Sarus cranes (Grus antigone) are the tallest members of the crane family, Gruidae. They are found in four geographically distinct regions: northwest India (Indian Sarus- Grus antigone antigone), southeast Asia (Burmese Sarus- Grus antigone sharpei) and northern Australia (Australian Sarus- Grus antigone gillae). Although the three subspecies are morphologically distinct, their genetic distinctness is unclear. In this study, I focused on control region sequences of mitochondrial DNA (mtDNA) to assess the genetic and phylogeographic distinctness of Sarus subspecies. I used samples from four fragmented populations, seven from India, 16 from southeast Asia, five from Myanmar and eight from Australia. Phylogenetic trees were estimated using two Brolga crane sequences (G. rubicunda) as outgroups. All phylogenetic trees had low resolution, but AMOVA showed that all four Sarus populations are differentiated from each other. Nested clade phylogenetic analysis showed that most of the southeast Asian haplotypes are found at the center, suggesting that the Thai population includes the maximum number of ancestral haplotypes. Sarus cranes probably originated in southeast Asia and migrated both north towards India and south towards Australia during the last glacial maximum.

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Crassostrea (Sacco, 1897) é o gênero mais importante do mundo de ostras de cultivo e consiste de 34 espécies distribuídas pelas regiões tropicais e temperadas do globo. C. gasar e C. rhizophorae são as duas espécies nativas que estão distribuídas ao longo de toda a costa do Brasil até o Caribe. C. gasar também ocorre na costa da Africa. Ainda que sua distribuição seja extensa e com disponibilidade abundante, o cultivo de ostras nativas no Brasil ainda é incipiente e a delimitação correta dos estoques mantém-se incerta. O sucesso do desenvolvimento da malacocultura, que é recomendada internacionalmente como forma sustentável de aquicultura, depende da resolução desses problemas. Assim, com o objetivo de determinar geneticamente seus estoques no Atlântico como também estimar sua história demográfica, dois diferentes marcadores moleculares foram empregados: sequências de DNA da região controle mitocondrial e loci de microssatélites espécie-especifícos, desenvolvidos no presente estudo. Foram sequenciados fragmentos da região controle de um total de 930 indivíduos de C. gasar e C. rhizophorae coletados em 32 localidades que incluíram o Caribe, a Guiana Francesa, a costa brasileira e a África. Também foram realizadas genotipagens de 1178 indivíduos, e ambas as espécies, com 9 e 11 loci de microssatélites para C. gasar e C. rhizophorae, respectivamente. Os dados genéticos foram analisados através de diferentes abordagens (índices de estruturação (FST) e de (Jost D), análise molecular de variância (AMOVA), análise espacial molecular de variância (SAMOVA), Bayesian Skyline Plots (BSP), análise fatorial de correspondência (AFC) e análise de atribuição Bayesiana (STRUCTURE)). Os resultados indicaram um padrão geral de estruturação, onde dois diferentes estoques foram detectados para ambas as espécies: grupos do norte e do sul, onde o Rio de Janeiro seria a região limitante entre os dois estoques. Os maiores valores dos índices de estruturação foram encontrados para C. gasar, indicando que esta espécie estaria mais estruturada do que C. rhizophorae. As análises demográficas indicaram uma provável expansão das populações durante o ultimo período glacial e uma possível origem americana das populações africanas. Todos os resultados sugeriram a existência de uma barreira geográfica próxima ao Rio de Janeiro, que poderia ser a cadeia de Vitória-Trindade e o fenômeno de ressurgência que ocorre em Cabo Frio (RJ). Esses resultados serão de grande utilidade para estabelecer critérios para seleção de sementes para cultivo ao longo da costa do Brasil que permitirá o manejo adequado dos estoques ostreícolas, prevenindo seu desaparecimento como já ocorrido em outros recifes no mundo. / Crassostrea (Sacco, 1897) is the most important genus of cultivated oysters in the world and consisting of 34 species distributed by tropical and temperate regions of the globe. C. gasar and C. rhizophorae are the two native species which have wide distribution along the entire Brazilian coast up to the Caribbean. C. gasar also occurs on coast of Africa. Despite its extensive distribution and abundant availability, cultivation of those oysters in Brazil is incipient, and the correct delimitation of the existing stocks is still uncertain. The successful development of malacoculture which is recommended internationally as an environmentally sustainable form of aquaculture depends on the resolution of these issues. Thus, in order to genetically determinate their stocks in the Atlantic and to estimate their demographic history, two different molecular markers were employed: sequences of the mitochondrial DNA control region and species-specific microsatellite loci, developed in the present study. We have sequenced a fragment of the mitochondrial control region from a total of 930 individuals of C. gasar and C. rhizophorae collected in 32 localities including the Caribbean, French Guyana, Brazilian coast and Africa. We have also genotyped 1178 individuals of both species with 9 and 11 loci of microsatellites for C. gasar and C. rhizophorae, respectively. Genetic data were analyzed with different approaches (fixation (FST) and differentiation (Jost D) indices, analysis of molecular variance (AMOVA), spatial analysis of molecular variance (SAMOVA), Bayesian Skyline Plots (BSP), factorial correspondence analysis (AFC) and Bayesian attribution analysis (STRUCTURE)). The results indicated a general structure pattern, where two different stocks were detected for both species: north and south groups, where Rio de Janeiro would be the limited region between them. Higher values of fixation indices were found for C. gasar, indicating that this species would be more structured than C. rhizophorae. Demographic analyses showed a probable expansion of populations during the last glacial period and a probable American origin of African populations. All results suggested the existence of a barrier next to Rio de Janeiro, which could be Vitoria-Trindade chain and the upwelling in the region of Cabo Frio (RJ). These results will be useful to establish criteria for the selection of seeds for cultivation along the Brazilian coast which will allow proper management of stocks of oysters preventing its disappearance as in other reefs around the world.

Goal of this Thesis is the comparison of the Grayling˘s genetic diversity. The complete mitochondrial DNA (mtDNA) control region (1083 base pairs) and gene for cytochrom B (1076 base pairs) were sequenced in 147 European grayling (Thymallus thymallus), from 21 populations in Czech Republic, Slovakia and Bosnia. In samples, 17 haplotypes were detected with average haplotype diversity Hd = 0,5480 and genic differentiation (FST) from 0,001 to the 0.9341. The most common haplotype TH1 was detected in 92 samples. An inferred intraspecific phylogenetic tree revealed three well-separated clades. One clade was represented by Danubian haplotypes from Slovakia. Second highly divergent clade contained individuals from river Vrbas in Bosnia, and the last biggest clade included haplotypes of all three sea basins from Czech Republic. We suppose that the gained results will be later utilized to the choice of suitable conservation measures that will lead to stabilization of the state of ancestral population of this ever more rare species in our region.

Submitted by Natalia de Souza Gonçalves (natalia.goncalves@ufpe.br) on 2016-09-23T13:58:51Z No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) Tese Emilly.pdf: 3694284 bytes, checksum: b1e6e78f9d75225d406cb1ffd3c9bc2b (MD5) / Made available in DSpace on 2016-09-23T13:58:51Z (GMT). No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) Tese Emilly.pdf: 3694284 bytes, checksum: b1e6e78f9d75225d406cb1ffd3c9bc2b (MD5) Previous issue date: 2016-02-26 / FACEPE / CAPES / CNPq / O beijupirá Rachycentron canadum, é um peixe pelágico marinho, migrador, cosmopolita que possui grande interesse comercial no mundo. O presente trabalho objetivou avaliar a existência de estruturação populacional interoceânica, analisar a diversidade genética e a conectividade entre as populações no Atlântico Sul, além de estimar a variabilidade e endogamia da espécie nas pisciculturas e na costa brasileira. Para isso foram utilizados exemplares do beijupirá ao longo de sua distribuição global (Atlântico, Índico e Pacífico), na costa brasileira e em quatro pisciculturas no Brasil analisados por meio de marcadores microssatélites e do DNAmt (citocromo b e D-loop). Os resultados obtidos na análise interoceânica indicam alta diversidade genética e moderada estruturação genético-populacional para o D-loop, rejeitando a hipótese de panmixia global da espécie. Na costa brasileira foi observada ausência de estruturação populacional, evidenciando conectividade e inexistência de barreiras que impeçam o fluxo gênico e a migração da espécie, revelando uma população panmítica intra-oceânica. Já nas pisciculturas do beijupirá no Brasil foi observada perda de diversidade genética e diferenciação genética entre as pisciculturas e os selvagens, apesar do cultivo recente da espécie. Diante disso, o gerenciamento da pesca tanto a nível mundial, quanto local, e o manejo da espécie nas estações de piscicultura devem considerar estas informações para a exploração sustentável e o comércio de indivíduos em termos regionais e globais, trazendo implicações para o manejo da espécie e sua conservação. / Cobia Rachycentron canadum, is a marine pelagic, migratory, cosmopolitan fish that has great commercial interest in the world. This study aimed to evaluate the existence of inter-oceanic population structure, analyze the genetic diversity and connectivity among populations in the South Atlantic, as well as to estimate the variability and inbreeding in cobia farms and the Brazilian coast. Specimens were collected throughout its global distribution (Atlantic, Indian and Pacific), the Brazilian coast and four aquaculture installations in Brazil using microsatellite markers and mtDNA (cytochrome b and D-loop). The results of the inter-oceanic analysis indicate high genetic diversity and moderate genetic population structure for the D-loop, rejecting the hypothesis of global panmixia. In the Brazilian coast the absence of population structure was observed, showing connectivity and lack of barriers that prevent gene flow and migration of species, revealing an intra-oceanic panmitic population. However, in the farmed cobia, a loss of genetic diversity was detected , besides genetic differentiation between farm and wild, despite the recent farming of the species. Thus, the fisheries management both globally and locally, and the maintenance of species in aquaculture installations should consider this information for the sustainable exploitation and trade of individuals in regional and global terms, bringing implications for the management of the species and its conservation.

Orientadores: Ana Maria Lima de Azeredo-Espin, Ana Claudia Lessinger / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-06T23:15:02Z (GMT). No. of bitstreams: 1 Oliveira_MarcosTuliode_M.pdf: 4922399 bytes, checksum: 9af5c489b44982daee534a4e0f7e937c (MD5) Previous issue date: 2006 / Resumo: o DNA mitocondrial (DNAmt) dos metazoários possui uma série de características, tais como organização circular, simples e compacta, conteúdo gênico conservado, herança predominantemente materna e ausência ou baixa taxa de eventos de recombinação, que fazem com que este genoma seja amplamente usado em diversos estudos evolutivos. Geralmente, o DNAmt animal possui 37 genes (13 codificadores de proteínas, 22 para RNAt e 2 para RNAr) e uma principal região não-codificadora, a região-controle. O objetivo do projeto foi o seqüenciamento e a caracterização estrutural e evolutiva de regiões gênicas e do genoma mitocondrial de espécies da família Muscidae (Diptera: Calyptratae), incluindo a mosca-dos chifres, Haematobia irritans, a mosca doméstica, Mosca domestica, a mosca menor das frutas, Atherigona orientalis, "the black dump fly", Ophyra aenescens, e a mosca-dos-estábulos, Stomoxys calcitrans. A estrutura da tese foi dividida em quatro capítulos. No primeiro capítulo, a seqüência completa do gene da subunidade I da cito cromo oxidase c (COI) foi caracterizada. COI é o gene mais seqüenciado entre os insetos e tem sido usado em diversos estudos evolutivos e taxonômicos. Este gene mostrou-se estruturalmente semelhante aos demais dípteros, incluindo o uso de um códon de iniciação não usual, TCG (serina). O segundo capítulo descreve um novo conjunto de oligonucleotídeos iniciadores que ajudou a amplificar e seqüenciar regiões do DNAmt de vários dípteros onde há alta chance de ocorrer rearranjos e/ou duplicações (regiões de "hot spots" ou "instabilidade estrutural" no DNAmt de artrópodes, que incluem a região-controle e agrupamentos de RNAt). O terceiro capítulo descreve a seqüência completa da região-controle de H. irritans, M domestica e A. orientalis, define padrões evolutivo-estruturais para moscas da subordem Brachycera e sugere a atuação de elementos cis-regulatórios no controle da replicação e transcrição do DNAmt de insetos. Ao tentar acessar a região-controle de O. aenescens e S. calcitrans, foi evidenciado um possível evento de rearranjo e/ou duplicação no genoma mitocondrial destas espécies envolvendo os genes que flanqueiam a região-controle. O quarto capítulo descreve uma análise comparativa entre os genomas mitocondriais de H. irritans (16078bp) e S. calcitrans (18Kb). Um conjunto de estratégias, incluindo amplificação via LongPCR, construção de bibliotecas de "shotgun", montagem, anotação e análises estruturais utilizando recursos de bioinformática, foi otimizada durante este trabalho. Os genomas mitocondriais de H. irritans e S. calcitrans possuem conteúdo e organização gênicos conservados, considerando-se o modelo ancestral proposto para artrópodes, exceto pela regiãocontrole de S. calcitrans (2,5Kb), que teve 60% de sua seqüência caracterizada, suficientes para indicar a ocorrência de duplicação gênica envolvendo elementos internos da região-controle e o gene de RNAt para isoleucina (I). A duplicação de 1 no DNAmt de S. calcitrans é muito semelhante a que ocorre no DNAmt de espécies de Chrysomya (Diptera: Calliphoridae), reforçando que esta região é um "hot spot" de duplicação no genoma mitocondrial de dípteros. Uma árvore filogenética usando os genes codificadores de proteínas foi inferida para a ordem Diptera e o resultado difere da filogenia tradicional proposta para o grupo / Abstract: The mitochondrial DNA (mtDNA) of Metazoan has features, such as circular, simple and compact organization, conserved gene content, predominantly maternal inheritance, and lack or low rate of recombination, which have made this genome widely used in a range of evolutionary studies. In general, animal mtDNA presents 37 genes (13 protein-coding genes, 22 genes for tRNA and 2 for rRNA) and a major non-coding region, the control region. The aim ofthis project was the sequencing and the structural and evolutionary characterization of gene regions and the mitochondrial genome of species from family Muscidae (Diptera: Calyptratae): the horn fly, Haematobia irritans; the house fly, Musca domestica; the pepper fruitfly, Atherigona orientalis; the black dump fly, Ophyra aenescens; and the stable fly, Stomoxys calcitrans. The structure of the thesis was divided in four chapters. In the first chapter, the complete sequence of the cytochrome c oxidase subunit I (COI) gene was characterized. COI is the most sequenced gene in insects and have been used in a wide range of evolutionary and taxonomic studies. This gene in Muscidae showed a structure similar to other dipterans, including the use of an uncommon start codon, TCG (serine). The second chapter describes a new set of primers that improved the amplification and sequencing of regions from many dipterans mtDNA in which there is a high probability of rearrangements andlor duplications occur (regions involved in structural "hot spots", including the control region and tRNA clusters). The third chapter describes the complete sequence of H. irritans, M domestica and A. orientalis, defines evolutionary and structural patterns for Brachyceran flies and suggests cis-regulatory elements for the mtDNA repÍication and transcription control in insects. Trying to access the control region of O. aenescens and S. calcitrans, a possible event of rearrangement andlor duplication in the mitochondrial genome of these species was evidenced involving the control region flanking genes. The fourth chapter describes a comparative analysis of H. irritans (l6078bp) and S. calcitrans (-18Kb) mitochondrial genomes. A set of strategies, including the amplification via Long-PCR, construction of a shotgun library, assemblage, annotation and structural analysis using bioinformatic tools, was optimized in this work. The mitochondrial genomes of H. irritans and S. calcitrans showed gene content and organization conserved regarding the ancestral model proposed to arthropods, except for S. calcitrans control region (-2.5Kb), which had 60% of its sequence characterized. This characterization indicated the occurrence of duplicated regions involving control region nternal elements and the tRNAgene for isoleucine (I). The duplication of 1 is very similar to that of Chrysomya (Diptera: Calliphoridae) mtDNA, reinforcing that this region is a duplication hot spot in the mitochondrial genome of dipterans. A phylogenetic tree using the protein-coding genes was inferred for the Diptera order and the results differ from the traditional phylogeny proposed for the grou / Mestrado / Genetica Animal e Evolução / Mestre em Genética e Biologia Molecular

Orientador: Ana Maria Lima de Azeredo-Espin / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-08T14:57:58Z (GMT). No. of bitstreams: 1 Duarte_GustavoTurqueto_M.pdf: 29004339 bytes, checksum: 8f4329468621fc63871c823f6f4664b1 (MD5) Previous issue date: 2007 / Resumo: As espécies da família Calliproridae, conhecidas como moscas varejeiras, apresentam ampla distribuição geográfica no Velho e Novo Mundo. Por serem causadores de miíases e vetores de doenças, muitas espécies possuem hábito sinantrópico, importância econômica, médico-sanitária e forense. Enquanto algumas espécies são pragas da pecuária e acarretam grande prejuízo econômico devido às infestações, outras são importantes para a entomologia forense, auxiliando na investigação de crimes e questões médico-legais. Neste contexto, os marcadores moleculares têm sido de grande valia para estudos genéticos relacionados à família Calliphoridae, sendo utilizados em estudos populacionais, evolutivos e biogeográficos, complementando análises ecológicas e sistemáticas. Dentre os marcadores moleculares, o DNA mitocondrial (DNAmt) tem mostrado potencial para estudos evolutivos relacionados à família Calliphoridae, devido a várias características, tais como: possuir uma estrutura genética simples, geralmente não apresentando íntrons, DNA repetitivo, elementos transponíveis e pseudogenes; exibir uma forma de transmissão predominantemente linear (herança materna); grande número de cópias e, finalmente, por apresentar maior taxa de substituição nucleotídica, quando comparada ao DNA nuclear. Na maioria das espécies animais, o DNAmt possui cerca de 16-20kb e apresenta 37 genes, dos quais 13 são codificadores de proteínas, 2 de subunidades ribossomais (rRNAs) e 22 de tRNAs. Neste genoma, a maior porção não codificadora é chamada região controle (RC), ou A+T em insetos, por ser rica nesses dois nucleotídeos. Bridências experimentais com insetos, crustáceos e vertebrados sugerem que essa região esteja relacionada à replicação e transcrição do genoma mitocondrial. Eventos de rearranjos gênicos envolvendo a região controle e os tRNAs adjacentes são relativamente freqüentes em insetos. Recentemente uma duplicação do gene para tRNA de isoleucina (tRNAIle) foi descrita em três espécies do gênero Chrysomya, não sendo encontrada nas demais espécies de Calliphoridae estudadas até então, sugerindo que a duplicação poderia ter se originado num evento evolutivo anterior à diversificação desse gênero e que seria um marcador molecular eficiente para sua identificação. Dessa forma, com o intuito de caracterizar a região controle do DNAmt m família Calliphoridae bem como a duplicação do tRNAIle, 15 espécies pertencentes a sete gêneros desta família foram analisadas. Nos califorídeos estudados, a região controle apresentou-se dividida em dois domínios com característica distintas: um conservado, devido à presença de blocos de seqüê ncia conservados além de estruturas conservadas em vários grupos de insetos, que podem estar relacionadas à replicação e transcrição do DNAmt; e um domínio variável, tanto em tamanho quanto em seqüência. Enquanto o domínio conservado apresentou potencial para estudos filogenéticos, o domínio variável apresentou características interessantes para estudos com estrutura de populações. A caracterização da RC de califorídeos também permitiu a identificação da duplicação do tRNAIle em outras duas espécies de Chrysomya, além de uma espécie do gênero Calliphora. Um segundo tipo de duplicação, envolvendo os tRNAIle e tRNAGln, foi identificada na espécie do gênero Phormia. Os dados sugerem que o domínio variável da região controle possa atuar como um "hot spot" para eventos de rearranjo. Para a avaliação do potencial para estudos filogenéticos do domínio conservado, foram analisadas as seqüências desse domínio da região controle de 26 indivíduos pertencentes a 18 espécies de califorídeos. Os resultados dão suporte à monofilia dás três subfamílias estudadas (Chrysomyinae, Luciliinae e Calliphorinae) corroborando estudos morfológicos e moleculares realizados previamente em Calliphoridae. Além disso, o domínio conservado da região controle mostrou-se um marcador eficiente para a identificação de espécies de califorídeos, mesmo quando espécies semelhantes morfologicamente foram comparadas. Os resultados obtidos indicam um potencial dessa região do genoma mitocondrial tanto para estudo com taxa com divergência recente como para o diagnóstico de espéciés de importância forense / Abstract: The species of family Calliphoridae, known as blowflies, present wide geographic distribution throughout Old and New World and many have synantropic habit, being of economic, medical, sanitary and forensic importance for causing myiasis and for being vectors of diseases. While some species are parasites of livestock and causes great economic prejudices, others are important for forensic entomology, helping in legal investigations. Molecular markers are providing valuable results on genetic-evolutive studies related to the family Calliphoridae, been used in population structure, evolutive and biogeographic studies, complementing ecological md systematic analyses. Among the molecular markers, the mitochondrial DNA have shown a great potential for evolutive studies related to family Calliphoridae, being many the features that make it a rich source of genotypic characters: simple genetic structure, which usually lacks introns, transposable elements and pseudogenes; its predominant1y maternal inheritance; high copy number and its higher rate of nucleotide substitution compared to nuclear DNA. In most animal species, mtDNA is a circular, double-stranded 16-20 kb molecule that generally contains 37 genes, being 13 protein-coding genes, two genes for subunits of ribosomal RNA (rRNA) and 22 transfer RNA (tRNA) genes. Within this genome, the major non-coding region is known as control region, or A+T region in insects for being rich in these nucleotides. Experimental evidences with insects, crustaceans and vertebrates suggest that this region is related to the replication and transcription of the mitochondrial genome. Rearrangements events involving the control region and its flanking tRNAs may be frequent in insects. In recent works, an isoleucine tRNA gene (tRNAIle) duplication was reported for three Chrysomya species, not been identified in the other calliphorids species studied so far, suggesting that the duplication may have occurred before the diversification of this genus and that it would be an efficient marker for its identification. Therefore, intending to characterize the control region of mitochondrial DNA in family Calliphoridae just as the tRNAIle duplication, 15 species belonging to seven genera of this family were analyzed. In the studied calliphorids, two domains were recognized in the control region: a conserved domain with conserved sequence blocks and conserved structures also identified in other insect groups, which relates the control region to the replication and transcription of mitochondrial DNA; and a variable domain that varies markedly in sequence and length Whereas the conserved domain has shown a potential for phylogenetic stud ies, the variable domain has interesting features for population studies. The characterization of the control region in various calliphorids species also showed the presence of the duplication of the tRNAIle in two other species of Chrysomya and in a species of genus Calliphora. A different duplication, involving the tRNAIle and tRNAGln, was identified in the species of genus Phormia. The present data suggests that the variable domain of the contraI region may act as a hot spot for rearrangement events. For evaluating the potential of the conserved domain for . phylogenetic studies, sequences of this domain were analyzed for 26 specimens belonging to 18 calliphorid species. The results supports the monophyly of the three subfamilies studied (Chrysomyinae, Luciliinae and Calliphorinae), corroborating previous morphologic and molecular studies. Moreover, the cohserved domain of control region showed to be I useful for calliphorids species identification, even when morphologic similar species were compared. The data reveals a potential of this region of the mitochondrial genome for studies with recent diverged taxa and also for the diagnosis of species with forensic importance / Mestrado / Genetica Animal e Evolução / Mestre em Genética e Biologia Molecular

Abstract The impact of hand-rearing on the morphology and physiology of captive and wild grey partridges (Perdix perdix) and capercaillies (Tetrao urogallus) was studied in three feeding trials conducted under laboratory conditions, and two comparative studies between wild and captive birds. Finally, wild and hand-reared grey partridges from several localities in Europe were sampled and the control region 1 of mitochondrial DNA was sequenced to reveal genetic variation between populations, as well as to compare wild and captive stocks. Wild capercaillies had heavier pectoral muscles, hearts, livers and gizzards, longer small intestines than hand-reared ones, and a higher cytochrome-c oxidase activity in muscle and heart. Invertebrates were essential to the growth, primary and temperature regulation development in grey partridge chicks. Fish was not sufficient to replace invertebrates in the diet. A change in diet from commercial to natural decreased the assimilation efficiency in the grey partridge. It also increased the mass of gizzard reflecting the need for greater grinding ability. Of hepatic P450 enzymes used in this study 7-ethoxyresorufin-0-deethylase and 7-pentoxyresorufin-0-deethylase differed between wild and hand-reared birds. Coumarin-7-hydroxylase activity was higher in grey partridges than capercaillies. Diet differences may have caused these differences. Quebracho tannin added to the diet lowered nitrogen concentration in caecal feces, and elevated the level of excreted tannin. Otherwise its effects were slight. Mitochondrial control region revealed 14 variable sites between two main lineages detected. Nucleotide and haplotype diversities varied greatly between populations. The markedly deep divergence between the two lineages indicated most probably post-glacial recolonisations from geographically isolated refuges. In Finland, wild birds represented the eastern lineage, while the farmstock represented the western lineage. Surprisingly little trace, contrary to expectations, from the large-scale releasing of imported partridges could be seen in the European populations.

>Magister Scientiae - MSc / The primary objective of this Masters project was to investigate the maternal ancient substructure of the Griqua population in South Africa. Genetic ancestry was determined by investigating ancestry informative single nucleotide polymorphisms. These are located in the control region of the mitochondrial genome. The auxiliary aim was to test the validity of the UWC 10plex system in relation to a sample group of Griqua males. This short tandem repeat multiplex targets specific mutations confined to paternal lineages. The Khoi Khoi or Hottentots were the first inhabitants in the Cape. Indigenous Khoi Khoi female slaves had offspring with the European settlers in the 1800s which resulted in the Griqua population group. The incorporated European paternal ancestry is what set the Griqua apart from the native population groups at that time. Colonisation events from the mid-17th to 19th Century and the apartheid regime resulted in land dispossession of the native population and an extensively mixed gene pool in South Africa. One hundred and seventy six (N=176) male and female Griqua people were collectively sampled in Kokstad (2012), Vredendal (2012 and 2013) and at the Griqua National Conference in Ratelgat (2013). All 176 samples were analysed using mtDNA control region Sanger sequencing. The sample group (N=176) was separated based on birthplace (Origin sample group and post-colonial sample group). The origin sample group consists of individuals whose ancestors were not part of the Griqua Trek to Northern regions of South Africa and were less likely to be exposed to colonial influences. Mutations within the hypervariable segments of the mtDNA control region were used to infer haplogroups with geographic-specific population data. In this way one can plot the extent of ancient Khoisan (L0d) and Bantu influences (L1-L5) as well as the influence of East (M, A, B, E) and West (N, R, J, H) Eurasian haplogroups in the maternal ancestry of the Griqua population group. The origin sample group showed 91% African ancestry (76.8% L0d) while the post-colonial group had 78% African ancestry (60% L0d). The origin sample group had 2% East Eurasian and 7% West Eurasian ancestry, while the post-colonial group contained 20% Eurasian ancestry. There is greater admixture in the post-colonial group which can be attributed to the integration of surrounding populations during settlement periods in parts of the Northern Cape and KwaZulu-Natal. The UWC 10plex STR kit was tested to see if it could discriminate between male individuals of this admixed sample group (N=91 males). The markers for this multiplex were selected according to their ability to differentiate between individuals of African descent. It proved to be a viable Y chromosome short tandem repeat testing tool, displaying a statistically significant discrimination capacity value of 0.966 and only having 3 shared haplotypes in the sample group of 91 Griqua males. / National Research Foundation (NRF)

Molecular tools, such as sequencing of the mitochondrial DNA Control Region (CR) and genotyping of highly variable nuclear microsatellites were applied to survey the genetic diversity, population structure and phylogeography of three shark species: the whale shark, Rhincodon typus; the bull shark, Carcharhinus leucas; and the nurse shark, Ginglymostoma cirratum. The highly migratory and pelagic whale shark exhibited the largest length variation yet reported for an elasmobranch CR (1143–1332 bp), and high haplotype (h = 0.974 ± 0.008) and nucleotide diversities(π = 0.011 ± 0.006). No geographical clustering of lineages was observed and the most common haplotype was distributed globally. The haplotype frequency, however, differed between the Atlantic and Indo-Pacific populations(AMOVA, ΦST = 0.107, P < 0.001). For the bull shark, both mtDNA CR and five microsatellite loci were surveyed for animals from the Gulf of Mexico, the East coast of Florida and the Brazilian coast. Strong genetic structure was observed between theBrazilian and all northern populations for the CR (ΦST > 0.8, P < 0.001), but not for the nuclear microsatellite. The results here presented are congruent with restricted maternal gene flow between populations as a consequence of female nursery site fidelity. The philopatric tendencies as well as the relatively low levels of genetic diversity raises concerns about the conservation of this species. Finally, for the western Atlantic nurse sharks the genetic diversity estimated in a 1,166 bp fragment of the mtDNA comprising partial cytochrome b, tRNAPro, tRNAThr, and partial CR was the second smallest ever recorded for sharks (h = 0.45 ± 0.04; π = 0.0004 ± 0.0004). The data indicated moderate but significant genetic structure with the mtDNA marker (ΦST = 0.22, P<0.05) and no substantial structure in eight microsatellite loci analyzed. A population bottleneck as recent as the lower Pleistocene might have eroded the nurse shark genetic diversity and also contributed to its relatively lower population structure. The data also indicated that dispersal rather than vicariance better explains the Atlantic distribution of nurse shark, and that the Pacific nurse shark might be a cryptic sister species to Ginglymostoma cirratum.

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