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Identifier

000431878

Title

Localizing selective sweeps using higher order Site Frequency Spectra: the 2-D SFS

Alternative Title

Εντοπισμός επιλεκτικής συμπαράσυρσης χρησιμοποιώντας μεγαλύτερης διάστασης φάσμα αλληλικών συχνοτήτων : 2D-SFS

Author

Μαλλιαρού, Μαρία

Thesis advisor

Παυλίδης, Παύλος

Reviewer

Νικολάου, Χριστόφορος
Λαδουκάκης, Εμμανουήλ

Abstract

When an allele is favored by natural selection, its frequency may increase in the population and linked neutral variants will increase their frequency as well a phenomenon called selective sweep. As the distance from the beneficial mutation increases, recombination will allow neutral variants to escape the so-called ‘hitchhiking effect’ of the beneficial mutation, thus, generating characteristic patterns of neutral variants, locally, around the target of natural selection. These patterns of neutral variants have been exploited in the last 20 years by computational methods that aim at localizing the action of positive selection on genomes obtained from natural populations. It is well-known that certain demographic models pose severe challenges on the detection of selective sweeps because they generate patterns of neutral variants that resemble those of a selective sweep. Considerable effort has been devoted to understanding the patterns of neutral variants generated by demographic models, solely. However, we still have no description of a selective sweep model in a population that has experienced demographic changes during its evolutionary history. Thus, even though neutrality is well-described, this is not the case for the model of positive selection. Here, we present a novel methodology for incorporating demography on the selection model of a selective sweep. We demonstrate that certain demographic models may change dramatically the well-known patterns of positive selection. To facilitate the detection of positive selection in non-isolated natural populations that have experienced demographic changes we implemented a selective sweep detection software, called SweeD-sim that extends Sweep Detector (SweeD) software. Moreover, to incorporate specific Linkage Disequilibrium patterns of genetic hitchhiking we have expanded our approach in two dimensions, creating a so called Two Dimensional Site Frequency Spectrum (2D-SFS) in hope of more significant results .

Language

English

Subject

Kernel density

Simulations

Εκτίμηση πυκνότητας με πυρήνες

Επιλεκτική συμπαράσυρση

Προσομοιώσεις

Issue date

2020-08-05

Collection

School/Department--School of Medicine--Department of Medicine--Post-graduate theses