Em sua distribuição autóctone, as abelhas Apis mellifera apresentam diversas diferenciações morfológicas, comportamentais e ecológicas, que as possibilitam habitar os mais variados ambientes, apresentando grande diversidade de subespécies adaptadas a cada região. Com a introdução das abelhas africanas Apis mellifera scutellata no Brasil, em 1956, surgiram populações polí-hibridas denominadas Africanizadas, sendo que essas abelhas se tornaram interessantes para várias atividades econômicas e essenciais para a apicultura no Brasil. Um local que se apresenta como um bom candidato para o entendimento da dinâmica populacional das abelhas Africanizadas é o Nordeste brasileiro, que, recentemente, tem apresentado grandes avanços na área da apicultura. A análise do DNA mitocondrial tem se mostrado muito útil por permitir a obtenção de polimorfismos genéticos diretamente do DNA, resultando em um rápido e preciso estudo da variabilidade existente. Evidências morfométricas também têm sido utilizadas para estimar a composição genética destas abelhas. Neste contexto, este trabalho tem como objetivo avaliar a variabilidade de abelhas Africanizadas em diferentes localidades do Nordeste brasileiro. Foram coletadas 10 operárias por colônia em várias localidades dentro dos Estados do Rio Grande do Norte, Piauí, Alagoas, Paraíba e Sergipe. Foram feitas análises de DNA Mitocondrial do gene COI e análises do padrão de venação da asa através de Morfometria Tradicional e Geométrica utilizando as localidades e os climas das regiões amostradas como marcadores. Para as análises de morfometria foram utilizadas cinco abelhas por colônia epara a análise molecular, foi utilizada uma abelha por colônia. Foram obtidos fragmentos de 624 pb e identificados 11 diferentes haplótipos, correspondentes a 9 sítios variáveis. Os resultados das análises morfométricas e moleculares quando classificados por localidade corroboram entre si, indicando ausência de estruturação populacional na área amostrada. Essa falta de estruturação populacional provavelmente está relacionada ao alto fluxo gênico entre as populações, que tem como principal fator as altas taxas de enxameação durante os períodos de seca no Nordeste. Outros fatores que provavelmente também estão envolvidos são a apicultura migratória existente na região e, em menor escala, o comercio de compra e venda de rainhas e enxames. Os resultados da análise morfométrica usando como classificador o clima da região amostrada, mostra certa estruturação entre os três climas amostrados (Tropical, Litorâneo Úmido e Semiárido), sugerindo grupos relativamente adaptados a estas condições ambientais, apesar de haver fluxo gênico entre eles. Outra explicação para tal fato pode ser a influência do ambiente na formação das características das asas. / In its native distribution, Apis mellifera exhibit various morphological, behavioral and ecological differences that allow them to inhabit various environments and show great diversity of subspecies adapted to each region. With the introduction of African bees Apis mellifera scutellata to Brazil in 1956, emerged hybrid populations called Africanized honey bees, and, overtime, these bees have become important for various economic activities and essential for beekeeping in Brazil. A good candidate for the understanding of population dynamics on Africanized bees is the Brazilian Northeast, which recently has made great advances in the field of beekeeping. The analysis of mitochondrial DNA has proved to be very useful for allowing obtaining genetic polymorphisms directly from DNA, resulting in a fast and accurate method to studies of variability. Morphometric evidence has also been used to estimate the genetic profile of these bees. In this context, this work aims to evaluate the variability of Africanized bees in different localities of Brazilian Northeast. Ten workers per colony were collected at various locations in the states of Rio Grande do Norte, Piauí, Alagoas, Sergipe and Paraiba. Mitochondrial DNA analysis of the COI gene and analysis of the venation pattern of the wing were made through Traditional and Geometric Morphometrics using as markers the localities and climates of the sampled regions. For the analyzes of morphometry were used five bees per colony and for molecular analysis one bee colony was used. Fragments of 624 bp were obtained and 11 different haplotypes were identified, corresponding to 9 variable sites. The results of morphometric and molecular analyzes by location corroborate each other, indicating the absence of population structuration in the sampled area. This is probably related to high gene flow among populations, whose main factor is probably the high rate of swarming during periods of drought in the Northeast. Other factors are probably also involved are migratory beekeeping existing in the region and, to a lesser extent, the trade of buying and selling queens and swarms. The results of morphometric analysis using classifier as the climate of the survey area, showing some structure between the three sampled climates (Tropical, Coastal Humid and Semiarid), suggesting relatively groups adapted to these environmental conditions, although there is gene flow between them. The influence of the environment in shaping the characteristics of the wings is also a possible explanation.

Mitochondrial DNA (mtDNA) has played a major role in human population studies over the past decade due to its maternal inheritance and negligible recombination (Macaulay, 1999). The mtDNA control region has been the focus of these studies due to the highly polymorphic nature of this non-coding region. Forensic scientists also use mtDNA to help determine the identity of missing individuals when nuclear DNA is not present. However, when skeletal remains are unclaimed, identification becomes near impossible. Therefore, mtDNA can play a valuable role in identification in terms of population affiliation, especially in conjunction with morphological analysis. The goals of this research were two-fold: 1) to determine population affiliation of unknown skeletal samples using phylogenetics and 2) to find a method of extraction that leaves a majority of the remains intact. This research depended on the donation of samples from sixteen skeletal remains from the Hillsborough County Medical Examiners office. Mitochondrial DNA from ten of these cases were extracted, amplified, and sequenced in order to determine population affiliation via phylogenetic analysis of hypervariable region I (HVR I). These sequences were aligned and compared to that of sequences in a pre-existing mtDNA control region database (Handt, 1998). The crania of the skeletal remains were measured and subsequently analyzed by the forensic anthropology program FORDISC 2.0 to morphologically determine population affiliation. A secondary morphological analysis included input of the measurements into SPSS, a statistical program package, as a separate discriminant function assessment. This analysis was dependent on a database of craniometrics from known individuals (Jantz, and Moore-Jansen, 2000). The results were compared to those of FORDISC 2.0 as well as that of the phylogenetic tree constructed using molecular techniques. This study will determine whether phylogenetic analysis is a legitimate way to determine population affiliation of unknown individuals, thereby benefiting future forensic studies.

Melongena corona and closely related congeners are a conspicuous part of the marine intertidal benthic communities of Florida and southeastern Alabama. Significant genetic differentiation among adjacent populations has been conjectured based on variation in shell morphology, habitat discontinuity, low levels of adult motility, and the presence of an aplanic lecithotrophic larval stage. Furthermore, studies of the highly variable shell morphology often have resulted in confusing specific and subspecific definitions of these gastropods, which are often referred to as the "corona complex". Variation in shell morphology may indicate local adaptation or environmentally induced phenotypic plasticity. In this study I utilized mitochondrial DNA sequences in order to reconstruct the phylogenetic relationships of crown conchs, and nuclear microsatellite loci to investigate the patterns of relatedness within and among populations inhabiting the southeastern United States. Approximately 500 individuals from 20 populations throughout the known range of the Crown Conch were genotyped at eight microsatellite loci. Additionally, a 1200bp portion of the cytochrome oxidase subunit I gene was sequenced along with a 490bp fragment of the 16s ribosomal gene from individuals representing all known species and subspecies of the genus Melongena. Phylogenetic analyses completed with these data provide no support for current taxonomic designations within this group and these genetic data indicate that the corona complex is composed of a single polymorphic species. Furthermore, microsatellite data reveal population structure consistent with restricted gene flow between extant populations and phylogeography heavily influenced by historical sea-level fluctuations during the Late Pleistocene.

Abstract not available

Freshwater systems offer important opportunities to investigate the consequences of intrinsic biological and extrinsic environmental factors on the distribution of genetic variation, and hence population genetic structure. Drainages serve to isolate populations and so preserve historical imprints of population processes. Nevertheless, dispersal between and within drainages is important if the biology of the species confers a good dispersal capability. Knowledge of the population genetic structure or phylogeographic patterns of Australia's freshwater fish fauna is generally depauperate, and the present study aimed to increase this knowledge by investigating patterns of genetic diversity in three Australian species of freshwater fish. I was interested in the relative importance of dispersal capability, the hierarchical nature of stream structure and the consequences of earth history events on patterns of genetic diversity among populations. I examined three species from three families of Australian freshwater fish, Pseudomugil signifer (Pseudomugilidae), Craterocephalus stercusmuscarum (Atherinidae) and Hypseleotris compressa (Gobiidae). These species are abundant, have wide overlapping distributions and qualitatively different dispersal capabilities. I was interested in attempting to unravel how the biological, environmental and historical factors had served to influence the patterns and extent of genetic diversity within each species, thereby inferring some of the important evolutionary processes which have affected Australia's freshwater fauna. I used allozyme and 500-650bp sequences from the ATPase6 mitochondrial DNA (mtDNA) gene to quantify the patterns of genetic variation at several hierarchical levels: within populations, among populations within drainages and among drainages. I collected fish at several spatial scales, from species wide to multiple samples within drainages; samples were collected from the Northern Territory, Queensland and New South Wales. The species with the highest potential for dispersal, H. compressa, exhibited the lowest levels of genetic differentiation as measured at several allozyme loci (H. compressa: FST=0.014; P. signifer FST=0.58; C. stercusmuscarum FST=0.74). Populations of H. compressa also had low levels of mtDNA differentiation, with many recently derived haplotypes which were widespread along the coast of Queensland. This suggested either considerable gene flow occurs or recent demographic change in the populations sampled. As there was no relationship between geographic distance and genetic differentiation, the populations appeared to be out of genetic drift - gene flow equilibrium, assuming the two-dimensional stepping stone model of gene flow. Estimating contemporary gene flow was thus difficult. It was apparent that there has been a recent population expansion and / or contraction of H. compressa populations. It was concluded that there has been considerably more connectivity among populations of H. compressa in the recent past than either of the other study species. Populations of P. signifer showed considerable genetic subdivision at different hierarchical levels throughout the sampled range, indicating gene flow was restricted, especially between separate drainages. Two widely divergent regional groups which had high ATPase6 sequence divergence and approximately concordant patterns at allozyme loci were identified. Interestingly, the groups mirrored previous taxonomic designations. There was also significant subdivision among drainages within regional groups. For example, the adjacent Mulgrave-Russell and Johnstone drainages had individuals with haplotypes that were reciprocally monophyletic and had large allozyme frequency differences. This allowed me to examine the patterns of genetic differentiation among populations within drainages of two essentially independent, but geographically close systems. There was as much allozyme differentiation among populations within subcatchments as there was between subcatchments within drainages, and significant isolation by distance among all populations sampled within a drainage. This suggested that the estuarine confluence between subcatchments was not a barrier to P. signifer, but that distance was an important component in the determination of the distribution of genetic diversity within drainages in P. signifer. There were three main areas of investigation for C. stercusmuscarum: comparing upland and lowland streams of the drainages in north Queensland, investigating the consequences of eustasy on coastal margin populations and examining the intriguing distribution of the two putative sub species, C. s. stercusmuscarum and C. s. fulvus in south east Queensland. First, as populations in upland areas of east coast flowing rivers are above large discontinuities in the river profile, their occurrence is presumably the result of gene flow to and / or from lowland areas, or the result of invasions via the diversion of western flowing rivers. Concordant patterns at both genetic markers revealed that the latter possibility was the most likely, with fixed allozyme differences between upland and lowland populations, and large mtDNA sequence divergence. Indeed, it appeared that there may have been two independent invasions into the upland areas of rivers in North Queensland. Second, lowland east coast populations also had large, although not as pronounced, levels of population subdivision. Lack of isolation by distance, but with a concomitant high level of genetic differentiation among many comparisons, was consistent with a scenario of many small, isolated subpopulations over the range. Interestingly, widespread populations in central Queensland coastal populations (drainages which receive the lowest rainfall) were relatively genetically similar. This was consistent with the widest part of the continental shelf which at periods of lower sea level apparently formed a large interconnected drainage, illustrating the effect of eustatic changes on populations inhabiting a continental margin. Third, putative C. s. fulvus in lowland coastal Queensland drainages were genetically more similar to a population of C. s. fulvus collected from a tributary of the Murray-Darling (western flowing) than they were to adjacent putative C. s. stercusmuscarum. This implied that populations in south east Queensland, north to approximately the Burnett River, appeared to be derived from western flowing streams, and not via dispersal from other lowland east coast populations. Determining the relative importance of intrinsic and extrinsic factors to the development of population genetic structure is a difficult task. The present study demonstrated that the species with the highest dispersal potential had the lowest levels of genetic differentiation, waterfalls can limit gene flow, eustasy acts to join and separate populations leading to complex genetic patterns and that drainage rearrangements are important in determining the distribution of genetic diversity of populations now inhabiting isolated drainages. A difficulty with generalising about population genetic structure in obligate freshwater animals is the unique history of not only each drainage, but also the streams within that drainage and the idiosyncratic biological dynamics of the populations inhabiting those drainages.

<p>Genetic variation within and among populations is a result of past and ongoing processes. Among the most important of such processes are dispersal, habitat fragmentation and selection. This thesis use neutral genetic variation as a tool to investigate these processes in three bird species.</p><p>In the Siberian jay, the timing of dispersal is dependent on social dominance among siblings. Mark-recapture data, radio-tracking and genetic variation was used to investigate whether timing of dispersal had an effect on dispersal distance. The results show that early dispersing individuals also disperse longer. In the same species, genetic correlation between neighbours was used to find areas with high production of philopatric individuals, which could be indicative of high habitat quality.</p><p>Great snipe populations in northern Europe have a breeding range divided into two regions. A Q_ST-F_STapproach was applied to study variation in selection between regions. Differentiation between the regions in neutral molecular markers was low, indicating high gene flow, or short time available for neutral divergence. Morphological divergence between the regions was high, and Q_ST > F_ST, which indicates divergent selection. Thus, neutral genetic markers can be misleading in identifying evolutionary significant units, and the Q_ST-F_ST approach might be valuable to identify targets for conservation.</p><p>Rock ptarmigan, or its ancestors, originated in Beringia, and spread throughout the Holarctic region. Their distribution has subsequently been affected by glaciations, most likely leading to withdrawals and re-colonisations. Neutral genetic variation among five populations around the northern Atlantic was investigated. There was strong genetic structure among the populations, and evidence that Scandinavian rock ptarmigan has been isolated from other populations for considerable time. Rock ptarmigan in Svalbard showed slightly lower genetic variation than others, and comparisons with other studies suggested an eastern colonisation route to Svalbard.</p>

Mitochondrial respiratory chain deficiency and increased oxidative stress have been closely associated with major age-associated neurodegenerative diseases. I hypothesized that mitochondrial oxidative phosphorylation defects or elevated oxidative stress, which could arise in a stochastic manner during our normal aging process, might modulate the formation of protein aggregates or production of misfolded proteins, contributing to the initiation of these diseases. To test this hypothesis, we (i) have developed and characterized mouse and cellular models of Alzheimer's and Huntington's diseases expressing aggregate-prone pathogenic proteins, beta-amyloid and mutant huntingtin (Chapters 1 and 2), (ii) have developed mouse models that exhibit neuron-specific defects in mitochondrial oxidative phosphorylation (Chapters 2 and 3), and (iii) have evaluated the alterations in the amount of aggregate loads upon genetic and pharmacological manipulations of mitochondrial oxidative phosphorylation activities (Chapters 1 and 2). The evaluation of the impacts of mitochondrial defects on the amount of huntingtin aggregates has revealed that a defect in complex III promotes the accumulation of huntingtin aggregates via the impairment of proteasome activity (Chapter 1). On the other hand, ablation of complex IV activity in a subset of postmitotic neurons revealed that complex IV deficiency does not promote either oxidative stress or the deposition of amyloid plaques in a mouse model of Alzheimer's disease, questioning the mitochondrial origin of Alzheimer's disease (Chapter 2). However, as shown previously, the tight correlation between oxidative stress and accumulation of amyloid plaques was found. Chapter 3 involved the generation of an improved mouse model, in which mitochondrial defects can be induced in a subset of forebrain neurons (cortex, hippocampus, and striatum) in a doxycycline-dependent manner. This system relies on the regulated expression of a mitochondria-targeted restriction enzyme, PstI, which digests mitochondrial DNA and thereby impairs the activity of oxidative phosphorylation. In conclusion, our studies highlighted the disease-specific complex pathways that may modulate the accumulation of misfolded proteins during aging. Future studies employing the newly-developed mouse model may reveal a contribution of age-associated global defects of oxidative phosphorylation to oxidative stress and neurodegenerative diseases.

Genetic variation within and among populations is a result of past and ongoing processes. Among the most important of such processes are dispersal, habitat fragmentation and selection. This thesis use neutral genetic variation as a tool to investigate these processes in three bird species. In the Siberian jay, the timing of dispersal is dependent on social dominance among siblings. Mark-recapture data, radio-tracking and genetic variation was used to investigate whether timing of dispersal had an effect on dispersal distance. The results show that early dispersing individuals also disperse longer. In the same species, genetic correlation between neighbours was used to find areas with high production of philopatric individuals, which could be indicative of high habitat quality. Great snipe populations in northern Europe have a breeding range divided into two regions. A QST-FST approach was applied to study variation in selection between regions. Differentiation between the regions in neutral molecular markers was low, indicating high gene flow, or short time available for neutral divergence. Morphological divergence between the regions was high, and QST &gt; FST, which indicates divergent selection. Thus, neutral genetic markers can be misleading in identifying evolutionary significant units, and the QST-FST approach might be valuable to identify targets for conservation. Rock ptarmigan, or its ancestors, originated in Beringia, and spread throughout the Holarctic region. Their distribution has subsequently been affected by glaciations, most likely leading to withdrawals and re-colonisations. Neutral genetic variation among five populations around the northern Atlantic was investigated. There was strong genetic structure among the populations, and evidence that Scandinavian rock ptarmigan has been isolated from other populations for considerable time. Rock ptarmigan in Svalbard showed slightly lower genetic variation than others, and comparisons with other studies suggested an eastern colonisation route to Svalbard.

Corals are the dominant species of the coral reefs. The diversity of species is classified by traditional morphological traits, especially relied on the calcious deposits-sclerites. The formation of sclerites may be affected by the environmental conditions; therefore, some controversies may exist. The ambiguities may be clarified with molecular approaches. Five soft coral species, Lobophytum pauciflorum, Sinularia leptoclado, Sinularia flexibilis, Sarcophyton sp., Nephthea erecta were chosen for this study. The total mitochondrial DNA sequences were determined by PCR and primer walking. The genome contains 18562 bp, 18732 bp, 18752 bp, 18806 bp, 18716 bp separately, which harbors 14 protein-coding genes (ATP6¡BATP8¡BCOI¡BCOII¡BCOIIII¡BCYTB¡BND1¡BND2¡BND3¡BND4¡BND4L¡BND5¡BND6¡BMSH), 2 rRNA and only 1 tRNA genes. The phylogenetic relationship of alcyonacea corals were analyzed and compared with published sequences. The possibility of using a short ¡§DNA bar-code sequence¡¨ of the mitochondria as an alternative for species identification may be feasible. We found the short DNA signature sequences for these five corals. They may speed up the identification of corals in the long run.

DNA as forensic evidence is valuable in criminal investigations. Implementation of new, sensitive and fast technologies is an important part of forensic genetic research. This thesis aims to evaluate new sensitive methods to apply in forensic DNA analysis including analysis of old skeletal remains. In Paper I and II, two novel systems for analysis of STRs, based on the Pyrosequencing technology, are presented. In Paper I, Y chromosomal STRs are analysed. Markers on the male specific Y chromosome are especially useful in analysis of DNA mixtures. In Paper II, ten autosomal STRs are genotyped. The systems are based on sequencing of STR loci instead of size determination of STR fragments as in routine analysis. This provides a higher resolution since sequence variants within the repeats can be detected. Determination of alleles is based on a termination recognition base. This is the base in the template strand that is excluded from the dispensation order in the sequencing of the complementary strand and therefore terminates the reaction. Furthermore, skeletal remains are often difficult to analyse, due to damaging effects from the surrounding environment on the DNA and the high risk of exogenous contamination. Analysis of mitochondrial DNA is useful on degraded samples and in Paper III, mtDNA analysis of 700 years old skeletal remains is performed to investigate a maternal relationship. The quantity and quality of DNA are essential in forensic genetics. In Paper IV the efficiency of DNA isolation is investigated. Soaking skeletal remains in bleach is efficient for decontamination but result in a lower DNA yield, especially on pulverised skull samples. In conclusion, this thesis presents novel sequencing systems for accurate and fast analysis of STR loci that can be useful in evaluation of new loci and database assembly as well as the utility of mtDNA in forensic genetics.