majority of the insular species inhabit the five western Canarian islands, where they constitute endemics to specific ecological habitats. A comprehensive molecular phylogeny of Tolpis is generated via DNA sequences of one nuclear ribosomal and two low-copy nuclear DNA markers. Considerable phylogenetic uncertainty among inferred tree topologies is detected, and incongruence between these topologies is resolved via statistical hypotheses testing. The extant diversity of the genus is identified to be the result of two independent colonization pathways and adaptive radiations on several islands. Moreover, potential hybridization is detected between species that inhabit different islands and archipelagoes, indicating a more widespread historical distribution of the genus. Details of the biogeographic history of Tolpis are inferred via ancestral area reconstructions under parsimony and likelihood optimality criteria. The hypothesis that Tolpis may have undergone a back-dispersal from an island to a continental habitat is also tested. Uncertainty in taxon cladograms owing to the presence of hybrid or allopolyploid taxa is characterized and a potential adjustment strategy evaluated. Averaging reconstruction results over all optimal phylogenetic trees and the manual pruning of cloned DNA sequences are found potential adjustment strategies against the impact of topological uncertainty owning to hybrid or allopolyploid taxa. Adjusted ancestral area reconstructions in Tolpis do not support the scenario that the genus has undergone a reverse colonization of the continent. In addition to the phylogenetic and biogeographic history of the genus, the diversity of symbiotic mycorrhizal fungi associated with Tolpis is characterized. A molecular survey using two nuclear ribosomal DNA markers and 454 pyrosequencing is performed. Particular emphasis is placed on the quality filtering of resulting fungal DNA sequences, the generation of operational taxonomic units, and their taxonomic assignment via similarity searches against DNA sequence databases. Numerous potentially novel fungal genotypes are identified. / text

L’inférence de génomes ancestraux est une étape essentielle pour l’étude de l’évolution des génomes. Connaissant les génomes d’espèces éteintes, on peut proposer des mécanismes biologiques expliquant les divergences entre les génomes des espèces modernes. Diverses méthodes visant à résoudre ce problème existent, se classant parmis deux grandes catégories : les méthodes de distance et les méthodes de synténie. L’état de l’art des distances génomiques ne permettant qu’un certain répertoire de réarrangements pour le moment, les méthodes de synténie sont donc plus appropriées en pratique. Nous proposons une méthode de synténie pour la reconstruction de génomes ancestraux basée sur une définition relaxée d’adjacences de gènes, permettant un contenu en gène inégal dans les génomes modernes causé par des pertes de gènes de même que des duplications de génomes entiers (DGE). Des simulations sont effectuées, démontrant une capacité de former une solution assemblée en un nombre réduit de régions ancestrales contigües par rapport à d’autres méthodes tout en gardant une bonne fiabilité. Des applications sur des données de levures et de plantes céréalières montrent des résultats en accord avec d’autres publications, notamment la présence de fusion imbriquée de chromosomes pendant l’évolution des céréales. / Ancestral genome inference is a decisive step for studying genome evolution. Knowing genomes from extinct species, one can propose biological mecanisms explaining divergences between extant species genomes. Various methods classified in two categories have been developped : distance based methods and synteny based methods. The state of the art of distance based methods only permit a certain repertoire of genomic rearrangements, thus synteny based methods are more appropriate in practice for the time being. We propose a synteny method for ancestral genome reconstruction based on a relaxed defenition of gene adjacencies, permitting unequal gene content in extant genomes caused by gene losses and whole genome duplications (WGD). Simulations results demonstrate our method’s ability to form a more assembled solution rather than a collection of contiguous ancestral regions (CAR) with respect to other methods, while maintaining a good reliability. Applications on data sets from yeasts and cereal species show results agreeing with other publications, notably the existence of nested chromosome fusion during the evolution of cereals.

There is an unmet medical need in the treatment of gout. This type of inflammatory arthritis can be efficiently alleviated by the enzyme uricase. This enzyme breaks down uric acid, the causative agent of gout, so it can be flushed from the body. In humans and the other great apes, uricase is a pseudogene and as such is inactive. Research on therapeutic uricases has focused on using enzymes from naturally occurring sources; however, these foreign proteins can be very antigenic and present a potentially life-threatening safety risk to patients. We address the challenges of developing a safer uricase therapeutic by exploiting evidence that, while inactive, the human pseudogene is expressed in the human body and may be recognized as self by the immune system. To develop a ﾓhuman-likeﾔ? uricase we apply the hybrid computational and experimental approach of Ancestral Sequence Reconstruction to search functional sequence space of uricase proteins to engineer an enzyme with high sequence identity to the human pseudogene, and possessing therapeutic levels of activity for the breakdown of uric acid. This dissertation describes the development and characterization of several uricase leads. The most active ancestral uricase possesses both enhanced in vitro and in vivo stability (in healthy rats) when assayed head-to-head Pegloticase, the only FDA approved uricase for the treatment of gout.

En aquest treball es pretén utilitzar la informació que deixa la recombinació al nostres genomes per fer inferències sobre la història evolutiva recent de les poblacions humanes. Per fer-ho, s’ha desenvolupat un mètode novedós, anomenat IRiS, que permet la detecció de recombinacions antigues específiques en un conjunt de seqüències. Hem validat extensivament IRiS i l'hem sotmès a diferents escenaris per tal d’avaluar-ne l’ eficàcia. Un cop els events de recombinació són detectats, es poden utilitzar com a marcadors genètics per estudiar els patrons de diversitat de les poblacions humanes. Finalment, hem aplicat aquesta innovadora aproximació a un conjunt de poblacions humanes del Vell Món, que varen ser genotipades específicament amb aquesta finalitat, aportant nous coneixements en la història evolutiva recent dels humans / The aim of this work is to use the information left by recombination in our genomes to make inferences on the recent evolutionary history of human populations. For that, a novel method called IRiS has been developed that allows detecting specific past recombination events in a set of extant sequences. IRiS is extensively validated and studied in whole set of different scenarios in order to assess its performance. Once recombination events are detected, they can be used as genetic markers to study the recombinational diversity patterns of human populations. We apply this innovative approach to a whole set of different human populations within the Old World that were specifically genotyped for this end and we provide new insights in the recent human evolutionary history of our species.

Submitted by Oliveira Santos Dilzaná (dilznana@yahoo.com.br) on 2016-08-03T15:40:53Z No. of bitstreams: 1 Dowyvan Gabriel Gaspar.pdf: 2985160 bytes, checksum: 2e12d0182be4cab4688470496a1147c5 (MD5) / Approved for entry into archive by Oliveira Santos Dilzaná (dilznana@yahoo.com.br) on 2016-08-08T11:47:18Z (GMT) No. of bitstreams: 1 Dowyvan Gabriel Gaspar.pdf: 2985160 bytes, checksum: 2e12d0182be4cab4688470496a1147c5 (MD5) / Made available in DSpace on 2016-08-08T11:47:18Z (GMT). No. of bitstreams: 1 Dowyvan Gabriel Gaspar.pdf: 2985160 bytes, checksum: 2e12d0182be4cab4688470496a1147c5 (MD5) / Este trabalho visa compreender a presença e métodos de ação da Igreja Universal do Reino de Deus em Maputo, Moçambique. Destaca-se sua história em contexto marcado por uma pluralidade étnico/religiosa, aspectos teológicos e sobretudo a aproximação entre a “Economia e a Religião”, operada pela IURD, sustentada na chamada “Teologia da Prosperidade”. A dissertação procura, de um lado, relacionar o perfil social dos crentes com sua atuação indicando métodos de proselitismo e arrecadação de recursos financeiros, e de outro, a busca de prosperidade financeira ainda nesta vida. The present work intends to understand the presence and methods of action by the Igreja Universal do Reino de Deus (Universal Church of God Kingdom) –IURD – in Maputo, Mozambique. It is stand out its history in Mozambique, historically marked by an ethnic and religious plurality, theological aspects and, above all, the nearness between the “Economy and Religion”, led by the IURD, supported in the so called “Theology of Prosperity”. This work tries to relate the social profile of the believers with its performance showing, in one hand, methods of proselytism and collection of financial resources and, in the other hand, the search for financial prosperity still along this life.

The island of Sri Lanka’s exceptional biodiversity and enigmatic biogeography begs investigation, as the island is key in understanding the evolution of the Asian tropical flora. Since the Jurassic, Sri Lanka has been subjected to remarkable tectonic changes, thus its flora could have been influenced by that of a number of nearby landmasses, as well giving Sri Lanka the potential to have played a wider role in the assemblage of floras elsewhere. Firstly, as Sri Lanka originated as a fragment of the supercontinent Gondwana, part of its flora may contain Gondwanan relict lineages. There is also the potential for immigration from Laurasia after the Deccan Plate collided with it 45-50 Mya. Further, Sri Lanka may harbour floristic elements from nearby land masses such as Africa and Southeast Asia as a result of long distance dispersals, and in situ speciation has the potential to have played an important role in enhancing the endemic Sri Lankan flora. I tested the relative contributions of the above hypotheses for the possible origins of the Sri Lankan flora using three representative families, Begoniaceae, Sapotaceae and Zingiberaceae. These families represent both herbaceous and woody elements, and have high diversity across the tropics. Dated molecular phylogenies were constructed for each family. I used recent analytical developments in geographic range evolution modelling and ancestral area reconstruction, incorporating a parameter J to test for founder event speciation. A fine scale area coding was used in order to obtain a better picture of the biogeography of continental Asia. Amongst all the models compared, a dispersal-extinction cladogenesis model incorporating founder event speciation proved to be the best fit for the data for all three families. The dates of origin for Sri Lankan lineages considerably post-date the Gondwanan break up, instead suggesting a geologically more recent entry followed by diversification of endemics within the island. The majority of Sri Lankan lineages have an origin in the Sunda Shelf (53%). Persistence of warm temperate and perhumid climate conditions in southwestern Sri Lanka resembling those of Peninsular Malaysia and Sumatra could have facilitated suitable habitats for these massive dispersals from the Sunda Shelf region. Some trans-oceanic long distance dispersals from Africa (11%) are also evidenced, again these are too young to accept a hypothesis of dispersal during the Deccan Plate’s migration close to the African coast during the late Cretaceous, but occurred later during the Miocene. Further, some lineages of Laurasian origin (20%) are evidenced in the Zingiberaceae with ancestral areas of China and Indochina, which is congruent with a post collision invasion. Among the families tested, dispersals have occurred stochastically, one during the Eocene, six during the Oligocene, seven during the Miocene, two during the Pliocene and one during the Pleistocene. The highest number of dispersals occurred during the Miocene when a warm climate was prevailing during the Miocene thermal maximum. My results confirm that in situ speciation is an important contributor to the Sri Lankan flora. More rapid radiation of endemics has occurred during Pliocene-Pleistocene; two endemics in Begoniaceae, ten endemics in Sapotaceae and ten endemics in Zingiberaceae have evolved in situ during this period. Sri Lanka will have been subjected to expansion and contraction of climatic and vegetation zones within the island during glacial and interglacial periods, potentially resulting in allopatric speciation. As a conclusion, long distance dispersals have played a prominent role in the evolution of the Sri Lankan flora. The young ages challenge the vicariant paradigm for the origin and current disjunct distributions of the world’s tropical lineages and provide strong evidence for a youthful tropics at the species level. The thesis contains six chapters; first two are introductory chapters, then there are three analytical chapters, one for each family, and finally a summary chapter is provided. Each analytical chapter is written as a stand-alone scientific publication, thus there is some repetition of relevant content in each.