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- All Subjects: Evolution
- Creators: School of Human Evolution & Social Change
My research is focused on the people of Turkana, a human pastoral population inhabiting Northwest Kenya. The people of Turkana are Nilotic people that are native to the Turkana district. There are currently no conclusive studies done on evidence for genetic lactase persistence in Turkana. Therefore, my research will be on the evolution of lactase persistence in the people of Turkana. The goal of this project is to investigate the evolutionary history of two genes with known involvement in lactase persistence, LCT and MCM6, in the Turkana. Variants in these genes have previously been identified to result in the ability to digest lactose post-weaning age. Furthermore, an additional study found that a closely related population to the Turkana, the Massai, showed stronger signals of recent selection for lactase persistence than Europeans in these genes. My goal is to characterize known variants associated with lactase persistence by calculating their allele frequencies in the Turkana and conduct selection scans to determine if LCT/MCM6 show signatures of positive selection. In doing this, we conducted a pilot study consisting of 10 female Turkana individuals and 10 females from four different populations from the 1000 genomes project namely: the Yoruba in Ibadan, Nigeria (YRI); Luhya in Webuye, Kenya; Utah Residents with Northern and Western European Ancestry (CEU); and the Southern Han Chinese. The allele frequency calculation suggested that the CEU (Utah Residents with Northern and Western European Ancestry) population had a higher lactase persistence associated allele frequency than all the other populations analyzed here, including the Turkana population. Our Tajima’s D calculations and analysis suggested that both the Turkana population and the four haplotype map populations shows signatures of positive selection in the same region. The iHS selection scans we conducted to detect signatures of positive selection on all five populations showed that the Southern Han Chinese (CHS), the LWK (Luhya in Webuye, Kenya) and the YRI (Yoruba in Ibadan, Nigeria) populations had stronger signatures of positive selection than the Turkana population. The LWK (Luhya in Webuye, Kenya) and the YRI (Yoruba in Ibadan, Nigeria) populations showed the strongest signatures of positive selection in this region. This project serves as a first step in the investigation of lactase persistence in the Turkana population and its evolution over time.
Bermuda Land Snails make up a genus called Poecilozonites that is endemic to Bermuda and is extensively present in its fossil record. These snails were also integral to the creation of the theory of punctuated equilibrium. The DNA of mollusks is difficult to sequence because of a class of proteins called mucopolysaccharides that are present in high concentrations in mollusk tissue, and are not removed with standard DNA extraction methods. They inhibit Polymerase Chain Reactions (PCRs) and interfere with Next Generation Sequencing methods. This paper will discuss the DNA extraction methods that were designed to remove the inhibitory proteins that were tested on another gastropod species (Pomacea canaliculata). These were chosen because they are invasive and while they are not pulmonates, they are similar enough to Bermuda Land Snails to reliably test extraction methods. The methods that were tested included two commercially available kits: the Qiagen Blood and Tissue Kit and the Omega Biotek Mollusc Extraction Kit, and one Hexadecyltrimethylammonium Bromide (CTAB) Extraction method that was modified for use on mollusk tissue. The Blood and Tissue kit produced some DNA, the mollusk kit produced almost none, and the CTAB Extraction Method produced the highest concentrations on average, and may prove to be the most viable option for future extractions. PCRs attempted with the extracted DNA have all failed, though it is likely due to an issue with reagents. Further spectrographic analysis of the DNA from the test extractions has shown that they were successful at removing mucopolysaccharides. When the protocol is optimized, it will be used to extract DNA from the tissue from six individuals from each of the two extant species of Bermuda Land Snails. This DNA will be used in several experiments involving Next Generation Sequencing, with the goal of assembling a variety of genome data. These data will then be used to a construct reference genome for Bermuda Land Snails. The genomes generated by this project will be used in population genetic analyses between individuals of the same species, and between individuals of different species. These analyses will then be used to aid in conservation efforts for the species.
Stellar mass loss has a high impact on the overall evolution of a star. The amount<br/>of mass lost during a star’s lifetime dictates which remnant will be left behind and how<br/>the circumstellar environment will be affected. Several rates of mass loss have been<br/>proposed for use in stellar evolution codes, yielding discrepant results from codes using<br/>different rates. In this paper, I compare the effect of varying the mass loss rate in the<br/>stellar evolution code TYCHO on the initial-final mass relation. I computed four sets of<br/>models with varying mass loss rates and metallicities. Due to a large number of models<br/>reaching the luminous blue variable stage, only the two lower metallicity groups were<br/>considered. Their mass loss was analyzed using Python. Luminosity, temperature, and<br/>radius were also compared. The initial-final mass relation plots showed that in the 1/10<br/>solar metallicity case, reducing the mass loss rate tended to increase the dependence of final mass on initial mass. The limited nature of these results implies a need for further study into the effects of using different mass loss rates in the code TYCHO.
Our cells need constant fuel and oxygen for the body to work properly and maintain cellular function. In high altitudes tissue oxygen levels fall and the body must work against this hypoxic challenge to maintain energetics and limit oxidative stress. Mammals living at high altitudes are challenged to sustain thermogenesis and aerobic exercise despite reduced amounts of available oxygen. Enhancements in oxidative capacity and oxygen diffusion capacity of skeletal muscle may be necessary to compensate for insufficient oxygen supply in tissues. Hypoxic conditions can cause a switch from aerobic metabolism to anaerobic metabolism. Due to previous research of Graham Scott and colleagues on “Adaptive Modifications of Muscle Phenotype in High-Altitude Deer Mice” and the SMack Lab at Arizona State University, the question of how low atmospheric oxygen levels affects the enzymatic activity in the gastrocnemius muscle of Gelada Monkeys compared to Rhesus Macaque Monkeys was researched. Lactate Dehydrogenase (LDH) activity was measured in the gastrocnemius tissue of 6 Gelada Monkeys (highland) and 6 Rhesus Macaque monkeys (lowland). LDH was expected to be greater in Gelada tissue samples due to heightened anaerobic metabolism in the presence of limited available oxygen in high altitude environments. Results showed higher LDH in Rhesus Macaque samples compared to Gelada samples, but this difference was not statistically significant. Despite nonsignificant data, this experiment is insightful into the effects of Hypoxic adaptation in skeletal muscle enzymatic activity in primates.
Cells have mechanisms in place to maintain the specific lipid composition of distinct organelles including vesicular transport by the endomembrane system and non-vesicular lipid transport by lipid transport proteins. Oxysterol Binding Proteins (OSBPs) are a family of lipid transport proteins that transfer lipids at various membrane contact sites (MCSs). OSBPs have been extensively investigated in human and yeast cells where twelve have been identified in Homo sapiens and seven in Saccharomyces cerevisiae. The evolutionary relationship between these well-characterized OSBPs is still unclear. Reconstructed OSBP phylogenies revealed that the ancestral Saccharomycotinan had four OSBPs, the ancestral Holomycotan had five OSBPs, the ancestral Holozoan had six OSBPs, the ancestral Opisthokont had three OSBPs, and the ancestral Eukaroyte had three OSBPs. Our analysis identified three clades of ancient OSBPs not present in animals or fungi.