<p>The aim of this study was to investigate the forensic usefulness of various Y-chromosome short tandem repeat loci among South African sub-populations. Three different sets of Y-chromosome short tandem repeat loci were chosen for investigation.</p>

Thesis (M. Med. Sc.)--University of Hong Kong, 2004. / Also available in print.

A análise do conteúdo gênico do cromossomo Y em 12 espécies de Drosophila com genoma sequenciado em 2008 mostrou que o Y é pouco conservado entre espécies e está em processo de aquisição de genes, o que contradiz o modelo atual de evolução de cromossomos sexuais que o descreve como um homólogo degenerado do X, com constante perda de genes. Este resultado inicial incitou o estudo espécies adicionais de Drosophila e de gêneros próximos. Uma dificuldade relevante para obtenção de espécimes é que muitos grupos taxonômicos de drosofilídeos não estão disponíveis nos &ldquo;stock-centers&rdquo;, e seus hábitos de vida são pouco conhecidos. Muitas espécies são encontradas na natureza associadas a fungos, flores, ou exsudados vegetais, e raramente são atraídas por isca com banana fermentada, que é o método usual de coleta de drosofilídeos. Os objetivos do presente trabalho foram: I) analisar o conteúdo gênico do cromossomo Y de drosofilídeos provenientes de substratos &ldquo;não usuais&rdquo;, II) determinar substratos de desenvolvimento larval e identificar espécies novas, e III) analisar a composição de bases de genes no Y. Os resultados revelam a natureza dinâmica de aquisição e perdas de genes do cromossomo Y na família Drosophilidae que, em poucos casos, inclui um movimento de todo o cromossomo (p.e., fusão do Y a um autossomo). Descrevemos uma nova espécie, Drosophila calatheae, cuja larva se desenvolve em flores do gênero Calathea (Marantaceae). Uma segunda espécie, provisoriamente codificada como Drosophila I4, e cujas larvas também se desenvolvem nessas flores, está em fase de descrição. A partir de análise morfológica, nenhuma dessas duas espécies pôde ser incluídas em algum dos grupos de espécies conhecidos. Uma filogenia molecular preliminar com dois genes do cromossomo Y (kl-3 and kl-5) sugere que ambas pertencem à radiação virilis-repleta e que D. calatheae tem relações (morfológicas e moleculares) com as espécies do grupo bromeliae. A análise do conteúdo GC de genes no Y mostrou que genes neste cromossomo são enriquecidos em AT em relação a genes autossômicos, e esta diferença na composição de bases é proporcional ao tempo que um gene está presente no Y. Portanto, o conteúdo GC pode servir como ferramenta no estudo da evolução do cromossomo Y ao determinar o estado ancestral de um gene (autossômico vs. ligado ao Y) e datar o movimento de genes entre esses dois compartimentos genômicos / The analyses of the Y chromosome gene content in 12 Drosophila species whose genome were sequenced in 2008 showed that the Y is not well conserved among species and is currently in the process of acquiring genes, contradicting the current model of sex chromosome evolution that describes the Y as a degenerate homolog of the X, in constant gene loss. This initial result prompted the study of additional Drosophila species and related genera. One of the difficulties in obtaining specimens is the fact that drosophilids from many taxonomic groups are not available in stock- centers and little is known about their ecology. Many species are found in nature associated with fungi, flowers, or plant exudates, and are rarely attracted to baits with fermented banana, the usual method of collecting drosophilids. The objectives of this study were: I) analysis of the Y chromosome gene content of species from \"unusual\" substrates, II) determination of drosophilids breeding / larval development sites, and III) analysis of the base composition of genes in the Y chromosome. The results emphasize the Y-chromosome dynamic nature of genes acquisition and loss in the family Drosophilidae, including a few cases of whole chromosome movements (p.e., Y-autosome fusion). We describe a new species, Drosophila calatheae, whose larvae develop in flowers of the genus Calathea (Marantaceae). Drosophila I4 (to be described) also breeds in these flowers. None of these two species could be included in a known taxonomic group of species. A phylogeny with two Y-chromosome genes (kl-3 and kl-5) suggests that they belong to the virilis-repleta radiation and D. calatheae is related to the bromeliae group. Analysis of base composition of Y-chromosome genes shows that they are AT-rich when compared to autosomal genes, and this difference is proportional to the time that a gene has been in the Y. Thus, GC content can be a tool to study the evolution of this chromosome

Magister Scientiae - MSc / The aim of this study was to investigate the forensic usefulness of various Y-chromosome short tandem repeat loci among South African sub-populations. Three different sets of Y-chromosome short tandem repeat loci were chosen for investigation. / South Africa

The Himalayan Mountain range encompasses an unparalleled landscape featuring some of the planet’s highest peaks, including Mount Everest. In the heart of this massive orographic barrier lies Nepal, sandwiched in the historically geostrategic position between the Tibetan plateau to the north and India in the south. Until recently, Nepalese and Tibetan populations remained poorly characterized genetically, partly because of their inaccessible geographical locations. In the present study, the genetic diversity of these two Himalayan populations is evaluated using different marker systems, including mitochondrial DNA (mtDNA) and Short Tandem Repeats (STRs) in the autosomes as well as on the Y-chromosome (Y-STR). While autosomal STRs are distributed throughout the genome and are biparentally inherited, the Y-chromosome and mtDNA are haploid markers and provide the paternal and maternal histories of the population, respectively. Fifteen autosomal STR loci were typed in 341 unrelated individuals from three Nepalese populations (188), namely Tamang (45), Newar (66) and Kathmandu (77), and a general collection from Tibet (153). These samples were also sequenced for the mtDNA control region and all of them were subsequently assigned to 75 different mtDNA haplogroups and sub-haplogroups by screening their diagnostic sites in the coding region using Restriction Fragment Length Polymorphism analysis and/or sequencing, thus achieving an unprecedented level of resolution. The results from the autosomal and mtDNA data suggest a Northeast Asian origin for the Himalayan populations, with significant genetic influence from the Indian subcontinent in Kathmandu and Newar, corroborating our previous Y-chromosome study. In contrast, Tibet displays a limited Indian component, suggesting that the Himalayan massif acted as a natural barrier for gene flow from the south. The presence of ancient Indian mtDNA lineages in Nepal implies that the region may have been inhabited by the earliest settlers who initially populated South Asia. In addition, seventeen Y-STR loci were analyzed in 350 Tibetan males from three culturally defined regions of historical Tibet: Amdo (88), Kham (109) and U-Tsang (153). The results demonstrate that the 17 Y-STR loci studied are highly polymorphic in all the three Tibetan populations examined and hence are useful for forensic cases, paternity testing and population genetic studies.

No description available.

No description available.

It is routine for the forensic scientist to obtain a genetic profile of an individual from DNA recovered from a biological stain deposited at a crime scene. In contrast, only a limited number of laboratories in the United States have the capability of performing Y-STR analysis in casework. In order to aid in facilitating the transfer of Y-STR technology to the crime laboratory community for operational use, a comparison between commercial products from three main vendors (Applied Biosystems AmpFLSTR Yfiler PCR Amplification Kit, Promega PowerPlex - Y System, Reliagene Y-PLEX 12) and two in-house Y-STR multiplexes (MPI and MPB) commenced. The main intention for this comparison was to ascertain whether commercial Y-STR kits are able to obtain a male profile from difficult samples which have been accomplished with our in-house Y-STR multiplexes; such as mixtures, post coital specimens, and environmental insults. To aid the crime laboratory community an in depth comparison of the three main commercial Y-STR kits began in hopes to glean information in circumstances where Y chromosome polymorphisms may need to be employed. For example, the ability to provide investigators with the numbers of semen donors in multiple rape cases, identification of the genetic profile of the male component in a male/female mixture, and identification of the genetic profile of the male component in an extended interval post-coital sample. The capability of typing Y-STR loci by the crime laboratory community could dramatically affect the admissibility of Y-STR evidence. Therefore, the comparison of commercially available kits is an imperative process by which the scientific community acquires the necessary information to assess the ability of a procedure to obtain reliable results, determine the conditions under which such results can be obtained and define the limitations of the procedure. Thus the information for the study could lend itself to a standard being established amongst Y-STR kits for operational use and/or the production of a new Y-STR kit. One example of how the comparison of the three main commercial Y-STR kits could directly impact a new standard being established is by examining post-coital samples and their extreme limits (>48 hrs) for each kit in which a full male genetic profile was observed and comparing it to other commercial Y-STR kit and in-house Y-STR multiplexes. This would help establish the types of cases where specific Y-STR kits would be most useful, and the parameters in which each kit is able to perform. Thus leading to the development of a highly sensitive Y-STR kit that would be more sufficient to perform with the variety of samples an operational crime laboratory would routinely analyze. The capability of typing Y-STR loci by the crime laboratory community could dramatically affect the admissibility of Y-STR evidence. Therefore, the comparison of commercially available kits is an imperative process in order to inform the forensic community of different Y-STR kits available and their performance through direct comparison using modified SWGDAM validation guidelines.

The South Pacific is a region of incredible biological, cultural and linguistic diversity, reflecting its early settlement by human populations. It has been a region of interest to scholars because of this diversity, as well as its unique geography and settlement history. Current evidence suggests there was an initial settlement of Near Oceania during the Pleistocene by Papuan-speaking foragers, followed by a later Holocene settlement of Remote Oceania by Oceanic-speaking agriculturalists. Previous studies of human biological variation have been used to illuminate the migration history of and population relationships within Oceania. In this study, I analyzed Y-chromosome (NRY) diversity in 842 unrelated males to more fully characterize the phylogeography of paternal genetic lineages in this region, using a large number of regionally informative markers on an intensive sample set from Northern Island Melanesia. This approach facilitated an analysis of NRY haplogroup distributions, an evaluation of the ancestral paternal genetic contribution to the region, and a comparison of regional NRY diversity with that observed at different genetic loci (e.g., mtDNA). This project is part of a collaborative effort by faculty and graduate students from the Temple University Department of Anthropology that focused on characterizing biological variation and genetic structure in Melanesia, and better resolving the phylogeographic specificity of Northern Island Melanesia. Overall, this study generated a higher resolution view of NRY haplogroup variation than detected in previous studies through the use of newly defined and very informative SNP markers. It also showed that there is a very small ancestral East Asian paternal contribution to this area, and a rather large proportion of older Melanesian NRY lineages present there. In addition, this study observed extraordinary NRY diversity within Northern Island Melanesia, as well as genetic structure influenced more by geography than linguistic variation. This structure and diversity was essentially equivalent to that noted for mtDNA data for this region. Finally, this study helped to resolve questions about the placement of the 50f2/c deletion within the larger NRY tree. Overall, this work has refined our understanding of the migration and demographic history of Northern Island Melanesia. / Anthropology

The contact zone between subspecies of house mouse Mus musculus musculus and Mus musculus domesticus is one of the most intensively studied hybrid zones. It is also due to extensive introgression of the Y chromosome of M. m. musculus subspecies to the genetic background of M. m. domesticus. One theory of the origin of the introgression explains it by intragenomic conflict between the sexes. With a set of variable microsatellite markers on the Y chromosome, I have examined the validity of this theory by simple approaches revealing the history of the introgression area. It turned out that overly big variability of our markers makes the revelation of this theory impossible. Our markers have been found suitable for use in the analysis of population structure of house mouse. Thanks to them, we can identify migrants between localities and estimate the level of closeness of the population structure in relation to migrants from the neighborhood. Populations in our analysis proved to be relatively closed and resistant to the influx of migrants. Despite the conclusions of previous research where the dispersion of males ran up to one kilometer, I have discovered a relatively large number of migrations to a distance of thirty kilometers. Keywords Mus musculus musculus, Mus musculus domesticus, Y chromosome,...