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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
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Μαλλιαρού, Μαρία
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Thesis advisor
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Παυλίδης, Παύλος
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Reviewer
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Νικολάου, Χριστόφορος
Λαδουκάκης, Εμμανουήλ
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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 .
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Language |
English |
Subject |
Kernel density |
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Simulations |
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Εκτίμηση πυκνότητας με πυρήνες |
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Επιλεκτική συμπαράσυρση |
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Προσομοιώσεις |
Issue date |
2020-08-05 |
Collection
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School/Department--School of Medicine--Department of Medicine--Post-graduate theses
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Type of Work--Post-graduate theses
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Permanent Link |
https://elocus.lib.uoc.gr//dlib/d/1/a/metadata-dlib-1599546920-42019-12642.tkl
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Views |
519 |