O tucumã-do-Amazonas (Astrocaryum aculeatum), da família Arecaceae, é uma espécie com ocorrência na Amazônia Ocidental e Central brasileira. Seu fruto é muito apreciado na região amazônica que consome a polpa na forma fresca. Sua produção é feita pelos agricultores extrativistas. Não existem informações dos parâmetros de diversidade e estrutura genética das populações naturais desta espécie, fundamental para o estabelecimento de estratégias adequadas no uso deste recurso genético, e para aumentar a eficiência da domesticação e seleção para um programa de melhoramento genético. Não é conhecido também como este extrativismo pode estar influenciando a diversidade entre estas populações ao nível dos genitores e progênies, o fluxo gênico e a estrutura genética espacial. Assim, o objetivo desta pesquisa foi caracterizar a estrutura e a diversidade genética de populações de A. aculeatum no Estado do Amazonas, utilizando marcadores microssatélites. Como objetivos específicos o estudo visou desenvolver iniciadores de microssatélites para A. aculeatum; avaliar a diversidade e a estrutura genética; determinar o fluxo gênico, bem como o grau de parentesco, a estrutura genética espacial (EGE) e o coeficiente de coancestria numa população. Os iniciadores de microssatélites foram isolados a partir de uma biblioteca genômica enriquecida e caracterizados usando 40 amostras provenientes de duas populações selvagens. Foram identificados 14 iniciadores de microssatélites, mostrando um alto polimorfismo nas populações avaliadas. Para estimar a diversidade e estrutura genética foram utilizadas amostras de material vegetal de 218 plantas distribuídas em 15 populações, localizadas em 14 municípios do estado de Amazonas. Foram identificados 101 alelos nos iniciadores, com média de 10,1 alelos. As médias das heterozigosidades observadas (HO) foram superiores às esperadas (HE) ao nível de população (HO=0,639, HE=0,557) e locos (HO=0,639; HE=0,594). Os baixos valores de FST (0,07) mostraram uma moderada estrutura populacional e a análise Bayesiana indicou um agrupamento mais adequado de k=4, o que foi confirmado pelas análises de PCoA. Para realizar o fluxo gênico, EGE e coeficiente de coancestria foram utilizadas 244 amostras de material vegetal, distribuídas entre 112 possíveis genitores, 12 matrizes e 120 progênies numa população. Foi detectada EGE significativa para os adultos até a distância de 50 m, indicando dispersão de sementes a curtas distâncias. A análise de paternidade detectou 9,2% de imigração de pólen. Não foram detectadas autofecundações e a distância média de polinização dentro da população foi de 81 m. Os índices de diversidade genética confirmaram a estratégia reprodutiva por alogamia da espécie, com níveis elevados de heterozigotos nas populações, e a estrutura genética sugere que a espécie teria iniciado o processo de formação das subpopulações há pouco tempo, tendo sido influenciada antes e após o início do desmatamento. O fluxo gênico detectado indica que a entrada de alelos na população através da imigração de pólen está contribuindo para manutenção da diversidade genética da população. Com relação à conservação da espécie, esta deve ser realizada ao nível das bacias hidrográficas, direcionando políticas de manejo para as bacias hidrográficas da Amazônia. Entretanto, dentro da população é importante a renovação com novas progênies selecionadas a partir de um espaçamento mínimo de 50 m entre plantas matrizes para diminuir as probabilidades de coletar sementes de plantas parentes. / The tucum palm (Astrocaryum aculeatum), family Arecaceae, is a species occurring in Western and Central Brazilian Amazon. Its fruit is widely appreciated in the Amazon region that consumes the pulp in fresh form. Its production is made by extractive farmers. There is no information on the genetic diversity and structure of natural populations of this species, fundamental to establishing adequate strategies in the use of this genetic resource, increase the efficiency of domestication and selection for a breeding program. It is also unknown the way this extrativism may be influencing to diversity of these populations at the level of the parents and offspring, as well as gene flow and spatial genetic structure. Therefore, the objective of this research was to characterize the structure and genetic diversity of populations of A. aculeatum in Amazonas State, using microsatellite markers. As specific objectives, the study aimed to develop microsatellite primers for A. aculeatum; evaluate the genetic diversity and structure; determine the gene flow, the degree of relationship or kinship, the spatial genetic structure (SGS) and the coefficient of coancestry in one population. The loci were isolated from a microsatellite-enriched genomic library and were characterized using 40 samples coming from two wild populations. Fourteen microsatellite primers were identified, showing a high polymorphism in the populations evaluated. To estimate the genetic diversity and structure we used samples of plant material from 218 plants distributed in 15 populations located in 14 municipalities of the state of Amazonas. A total of 101 alleles were identified in the primers, with an average of 10.1 alleles. The averages of the observed heterozygosities (HO) were higher than the expected heterozygosities (HE) at the population (HO=0.639; HE=0.557) and loci (HO=0.639; HE=0.594) levels. The low values of FST (0.07) showed a moderate population structure and the Bayesian analysis indicated as the most suitable a cluster of k=4, confirmed by the groups formed in the PCoA. To conduct gene flow, SGS and the coefficient of coancestry, 244 samples of plant material were used, distributed among 112 possible progenitors, 12 matrices and 120 progenies in a population. A significant SGS was detected for adult trees up to the distance of 50 m, indicating seed dispersal over short distances. Paternity analysis indicated 9.2% of pollen immigration. Selfing was not detected and the average distance of pollination within the population was 81 m. The genetic diversity indices confirmed the outcrossing reproductive strategy of the species with high levels of heterozygotes in the populations, and the genetic structure suggests that the species would have started the process of formation of subpopulations a short time ago, being influenced before and after the start of deforestation. The gene flow detected indicates that the entry of alleles in the population through pollen immigration is contributing to the maintenance of genetic diversity of the population. With respect to the conservation of the species, it should be performed at the level of the river basins, directing management policies for the river basins of the Amazon. However, within the population it is important to renew with new progenies selected from a minimum spacing of 50 m between plant matrices to decrease the probability of collecting seeds from plant relatives.

Cette thèse porte sur le décryptage des causes des variations des taux de substitution moléculaires entre lignées. D'un point de vue théorique, différentes hypothèses sont souvent basées sur des distributions des valeurs sélectives des mutations assez simplistes. En utilisant le modèle géométrique de Fisher, nous avons pu dériver des expressions pour cette distribution, et mettre en évidence l'importance de la complexité phénotypique et de la pléiotropie des mutations. Les variations entre espèces de la proportion de changements d'amino-acides qui sont adaptatifs sont souvent interprétées comme une conséquence de différences de taille de population. Par des simulations, nous avons démontré que la taille efficace des populations n'a qu'une influence faible sur la variation de ces taux, et que les changements environnementaux et la complexité phénotypique peuvent avoir un effet plus important. En ce qui concerne les taux de substitution synonymes, une relation inverse avec la masse corporelle est souvent décrite chez les vertébrés endothermes. Pour déterminer si cette relation est aussi valable chez les vertébrés ectothermes, nous avons suivi une approche comparative portant sur les tortues. Nous avons estimé les taux de substitution synonymes chez 224 espèces, que nous avons ensuite comparé à la masse corporelle (et autres traits d'histoire de vie) et à une variable environnementale (la latitude). Nos résultats démontrent que les taux d'évolution moléculaires sont fortement corrélés aux conditions environnementales et non pas à des traits d'histoire de vie. / The main objective of the present thesis is to elucidate the causes of variations in rates of molecular evolution among lineages, and in particular, to understand how factors connected to mutation, selection and genetic drift can influence these variations.

The Tatra chamois (Rupicapra rupicapra tatrica), an endemic mountain ungulate, occurs in the High Tatra Mts. (northern Slovakia and southern Poland). In the second part of the 20th century several chamois introductions occurred in Slovakia: Tatra chamois (from the High Tatra Mts.) were introduced into the Low Tatra Mts., while Alpine chamois (R. r. rupicapra) into the Veľká Fatra and Slovenský raj Mts. The High Tatra Mts. population underwent several population declines (bottlenecks) and all other Slovak populations were founded from only a few individuals (founder effect). Moreover, because the Low Tatra, Veľká Fatra and Slovenský raj are neighbouring mountain ranges, there is a potential risk of migration and hybridisation between the subspecies. Using 18 microsatellite loci, we studied neutral genetic variability, structure and potential hybridisation in chamois populations in Slovakia. The study is based on 193 samples: 95 tissue and 5 blood samples, and 88 faecal and 5 hair samples. Low genetic variability was found in all populations, the lowest one in High Tatra Mts. population. High values of fixation index, the number of private alleles, and factorial correspondence analysis indicated strong differentiation between the studied populations. Bayesian clustering divided Slovak chamois...

Killer whales are the oceans’ apex predator and are known to have important effects on ecosystems. At Subantarctic Marion Island, southern Indian Ocean, they have only been studied opportunistically, resulting in limited knowledge of their ecosystem impact here. This dissertation describes the prey and seasonal abundance, estimates the population size and assesses the predatory impact of killer whales on seals and penguins at Marion Island, using dedicated and opportunistic shore-based observations and photographic identification, from 2006 to 2009. During 823 sightings of killer whales at Marion Island (2006 to 2009) 48 predation events were recorded; in only 10 cases could prey be identified. Killer whales fed on fur seals, elephant seals and penguins. Constant effort (dedicated) observations (259 hours, 2008 to 2009) showed that killer whale abundance, which peaked in September to December with a secondary peak in April to May, is linked to the abundance of seals and penguins. Mark-recapture analyses were performed using nearly 10 000 photographs taken from 2006 to 2009. Following careful quality control criteria 37 individuals were identified and a population size of 42 (95% CI = 35-50) individuals estimated using the open population POPAN parameterization in the software program MARK. The analytical approach is more rigorous than that used in any previous population size assessment at Marion Island. Finally, the above data were integrated to assess whether top-down control of seal and penguin populations at Marion Island is generally plausible using a simple process of elimination. Based on published data I predicted the energetic ingestion requirements of adult male and female killer whales as 1 394 MJ.day-1 and 1 028 MJ.day-1, respectively. Expanding these requirements to the 37 killer whales photographically identified at Marion Island, the population requires 40 600MJ.day-1. Based on available energy density and mass data, I predicted the energy content of available seal and penguin prey and calculated the rates at which killer whales would consume these prey in various scenarios. Penguins and Subantarctic fur seals are relatively insensitive to killer whale predation owing to their large population sizes (10 000s to 100 000s), conversely, the smaller populations (100s to 1 000s) of Antarctic fur seals and southern elephant seals are sensitive to predation, particularly the latter as they have a high energy content (approximately 2 000 to 9 000 MJ). Populations of these seals are currently increasing or stable and I conclude that presently killer whale predation is not driving population declines, although they clearly have the potential for regulation of these smaller populations. Thus, if population sizes were reduced by bottom-up processes, if killer whale diet shifted, or if prey availability changed, top-down control by killer whales could become significant. This study provides baseline information for the informed management and conservation of killer whales at Marion Island, identifies avenues for further research, and provides a foundation for the continuation of structured and dedicated killer whale research at Marion Island. / Dissertation (MSc)--University of Pretoria, 2011. / Zoology and Entomology / unrestricted

A urbanização e a expansão das fronteiras agrícolas na região Neotropical estão entre as principais forças causadoras da degradação ambiental em hábitats abertos naturais. Inferências e estimativas de abundância são críticas para quantificação de dinâmicas populacionais e impactos de mudanças ambientais. Contudo, a detecção imperfeita e outros fenômenos que causam inflação de zeros podem induzir erros de estimativas e dificultar a identificação de padrões ecológicos. Examinamos como a consideração desses fenômenos em dados de contagens de indivíduos não marcados pode informar na escolha do método apropriado para estimativas populacionais. Revisamos métodos estabelecidos (modelos lineares generalizados [GLMs] e amostragem de distância [distance sampling]) e emergentes que usam modelos hierárquicos baseados em misturas (N-mixture; modelo de Royle-Nichols [RN], e N-mixture básico, zero inflacionado, espacialmente explicito, visita única, e multiespécies) para estimar a abundância de populações não marcadas. Como estudo de caso, aplicamos o método N-mixture baseado em visitas únicas para modelar dados de contagens de aves de rapina em estradas e investigar como transformações de habitat no Cerrado e Pantanal do Mato Grosso do Sul afetaram as populações de 12 espécies em uma escala regional (>300.000 km2). Os métodos diferem nos pré-requisitos de desenho amostral, e a sua adequabilidade depender da espécie em questão, da escala e objetivos do estudo, e considerações financeiras e logísticas, que devem ser avaliados para que verbas, tempo e esforço sejam utilizados com eficiência. No estudo de caso, a detecção de todas as espécies foi influenciada pela horário de amostragem, com efeitos congruentes com expectativas baseadas no comportamentos de forregeamento e de voo. A vegetação fechada e carcaças também influenciaram a detecção de algumas espécies. A abundância da maioria das espécies foi negativamente influenciada pela conversão de habitats naturais para antrópicos, particularmente pastagens e plantações de soja e cana-de-açúcar, até mesmo para espécies generalistas consideradas como indicadores ruins da qualidade de hábitats. A proteção dos hábitats naturais remanescentes é essencial para prevenir um declínio ainda maior das populações de aves de rapina na área de estudo, especialmente no domínio do Cerrado / Urbanization and the expansion of agricultural frontiers are among the main forces driving the degradation of natural habitats in Neotropical open habitats. Inference and estimates of abundance are critical for quantifying population dynamics and the impacts of environmental change. Yet imperfect detection and other phenomena that cause zero inflation can induce estimation error and obscure ecological patterns. We examine how detection error and zero-inflation in count data of unmarked individuals inform the choice of analytical method for estimating population size. We review established (GLMs and distance sampling) and emerging methods that use N-mixture models (Royle-Nichols model, and basic, zero-inflated, temporary emigration, beta-binomial, generalized open-population, spatially explicit, single-visit and multispecies) to estimate abundance of unmarked populations. As a case study, we employed a single visit N-mixture approach to model roadside raptor count data and investigate how land-use transformations in the Cerrado and Pantanal domains in Brazil have affected the populations of 12 species on a regional scale (>300,000 km2). Methods differ in sampling design requirements, and their suitability will depend on the study species, scale and objectives of the study, and financial and logistical considerations, which should be evaluated to use funds, time and effort efficiently. In the case study, detection of all species was influenced by time of day, with effects that follow expectations based on foraging and flying behavior. Closed vegetation on and carcasses found during surveys also influenced detection of some species. Abundance of most species was negatively influenced by conversion of natural Cerrado and Pantanal habitats to anthropogenic uses, particularly pastures, soybean and sugar cane plantations, even for generalist species usually considered poor habitat-quality indicators. Protection of the remaining natural habitats is essential to prevent further decline of raptor populations in the study area, especially in the Cerrado domain

In the late 1980s the endangered Chatham Island oystercatcher (Haematopus chathamensis) (CIO) was estimated at less than 110 individuals. Endemic to the Chatham Islands, New Zealand, it was feared to be declining and, based on existing productivity estimates, in danger of extinction within 50-70 years. These declines were thought to be caused by numerous changes since the arrival of humans, including the introduction of several terrestrial predators, the establishment of marram grass (Ammophila arenaria) which changes dune profiles, and increased disturbance along the coastline. The New Zealand Department of Conservation has undertaken recovery planning and conservation management to increase CIO numbers since the late 1980s. Recovery planning raised some key research questions concerning the population dynamics, habitat selection, and breeding biology of Chatham Island oystercatcher (CIO), and the critical factors currently limiting the population. The objectives of this study were to collect and interpret data on: 1) population size, trends, and distribution across the Chathams, 2) basic breeding parameters, 3) recruitment and mortality rates, 4) habitat selection at the general, territorial and nest-site levels, 5) habitat factors that are correlated with territory quality, and 6) cues that elicit territorial behaviour in CIO.

Made available in DSpace on 2016-06-02T20:04:51Z (GMT). No. of bitstreams: 1 4032.pdf: 1016886 bytes, checksum: 6e1eb83f197a88332f8951b054c1f01a (MD5) Previous issue date: 2011-11-18 / Financiadora de Estudos e Projetos / The capture-recapture process, largely used in the estimation of the number of elements of animal population, is also applied to other branches of knowledge like Epidemiology, Linguistics, Software reliability, Ecology, among others. One of the _rst applications of this method was done by Laplace in 1783, with aim at estimate the number of inhabitants of France. Later, Carl G. J. Petersen in 1889 and Lincoln in 1930 applied the same estimator in the context of animal populations. This estimator has being known in literature as _Lincoln-Petersen_ estimator. In the mid-twentieth century several researchers dedicated themselves to the formulation of statistical models appropriated for the estimation of population size, which caused a substantial increase in the amount of theoretical and applied works on the subject. The capture-recapture models are constructed under certain assumptions relating to the population, the sampling procedure and the experimental conditions. The main assumption that distinguishes models concerns the change in the number of individuals in the population during the period of the experiment. Models that allow for births, deaths or migration are called open population models, while models that does not allow for these events to occur are called closed population models. In this work, the goal is to characterize likelihood functions obtained by applying methods of elimination of nuissance parameters in the case of closed population models. Based on these likelihood functions, we discuss methods for point and interval estimation of the population size. The estimation methods are illustrated on a real data-set and their frequentist properties are analised via Monte Carlo simulation. / O processo de captura-recaptura, amplamente utilizado na estimação do número de elementos de uma população de animais, é também aplicado a outras áreas do conhecimento como Epidemiologia, Linguística, Con_abilidade de Software, Ecologia, entre outras. Uma das primeiras aplicações deste método foi feita por Laplace em 1783, com o objetivo de estimar o número de habitantes da França. Posteriormente, Carl G. J. Petersen em 1889 e Lincoln em 1930 utilizaram o mesmo estimador no contexto de popula ções de animais. Este estimador _cou conhecido na literatura como o estimador de _Lincoln-Petersen_. Em meados do século XX muitos pesquisadores se dedicaram à formula ção de modelos estatísticos adequados à estimação do tamanho populacional, o que causou um aumento substancial da quantidade de trabalhos teóricos e aplicados sobre o tema. Os modelos de captura-recaptura são construídos sob certas hipóteses relativas à população, ao processo de amostragem e às condições experimentais. A principal hipótese que diferencia os modelos diz respeito à mudança do número de indivíduos da popula- ção durante o período do experimento. Os modelos que permitem que haja nascimentos, mortes ou migração são chamados de modelos para população aberta, enquanto que os modelos em que tais eventos não são permitidos são chamados de modelos para popula- ção fechada. Neste trabalho, o objetivo é caracterizar o comportamento de funções de verossimilhança obtidas por meio da utilização de métodos de eliminação de parâmetros perturbadores, no caso de modelos para população fechada. Baseado nestas funções de verossimilhança, discutimos métodos de estimação pontual e intervalar para o tamanho populacional. Os métodos de estimação são ilustrados através de um conjunto de dados reais e suas propriedades frequentistas são analisadas via simulação de Monte Carlo.

A urbanização e a expansão das fronteiras agrícolas na região Neotropical estão entre as principais forças causadoras da degradação ambiental em hábitats abertos naturais. Inferências e estimativas de abundância são críticas para quantificação de dinâmicas populacionais e impactos de mudanças ambientais. Contudo, a detecção imperfeita e outros fenômenos que causam inflação de zeros podem induzir erros de estimativas e dificultar a identificação de padrões ecológicos. Examinamos como a consideração desses fenômenos em dados de contagens de indivíduos não marcados pode informar na escolha do método apropriado para estimativas populacionais. Revisamos métodos estabelecidos (modelos lineares generalizados [GLMs] e amostragem de distância [distance sampling]) e emergentes que usam modelos hierárquicos baseados em misturas (N-mixture; modelo de Royle-Nichols [RN], e N-mixture básico, zero inflacionado, espacialmente explicito, visita única, e multiespécies) para estimar a abundância de populações não marcadas. Como estudo de caso, aplicamos o método N-mixture baseado em visitas únicas para modelar dados de contagens de aves de rapina em estradas e investigar como transformações de habitat no Cerrado e Pantanal do Mato Grosso do Sul afetaram as populações de 12 espécies em uma escala regional (>300.000 km2). Os métodos diferem nos pré-requisitos de desenho amostral, e a sua adequabilidade depender da espécie em questão, da escala e objetivos do estudo, e considerações financeiras e logísticas, que devem ser avaliados para que verbas, tempo e esforço sejam utilizados com eficiência. No estudo de caso, a detecção de todas as espécies foi influenciada pela horário de amostragem, com efeitos congruentes com expectativas baseadas no comportamentos de forregeamento e de voo. A vegetação fechada e carcaças também influenciaram a detecção de algumas espécies. A abundância da maioria das espécies foi negativamente influenciada pela conversão de habitats naturais para antrópicos, particularmente pastagens e plantações de soja e cana-de-açúcar, até mesmo para espécies generalistas consideradas como indicadores ruins da qualidade de hábitats. A proteção dos hábitats naturais remanescentes é essencial para prevenir um declínio ainda maior das populações de aves de rapina na área de estudo, especialmente no domínio do Cerrado / Urbanization and the expansion of agricultural frontiers are among the main forces driving the degradation of natural habitats in Neotropical open habitats. Inference and estimates of abundance are critical for quantifying population dynamics and the impacts of environmental change. Yet imperfect detection and other phenomena that cause zero inflation can induce estimation error and obscure ecological patterns. We examine how detection error and zero-inflation in count data of unmarked individuals inform the choice of analytical method for estimating population size. We review established (GLMs and distance sampling) and emerging methods that use N-mixture models (Royle-Nichols model, and basic, zero-inflated, temporary emigration, beta-binomial, generalized open-population, spatially explicit, single-visit and multispecies) to estimate abundance of unmarked populations. As a case study, we employed a single visit N-mixture approach to model roadside raptor count data and investigate how land-use transformations in the Cerrado and Pantanal domains in Brazil have affected the populations of 12 species on a regional scale (>300,000 km2). Methods differ in sampling design requirements, and their suitability will depend on the study species, scale and objectives of the study, and financial and logistical considerations, which should be evaluated to use funds, time and effort efficiently. In the case study, detection of all species was influenced by time of day, with effects that follow expectations based on foraging and flying behavior. Closed vegetation on and carcasses found during surveys also influenced detection of some species. Abundance of most species was negatively influenced by conversion of natural Cerrado and Pantanal habitats to anthropogenic uses, particularly pastures, soybean and sugar cane plantations, even for generalist species usually considered poor habitat-quality indicators. Protection of the remaining natural habitats is essential to prevent further decline of raptor populations in the study area, especially in the Cerrado domain

[For the Abstract, please see the PDF files below, namely "front.pdf"] CONTENTS. Chapter 1 Introduction. Chapter 2 Gross and microscopic visceral anatomy of the male Cape fur seal with reference to organ size and growth. Chapter 3 Age determination and growth in the male Cape fur seal: part one, external body. Chapter 4 Age determination and growth in the male Cape fur seal: part two, skull. Chapter 5 Age determination and growth in the male Cape fur seal: part three, baculum. Chapter 6 Suture age as an indicator of physiological age in the male Cape fur seal. Chapter 7 Sexual dimorphism in the adult Cape fur seal: standard body length and skull morphology. Chapter 8 Reproduction in the male Cape fur seal: age at puberty and annual cycle of the testis. Chapter 9 Diet and foraging behaviour of the Cape fur seal. Chapter 10(a) The Impact of the fur seal industry on the distribution and abundance of Cape fur seals. Chapter 10(b) South African Airforce wildlife rescue: Cape fur seal pups washed from Black Rocks, Algoa Bay, during heavy seas, December 1976. Chapter 11(a) Operational interactions between Cape fur seals and fisheries: part one, trawl fishing. Chapter 11(b) Operational interactions between Cape fur seals and fisheries: part two, squid jigging and line fishing. Chapter 11(c) Operational interactions between Cape fur seals and fisheries: part three, entanglement in man-made debris. Chapter 12 Concentrations of heavy metals (Cd, Cu, Pb, Ni & Zn) and organochlorine contaminants (PCBs, DDT, DDE & DDD) in the blubber of Cape fur seals. Chapter 13 Endoparasites of the Cape fur seal. Chapter 14(a) Preliminary investigations of shark predation on Cape fur seals. Chapter 14(b) Aggressive behaviour of an adult male Cape fur seal towards a great white shark Carcharodon carcharias. Chapter 15 Conclusions and future directions.

No description available.