Made available in DSpace on 2014-12-17T15:36:35Z (GMT). No. of bitstreams: 1 SebastiaoFS.pdf: 2551917 bytes, checksum: 3538250a323b39c32585d41d316bcb6a (MD5) Previous issue date: 2009-09-08 / Conselho Nacional de Desenvolvimento Cient?fico e Tecnol?gico / The primary and accessory optic systems comprise two set of retinorecipient neural clusters. In this study, these visual related centers in the rock cavy were evaluated by using the retinal innervations pattern and Nissl staining cytoarchigtecture. After unilateral intraocular injection of cholera toxin B subunit and immunohistochemical reaction of coronal and sagittal sections from the diencephalon and midbrain region of rock cavy. Three subcortical centres of primary visual system were identified, superior colliculus, lateral geniculate complex and pretectal complex. The lateral geniculate complex is formed by a series of nuclei receiving direct visual information from the retina, dorsal lateral geniculate nucleus, intergeniculate leaflet and ventral lateral geniculate nucleus. The pretectal complex is formed by series of pretectal nuclei, medial pretectal nucleus, olivary pretectal nucleus, posterior pretectal nucleus, nucleus of the optic tract and anterior pretectal nucleus. In the accessory optic system, retinal terminals were observed in the dorsal terminal, lateral terminal and medial terminal nuclei as well as in the interstitial nucleus of the superior fasciculus, posterior fibres. All retinorecipient nuclei received bilateral input, with a contralateral predominance. This is the first study of this nature in the rock cavy and the results are compared with the data obtained for other species. The investigation represents a contribution to the knowledge regarding the organization of visual optic systems in relation to the biology of species. / Os sistemas visual prim?rio e ?ptico acess?rio compreendem dois conjuntos de grupamentos neurais, que recebem proje??o direta da retina. Nesse estudo, estes dois sistemas foram avaliados com rela??o a citoarquitetura e padr?o de inerva??o retiniana, usando como tra?ador neural anter?grado, a subunidade B da toxina col?rica revelada por imunoistoqu?mica para detectar este tra?ador em terminais sobre grupamentos neuronais (alvos) no enc?falo do moc? (Kerodon rupestris), um roedor nativo do Nordeste Brasileiro. Os resultados permitiram identificar os componentes do sistema visual prim?rio o complexo geniculado lateral, o complexo pr?-tectal e o col?culo superior. O complexo geniculado lateral cont?m o n?cleo geniculado lateral dorsal, o n?cleo geniculado lateral ventral e o folheto intergeniculado. Todos recebem fibras da retina com predomin?ncia contralateral, menos intensa para o folheto intergeniculado. O complexo pr?-tectal cont?m os n?cleos pr?-tectal anterior, pr?-tectal medial, pr?-tectal posterior, olivar pr?-tectal e n?cleo do trato ?ptico, os quais recebem proje??o retiniana predominantemente contralateral. Do mesmo modo, o col?culo superior recebe fibras da retina contralateral nas camadas superficiais. Tamb?m foi identificado o sistema ?ptico acess?rio completo no moc?, constitu?do pelos n?cleos terminal medial, terminal lateral, terminal dorsal e intersticial do fasc?culo superior posterior. Esses n?cleos recebem inerva??o retiniana com forte predomin?ncia contralateral, sendo que o n?cleo terminal medial, embora preserve a predomin?ncia contralateral, exibe uma evidente inerva??o ipsolateral.

It appears to be unanimous that alien species in island environments tend to cause considerably more negative than positive impacts. To assess the potential level of threat aliens may pose to the native environment, understanding a species’ population structure and dynamics is of ultimate importance. Assessing both impacts and consequences of management interventions to alien species is likewise only possible through the comprehension of its population structure and dynamics. This can be achieved by estimating the number of individuals in the study site, as well as other population parameters through time, applying population models such as capture-recapture to the collected datasets. Nonetheless, alien species that have low capture rates, such as small mammals, might present a considerable obstacle for conservation, as available capturerecapture models need a relatively large dataset to precisely and accurately estimate population parameters. To improve accuracy and precision of estimates that use sparse datasets, the present study developed an integrated concurrent marking-observation capture-recapture model (C-MOM). The model proposed here, contrary to the commonly available mark-recapture and mark-resight models, allows for two different datasets (i.e. a capture-recapture and a population count) to be integrated, as well as for marking and observation (recapture) data to be collected simultaneously. While few models can integrate different datasets, no model is known to allow for concomitant capture-markobservation activities. To assess the performance of the C-MOM when estimating population parameters for sparse datasets, a virtual ecology study was carried out. The population dynamics of a small rodent, the rock cavy (Kerodon rupestris), as well as capture-recapture and population count datasets, were simulated under different scenarios. The sampled datasets were then analyzed by the C-MOM, and by two other established statistical models: a classical mark recapture (CMR) (based on the Jolly-Seber model), and a zero-truncated Poisson log-normal mixed effects (ZPNE), the only integrated mark-resight model that allows for recapture sampling with replacement. Estimates of population parameters provided by the three models were then compared in terms of bias, precision and accuracy. C-MOM and ZPNE models were afterwards applied to real data collected on a rock cavy colony in the island of Fernando de Noronha. The estimated parameters were used to extrapolate the number of individuals in the rock cavy colony to the whole population in the island. Subsequently, these results were used to develop a risk assessment for the species by modelling historical and management scenarios, simulating both the establishment of the species in the island, and the consequences of different management interventions applied to it. The virtual ecology study showed that, in comparison to the CMR and the ZPNE, the C-MOM presented improved accuracy without overestimating the precision of population parameter’s estimates. The last also presented reduced amplitude of the calculated credible interval at 95% when applied to real data in comparison to the ZPNE. While the extrapolation of C-MOM estimates suggests that the rock cavy population in Fernando de Noronha is 6,652 ± 1,587, ZPNE estimates are of 5,854 ± 3,269 individuals. In the risk assessment, historical simulation models demonstrated that even though different combinations of uncertainty in reproductive parameters of the rock cavy might be possible for the species, these did not interfere significantly in either establishment or spread of the rock cavy population in the island. Moreover, historical yearly mortality has most likely been under 30%. Regarding the species’ management simulations, the most effective management interventions to achieve population extinction were spaying and neutering of both sexes, although harvest effort presented the highest influence on this populations’ extirpation. Nonetheless, the relative influence of female and both sexes’ based interventions did not differ significantly regarding the frequency of extinction of stochastic replicates’. Moreover, none of the management interventions guaranteed the population extinction within the time span and harvest effort proposed for the management program. Neutering of both sexes was most inversely influential on time to extinction of this population, followed by removal of both sexes. Briefly, the C-MOM has proven to be a resourceful and precise model to estimate population parameters when low capture rates result in sparse datasets. Moreover, the rock cavy is well established in the island and likely at carrying capacity. In general, the risk assessment showed that the management interventions in the time span and harvest effort simulated in the present study were ineffective to extinguish the rock cavy population in Fernando de Noronha. Considering this, as well as the importance of investigating other vital factors to decide in favour of or contrary to the management of this species, it is recommended that both an impact assessment of the rock cavy and a cost-effectiveness analysis of the management interventions should be performed to complement the current study.:Acknowledgement III Abstract IV Zusammenfassung VI Resumen IX Table of Contents XII List of Tables and Figures XIV List of Abbreviations XIX 1. Introduction 1 1.1. Invasive alien species and their consequences 1 1.2. Population dynamics analysis 2 Capture-recapture models 3 Observation models 4 Integrated population models 5 Software 7 Model analysis 8 1.3. Fernando de Noronha and the rock cavy 10 1.4. Objectives 12 Overall Objectives 12 Specific Objectives 13 2. Study Framework 15 3. Methods 19 3.1. Study area 19 3.2. Study case species 21 3.3. Research Steps 24 RESEARCH STEP I: Comparing the C-MOM to established models – does this concurrent marking-observation model produces accurate estimates of population parameters for sparse datasets? 24 RESEARCH STEP II: C-MOM application to a real case study 40 RESEARCH STEP III: The rock cavy population in Fernando de Noronha 45 RESEARCH STEP IV: The colonization and eradication of the rock cavy in Fernando de Noronha 47 4. Results 63 4.1. RESEARCH STEP I: Comparing the C-MOM to established models – does this concurrent marking-observation model produces accurate estimates of population parameters for sparse datasets? 63 4.2. RESEARCH STEP II: C-MOM application to a real case study 72 4.3. RESEARCH STEP III: The rock cavy population in Fernando de Noronha 73 4.4. RESEARCH STEP IV: The colonization and eradication of the rock cavy in Fernando de Noronha 74 Sensitivity analysis 74 Simulation experiments 80 5. Discussion 83 5.1. Bias, precision and accuracy of population dynamic models for sparse datasets 85 Simulated data 85 Study case 90 5.2. Advantages and disadvantages of the C-MOM approach 93 5.3. Development and applications of the integrated models and the C-MOM 96 5.4. The reversed use of the PVA software Vortex to simulate AS and IAS populations’ extinction 97 5.5. Status of the rock cavy population in the island of Fernando de Noronha 100 The colonization of the rock cavy in Fernando de Noronha 101 Management of the rock cavy in Fernando de Noronha 104 Study case limitations and future researches 112 6. Conclusion 116 References 118 Appendices 124 APPENDIX I – Assessment of biological invasions 124 APPENDIX II – Population dynamics simulation and dataset sampling 125 APPENDIX III – CMR and C-MOM model codes in R 134 APPENDIX IV – ZPNE model code in R 138 APPENDIX V – C-MOM model used for real datasets 143 APPENDIX VI – Rock cavy colony sizes and number of individuals in Fernando de Noronha 145 APPENDIX VII – Parameter’s ranking of C-MOM, CMR and ZPNE models 148 APPENDIX VIII – Bias, precision and accuracy table 149

Made available in DSpace on 2014-12-17T15:36:32Z (GMT). No. of bitstreams: 1 ExpeditoSNJ.pdf: 2182833 bytes, checksum: 1d14b6b7f5a8b99dccd3ec09fd418133 (MD5) Previous issue date: 2007-12-07 / Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior / In this study, two circadian related centres, the suprachiasmatic nucleus (SCN) and the intergeniculate leaflet (IGL) were evaluated in respect to their cytoarchitecture, retinal afferents and chemical content of major cells and axon terminals with a tract tracer and immunohistochemical techniques in the rock cavy (Kerodon rupestris), a Brazilian caviidae rodent species. The rock cavy SCN is innervated in its ventral portion by terminals from the predominantly contralateral retina. It also contains neurophisin and vasoactive intestinal polypeptide immunoreactive cell bodies and neuropeptide Y and enkephalin immunopositive fibres and terminals and is marked by intense GFAP immunoreactivity. The IGL receives a predominantly contralateral retinal projection, contains neuropeptide Y and nitric oxide synthase producing neurons and enkephalin immunopositive terminals and is characterized by dense GFAP immunoreactivity. This is the first report examining the neural circadian system in a crepuscular rodent species for which circadian properties have been described. The results are discussed comparing with what has been described for other species and in the context of the functional significance of these centres / O sistema de temporiza??o circadiana compreende um conjunto de estruturas neurais diferenciadas, que incluem um marcapasso central, o qual produz ritmicidade na aus?ncia de est?mulos externos; vias de entrada, incluindo as afer?ncias retininas, que permitem a sincroniza??o dos ritmos aos ciclos ambientais; e vias de sa?da, que conectam o marca-passo aos efetores comportamentais. Entre os componentes centrais do sistema de temporiza??o circadiana de mam?feros, destaca-se o n?cleo supraquiasm?tico (NSQ) do hipot?lamo, at? o presente o ?nico marca-passo circadiano formalmente comprovado, e o folheto intergeniculado (FIG) do complexo geniculado lateral do t?lamo, que atua como modulador do marca-passo. Neste estudo, estes dois centros foram avaliados com rela??o a sua citoarquitetura, padr?o de inerva??o retiniana e conte?do neuroqu?mico de c?lulas e terminais ax?nicos, usando um tra?ador neural e t?cnicas imuno-histoqu?micas no moc? (Kerodon rupestris), um roedor nativo do Nordeste Brasileiro, cuja atividade locomotora exibe um padr?o circadiano predominantemente crepuscular. O NSQ do moc? ? inervado em sua por??o ventrolateral por terminais da retina predominantemente contralateral. O NSQ ? dotado de neur?nios contendo neurofisina (NPH) e polipept?deo intestinal vasoativo (VIP) e as prote?nas ligantes de c?lcio calbindina (CB) e cal-retinina (CR), terminais imunorreativos a neuropept?deo Y (NPY) e encefalina (ENK) e ? tamb?m marcado por imunorreatividade ? prote?na ac?dica fibrilar glial (GFAP). O FIG recebe uma proje??o retiniana predominantemente contralateral, cont?m neur?nios produtores de NPY, CB e CR, terminais positivos para ENK e ? marcado por imunorreatividade a GFAP. Este ? o primeiro trabalho a examinar o sistema de temporiza??o circadiana (STC) numa esp?cie de roedor crepuscular, para o qual as propriedades formais dos ritmos circadianos tenham sido descritas. Os resultados s?o comparados com resultados previamente descritos em outras esp?cies diurnas e noturnas e discutidos no seu contexto funcional