Thesis (Ph. D.)--State University of New York at Binghamton, Department of Anthropology, 2009. / Includes bibliographical references.

published_or_final_version / Pathology / Master / Master of Philosophy

The purpose of this study was to analyze the frequency distributions of alleles at the 3$ sp prime$HVR (hypervariable region) and 5$ sp prime$HVR, two highly polymorphic regions on chromosome 16p. About 300 DNA samples from individuals of East Asian, French Canadian, Greek, Italian, Jewish and Middle Eastern origin were analyzed by hybridization to probes for the 3$ sp prime$HVR and 5$ sp prime$HVR. / The distributions of alleles at both loci are skewed with the long tail towards the larger alleles. The observed heterozygosity at the 3$ sp prime$HVR locus for 281 individuals was 0.91, ranging from 0.85 in the Jewish group to 1.00 among French Canadians and East Asians. Statistical analysis demonstrated significant variation among some of the ethnic groups. / The observed heterozygosity at the 5$ sp prime$HVR locus in 225 individuals was 0.75. Heterozygosity varied from 0.91 in East Asians to 0.61 of Middle Eastern samples studied. 28% of samples also display a RsaI site polymorphism near the 5$ sp prime$HVR locus. / Genetic distance analysis demonstrated that the largest distance at these two loci exists between the Jews and East Asians (D = 0.119). / Both the 3$ sp prime$HVR and the 5$ sp prime$HVR are extremely variable in all the populations studied, and thus will serve as informative markers for chromosome 16p for clinical as well as population studies.

Denaturing gradient gel electrophoresis (DGGE) and sequencing of the PAH locus has found 38 different mutations on 141 chromosomes in the PKU patients resident in Quebec; mutation analysis is now 92.5% complete. Two novel disease producing alleles (K421, R157N) and one silent allele (IVS6 nt-55) were discovered in this project; these mutations remain unique to the Quebec population. Three novel mutation-(haplotype) combinations were also found (S67P (H1), G218V (H2), V245A (H7)); they are not at hypermutable sites and are therefore compatible with a single homologous recombination event between two different haplotypes. Whereas mutation types (missense 64%, nonsense 6%, splice 9%, frameshifts 6%, silent 15%), resemble those in world populations, the Quebec allele profile differs from that of any European population, reflecting range expansion, founder effects, genetic drift and assimilation. Furthermore, when analyzed by geographic region a stratification of PAH alleles is apparent, reflecting the different demographic histories of Western and Eastern Quebec and Montreal.

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El trabajo realizado trata de estudiar la diversidad del genoma mitocondrial humano en poblaciones humanas de diferentes áreas geográficas que habían sido hasta ahora poco o nada estudiadas. Los grupos de poblaciones humanos estudiados en este trabajo esta formado por las poblaciones del oeste del Mediterráneo, de l'África sub-Sahariana, de la Isla de La Reunión, y de l'Asia. Cada una de estas poblaciones pertenecen a un entorno geográfico diferente y han padecido diferentes y numerosos movimientos de poblaciones que han modulado su composición genética. El análisis de diferentes polimorfismos del genoma mitocondrial han permitido entender los factores poblacionales, tal como la migración, la mezcla genética, la deriva genética, los efectos fundadores, y inferir la historia d la poblaciones bajo estudio, La metodología utilizada incluye diferentes tipos de técnicas adaptadas a los diferentes tipos de polimorfismos estudiados. La técnica aplicadas fueron la secuenciación, el análisis de fragmentos y la técnica de SNaPshot. Los resultados obtenidos han aportado un conocimiento nuevo de las poblaciones que han modulado la diversidad genética de los grandes grupos humanos a nivel continental pero también a un nivel mas regional.

Natural selection has played an important role in shaping human genetic variation, thus, finding variants that have been targeted by positive selection can provide insights about which genes influence human phenotypic variability. In this work we conduct a genome-wide survey of protein-coding genes comparing humans, chimpanzees, and closely related species in order to detect the fraction of genes undergoing positive selection on the human lineage, and further investigate intraspecific variation in a subset of candidate genes in the search of recent selective events in worldwide human populations. Our results suggest that most of the genes implicated in selective events during early human evolution differ from those involved in recent human adaptations, implying distinct selective pressures during varying stages of human evolutionary history. We also found three genome regions with evidence of recent positive selection, which were dissected to propose targets of selection and discuss on the possible underlying selective pressures in each case. / La selección natural ha moldeado de forma importante la variación genética humana, por lo que encontrar variantes que hayan sido seleccionadas positivamente puede dar indicios acerca de los genes que determinan la diversidad fenotípica humana. En este trabajo comparamos los genes del genoma humano, del chimpancé y de varias especies cercanamente emparentadas para detectar aquellos genes bajo selección positiva en el linaje humano, y posteriormente evaluar la variación intraespecífica en un subconjunto de genes con la intención de buscar eventos de selección reciente en poblaciones humanas de todo el mundo. Nuestros resultados sugieren que la mayoría de genes implicados en eventos selectivos durante la evolución temprana del hombre no son los mismos que aquellos involucrados en adaptaciones humanas recientes, lo que implica la existencia de diferentes presiones selectivas a lo largo de las distintas etapas de la historia evolutiva humana. También encontramos tres regiones genómicas con evidencias de selección positiva reciente, las cuales fueron analizadas en profundidad para proponer posibles dianas de selección y discutir las presiones selectivas subyacentes en cada caso.

Les événements fondateurs et les expansions territoriales peuvent promouvoir une cascade de changements génétiques et ont ainsi pu jouer un rôle important au cours de l’histoire évolutive de l’Homme moderne. Or, chez les populations humaines, les conséquences évolutives et la dynamique démographique des processus de colonisation demeurent largement méconnues et difficiles à étudier. Dans cette thèse, nous avons utilisé les généalogies de la population fondatrice canadienne-française ainsi que des données génomiques pour étudier ces questions. Les analyses génomiques et généalogiques, remarquablement concordantes, ont dévoilé un nouveau portrait détaillé de la structure de la population du Québec, incluant un continuum de diversité génétique dans l’axe ouest/est et des sous-populations significativement différenciées. L’analyse de l’immigration fondatrice a montré que virtuellement tous les Canadiens français sont métissés. Allant à l’encontre d’une prétendue homogénéité génétique de la population, nos résultats démontrent que le peuplement des régions a engendré une rapide différentiation génétique et expliquent certaines signatures régionales de l’effet fondateur. De plus, en suivant les changements évolutifs dans les généalogies, nous avons montré que les caractéristiques des peuplements fondateurs peuvent affecter les traits liés à la fécondité et au succès reproducteur. Cette thèse offre une meilleure compréhension du patrimoine génétique du Québec et apporte des éléments de réponse sur les conséquences évolutives des événements fondateurs. / Founding events and range expansions can promote a cascade of genetic changes and may have played an important role in the evolutionary history of modern humans. Yet the evolutionary consequences and demographic dynamics of these colonization processes remain poorly documented and challenging to study in human populations. In this thesis, we used deep-rooted genealogies from the French Canadian founder population in addition to genomic data to address these questions. Genomic and genealogical analyses were remarkably concordant and revealed a new portrait of Quebec fine-scale population structure, including a continuum of genetic diversity in the west/east axis and sub-populations significantly differentiated. The analysis of the founding immigration showed that virtually all French Canadians are admixed. Contrary to the idea of homogeneity of the population, our results demonstrate that the regional settlement histories led to a rapid genetic differentiation and explain some regional signatures of the founder effect. By monitoring evolutionary changes in real genealogies, we show that founding events impact fertility traits and reproductive success. This thesis leads to a better understanding of the genetic heritage of Quebec and provides insights on how peopling of new territories shaped human evolution.