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Identifier |
000448414 |
Title |
Inference of population relations using ancient genomes : challenges, biases and imputation approaches in dimensionality reduction methodologies |
Alternative Title |
Εξαγωγή συμπερασμάτων πληθυσμιακών σχέσεων χρησιμοποιώντας αρχαία γονιδιώματα: προκλήσεις, μεροληψίες, και προσεγγίσεις για ανάκτηση της ελλιπούς πληροφορίας σε μεθόδους μείωσης διαστάσεων |
Author
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Παπαδοπούλου, Αγγελική Β.
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Thesis advisor
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Παυλίδης, Παύλος
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Reviewer
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Ηλιόπουλος, Ιωάννης
Νικολάου, Χριστόφορος
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Abstract |
Ancient DNA (aDNA), derived mainly from archaeological findings, is a snapshot into the past, enabling researchers to obtain insights into the human evolutionary history. Due to its age, aDNA is highly degraded and damaged, leading
to limited, often low-quality, extracted information. aDNA studies unravel the
complex evolutionary history of human demography, such as the past population
size changes, gene flow events as well as adaptive processes that contributed to
the survival of our species. The demographic inference of ancient populations
sheds light on the genetic relationships between them assisting us to understand
the present-day structure and the common origins of human populations. In this
study, we describe and evaluate widely-used methods for the inference of population structure, focusing on the Dimensionality Reduction techniques. We highlight the biases, introduced by the inevitable missing data in aDNA. We propose
a novel imputation approach that is based on the phylogeny of the samples under study. Using simulations, we tested the accuracy of our imputation approach
and we showed that is superior to the widely-used mean imputation and has a
similar performance to the state-of-the-art kNN imputation. In conclusion, this
thesis draws attention to the challenges accompanying the usage and analysis of
aDNA data to infer population relationships and, in addition, proposes a novel
imputation approach to retrieve the missing information of aDNA genotypes.
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Language |
English |
Subject |
Ancient DNA |
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PCA |
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Population structure |
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Πληθυσμιακή δομή |
Issue date |
2022-07-29 |
Collection
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School/Department--School of Sciences and Engineering--Department of Biology--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/3/1/d/metadata-dlib-1653043290-440610-14066.tkl
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Views |
448 |