A dissertation submitted to the faculty of Health Sciences, University of the Witwatersrand, Johannesburg, in fulfilment of the requirements for the degree of Master of Science in Medicine in the Division of Human Genetics. / Genetic polymorphisms within the non-recombining portion of Y-chromosome (NRY) preserve a record of human paternal genetic heritage that has persisted to the present, allowing human evolutionary inference, population affinity and demographic history, to be elucidated. To elucidate the geographic origins of the paternal ancestry of the present- day South African (SA) ‘Coloured’ population, a total sample of 167 individuals consisting of Cape Malay (N=54) and ‘Coloured’ groups from Cape Town (N=48) and Johannesburg (N=65) were analysed at 21 binary and eight short tandem repeat (STR) polymorphic loci within NRY. A SA White sample (present study, N=97) as well as other presumed parental populations were included for comparative analysis. Haplotypes constructed using both biallelic haplogroup and STR haplotype data assisted in resolving the geographic regions of origin of Y-chromosome in these groups. Altogether the proportions of African, European and Asian contributions were estimated to be 0%, 18.5% and 46.3% in the Cape Malay, 31.3%, 25% and 20.1% in the Cape ‘Coloureds’, and 24.6%, 40% and 16.9%, in the ‘Coloured’ group from Johannesburg. Those haplotypes that could not be unambiguously resolved to European or Asian origins were referred to as Eurasian lineages, and constituted 35.2%, 22.9% and 18.5% of Y- chromosomes in the Cape Malays, Cape ‘Coloureds’ and Johannesburg ‘Coloureds’, respectively. While the ‘Coloured’ groups currently residing in Cape Town and Johannesburg were not significantly different from each other, both groups were significantly different from the Cape Malay population. This was further supported from the association of these groups in population trees. For the most part, these data corroborate historical data concerning the history of ‘Coloured’ populations, but is the first study to show how males have contributed in shaping the gene pool of the ‘Coloured’ population from South Africa. / WHSLYP2016

No description available.

The genetic component of mammalian male fertility is complex and involves thousands of genes. The majority of these genes are distributed on autosomes and the X chromosome, while a small number are located on the Y chromosome. Human and mouse studies demonstrate that the most critical Y-linked male fertility genes are present in multiple copies, show testis-specific expression and are different between species. In the equine industry, where stallions are selected according to pedigrees and athletic abilities but not for reproductive performance, reduced fertility of many breeding stallions is a recognized problem. Therefore, the aim of the present research was to acquire comprehensive information about the organization of the horse Y chromosome (ECAY), identify Y-linked genes and investigate potential candidate genes regulating stallion fertility. To achieve theses goals, a direct cDNA (complementary DNA) selection procedure was used to isolate Y-linked genes from horse testes and 29 Y-specific genes were identified. All 29 genes were mapped to ECAY and their sequences were used to further expand the existing map. Copy number analysis identified 15 multicopy genes of which 9 were novel transcripts. Gene expression analysis on a panel of selected body tissues showed that some ECAY genes are expressed exclusively in testes while others show ubiquitous or intermediate expression. Quantitative Real-Time PCR using primers for 9 testis-specific multicopy genes revealed 5 genes with statistically significant differential expression in testis of normal fertile stallions and stallions with impaired fertility. Gene copy number analysis showed that the average copy number of 4 such genes was decreased in subfertile/infertile stallions compared to normal animals. Taken together, this research generated the first comprehensive physical gene map for the horse Y chromosome and identified a number of candidate genes for stallion fertility. The findings essentially expand our knowledge about Y chromosome genes in horses, open a new avenue for investigating the potential role of ECAY genes in stallion fertility which contribute to the development of molecular tools for the assessment of fertility in stallions.

published_or_final_version / Medical Sciences / Master / Master of Medical Sciences

Indonesia, a vast archipelago nation and home to a wide range of cultural, linguistic and genetic diversity, has been a navel of intercultural and interregional interaction between the Asian and the Pacific worlds since prehistoric times. By analyzing the genetic profile of Indonesian people across the archipelago, this dissertation aims to elucidate the colonization history of Indonesia and to assess the effect of social practices on the Indonesian gene pool. Genetic diversity has revealed the complex settlement history of the Indonesian archipelago, starting from the initial colonization of Indonesia ~50 kya, multiple migrations by hunter-gatherers from mainland Asia during the Paleolithic era, followed by a major Neolithic expansion of Austronesian-speaking farmers from a putative homeland of Taiwan, and historic era migrations that involved several foreign invasions via trading and the spread of major religions. The survival of older lineages in western and eastern Indonesia showed that these later expansions into the archipelago did not replace the gene pool of the previous inhabitants. Although most Indonesian communities today practice patrilocality, which is supported by genetic diversity and population structure analyses, matrilineal descent systems are thought to have dominated ancestral Austronesian societies. Preserving a rich Austronesian cultural heritage, such as matrilocal marriage practices, has particularly affected the genetic diversity and population structure of Timor. The dominance of Asian female lineages is apparent on the X chromosome compared to the autosomes, suggesting that female migrants played a leading role during the period of Asian immigration into Timor. Matrilocality may have been a driving force behind this admixture bias during the Austronesian expansion. This finding provides support for an Austronesian `house society' model in which the Austronesian expansion led to the dispersal of matrilocal societies with small numbers of neighboring non-Austronesian males marrying into Austronesian matrilocal, matrilineal houses. This study has revealed that the colonization history of Indonesia does not seem to comprise merely a Melanesian substratum with a single expansion of Austronesian speakers, yet rather involves multiple waves of human migration, coupled with an extensive admixture process.

Thesis (Ph. D.)--University of Tartu, 2004. / Includes reprints of 4 previously published articles. Includes bibliographical references (p. 48-59).

Thesis (M.S.)--University of Akron, Dept. of Biology, 2009. / "August, 2009." Title from electronic thesis title page (viewed 10/7/2009). Advisor, Amy Milsted; Committee members, Monte Turner, Richard Londraville; Department Chair, Monte Turner; Dean of the College, Chand Midha; Dean of the Graduate School, George R. Newkome. Includes bibliographical references.

Thesis (M. Med. Sc.)--University of Hong Kong, 2005.

Made available in DSpace on 2014-06-11T19:23:01Z (GMT). No. of bitstreams: 0 Previous issue date: 2012-04-20Bitstream added on 2014-06-13T20:29:39Z : No. of bitstreams: 1 figueiredo_rf_me_arafcf.pdf: 495174 bytes, checksum: 7ab0836eb29809e44df113c6faa89bdc (MD5) / Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) / Universidade Estadual Paulista (UNESP) / A identificação humana pela análise de DNA utiliza o perfil genético de um indivíduo baseado no estudo de uma combinação de marcadores que são herdados de seus progenitores. Os marcadores genéticos mais utilizados na rotina forense estão presentes nos cromossomos autossomos, porém, os marcadores presentes nos cromossomos sexuais (X e Y) e no DNA mitocondrial auxiliam as análises de forma eficiente. Assim, os marcadores do cromossomo Y têm sido muito estudados, pois além do campo forense, estes possuem várias aplicações no campo evolucionário, como na compreensão da genética populacional e exploração da história da evolução humana. Duas categorias principais são atualmente utilizadas para examinar o cromossomo Y: loci bialélico (polimorfismos de nucleotídeo único – SNPs – e inserção Alu) e loci multialélico (minissatélites e microssatélites – STRs). SNPs possuem várias vantagens em relação aos STRs, principalmente com amostras degradadas ou em pequena quantidade, devido a sua alta frequência, simplicidade, menor tamanho e baixa taxa de mutação. Assim, visando à ampliação dos dados da população brasileira em relação aos marcadores genéticos, este estudo teve por objetivo identificar os maiores haplogrupos existentes na população do Estado do Espírito Santo e avaliar as contribuições de Africanos, Ameríndios e Europeus na sua formação, uma vez que esse estado recebeu imigrantes de várias origens. Para isso, foram estudados 35 Y-SNPs em 255 amostras de indivíduos do sexo masculino nascidos no Estado do Espírito Santo - Brasil. A genotipagem foi realizada por PCR seguida por minisequenciamento (SNaPshot Multiplex) e detecção por eletroforese capilar no analisador genético ABI3500 (Applied Biosystems by Life Technologies). Dos 38 haplogrupos possíveis de serem classificados... / Human identification by DNA analysis uses the genetic profile of an individual studying a combination of markers inherited from their parents. The genetic markers most widely used in routine forensic are present in the autosomes, however, the markers present in sex chromosomes (X and Y) and mitochondrial DNA helps analysis efficiently. Thus, the Y chromosome markers have been widely studied because beyond the forensic field, they have several applications in the field of evolution, such as in the understanding of population genetics and exploitation of human evolutionary history. Two main categories are currently used to examine the Y chromosome: biallelic loci (single nucleotide polymorphisms - SNPs - and Alu insertion) and multiallelic loci (minisatellites and microsatellites - STRs). SNPs have several advantages over STRs, especially with degraded or in small quantities samples, due to its high frequency, simplicity, small size and low mutation rate. Thus, aiming to increase the data of the brazilian population related to genetic markers, the objective of this study was to identify the major haplogroups existing in the population of Espirito Santo and evaluate the contribution of Africans, Amerindians and Europeans in their formation, since this state has received immigrants from various origins. For this purpose, 35 Y-SNPs in 255 blood samples from male individuals born in Espirito Santo State-Brazil. Genotyping was performed by PCR followed by minisequencing reaction (SNaPshot Multiplex) and detection by capillary electrophoresis on ABI3500 genetic analyzer (Applied Biosystems by Life Technologies). Of the 38 possible haplogroups to be classified with the 35 SNPs studied, only 19 were detected in this sample. The haplogroup diversity was 0.7794±0.0229 and the most frequent haplogroup was... (Complete abstract click electronic access below)

Orientador: Regina Maria Barretto Cicarelli / Banca: Greiciane Gaburro Paneto / Banca: Raquel Mantuaneli Scarel Caminaga / Resumo: A identificação humana pela análise de DNA utiliza o perfil genético de um indivíduo baseado no estudo de uma combinação de marcadores que são herdados de seus progenitores. Os marcadores genéticos mais utilizados na rotina forense estão presentes nos cromossomos autossomos, porém, os marcadores presentes nos cromossomos sexuais (X e Y) e no DNA mitocondrial auxiliam as análises de forma eficiente. Assim, os marcadores do cromossomo Y têm sido muito estudados, pois além do campo forense, estes possuem várias aplicações no campo evolucionário, como na compreensão da genética populacional e exploração da história da evolução humana. Duas categorias principais são atualmente utilizadas para examinar o cromossomo Y: loci bialélico (polimorfismos de nucleotídeo único - SNPs - e inserção Alu) e loci multialélico (minissatélites e microssatélites - STRs). SNPs possuem várias vantagens em relação aos STRs, principalmente com amostras degradadas ou em pequena quantidade, devido a sua alta frequência, simplicidade, menor tamanho e baixa taxa de mutação. Assim, visando à ampliação dos dados da população brasileira em relação aos marcadores genéticos, este estudo teve por objetivo identificar os maiores haplogrupos existentes na população do Estado do Espírito Santo e avaliar as contribuições de Africanos, Ameríndios e Europeus na sua formação, uma vez que esse estado recebeu imigrantes de várias origens. Para isso, foram estudados 35 Y-SNPs em 255 amostras de indivíduos do sexo masculino nascidos no Estado do Espírito Santo - Brasil. A genotipagem foi realizada por PCR seguida por minisequenciamento (SNaPshot Multiplex) e detecção por eletroforese capilar no analisador genético ABI3500 (Applied Biosystems by Life Technologies). Dos 38 haplogrupos possíveis de serem classificados... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Human identification by DNA analysis uses the genetic profile of an individual studying a combination of markers inherited from their parents. The genetic markers most widely used in routine forensic are present in the autosomes, however, the markers present in sex chromosomes (X and Y) and mitochondrial DNA helps analysis efficiently. Thus, the Y chromosome markers have been widely studied because beyond the forensic field, they have several applications in the field of evolution, such as in the understanding of population genetics and exploitation of human evolutionary history. Two main categories are currently used to examine the Y chromosome: biallelic loci (single nucleotide polymorphisms - SNPs - and Alu insertion) and multiallelic loci (minisatellites and microsatellites - STRs). SNPs have several advantages over STRs, especially with degraded or in small quantities samples, due to its high frequency, simplicity, small size and low mutation rate. Thus, aiming to increase the data of the brazilian population related to genetic markers, the objective of this study was to identify the major haplogroups existing in the population of Espirito Santo and evaluate the contribution of Africans, Amerindians and Europeans in their formation, since this state has received immigrants from various origins. For this purpose, 35 Y-SNPs in 255 blood samples from male individuals born in Espirito Santo State-Brazil. Genotyping was performed by PCR followed by minisequencing reaction (SNaPshot Multiplex) and detection by capillary electrophoresis on ABI3500 genetic analyzer (Applied Biosystems by Life Technologies). Of the 38 possible haplogroups to be classified with the 35 SNPs studied, only 19 were detected in this sample. The haplogroup diversity was 0.7794±0.0229 and the most frequent haplogroup was... (Complete abstract click electronic access below) / Mestre