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Several questions regarding the nature of extinction in the fossil record of marine invertebrates were investigated using statistical methods and familial diversity data. First, a series of analyses were performed to determine whether the magnitudes of mass extinctions were statistically distinguishable from the magnitudes of background extinctions. The expected proportions of familial extinction for each order in a stage (based on an estimate of the ordinal probability of familial extinction for each of 134 orders) were compared to the observed proportions of familial extinction in the stage using a simple X2 goodness-of-fit test. The results indicate that eight stages in the Phanerozoic had a statistically significant excess of extinction. A second set of X2 analyses was done using estimates of per taxon familial extinction rates for the orders, rather than familial extinction probabilities. The X2 tests resulted in four additional stages that contained a statistically significant surplus of familial extinction. To test the results further, a set of bootstrapping analyses was done for each of five different extinction metrics. Two stages, the Ashgillian and the Dzhulfian, had a statistically significant excess of extinction in both Xl analyses and in four out of five of the bootstrapping analyses. Two additional stages, the Guadelupian and the Maestrichtian, had a statistically significant magnitude of extinction in every analysis. Thus, the results provide strong support for the argument that mass extinctions comprise a distinct group of evolutionary phenomena. Familial extinction rates have declined from the early Phanerozoic to the Recent. Some have suggested that familial extinction rates have been constant through time within most major taxonomic groups and that the decline in familial extinction rates is the result of the successive elimination of groups with relatively high familial extinction rates (a process referred to as taxon sorting). A model of total familial extinction rates through time based on stationary probabilities of familial extinction within orders closely mimics the observed decline in total familial extinction rates supporting the taxon sorting hypothesis. Linear regressions of the familial extinction probabilities of orders versus the geologic time of both their first and their last occurrences suggest that the observed decline in extinction rates resulted from the early elimination of orders with characteristically high probabilities of extinction, and the later origination of orders with relatively low probabilities of extinction. In addition, a statistical analysis comparing the evolutionary volatility of extinct versus extant taxa suggests that extinct orders had greater volatility in their diversity histories which may have contributed to their early demise. The taxonomic selectivity of both background and mass extinctions was investigated using simple X2 analyses. The results suggest that familial extinction during mass extinctions was taxonomically more selective than extinction during background extinctions. In addition, the magnitude of familial extinction experienced by an order in a stage was compared to the familial extinction probability estimated for the order using the binomial theorem. Then, those orders that suffered an unusual excess of familial extinction during particular stratigraphic stages were separated from the remaining orders in the stage. The results suggest that sessile filter feeders (particularly those groups important in ancient reefs) and pelagic groups suffered the greatest during intervals of mass extinction. Finally, the potential relationship of familial diversity to both sea level and I7Sr/86Sr ratios was statistically examined using linear regression techniques. No statistically significant correlation was found between sea level and familial diversity. However, a significant correlation was discovered between diversity and I7Sr /86Sr ratios. Strontium ratios are believed to be an indirect measure of the aerial extent of exposed continental crust. Thus, the relationship between 17 Sr/86Sr ratios and diversity suggests that familial diversity has been a function of 1) the aerial extent of epeiric seas and 2) the amount of clastic material being supplied to these seas. The last factor could have affected familial diversity by restricting normally diverse, shallow carbonate environments. / Master of Science

This thesis attempted a cross-species replication of Bland, et. al., 2018. Human participants went through a computerized, automated shaping procedure that trained them to click on and discriminate between a blue square (SD) and red square (S-delta) on a VR 12 schedule of reinforcement. Three conditions were then presented to the participants consisting of a baseline, punishment, and control condition. In the punishment and control conditions, the SD was replaced by the S-delta or a novel stimulus respectively for 1-second on a VR 5 schedule. With each click, the reaction time and specific object clicked on were recorded. While the present study partially replicated the effect seen in earlier research, our results suggest that, depending on the lens of analysis used, either a punishment or an extinction effect may be causing the results seen.

The capercaillie is the largest member of the grouse family extant in Scotland. This species is reported to have become extinct during the 1700s. It is also reported to have been reintroduced to Scotland from Sweden during the 1800s. There have been many assertions made about the underlying causes of the decline of the species; however the specific causal factors remain unknown. The reintroduction of the capercaillie to Scotland in the 1800s is the only successful reintroduction of a grouse species ever to have occurred in the world. The specific factors behind the success of the reintroduction also remain unknown. This thesis examines the extent to which a selection of historical documentary evidence can help to establish both the causes of the 18th century decline of the capercaillie in Scotland and the successes of the 19th century reintroduction. The methodology of this thesis incorporates facets from the fields of both environmental science and history. The methodology includes three steps. The first step involves the selection of a series of potential critical factors that may have been responsible for the decline of the species in the 1700s; these critical factors were selected from the present day understanding of the ecology and the behaviour of the capercaillie. The second step of the methodology includes the surveying of a series of historical documentary sources. From these surveys historical observations of the species were gathered. The historical documentary sources selected for examination in this thesis include what are referred to here as ‘primary historical source material’ and ‘secondary historical source material’. The majority of the primary historical source material was gathered from the hand written manuscripts of the Breadalbane estate, held at the National Archives of Scotland (NAS) and the Atholl estate held at the Blair Castle Charter Room in Blair Atholl. Other select primary historical source material consulted to a lesser extent, due to time constraints, includes the Forfeited Estates (1745) Inventory and the Baron Court Records for Strathspey and Urquhart (1617–1683) from the Grant estate muniments; both held at the NAS. The secondary historical source material was gathered from published and edited literary collections that include historical accounts of the species. The third and final step of the methodology involves the synthesis of both the historical and environmental information in order to establish to what extent the causes of both the decline of the species in the 1700s and success of its reintroduction in the 1800s can be realised. The findings from this thesis assert that the capercaillie was resident in Scotland from, at least, the end of the Medieval. Moving forward from the Middle Ages this thesis presents observations of the capercaillie throughout the historical period. These observations of the capercaillie appear in many different historical accounts. In some instances these observations are fleeting and do not form the main subject of the particular document in question. In other instances accounts of the species are much more detailed and include references to the ecology and behaviour of the bird. The level of detail included in an observation aside, the frequency with which the species is referred to in the sample of historical documents suggests that sections of the Scottish human population were familiar with the species, in various locations and at various times throughout history. By the 17th century the capercaillie is reported as beginning to become rare in some locations while still remaining comparatively abundant in others. The number of instances where the species is referred to as becoming rare in the historical documents increases between the 17th and the 19th centuries. Despite the reported scarceness of the species in Scotland from around the 17th century onwards, the capercaillie is recorded as persisting in Scotland until around the end of the 1700s. By the early 1800s the number of observations of the species in the secondary historical source material increases. All of the observations in the secondary sources from the early 1800s record the absence of the species from localities and regions of Scotland. No new evidence was found in either the primary or secondary historical source material to challenge the supposition that the capercaillie did become extinct in Scotland after 1785. No detailed quantitative data was available for analysis of the decline of the species. Thus, to investigate the extent to which the historical accounts can help explain the specific causal factors of the reported decline, a synthesis of the environmental and historical data was necessary. The findings of this synthesis suggest that the naturally occurring Scottish population of capercaillie probably persisted in the form of a metapopulation. The two hundred years between the 17th and 19th century most likely saw the extinction of capercaillie sub-populations, before the loss of the overall population of capercaillie around 1785. The sample historical documentary evidence alludes to this pattern of local and/or regional extinction of sub-populations. The cause or causes of the extinction of these sub-populations has focussed on five limiting or critical factors known to affect the species today. These five factors are climate change, particularly weather effects associated with the Little Ice Age, habitat loss and deterioration, disturbance, human hunting and predation by species other than humans also contributed to the species’ extinction. The extent to which these critical factors affected each sub-population would have varied between regions of Scotland occupied by the capercaillie in history. This thesis proposes that there was no single or combination of specific critical factors that were ultimately responsible for the decline of the capercaillie in Scotland during the 1700s. In some areas the capercaillie sub-populations would have most likely died out as a result of habitat loss and deterioration and climate change. Whereas in others predation and inbreeding may have been the critical factors responsible for the species’ demise. More detailed information referring to the capercaillie was found in the historical documentary source material for the period post-extinction (i.e. 1800 onwards). Contrary to popular understanding numerous attempts to reintroduce the capercaillie to Scotland were carried out before the Marquis of Breadalbane’s successful programme in 1837. The historical documentary evidence reports early attempts to reintroduce the species to locations such as the Isle of Arran in 1807, on the Duke of Atholl’s estate in 1822 and on the Earl of Mar’s estate in 1824. None of these reintroduction programmes are reported to have been successful in establishing a ‘wild’ population. However, in some instances the captive rearing programmes initiated did bear some fruit and captive reared birds were sent from Dunkeld by the Duke of Atholl to Kenmore and were used in Breadalbane’s successful reintroduction in 1837. The historical documents report two causes for the failure of these early reintroduction attempts. The first is the sudden death of captive birds, most likely as a result of choking due to stress as observed in recent rearing programmes (i.e. Moss 1986). The reintroduced Arran population is reported to have become extinct in this fashion. The second reported cause of failure is predation by species other than man. For example the entire population of birds brought to Scotland by the Earl of Mar were predated when released on his estate. This thesis offers two critical factors as explanations for the remarkable success of the capercaillie’s reintroduction to Scotland in the 19th century. The first is the method by which the reintroduction was carried out; specifically, the re-establishment of a series of capercaillie sub-populations in different regions of Scotland.

Submitted by Luciana Ferreira (lucgeral@gmail.com) on 2018-08-28T11:09:57Z No. of bitstreams: 2 Tese - Flávia de Figueiredo Machado - 2018.pdf: 3861358 bytes, checksum: d1d99c2f2391b7000da1d2f269179035 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Approved for entry into archive by Luciana Ferreira (lucgeral@gmail.com) on 2018-08-28T11:16:05Z (GMT) No. of bitstreams: 2 Tese - Flávia de Figueiredo Machado - 2018.pdf: 3861358 bytes, checksum: d1d99c2f2391b7000da1d2f269179035 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Made available in DSpace on 2018-08-28T11:16:05Z (GMT). No. of bitstreams: 2 Tese - Flávia de Figueiredo Machado - 2018.pdf: 3861358 bytes, checksum: d1d99c2f2391b7000da1d2f269179035 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Previous issue date: 2018-05-28 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / (Sem resumo em outra língua) / Nesta tese tive o objetivo de investigar os fatores relacionados ao risco de extinção em primatas, assim como as tendências e vieses nos esforços de pesquisas voltadas para a conservação do grupo. No primeiro capítulo, por meio de uma cienciometria, mostrei quais são os temas, abordagens e espécies mais estudadas, bem como as instituições e locais que mais realizam esses estudos. Demonstrei que os esforços de pesquisa com conservação de primatas não têm sido motivados pelo status de conservação das espécies e tamanho da sua distribuição, e sim pelo peso corporal e idade (tempo desde a sua descrição). No segundo capítulo, testei se a dieta de primatas pode predizer o risco de extinção das espécies, mensurando dieta de diferentes maneiras: amplitude de dieta, diversidade de dieta, tipo de dieta e disparidade de itens. Concluí que a dieta prediz o risco de extinção, mas apenas pela métrica de disparidade de itens, sendo que espécies capazes de consumir itens mais diferentes entre si estarão menos propensas à extinção. No terceiro e último capítulo, avaliei os padrões de risco de extinção em primatas. Incluí variáveis intrínsecas e extrínsecas em modelos que particionam a variância em componentes espaciais, filogenéticas e independentes. Mostrei que espécies próximas na filogenia e no espaço tendem a apresentar status de ameaça semelhantes. Além disso, encontrei que a região Madagascar é a pior para os primatas e que o tempo de desmame, tamanho da distribuição geográfica e fatores como “human footprint” e pobreza humana influenciam no risco de extinção das espécies. Por fim, demonstrei que o espaço possui grande influência no risco de extinção de primatas, não devendo ser ignorado nesse tipo de análise.

Les raies d'absorption de quasars sont des outils efficaces pour étudier le milieu interstellaire dans les galaxies. Dans ce travail, nous étudions un échantillon de soixante-six systèmes absorbants à z<1.5 sélectionnés pour la présence de raies d'absorption de CI intenses dans leurs spectres SDSS. Ils sont observés par les spectrographes X-shooter et UVES du VLT de l'ESO. Nous étudions en tout 17 systèmes observés par X-shooter. Nous déduisons la métallicité, la déplétion par la poussière, le taux d'extinction par la poussière et le taux d'absorption des raies de MgII, MgI, CaII et NaI décalées dans l'infrarouge proche. Nous détectons neuf raies d'absorption de CaII avec W(CaII λ3934)>0.23Å. Nous détectons dix raies d'absorption de NaI dans quatorze systèmes susceptibles d'en montrer. La largeur équivalente médiane de W(NaI λ5891)=0.68Å est plus grande que celles observées dans des nuages proches ayant des densités-colonnes de HI similaires ou dans des systèmes CaII à z<0.7 détectés par le SDSS. La présence systématique de raies d'absorption de NaI dans ces systèmes CI suggère fortement que le gaz environnant est neutre et froid, et donc peut faire partie du gaz moléculaire diffus dans le milieu interstellaire de galaxies à fort décalage vers le rouge. Les raies d'absorption de MgII s'étalent sur plus de 400km/s en Δv pour la moitié de l'échantillon; trois systèmes ont un Δv supérieur à 500 km/s. Tout ceci suggère qu'une fraction importante du gaz froid à fort décalage vers le rouge émane d'environnements perturbés. Nous détectons de l'hydrogène moléculaire dans tous les systèmes dans la limite de détection. / Quasar absorption lines are a powerful tool to study the interstellar medium(ISM) in the galaxies. We study a sample of 66 z >1.5 absorbers selected based on the presence of strong CI absorption lines in SDSS spectra and observed with the ESO-VLT spectrograph X-shooter/UVES. I study 17 systems that are re-observed by X-shooter. I derive metallicities, depletion onto dust, extinction by dust and analyse the absorption from MgII, MgI, CaII and NaI that are redshifted into the near infrared wavelength range. I detect 9 CaII absorptions with W(CaII λ3934) > 0.23 Å out of 14 systems. I detect 10 NaI absorptions in the 11 systems where we could observe this absorption. The median equivalent width (W(NaI λ5891) = 0.68 Å) is larger than what is observed in local clouds with similar HI column densities but also in z<0.7 CaII systems detected in the SDSS. The systematic presence of NaI absorption in these CI systems strongly suggests that the gas is neutral and cold, maybe part of the diffuse molecular gas in the ISM of high-redshift galaxies. The MgII absorptions are spread over more than Δv ~ 400 km/s for half of the systems; three absorbers have Δv > 500 km/s. The kinematics is strongly perturbed for most of these systems which probably do not arise in quiet disks and must be close to regions with intense star formation activity. All this suggests that a large fraction of the cold gas at high redshift arises in disturbed environments. We detect molecular hydrogen in all the systems within the detection limit.

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