E-Locus - Institutional Repository of the University of Crete

Home Search

Results - Details

Search command : Author="Νικολάου" And Author="Χριστόφορος"

Current Record: 7 of 29

[Add to Basket]

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

Παπαδοπούλου, Αγγελική Β.

Thesis advisor

Παυλίδης, Παύλος

Reviewer

Ηλιόπουλος, Ιωάννης
Νικολάου, Χριστόφορος

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.

Language

English

Subject

Ancient DNA

PCA

Population structure

Πληθυσμιακή δομή

Issue date

2022-07-29

Collection

School/Department--School of Sciences and Engineering--Department of Biology--Post-graduate theses

Type of Work--Post-graduate theses