In order to determine if there is a shared biological lineage among four east central Indiana skeletal populations, the remains have been subjected to nonmetric trait analysis. This technique examines the directly observable manifestations of the genome on the skeleton in order to determine if two or more groups have a shared genetic background beyond the genes that all humans share. This information supplements the archaeological information already available from the cultural remains of these groups, in addition to the metrical data. / Department of Anthropology

Human populations in Africa have high levels of genetic, cultural and linguistic diversity. Despite this, only a small proportion of African populations have been studied from a genetics perspective. There is a particular dearth of information for Southern Africa, even though this region is one of the few places where hunter-gatherer, pastoralist and farmer populations remain, and where interaction between these groups can be studied. This thesis analyses novel populations from Lesotho, Namibia and South Africa, for both maternal and paternal markers, in order to provide a more accurate understanding of the history of this region. Analysis of biodemographic data for these populations highlights signatures of specific cultural traits. Interestingly, contrary to expectations, results indicate that in the patrilocal Basotho there are no differences in within and between area mtDNA and NRY variation, despite observations of a higher female than male migration rate. Females move preferentially at shorter distances than males, minimising the impact of the higher female migration rate. Further analysis of the Southern African samples indicates that the genetic composition of these populations is different to previously studied populations from Sub-Saharan Africa. Notably, there is a significantly higher maternal hunter-gatherer component, potentially as a result of an archeologically defined static frontier which existed along the Maloti/Drakensberg escarpment. Analysis of Namibian samples provides additional information about the history of populations with different lifestyles in the region, with support for a link between Southern Africa pastoralists and East Africa, while other Namibian populations appear genetically different from previously studied populations. Overall, this work demonstrates the diversity of populations in Southern Africa, improves understanding of the history of this region, and also emphasises the value of having access to geographically and ethnically well-defined samples.

The aim of this dissertation is to describe socioeconomic development of Central - Bohemian region and one of the Operational program, which is the Joint Regional Operational Programme (JROP). It contains the comparison of the chosen demographic and socioeconomic indicators during the period 2000-2009 and the benefits of JROP in the Central - Bohemian region. The dissertation is divided into two main parts. In the first one is presented Central - Bohemia region, and the description of the covered indicators, e.g. the structure of the inhabitants in detail of sex and age, natality, structure of abortions, marriages, divorces, migration, and the measurement of these indicators. Further, the basic socioeconomic parameters as the labor market and the associated unemployment, trend of the GDP, transport infrastructure, and opportunities in tourism are described, followed by description of particular Priorities of the operational program. In the analytical part, the comparison and evaluation of the covered indicators in detail of districts in Central Bohemia Region and successfulness of JROP priority axis covering all the Central Bohemian Region is included. Successful projects, amount of paid financial sources to final beneficiaries in detail of particular regions according to priorities.

Advances in the genetic analysis of humans have revealed a surprising abundance of local relatedness between purportedly unrelated individuals. Where common mutations classically inform us of ancient relationships, such segments of pairwise identical by descent (IBD) sharing from a common ancestor are the observable traces of recent inter-mating. Combining these two distinct sources of information can help disentangle the complex genetic structure and flux in human populations. When considered together with a heritable trait, the segments can also be used to interrogate unascertained rare variation and help in locating trait-effecting loci. This work presents methods for comprehensive analysis of population-wide IBD and explores applications to disease and the understanding of recent genetic variation. We propose several strategies for efficient detection of IBD segments in population genotype data. Our novel seed-based algorithm, GERMLINE, can reduce the computational burden of finding pairwise segments from quadratic to nearly linear time in a general population. We demonstrate that this approach is several orders of magnitude faster than the available all-pairs methods while maintaining higher accuracy. Next, we extended the GERMLINE technique to process cohorts of unlimited size by adaptively adjusting the search mechanism to meet resource restrictions. We confirm its effectiveness with an analysis of 50,000 individuals where contemporary methods can only process a few thousand. One draw-back of these two algorithms is the dependence on phased haplotype data as input - a constraint that becomes more difficult with large populations. We propose a solution to this problem with an algorithm that analyzes genotype data directly by exploring all potential haplotypes and scoring each putative segment based on linkage-disequilibrium. This solution significantly outperforms available methods when applied to full sequence data and is computationally efficient enough to analyze thousands of sequenced genomes where current methods can only determine haplotypes for several hundred. Secondly, we outline two algorithms for analyzing available IBD segments to increase our understanding of rare variation and complex disease. Motivated by whole-genome sequencing, we present the INFOSTIP algorithm, which uses IBD segments to optimize the selection of individuals for complete population ascertainment. In simulations, we show that INFOSTIP selection can significantly increase variant inference accuracy over random sampling and posit inference of 60% of an isolated population from 1% optimally selected individuals. Seeking to move beyond pairwise IBD segment analysis, we describe the DASH algorithm, which groups shared segments into IBD "clusters" that are likely to be commonly co-inherited and uses them as proxies for un-typed variation. In simulated disease studies, we show this reference-free approach to be much more powerful for detecting rare causal variants than either traditional single-marker analysis or imputation from a general reference panel. Applying the DASH algorithm to disease traits from different populations, we identify multiple novel loci of association. Together, these novel techniques integrate the power of population and disease genetics.

The Aedes aegypti mosquito is the vector for four infectious diseases of global concern – Yellow Fever, Dengue, Chikungunya, and Zikavirus. Previous attempts to model the expansion of the vector habitat due to global climate change have rarely included characteristics related to the human populations on which this mosquito is dependent. The purpose of this research was to determine whether the inclusion of human population density improves model performance while creating risk maps that can be used to determine where humans are most likely to be exposed to the vector in the future. The resulting model demonstrated that the inclusion of human population density improves the predictive power for A. aegypti and should be considered during model development. Maps produced by the model were also suitable for identifying regions where human populations are most likely to experience increased risk. Finally, two areas at risk of expansion were highlighted as a case study in pairing risk mapping with evidence-based intervention strategies to identify sites that would benefit from mosquito-control efforts. In this case, a low-cost program of insecticide-treated covers for water storage containers would likely work well in both Minas Gerais, Brazil and Northwestern Province, Zambia to mitigate mosquito risk. This research demonstrates that human population characteristic not only improve model fit but also increase the extent to which risk maps are actionable by aiding in targeting interventions.

No description available.

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.