Submitted by Danielle Karla Martins Silva (danielle.martins@ufpe.br) on 2015-03-03T18:04:36Z No. of bitstreams: 2 Tese Gondolo ppgba 2012.pdf: 13206403 bytes, checksum: 031790e8079da8f2469064fa538a3223 (MD5) license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) / Made available in DSpace on 2015-03-03T18:04:36Z (GMT). No. of bitstreams: 2 Tese Gondolo ppgba 2012.pdf: 13206403 bytes, checksum: 031790e8079da8f2469064fa538a3223 (MD5) license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) Previous issue date: 2012 / FACEPE / Os padrões de estruturação populacional podem ser entendidos pela dinâmica das populações, e tal entendimento passa pela distinção de unidades evolutivas e compreensão dos padrões de conectividade. A tainha (parati), Mugil curema, objeto do presente trabalho, apresentase como modelo para estudos de conectividade populacional, uma vez que existem evidências consolidadas acerca da existência de um potencial complexo de espécies ou de populações disjuntas. Revelar o patamar de variação genética-morfológica da espécie, bem como descobrir como e em que nível a variabilidade genética se apresenta ao longo da região é o objetivo central do presente estudo. A espécie foi estudada nos estuários dos rios Potengi/RN, Paraíba do Norte/PB, Canal de Santa Cruz/PE, Formoso/PE, São Francisco/AL e Ribeira de Iguape/SP. A variabilidade genética foi acessada por PCR, pelo uso de marcadores moleculares PCR-RFLP do gene Citocromo Oxidase Subunidade I e ISSRs, foram observadas as histórias genéticodemográfica da espécie na região, sendo desenvolvidas análises de agrupamento e mensurados parâmetros genético-populacionais. A diferenciação em tamanho e forma dos indivíduos foi realizada pela morfometria geométrica. Tanto os dados obtidos da região mitocondrial, assim como os colhidos da região nuclear do genoma da espécie evidenciaram alto grau de estruturação populacional. Em menor grau, mas também evidente, foi observada diferenciação morfológica entre os exemplares dos diferentes estuários. Pode-se concluir que as populações de Mugil curema encontram-se em processo de diversificação, sugerindo um possível complexo de espécies sob a denominação Mugil curema. Além disso, uma das populações deste complexo é genético-evolutivamente mais relacionada com Mugil hospes do que com duas outras populações da própria espécie. Perante os resultados obtidos, o manejo das populações de Mugil curema no litoral brasileiro deve ser abordado de forma muito cuidadosa e específica, uma vez que a diversificação populacional deste taxon é conspícua e de forma geral é notório que os seis estuários não podem ser regidos pelas mesmas ações e medidas para a conservação do estoque de tainhas.

This thesis is dedicated to an archaeogenetic study of five prehistoric individuals. The sample material comes from central Yakutia, also called Sakha Republic, in the north-eastern part of Russia. The main focus of this study has been the analysis of five mitochondrial genomes, retrieved from osteological material (human bones and teeth), having an estimated age of 6845 BP to 2490 BP. The dates fall within Neolithic, Bronze Age and Early Iron Age. A brief presentation for each individual’s archaeological profile and interpretation of the burial will be provided. While a series of interpretive tests with the mitochondrial DNA material were performed and the results are presented. The neolitization of the north-eastern Eurasia will also be discussed. The correlation between the Neolithic Age, Bronze Age and Early Iron Age populations will be proposed, as well as their connections to modern populations.

Submitted by Fabio Sobreira Campos da Costa (fabio.sobreira@ufpe.br) on 2016-04-12T12:41:55Z No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) Tese Taciana Martins Barbosa Biblioteca Central.pdf: 2266957 bytes, checksum: c72479b848ff65eb617cd5065338256f (MD5) / Made available in DSpace on 2016-04-12T12:41:55Z (GMT). No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) Tese Taciana Martins Barbosa Biblioteca Central.pdf: 2266957 bytes, checksum: c72479b848ff65eb617cd5065338256f (MD5) Previous issue date: 2015-08-31 / FACEPE / O octocoral Carijoa riisei é um cnidário colonial que possui ampla distribuição geográfica no Oceano Atlântico Sul, Caribe, Pacífico e Indo-Pacífico. Com intuito de conhecer a estrutura e a conectividade das populações da espécie, abordagens diferentes foram realizadas. Em pequena escala geográfica espacial (6-125 km) a partir de diferentes ambientes (recifes costeiros, naufrágios e estuários) da costa de Pernambuco (Brasil), análises do DNAmt, morfológicas e reprodutivas foram realizadas. Verificou-se que houve variação morfológica em 10 dos 11 caracteres morfológicos avaliados quando comparadas as localidades estudadas. No entanto, não há diferenciação genética entre as sete populações estudadas devido ao alto fluxo gênico, indicando que a espécie em Pernambuco consiste em uma população panmítica. Portanto, a alta variabilidade morfológica de C. riisei encontrada neste estudo é devido à plasticidade fenotípica em resposta às mudanças ambientais e não ao acúmulo de diferenças genéticas devido à interrupção do fluxo gênico entre as populações. Para análise em grande escala geográfica espacial (108-2781 km), o exame da conectividade genética por meio do DNAmt foi realizado em populações do Atlântico Sul/Brasil e comparado com resultados encontrados de outras regiões do Atlântico (Leste e Norte) e do mundo (Pacífico/Havaí e Indo-Pacífico). Estruturação genética foi observada em duas das seis populações estudadas no Atlântico Sul/Brasil. Contudo, foi verificado fluxo gênico suficiente para conectar todas as populações, tanto dentro do Atlântico Sul, como entre as populações desta região com as demais. O Atlântico Sul apresentou a maior diversidade genética entre todas as regiões do Atlântico estudadas. Quando a comparação é realizada entre as regiões geográficas do mundo, a maior diversidade genética foi encontrada no Indo-Pacífico e a menor no Atlântico Norte. De acordo com esses resultados e aliado com o que existe na literatura, encontra-se suporte à ideia de que C. riisei é nativa do Indo-Pacífico. A conectividade genética das populações em organismos sésseis é alcançada pela dispersão larval. Este estudo descreve pela primeira vez a embriogênese, desenvolvimento e assentamento larval de C. riisei. Foram recolhidas colônias na costa norte de São Paulo, Brasil e mantidos vivos em aquários. Através da observação direta, verificou-se que a liberação dos gametas predominantemente ocorreram entre 05h00-10h00. A fertilização é externa e os ovos fertilizados tem um diâmetro médio de 403 ± 6,0 μm, apresentando geralmente flutuabilidade positiva. As clivagens são superficiais, o primeiro ciclo de divisão ocorre perto de 3h30-5 h após a liberação dos gametas. A divisão citoplasmática é rápida (15-20 min), facilmente visível nas fases de 16 e 32 células. As larvas plânulas são formadas entre 27-36 h após a liberação dos gametas; podem nadar por toda a coluna dágua e atingir 1,8 mm de comprimento. As plânulas assentam entre 10-18 dias após a liberação dos gametas. O pólipo primário é translúcido, e os tentáculos emergem como oito pequenos botões arredondados. Portanto, a espécie tende a ter um potencial de dispersão de longa distância, que aliado ao nível considerável de variação morfológica (que favorece a adaptação da espécie em condições ecológicas heterogêneas) e a conectividade ocorrendo entre populações em pequena e grande escala geográfica espacial, auxiliam a compreender a ampla distribuição deste octocoral. / The octocoral Carijoa riisei is widely spread in the South Atlantic Ocean, Caribbean, Pacific and Indo-Pacific. Seeking to know the structure and connectivity of populations of the species, different approaches have been undertaken. In small spatial geographic scale (6-125 km) from different environments (coastal reefs, shipwrecks and estuaries) from the coast of Pernambuco (Brazil), analysis of mtDNA, morphological and reproductive were held. It was found that there is morphological variation in 10 of 11 morphological characters evaluated when compared the locations studied. However, there is no genetic differentiation among the populations studied due to high gene flow, indicating that the species in Pernambuco consists of a panmitic population. Therefore, the high morphological variability of C. riisei found in this study is due to phenotypic plasticity in response to environmental changes and not the accumulation of genetic differences due to the interruption of gene flow between populations. For analysis in large spatial geographic scale (108-2781 km), examination of genetic connectivity through mtDNA was held in South Atlantic/Brazil populations and compared with results from other regions of the Atlantic (East and North) and the world (Pacific/Hawaii and Indo-Pacific). Genetic structure was observed in two of the six studied populations in the South Atlantic/Brazil. However, it was found sufficient gene flow to connect all populations, both within the South Atlantic, as among populations of this region with others. The South Atlantic showed the highest genetic diversity among all regions of the Atlantic studied. When a comparison is performed among the geographic regions of the world, the greatest genetic diversity was found in the Indo-Pacific and the smallest in the North Atlantic. According to these results and allied with what exists in the literature, it supports the idea that C. riisei is native to the Indo-Pacific. Genetic connectivity of populations in sessile organisms is achieved by larval dispersal. This study describes for the first time embryogenesis, development and larval settlement of this octocoral. Colonies were collected on the north coast of São Paulo, Brazil and kept alive in aquariums. Through direct observation, it was found that spawns predominantly occurred in the morning between 05h00-10h00. The fertilization is external and fertilized eggs have an average diameter of 403 ± 6.0 μm, usually presenting positive buoyancy. The cleavages are superficial, the first division cycle occurs near 3h30-5 h after spawning. The cytoplasmic division is rapid (15-20 min), easily visible in stages 16 and 32 cells. The larvae planula are formed 27-36 h after spawning; can swim throughout the water column and reach a length of 1.8 mm. Planulae settle 10-18 days after spawning. The primary polyp is translucent, and the tentacles emerge as eight small round buttons. Therefore, the species tends to have a potential for long-distance dispersal, that coupled with the considerable level of morphological variation (that favors the adaptation of the species in heterogeneous ecological conditions) and connectivity between populations occurring in small and large spatial geographic scale assists to understand the wide distribution of this octocoral.

A espécie Bos indicus, particularmente a raça Nelore, é grande maioria no rebanho bovino da região acima do trópico no Brasil. Embora a habilidade desses animais em resistir às doenças parasitárias, condições climáticas e pastagens de baixa qualidade enalteçam a utilização em larga escala desta raça, estes animais não são considerados bons conversores de alimento e, conseqüentemente, precoces em comparação aos seus homólogos Bos taurus. Durante a formação das raças zebuínas brasileiras, houve uma participação das linhas maternas de Bos taurus, que pode ser demonstrada pela contribuição majoritária do genoma mitocondrial desta subespécie. Embora em escala muito menor, estima-se que exista também uma participação destas linhas maternas no genoma nuclear. O objetivo deste trabalho foi iniciar os estudos para estimar esta participação. Para os estudos foram utilizados 104 animais da raça Nelore e 8 animais de diferentes raças européias. Cinco regiões do DNA que produzem fragmentos microssatélites taurus/indicus específicos (HEL1, HEL9, ETH225, ILSTS005 e INRA063) foram amplificadas com a utilização de primers marcados com sondas fluorescentes. Os fragmentos foram submetidos à eletroforese em gel de poliacrilamida desnaturante 6% e visualizados após excitação com laser. No total foram encontrados 23 alelos para os microssatélites analisados o que representa uma média de 4,6±1,82 alelos por locus. Amplificou-se também uma região do DNA satélite 1711b que posteriormente foi digerida com a enzima de restrição Msp I. Verificou-se a existência de três possíveis genótipos entre os animais Nelore mtDNA Bos taurus e mtDNA Bos indicus. Os animais europeus analisados apresentaram sempre o mesmo padrão de restrição. A comparação dos componentes de variância do tamanho dos alelos intra e inter população usando os fragmentos microssatélites permitem a separação dos animais Bos taurus dos animais Nelore, mas não dos Nelore de origem materna distinta. No entanto, a freqüência de alelos indicus específicos nos microssatélites e de padrões de digestão do DNA satélite também indicus específicos sugerem uma participação da ordem de aproximadamente 6% do genoma taurus na população de gado Nelore. / Bos indicus specie, especially Nellore breed is responsible for the majority of Brazilian tropical herd. These animals are notably capable to endure parasite infection as well as hot weather and low quality feed. In one hand this qualities suggest the large scale application of this breed, but in other hand this same breed is well characterized as bad food converter and consequently far from having good precocity status compared with its Bos taurus homologues. It has been reported a matrilineal European participation in Zebu cattle since its introduction in American lands. This hybridization is confirmed by the majority contribution of Bos taurus mtDNA in these animals. Although in a much lower frequency, we hypothesize a Bos taurus cow participation in nuclei genome. The main aim of this work was to give the firsts steps towards the estimation of this participation. A total of 104 Nellore and 8 animals of different European breeds were used for DNA analysis. Five microsatellites fragments (HEL1, HEL9, ETH225, ILSTS005 e INRA063) were amplified applying primers with fluorescent dye. Amplified fragments were used in 6% polyacrilamide electrophoresis and visualized after laser excitation. Overall 23 alleles were detected averaging 4.6±1,82/locus. Variance components of microsatellites allele size comparisons allowed the formation of two clusters separating both subspecies. No significant variation was observed between Nellore with different maternal origins. A satellite 1711b DNA was also amplified and digested with the restriction enzyme Msp I. Three possible genotypes were identified in Nellore animals harboring B. taurus and B. indicus mtDNA. European originated animals always showed the same restriction pattern. Finally B. indicus specific microsatellite allele and satellite 1711b digestion patterns frequency allowed the estimation of 6% of B. taurus contribution in purebred Nellore. These results are discussed in terms of application in cattle genetic improvement.

Orientador: Lilian Madi-Ravazzi / Resumo: As mudanças climáticas ocorridas no Pleistoceno afetaram a distribuição e os padrões de diversificação populacionais e são conhecidas como um dos potenciais impulsionadores da alta diversidade encontrada na região Neotropical. Drosophila sturtevanti pertence ao subgrupo sturtevanti do grupo saltans de Drosophila e é uma das espécies com distribuição geográfica mais ampla dentro do grupo, ocorrendo em áreas florestais de diferentes biomas. Além disso, essa espécie apresenta altos níveis de variabilidade genética para diversos marcadores, constituindo um excelente modelo para estudos de estrutura populacional, diversificação e adaptação em diferentes cenários. O objetivo desse estudo foi analisar a diferenciação genética, usando os genes Citocromo Oxidase subunidades I e II em 163 indivíduos provenientes de 21 populações de D. sturtevanti coletados em fragmentos florestais da América Central ao sul do Brasil, com ênfase na Mata Atlântica. Nossos resultados moleculares mostram que as populações de D. sturtevanti estão estruturadas na América do Sul e sua distribuição mostra uma correlação significativa com variáveis geográficas e climáticas, principalmente temperatura e umidade. Além disso, os eventos de divergência entre os grupos geográficos sugerem associação significante com as oscilações paleoclimáticas ocorridas desde o Pleistoceno tardio e, esses eventos, provavelmente moldaram a distribuição geográfica dos haplogrupos de acordo com variáveis ambientais, principalmente te... (Resumo completo, clicar acesso eletrônico abaixo) / Doutor

In most tropical river systems there has been a lack of integrated ecological research to investigate the dynamics and impacts of invasive species on recipient river systems. This is in sharp contrast to temperate river systems. This thesis investigated the nature, extent, and impact of Nile tilapia, Oreochromis niloticus (Linnaeus, 1758), on indigenous congenerics within the Limpopo River basin in northern South Africa. An integrated approach was adopted to gain a better understanding of factors that allow Nile tilapia to be a successful invader and also to gain an insight into its invasion rate and conservation implications within South Africa. Morphometric and genetic variation between Nile tilapia, indigenous congenerics and their associated hybrids were determined. Intermediate meristic characters obscured the identification of hybrid specimens from pure morpho-specimens and species identity was only confirmed through mtDNA analysis. Preliminary evidence points to unidirectional hybridization among Oreochromis congeners in the Limpopo River system. The hypothesis that bigger Nile tilapia males may have a competitive advantage over spawning grounds and in female mate choice is proposed. The trophic ecology of Nile tilapia was investigated using both stomach contents and stable isotope analysis. A high similarity in stomach contents was observed but interspecific differences were revealed in the isotopic composition of diets that suggest fine scale patterns of resource partitioning that could be achieved by the ability of fish to selectively feed on what is immediately available and the ability to perceive the dynamics that determine food resource availability. Ecological niche models were used to determine the potential invasive range of Nile tilapia and revealed broad invasive potential over most river systems in southern Africa that overlapped the natural range of endemic congenerics. It was noted that model performance and the degree of niche conservatism varied significantly with variable selection and spatial extent of study area. This implied that the spatial distribution of suitable and unsuitable environmental variables varied between the native and introduced ranges of Nile tilapia and also indicated the ability of Nile tilapia to survive in conditions incongruent with its native range. The extreme hardiness and adaptive life history characteristics of Nile tilapia have probably predisposed it to be a successful invader in novel systems within southern Africa. Lastly, a qualitative risk assessment method was developed as a potential application to determine the risk of establishment and spread of the invasive Nile tilapia. Results showed that in the absence of quantitative data on ecosystem structure and functioning, habitat suitability analysis in terms of known physiological tolerance limits to minimum water temperature, presence or absence of dams, seasonality of river flows and the presence of indigenous fish species of concern could be adequate for identifying vulnerable river systems. The model developed also provides an objective method that is easy to implement, modify and improve on as new data become available. Furthermore, the model can be applied to highlight areas of uncertainty where future research should be directed. / Thesis (PhD)--University of Pretoria, 2012. / Zoology and Entomology / Unrestricted

Mitochondria are organelles present in most eukaryotic cells. They generate most of the cells adenosine triphosphate (ATP) supply which make them essential for cell viability. It is assumed that they are derived from a proteobacterial ancestor as they retain their own, drastically small genome. The importance in studying mitochondrial genome evolution came from the discovery of a large number of human diseases that are caused by mitochondrial dysfunction (e.g., Parkinson and Alzheimer). Many of these diseases are a result of a mutation in one of the mitochondrial genes or a defective mitochondrial DNA (mtDNA) maintenance, mostly caused by genetic defects in proteins involved in mtDNA replication. In order to explore the diversity and understand the evolution of mitochondrial genomes (mitogenomes) in animals, multiple methods have been developed in this study to deal with two biological problems related to the mitochondrial genome evolution. A new method for identifying the mitochondrial origins of replication is presented. This method deals with the problem of determining the origins of replication, which despite many previous efforts has remained non-trivial even in the small genomes of animal mitochondria. The replication mechanism is of central interest to understand the evolution of mitochondrial genomes since it allows the duplication of the genetic information. The extensive work that has been done to study the replication of mitochondrial genomes has generated the assumption of the strand displacement model (SDM) also known as the standard model of replication that is known to leave the mitochondrial H-strand in a single stranded state exposing it to mutation and damage. Later on, other models of replication have been suggested such as the strand coupled bidirectional replication model, its refinement which assumes the bidirectional mode but with a unidirectional start, and the \"RNA incorporation throughout the lagging strand\" (RITOLS) model proposed as a refinement of the strand displacement model. Based on the observation that the GC-skew is correlated with the distance from the replication origins in the light of the strand displacement model of replication, a new computational method to infer the position of both the heavy strand and the light strand origins from nucleotide skew data has been developed. The method has been applied in a comprehensive survey of deuterostome mitochondria where conserved positions of the replication origins for the vast majority of vertebrates and cephalochordates have been inferred. Deviations from the consensus picture are presumably associated with genome rearrangements. Additionally, two methods for the identification of tRNA remolding events throughout Metazoa have been developed. Remolding changes the identity of a tRNA by a duplication and a point mutation(s) of the anticodon. This new tRNA takes the identity of another tRNA which is then lost. This can lead to artifacts in the annotation of mitogenomes and thus in studies of mitogenomic evolution. In this work, novel methods are developed to detect tRNA remolding in large-scale data sets. The first method represents an extension of the similarity-based approach to determine remolding candidates with high confidence. This approach uses an extended set of criteria based on both sequence and structural similarities of the tRNAs in conjunction with statistical tests. The second method is a novel phylogeny-based likelihood method which evaluates specific topologies of gene phylogenies of the two tRNA families relevant to a putative remolding event. Both methods have been applied to survey tRNA remolding throughout animal evolution. At least three novel remolding events are identified in addition to the ones previously mentioned in the literature. A detailed analysis of these remoldings showed that many of them are derived ancestral events.

Earth-boring dung beetles of the genus Lethrus Scopoli, 1777 belong to the family Geotrupidae, classified into three subfamilies (Geotrupinae, Lethrinae a Taurocerastinae). The description of about 120 species, divided into nine subgenera, is based on morphology and geographic distribution. Shape of mandibles, ventral mandible processes, pronotum and structure of external male genitalia are used as diagnostic morphological characters for taxa. The richest species diversity is known from Central Asia. The distribution area reaches, in the east, up to Mongolia and China, and in the west, up to Southeast Europe. All species are robust, relatively large flightless beetles with low dispersial ability. They feed on parts of fresh plants instead of feces like other dung beetles. Master thesis is focused on the species distributed in the Eastern Mediterranean and Central Europe. This area is inhabited only by nominotypical subgenus Lethrus. The main goal of thesis is to clear up phylogenetic relationships between species of subgenus and speciation events using molecular genetic methods. We have examined 91 samples of the genus Lethrus using two mitochondrial genes - cytochrome b (382 bp, 80 sequences), cytochrome oxidase I (815 bp, 87 sequences) and nuclear gene 28S rDNA (D2-D5) (1100 bp, 11 sequences)....

The first method for DNA analysis in forensics was presented in 1985. Since then, the introduction of the polymerase chain reaction (PCR) has rendered possible the analysis of small amounts of DNA and automated sequencing and fragment analysis techniques have facilitated the analyses. In most cases short tandemly repeated regions (STRs) of nuclear DNA are analysed in forensic investigations, but all samples cannot be successfully analysed using this method. For samples containing minute amounts of DNA or degraded DNA, such as shed hairs, analysis of mitochondrial DNA (mtDNA) is generally more successful due to the presence of thousands of copies of mtDNA molecules per cell. In Sweden, ~40 % of all households have cats or dogs. With ~9 million humans shedding ~100 scalp hairs per day, and ~1.6 million cats and ~1 million dogs shedding hairs it is not surprising that shed hairs are one of the most common biological evidence found at crime scenes. However, the match probability for domestic dog mtDNA analysis has only been investigated in a few minor studies. Furthermore, although breed –sequence correlations of the noncoding mtDNA control region (CR) have been analysed in a few studies, showing limited correlations, no largescale studies have been performed previously. Thus, there have not been any comprehensive studies of forensic informativity of dog mtDNA. In the two papers presented in this thesis we have tried to lay a foundation for forensic use of analysis of domestic dog mtDNA. In the first paper, CR sequences were analysed and the exclusion capacity was investigated for a number of different populations. This is also the first comprehensive study of the correlation between mtDNA CR type and breed, type, and geographic origin of domestic dogs. Since the exclusion capacity for analysis of domestic dog CR sequences is relatively low, it was investigated in the second paper to what extent the discrimination power is improved by analysis of coding sequence. The exclusion capacity improved considerably when 3,000 base pairs of coding sequences where analysed in addition to CR sequences. This study will hopefully work as a basis for future development of analysis of dog mtDNA for forensic purposes. / QC 20101123

No description available.