Perceptions of water conditions and management in the Sonora River Basin, Sonora, Mexico

The effects of climate change are expected to be very severe in arid regions. The Sonora River Basin, in the northwestern state of Sonora, Mexico, is likely to be severely affected. Some of the anticipated effects include precipitation variability, intense storm events, higher overall temperatures, and less available water. In addition, population in Sonora, specifically the capital city of Hermosillo, is increasing at a 1.5% rate and current populations are near 700,000. With the reduction in water availability and an increase in population, Sonora, Mexico is expected to experience severe water resource issues in the near future. In anticipation of these changes, research is being conducted in an attempt to improve water management in the Sonora River Basin, located in the northwestern part of Sonora. This research involves participatory modeling techniques designed to increase water manager awareness of hydrological models and their use as integrative tools for water resource management. This study was conducted as preliminary research for the participatory modeling grant in order to gather useful information on the population being studied. This thesis presents research from thirty-four in-depth interviews with water managers, citizens, and agricultural producers in Sonora, Mexico. Data was collected on perceptions of water quantity and quality in the basin, thoughts on current water management practices, perceptions of climate change and its management, experience with, knowledge of, and trust in hydrological models as water management tools. Results showed that the majority of interviewees thought there was not enough water to satisfy their daily needs. Most respondents also agreed that the water available was of good quality, but that current management of water resources was ineffective. Nearly all interviewees were aware of climate change and thought it to be anthropogenic. May reported experiencing higher temperatures, precipitation changes, and higher water scarcity and attributed those fluctuations to climate change. 65% of interviewees were at least somewhat familiar with hydrological models, though only 28% had ever used them or their output. Even with model usage results being low, 100% of respondents believed hydrological models to be very useful water management tools. Understanding how water, climate change, and hydrological models are perceived by this population of people is essential to improving their water management practices in the face of climate change.

Genetic association studies under the population stratification, family pedigree and application to genome-wide association studies

This dissertation has three separate parts: the first part deals with the general pedigree association testing incorporating continuous covariates; the second part deals with the association tests under population stratification using the conditional likelihood tests; the third part deals with the genome-wide association studies based on the real rheumatoid arthritis (RA) disease data sets from Genetic Analysis Workshop 16 (GAW16) problem 1. Many statistical tests are developed to test the linkage and association using either case-control status or phenotype covariates for family data structure, separately. Those univariate analyses might not use all the information coming from the family members in practical studies. On the other hand, the human complex disease do not have a clear inheritance pattern, there might exist the gene interactions or act independently. In part I, the new proposed approach MPDT is focused on how to use both the case control information as well as the phenotype covariates. This approach can be applied to detect multiple marker effects. Based on the two existing popular statistics in family studies for case-control and quantitative traits respectively, the new approach could be used in the simple family structure data set as well as general pedigree structure. The combined statistics are calculated using the two statistics; A permutation procedure is applied for assessing the p-value with adjustment from the Bonferroni for the multiple markers. We use simulation studies to evaluate the type I error rates and the powers of the proposed approach. Our results show that the combined test using both case-control information and phenotype covariates not only has the correct type I error rates but also is more powerful than the other existing methods. For multiple marker interactions, our proposed method is also very powerful. Selective genotyping is an economical strategy in detecting and mapping quantitative trait loci in the genetic dissection of complex disease. When the samples arise from different ethnic groups or an admixture population, all the existing selective genotyping methods may result in spurious association due to different ancestry distributions. The problem can be more serious when the sample size is large, a general requirement to obtain sufficient power to detect modest genetic effects for most complex traits. In part II, I describe a useful strategy in selective genotyping while population stratification is present. Our procedure used a principal component based approach to eliminate any effect of population stratification. The paper evaluates the performance of our procedure using both simulated data from an early study data sets and also the HapMap data sets in a variety of population admixture models generated from empirical data. There are one binary trait and two continuous traits in the rheumatoid arthritis dataset of Problem 1 in the Genetic Analysis Workshop 16 (GAW16): RA status, AntiCCP and IgM. To allow multiple traits, we suggest a set of SNP-level F statistics by the concept of multiple-correlation to measure the genetic association between multiple trait values and SNP-specific genotypic scores and obtain their null distributions. Hereby, we perform 6 genome-wide association analyses using the novel one- and two-stage approaches which are based on single, double and triple traits. Incorporating all these 6 analyses, we successfully validate the SNPs which have been identified to be responsible for rheumatoid arthritis in the literature and detect more disease susceptibility SNPs for follow-up studies in the future. Except for chromosome 13 and 18, each of the others is found to harbour susceptible genetic regions for rheumatoid arthritis or related diseases, i.e., lupus erythematosus. This topic is discussed in part III.