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Stanford CS 374 - Human Evolution

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CS 374 Lecture 5 Human Evolution Lecturer: Sharareh Noorbaloochi Scribe: Wissam Kazan Human Evolution Papers: 1. Benjamin F. Voight, Sridhar Kudaravalli, Xiaoquan Wen, Jonathan K. Pritchard, “A Map of Recent Positive Selection in the Human Genome”, PLOSBiology, March 2006, Volume 4, Issue 3, e72. 2. P. C. Sabeti, S. F. Schaffner, B. Fry, J. Lohmueller, P. Varilly, O. Shamovsky, A. Palma, T. S. Mikkelsen, D. Altshuler, E. S. Lander, “Positive Natural Selection in the Human Lineage”, www.sciencemag.org, 16 June 2006 Table of Contents: 1. Introduction..................................................................................................................... 2 2. Human Genetic Variations.......................................................................................... 2 3. SNP (Single Nucleotide Polymorphism) ........................................................................ 3 3.1 Haplotype.................................................................................................................. 3 3.2 SNP Maps ................................................................................................................. 4 3.3 Effect of SNPs on protein structures......................................................................... 4 4. HapMap Project .............................................................................................................. 6 4.1 Construction of the HapMap..................................................................................... 6 5. Genetic Variations .......................................................................................................... 7 5.1 Definitions................................................................................................................. 7 5.2 Linkage Disequilibrium ............................................................................................ 8 6. Neutral Evolution versus Positive Natural Selection...................................................... 9 6.1 Neutral Evolution...................................................................................................... 9 6.2 Positive Natural Selection......................................................................................... 9 6.3 Detecting Selection................................................................................................. 10 6.3.1 High proportion of function altering mutations............................................... 10 6.3.2 Reduction in genetic diversity ......................................................................... 11 6.3.3 High Frequency derived alleles ( age < 80K years)......................................... 12 6.3.4 Long Haplotypes.............................................................................................. 12 6.3.5 Difference between populations (age <50K to 75K years).............................. 13 6.3.6 Signature of Selections .................................................................................... 14 6.4 Genome-Wide Studies ............................................................................................ 14 6.5 Finding selective sweeps......................................................................................... 14 6.5.1 Description....................................................................................................... 14 6.5.2 Relationship between allele’s frequencies and extent of linkage disequilibrium................................................................................................................................... 15CS 374 Lecture 5 Human Evolution Lecturer: Sharareh Noorbaloochi Scribe: Wissam Kazan 1. Introduction Many environmental changes and alteration in the way of living has been experienced in the evolution of existing human populations. Starting 100,000 years ago with the emigration of Humans from Africa to the rest of the globe straining the human race to acclimatize to new environments and atmospheres, to 14,000 years ago where the population experienced a major global warming event increasing the world’s temperature to the actual level, the human race has showed many evolutionary changes and adaptations. They moved from a hunting society to a farming one, for example. Due the latter change, the new environment increased the risk of diseases caused by livestock. Due to all those modifications, there has been a natural selection of new genotypes that would be more appropriate to the new environment, mutations that would help the human race to overcome all those difficulties. Examples of such genes are: [1] • G6PD which is a gene that helps for the resistance to malaria • Lactase gene in response to dairy farming • MCPH1 and ASPM that help for brain development In human beings, 99.9% of the bases are the same, but the remaining 0.1% is what makes a person unique. They code the different attributes, characteristics and traits of a person. The variations in the human genome that makes on sequence different than the other can either be harmful, harmless or latent. Harmful variations are likely to cause diabetes, cancer, heart disease, hemophilia and other diseases. Harmless variations are mainly variations in the phenotype of a person. Latent variations are found in coding and regulatory regions, they are known not to be harmful on their own but they become harmful under certain conditions. 2. Human Genetic Variations There are two types of genetic mutations: Single Base mutation: substitution of one nucleotide with another. The Single Nucleotide Polymorphism (SNP) is one of the most common types of genetic variations. The international HapMAP project constitutes the basis for a major portion of the genetic diversity in the human race, having around 10,000,000 SNPs estimated. Insertion or deletion of one or more nucleotides: Tandem Repeat Polymorphisms and Insertion/Deletion Polymorphisms are examples.CS 374 Lecture 5 Human Evolution Lecturer: Sharareh Noorbaloochi Scribe: Wissam Kazan 3. SNP (Single Nucleotide Polymorphism) A SNP is defined as a single base change in a DNA sequence that occurs in a significant proportion (> 1%) of a large population. It might result in changing the DNA sequence. They can be found in coding and non-coding regions and they occur with a very high frequency: about 1 in 1200 bases on average, which results in approximately 10 million SNPs


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Stanford CS 374 - Human Evolution

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