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Identifier	000397229
Title	Detecting positive selection using pair of consecutive SNPs
Author	Χριστοδουλάκη, Ειρήνη Ε.
Thesis advisor	Παυλίδης, Παύλος
Abstract	An interesting research topic in population genetics is the detection of loci that are targets of positive selection using Single Nucleotide Polymorphism (SNP) data. Many tests have been developed for the identification of genomic signatures of positive selection based on the skew of the distribution of SNP frequencies (Site Frequency Spectrum or SFS) that is caused by selection. There are several methods to detect strong positive selection or in other words, a selective sweep event. Current methods for detecting selective sweeps based on SFS do not take into consideration the linkage disequilibrium in combination with the skew in the allele frequencies in SFS. In this study we describe a model that combines both genomic signatures of positive selection, that is, LD and the skewed patterns of allele frequencies. By extensive simulations we show that is possible to detect a selective sweep by using the joint distribution of the allele frequencies of pairs of polymorphic sites (joint-SFS). Furthermore, we show that using pairs of SNPs, instead of independent sites, results in higher efficiency to detect selective sweeps. Furthermore, we try to find a mathematical formula that calculates the probability of observing a pair of Single Nucleotide Polymorphisms (SNPs) at a certain distance from a positively selected site, using a diffusion approximation.
Language	English
Issue date	2015-11-20
Collection	School/Department--School of Sciences and Engineering--Department of Biology--Post-graduate theses
	Type of Work--Post-graduate theses
Permanent Link	https://elocus.lib.uoc.gr//dlib/f/2/b/metadata-dlib-1447936666-587183-15718.tkl
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