Not much is known about the mechanisms affecting the genetic composition of populations of different species. To investi­gate one of these potential mechanisms, mating behaviour, the fruit fly Drosophila melanogaster, was chosen as an experimen­tal animal. To quantify mating behaviour in easily measurable parameters, it was subdivided into several distinct components; mating activity, mating time, mating competition ability and male mating capacity. As behavioural components to a great extent are influenced by environmental conditions all experiments were performed under controlled temperature and humidity. All components of mating behaviour were estimated by introducing females and males into mating chambers. Mating behaviour seems to be one of the major factors affect­ing the genetic composition of Drosophila melanogaster popula­tions. The experiments performed showed that differences in mating properties led to a substantial sexual selection among the genotypes. This selection was of a stabilizing type with regard to characters associated to bristle number and Y chromo­somal chromatin. This selection situation seems to warrant the retention of intermediate phenotypes in a population and will therefore contribute to the genetic variation present. Differences in mating properties were also shown to be able to maintain a balanced polymorphism for allozyme variants in populations. This maintenance was obtained through different forms of balancing selection as heterozygous superiority in sexual activity and balancing selection between female and male genotypes. Heterozygous superiority or overdominance in fitness always leads to balanced polymorphism through segre­gation of individuals with lowered fitness. The balancing selection between the female and male genotypes is best looked upon as a form of marginal overdominance, conferring the aver­aged highest fitness to the heterozygous genotype, thereby maintaining the polymorphism of the population. / <p>Härtill 5 uppsatser</p> / digitalisering@umu

Following their dispersal out of Africa, humans colonised all continents of the world save one, Antarctica. Whilst Europe was initially peopled soon after this exodus, paleoclimatic, archaeological, and historical evidence suggest that successive waves and migrations of people have contributed to the population resident in Europe today. I therefore examined the impact of past events on the European population through the analysis of DNA sampled both from contemporary Europeans, and from worldwide populations pertinent to its history. I genotyped and analysed data from the Y chromosomes of over 2,000 haplogroup R-M269 European men from over 30 different populations and, in combination with comparable datasets gathered from the literature, show that there it is not possible to assign a date to the origin of this lineage in Europe, and thus that any conclusion as to the ancient or recent spread of this lineage in Europe is unfounded. I also show that commonly used Y chromosome lineage dating techniques based on STR variation are biased by the markers used and conclusions based on such dates should be viewed with a large amount of caution. I next use genome-wide SNP data from 1,550 individuals from 95 worldwide populations to explore the population structure of Europe and present an analysis of the detailed structure of Europe in a novel analytical framework using ChromoPainter and fineSTRUCTURE. Admixture analysis based this data reveals distinct genomic inputs to peripheral European populations, from North Africa, Sub-Saharan Africa, the Middle East, and East Asia, and provides dates for this admixture within the last 1,000 years that correspond to the emergence and decline of empires and kingdoms in these regions of Europe. This novel analysis highlights the importance of recent historical events on European population structure, but also suggests a degree of ancient structure across European populations. Taken together, these analyses demonstrate the substantial effects of both ancient and recent migrations and mixture on the contemporary genetic structure of Europe.

Este trabalho tem como objetivo a determinação da freqüência alélica de 12 microssatélites do cromossomo Y na população de Araraquara e da Grande São Paulo, tendo em vista a necessidade de ampliação dos dados referentes a estes marcadores devido a sua crescente aplicação em diferentes áreas, entre elas a forense na qual a utilização destes microssatélites torna-se muitas vezes a única ferramenta disponível para resolução de casos. Para isto foram tipados 200 indivíduos, que não apresentavam relação de parentesco, divididos em quatro grupos de acordo com autoclassificação de cor (branco, preto, pardo ou oriental). Foram coletadas destes indivíduos amostras de sangue ou saliva a partir das quais foi feita extração do DNA utilizando diferentes protocolos de acordo com o tipo de amostra, seguida da amplificação dos 12 locos do cromossomo Y através do PowerPlex® Y System (Promega) de acordo com instruções do fabricante. Os produtos da amplificação foram submetidos a eletroforese em gel de poliacrilamida desnaturante a 6%, no seqüenciador ABI377 (Applied Biosystems) para obtenção dos perfis de cada loco. Os quais foram analisados com a utilização do software GeneScan ver. 2.1 (Applied Biosystems). Foi realizado o cálculo das freqüências alélicas e diversidade gênica de cada loco, assim como da diversidade haplotípica e capacidade de discriminação para cada grupo e para a amostra total. A comparação entre os resultados obtidos demonstrou que a variação dentro de cada grupo é maior que a variação entre os grupos. Os resultados obtidos foram enviados ao banco de dados mundial do cromossomo Y (Y-STR Haplotype Reference Database). / The aim of this study is to determine the allelic frequency of 12 microsatellites of the Y chromosome in Grande São Paulo and Araraquara population, in face of the amplification necessity of these markers data due to the increasing application of these markers on different fields, including the forensic on which the use of them is sometimes the only way to solve crime cases. For this purpose it was typed 200 unrelated individuals divided according to self report in four groups based on color skin (white, black, mulatto or yellow). Blood or buccal swab samples were collected and submitted to DNA extraction with different protocols according to the kind of sample. Subsequent amplification of 12 Y-STR was proceeded using the PowerPlex® Y System (Promega) following the manufacture’s protocol. The amplification products were submitted to electrophoresis in 6% polyacrilamid gel on ABI377 sequencer (Applied Biosystems) to obtain the profile of each locus. The results were analyzed with GeneScan ver. 2.1 software (Applied Biosystems). The allelic frequency and gene diversity of each locus as well as the haplotypic diversity and discrimination capacity was calculated for each group and for total sample. The comparison among the results showed that the variation inside the groups is higher than between groups. The haplotypes observed on this sample were sent to Y-STR Haplotype Reference Database.

Made available in DSpace on 2016-08-10T10:38:58Z (GMT). No. of bitstreams: 1 ISABELLA LACERDA FERNANDES.pdf: 1467834 bytes, checksum: 985b4aa7bf961993ef7672d3838bc086 (MD5) Previous issue date: 2015-03-31 / Microsatellite markers are short sequences, repetitive, highly polymorphic and hereditary present in the DNA, which follow the Mendelian pattern of segregation. Due to its haplotype heritage has been used to trace the paternal line to be passed from generation to generation without any changes, except in cases of mutation. The stepwise mutation model is more acceptable to mutation in microsatellite markers, assuming that each mutational event the length of a microsatellite changes by one or a few repeating units due to slippage process, which occurs during replication DNA. This study aimed to estimate the rates of change of microsatellite markers of the Y chromosome in a sample of the population and its implications in human identification process. It is a molecular study, which was conducted at Biocroma Laboratory in partnership with LaGene and Replicon in Goiânia-Goiás. Samples of study were selected from 80 cases of investigation of paternity by DNA analysis, undergo mutation analysis in the Y chromosome haplotypes with molecular amplification system PowerPlex® Y23 System - Promega Corporation. Were identified 15 records of germline mutations in the Y chromosome between alleged parents and children related to suspected samples. The results have identified 9 mutations gain and 6 mutations loss of repetitions numbers. The DYS576 marker had the highest number of reported mutations (20%), followed by DYS570, which identified two mutations (13.33%). The markers DYS389 II, DYS391, DYS481, DYS549, DYS438, DYS439, DYS393, DYS458, DYS385 a - b DYS456 showed only 1 (6.66%) mutation record each. In the other markers, DYS389 I, DYS448, DYS19, DYS533, DYS437, DYS635, DYS390, DYS392, DYS643 and Y-GATA-H4 mutations were not identified in the samples analyzed in this study. Thus the identification of mutations increases the tools that are used in genetic analysis link laboratories and can deliver a more reliable result minimizing potential errors in the analyzes. / Os marcadores microssatélites são sequências curtas, repetitivas, altamente polimórficas e hereditárias presentes no DNA, que seguem o padrão mendeliano de segregação. Devido a sua herança haplotípica tem sido utilizado para rastrear a linhagem paterna por ser passado de geração em geração sem nenhuma alteração, exceto em casos de mutação. O modelo step-wise mutation é o mais aceito para mutação nos marcadores microssatélites, admitindo-se que, a cada evento mutacional o comprimento de um microssatélite altera por uma ou poucas unidades de repetição devido ao processo de slippage, que ocorre durante a replicação do DNA. Este trabalho teve como objetivo estimar as taxas de mutações dos marcadores microssatélites do cromossomo Y em uma amostra da população brasileira e suas implicações no processo de identificação humana. Trata-se de um estudo molecular, que foi conduzido no Laboratório Biocroma em parceria com o LaGene e Replicon em Goiânia-Goiás. As amostras de estudo foram selecionadas de 80 casos de investigação de paternidade pela análise do DNA, submetidos a análise de mutações nos haplótipos do cromossomo Y com o sistema de amplificação molecular PowerPlex® Y23 System Promega Corporation. Foram identificados 15 registros de mutações germinativas no cromossomo Y entre supostos pais e supostos filhos referentes às amostras analisadas. Os resultados obtidos permitiram identificar 9 mutações de ganho e 6 mutações de perda de números de repetições. O marcador DYS576 apresentou o maior número de mutações registrados (20%), seguido pelo DYS570, que permitiu identificar 2 mutações (13,33%). Os marcadores DYS389 II, DYS391, DYS481, DYS549, DYS438, DYS439, DYS393, DYS458, DYS385 a-b e DYS456 apresentaram apenas 1 (6,66%) registro de mutação cada. Nos demais marcadores, DYS389 I, DYS448, DYS19, DYS533, DYS437, DYS635, DYS390, DYS392, DYS643 e Y-GATA-H4 não foram identificadas mutações nas amostras analisadas neste estudo. Desta forma a identificação das mutações aumenta as ferramentas que são utilizadas nos laboratórios de análise de vínculo genético e que podem garantir um resultado mais confiável minimizando possíveis erros nas análises.

Made available in DSpace on 2016-08-10T10:39:20Z (GMT). No. of bitstreams: 1 Ricardo Goulart Rodovalho.pdf: 490214 bytes, checksum: 86f31d10876ac161981506bf61d01362 (MD5) Previous issue date: 2008-03-27 / Male infertility is under a difficult condition of treatment, because it is not a single entity, but reflecting a variety of different pathological conditions, preventing a unique strategy of treatment. Structural changes in Y chromosome have been responsible for male infertility. We examined 26 family members of 13 patients with male infertility and had deletions in the AZF region. In the family 01, a father and a brother did not present a microdeletion. However, one son present a microdeletion in AZFa (sY84) and spermogram azoospermic but the another son present a microdeletion in AZFa (sY84) and AZFb (sY127) and a normal spermogram. The father of the family 02, a severe oligozoospermic man, presented a microdeletion in AZFa (sY84) and his son, conceived by ICSI process, also presented the same microdeletion. In the other families, only the men with changed spermogram had presented the microdeletion. Probably, in family 01, the father and the brother without microdeletions can to present microdeletions of previous or posterior regions to that one analyzed. The treatment with ICSI can lead to the vertical transmission of microdeletions in AZF region and also it can cause in the expansion of the mutation de novo . This result reinforces the need for an investigation of Y chromosome microdeletion in individual candidates for assisted reproduction, as well as a tracking genetic counseling. / A infertilidade masculina é considerada uma condição de difícil tratamento, o que ocorre pelo fato dela não ser uma entidade única, mas refletir uma variedade de diferentes condições patológicas, dificultando uma estratégia única de tratamento. Alterações estruturais no cromossomo Y têm sido o principal responsável pela infertilidade masculina. Nós investigamos 26 familiares de 13 pacientes portadores de infertilidade masculina que apresentaram deleções na região AZF. Na família 01, o pai e um irmão não apresentaram microdeleção. Entretanto um filho apresentou microdeleção em AZFa (sY84) e espermograma azoospérmico, mas o outro filho apresentou microdeleção em AZFa (sY84) e AZFb (sY127) e um espermograma normal. O pai da família 02, oligozoospérmico severo, apresentou microdeleção na região AZFa (sY84) e seu filho, gerado através da ICSI, também apresentou a mesma microdeleção. Nas outras famílias, apenas os homens com espermograma alterado apresentaram a microdeleção. Provavelmente, na família 01, o pai e o irmão sem microdeleção podem apresentar microdeleções em regiões anteriores ou posteriores àquela analisada. O tratamento com ICSI pode levar à transmissão vertical de microdeleções da região AZF e também pode ocasionar na expansão da mutação de novo . Este resultado reforça a necessidade de uma investigação de microdeleção do cromossomo Y em indivíduos candidatos a reprodução assistida, assim como um acompanhamento e aconselhamento genético.

Este trabalho teve como meta principal contribuir para elucidar algumas das questões em aberto pertinentes à história evolutiva e antropológica de populações nativas americanas. Para isso investigou-se marcadores uniparentais paternos, ligados à NRY, e materno, mtDNA. Para o cromossomo Y foram investigados 108 indivíduos (85 sulameríndios de 16 tribos, pertencentes a 5 grupos lingüísticos, além de 23 asiáticos (siberianos), compreendendo 6 grupos étnicos distintos). Para o mtDNA foram investigados 160 indivíduos (homens e mulheres), compreendendo 10 tribos sulamericanas, pertencentes a 5 grupos lingüísticos distintos. Para o cromossomo Y foram utilizados 26 marcadores (SNPs). Para o mtDNA a região controladora-RC (HVS-I: da posição 16.024 até 16.569, e HVS-II: da posição 001 até 576) e a região imediatamente 5’ à região controladora foram seqüenciadas. Foi possível determinar para o cromossomo Y que Q1a3a* (autóctone nativo-americano, de provável origem beringiana) está fixado em 63% das tribos; o haplogrupo Q1a3*, que por outro lado também é encontrado na Ásia, foi observado entre os Araweté (25%), Jamamadi (100%), Lengua (25%) e esquimós asiáticos (17%). Merece destaque que Q1a3* parece ser o que até agora era identificado como sendo apenas “haplogrupo Q*”, ou seja, cromossomo Y portador do alelo derivado no loco M242, mas com alelo ancestral para o M3. Nenhuma das novas mutações mencionadas na atual árvore filogenética do cromossomo Y (com exceção do M346, que define Q1a3*) foram encontradas. O seqüenciamento de regiões do cromossomo Y não revelou nenhuma nova mutação. No caso do mtDNA, os indígenas do tronco Ge mostram os haplogrupos B e A como sendo os mais freqüentes, enquanto que nos Tupi esses haplogrupos apresentam freqüências mais elevadas apenas em regiões bastante restritas, ficando o haplogrupo D como o mais freqüente. Cabe salientar que o haplogrupo C apresenta freqüência muito baixa tanto para os Ge quanto para os Tupi, sendo que freqüências um pouco mais elevadas estão quase que geograficamente opostas, ficando no sul do Brasil para os Ge e no norte para os Tupi. Avaliando o modelo de fissão-fusão pôde-se sugerir que: 1) As linhagens mitocondriais tribo-específicas dentro das tribos Kayapó aqui investigadas dificilmente representariam linhagens autóctones, já que o tempo de surgimento de cada tribo por processo de fissão é pequeno para comportar uma rede de novas mutações. As especificidades poderiam estar vinculadas ao modelo de fissão envolvendo grupos de pessoas aparentadas via materna. Nesse caso, grupos de parentes carregariam para fora do grupo parental todas as seqüências pertencentes a uma determinada linhagem. Assim a linhagem estaria presente somente no grupo derivado e não mais no parental; 2) Perda de linhagens parentais na dispersão e/ou por deriva na formação do novo grupo, o que resultaria na diferença encontrada entre os grupos derivados; 3) Embora não se possa excluir alguma fusão posterir a fissão, a quantidade de linhages exclusivas nas tribos Kayapó estaria indicando relativo isolamento dos grupos depois da fissão (ausência ou baixa freqüência de fluxo gênico entre os grupos fissionados levando à relativa baixa freqüência de linhagens compartilhadas), o que denota o fato do fenômeno ser recente (atritos ainda presentes na memória coletiva e/ou familiar dos grupos fissionados) como estabelecido pelos dados históricos (início do século XVII). Esse fato poderia sugerir que a fusão demanda mais tempo para ocorrer; 4) O compartilhamento das linhagens mais comuns, normalmente na raiz das networks, entre os Tupi e os Ge, parece denotar mais ancestralidade comum do que importante fluxo gênico depois da formação desses dois grandes estoques lingüísticos. / This work has as its main aim to elucidate some of the still open questions about the evolutive and anthropological history of the Native American populations. Paternal uniparental markers, in the NRY, and maternal, mtDNA, were investigated to do that. For the Y chromosome, 108 individuals were investigated (85 South-Amerindians from 16 tribes, belonging to 5 linguistic groups, and 23 Asians (Siberians), covering 6 distinct ethnical groups). For the mtDNA, 160 individuals (men and women) were evaluated, covering 10 South-American tribes, belonging to 5 distinct linguistic groups. For the Y chromosome 26 SNPs were tested and some regions sequenced. For the mtDNA the control region-CR (HVS-I: from position 16.024 to 16.569, and HVS-II: from position 001 to 576) and the region immediately 5’ of the control region were sequenced. It was possible to determine that Q1a3a* (a Native American autoctonous chromosome, probably of Beringian origin) is fixed in 63% of the tribes; the haplogroup Q1a3*, which, moreover, is also encountered in Asia, was observed in Araweté (25%), Jamamadi (100%), Lengua (25%) and Asian Eskimos (17%). It is worth mentioning that Q1a3* appears to be what until now has been identified as “haplogroup Q*” only, that is, Y chromosome carrier of the derived allele in the M242 locus, but with an ancestral allele for M3. Any of the new mutations mentioned in the current Y chromosome phylogenetic tree (except M346, which defines Q1a3*) were encountered. Sequencing of Y chromosome regions hasn’t revealed any new mutation. In the mtDNA’s case, the Ge indians show the haplogroups B and A as the most frequent ones, while in the Tupi indians these haplogroups show high frequencies only in very restrict regions, being haplogroup D the most frequent. It should be noted that haplogroup C shows very low frequency in both Ge and Tupi, the slightly higher frequencies occuping almost geographically opposite locations, at the South of Brazil for the Ge and on the North for the Tupi. On evaluating the fission-fusion model it could be suggested that: 1) Tribe-specific lineages in the Kayapó tribes investigated here would hardly represent autoctonous lineages, since the time of emergence of each tribe by fission process is small to bear a web of new mutations. The specificities could be related to the fission model involving maternally related groups of people. In this case, groups of relatives would carry out of the parental group all the sequences belonging to a determined lineage. Therefore the lineage would be present only in the derived group and not in the parental anymore; 2) Loss of parental lineages in the dispersion and/or by drift in the new group’s formation, which would result in the differences found between the derived groups; 3) Though some fusion posterior to the fission cannot be excluded, the amount of exclusive lineages in the Kayapó tribes would indicate a relative isolation of the groups after the fission (absence or low frequency of gene flow between the fissioned groups leading to relative low frequency of the shared lineages), which denotes the fact of the phenomenon being recent (struggles still present in the collective and/or familiar memories of the fissioned groups) as estabilished by historical data (beginning of the XVII century). This fact could suggest that the fusion demands more time to occur; 4) The sharing of the more common lineages, normally in the networks’ nodes, between Tupi and Ge, appears to denote more common ancestrality than important gene flow after the formation of these two great linguistic stocks.

>Magister Scientiae - MSc / The objective of this study is to deduce paternal ancestry using ancestry informative single nucleotide polymorphisms (SNPs) by means of High Resolution Melting (HRM). This was completed by producing a multiplex system that was designed in a hierarchical manner according to the YSNP tree. This project mainly focused on African ancestry and was used to infer paternal ancestral lineages on the Johannesburg Coloured population. South Africa has a diverse population that has ancestral history from across the globe. The South African Coloured population is the most admixed population as it is derived from at least five different population groups: these being Khoisan, Bantu, Europeans, Indians and Southeast Asians. There have been studies done on the Western Cape/ Cape Town Coloured populations before but this study focused on the Johannesburg Coloured population.

Magister Scientiae - MSc (Biotechnology) / The objective of this study is to deduce paternal ancestry using ancestry informative single nucleotide polymorphisms (SNPs) by means of High Resolution Melting (HRM). This was completed by producing a multiplex system that was designed in a hierarchical manner according to the YSNP tree. This project mainly focused on African ancestry and was used to infer paternal ancestral lineages on the Johannesburg Coloured population. South Africa has a diverse population that has ancestral history from across the globe. The South African Coloured population is the most admixed population as it is derived from at least five different population groups: these being Khoisan, Bantu, Europeans, Indians and Southeast Asians. There have been studies done on the Western Cape/ Cape Town Coloured populations before but this study focused on the Johannesburg Coloured population. The first step was to design the multiplex system. This was done by using inhouse SNPs. A total of seven multiplexes were designed and optimised, each consisting of two, three or four different SNPs respectively. A total of 143 saliva and buccal samples were collected from male Johannesburg Coloureds. DNA was extracted from the saliva samples using an optimised organic method. DNA was extracted from the buccal samples using an optimised salting out method. DNA was successfully extracted from 77 of the male samples. A total of 69 samples were screened using Multiplex 1; of the 69 samples 56 samples were successfully screened to infer the paternal lineage of the samples. The results show that the most frequent haplogroup of the Johannesburg male samples was haplogroup CF (39%). The second most frequent haplogroup was haplogroup DE (38%). Under further analysis of haplogroup DE it was seen that 37% of those samples were derived for the haplogroup E1b1b.

<p>Sex chromosomes are useful in elucidating the evolutionary factors affecting diversity and divergence. In particular, Y chromosome analyses may complement studies using mitochondrial DNA for inferring sex-specific population genetic processes.</p><p>Y chromosome studies have been scarce due to limited access to genetic markers and the dynamic evolution of Y. Conserved Y-specific primers that could amplify a diverse set of mammalian species were developed from comparison of gametologous X and Y sequences. Y-specific sequence, generally more than one kb, was amplified for all 20 species examined.</p><p>Intraspecific diversity on mammalian Y was found to be reduced even when male-biased mutation rate and effective population size were corrected for. A number of factors can cause this low variation on Y of which selection on a haploid chromosome seems most important.</p><p>The field vole (<i>Microtus agrestis</i>), a common and well-studied small mammal in Eurasia, was examined for X and Y variability. Earlier studies on mtDNA had shown that the field vole is separated in two distinct lineages in Europe. The X and Y chromosome sequences confirmed the deep split and suggested that the two lineages of field vole should be reclassified as two separate species.</p><p>Two distinct Y chromosome haplogroups were found in modern European cattle, distributed among breeds according to a north-south gradient. Ancient DNA analysis of European aurochsen showed the northern haplogroup to be the most common, possibly indicating local hybridization between domestic cows and wild aurochs bulls in Europe.</p>

<p>Management of wolves is a complex issue, and molecular genetics is an important tool in this work. Molecular genetics can provide important information at the species, population and individual level, which can be essential for the development of management programs aiming at the long term survival of wolf populations.</p><p>In this thesis I developed new genetic markers on the canine Y chromosome to estimate the number of founders of the Scandinavian wolf population. This knowledge is important to reconstruct the history of the population and to design the most appropriate conservation strategies. Next, genetic markers with different pattern of inheritance have been used to identify hybrids between wolves and dogs. This allowed us to determine the direction of hybridization and to evaluate its possible impact on the gene pool of a wolf population. Furthermore, I also developed a method for a more reliable identification of the predator responsible of an attack by using saliva remains left on the prey. Since predation on livestock is perhaps the main reason for the negative opinions about the predator, the correct identification of the responsible for an attack (wolf, dog or hybrid) is essential. </p><p>Finally, this thesis has also been focusing on the domestication of dogs. By using Y chromosome markers (paternally inherited), it has been possible to complement previous studies based on mtDNA sequences (maternally inherited) and autosomal markers (inherited from both parents). In this way I have obtained a more complete picture of the domestication process and of the origin of breeds. This has shown that there has been a bias in the contribution of the two sexes in the origin of dog breeds (fewer males then females contributing to each breed) and that the origin of dogs was not marked by extensive backcrosses with male wolves over the entire species range.</p>