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Full genomic Y chromosomal variation in southern African Khoe-San populations
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.ORCID iD: 0000-0002-9122-4530
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.ORCID iD: 0000-0002-6456-8055
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(English)Manuscript (preprint) (Other academic)
National Category
Genetics Evolutionary Biology
Identifiers
URN: urn:nbn:se:uu:diva-361124OAI: oai:DiVA.org:uu-361124DiVA, id: diva2:1249922
Available from: 2018-09-20 Created: 2018-09-20 Last updated: 2018-09-20
In thesis
1. Population Genetics of Human Genomic Elements
Open this publication in new window or tab >>Population Genetics of Human Genomic Elements
2018 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The genomes of living organisms are composed of a multitude of functional units, which interact with each other and their environment in a highly regulated fashion, to facilitate the expression of an enduring (and evolving) phenotype. Several approaches have emerged in the effort to identify these functional units and explore their activities. In this thesis, I have taken a population genetics approach; evaluating how the distribution of genetic variation in the human genome has been shaped through the actions of natural selection on functional genomic elements. In the first paper, I interrogate a catalogue of elements derived from biochemical signatures for signals of selection; finding significant signals of purifying selection on regulatory elements, independent of linked-purifying selection. In the second paper, I explore the pseudogene class of genomic elements, and find that a large proportion of a particular subclass, transcribed duplicated pseudogenes, has experienced significant amounts of positive selection. In the third paper, I focus on protein coding genes and variants that disrupt their open reading frames. Specifically, I examine the distribution of loss-of-function variants in the Khoe-San population; gauging their functional significance and exploring the biological roles of affected genes. In the final paper, instead of using population genetics to uncover and explore genomic elements, I use a major genomic element – the Y chromosome – as an effective tool to study the evolutionary history of a human population.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2018. p. 58
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 1724
Keywords
population genetics, human genome, functional elements, natural selection, pseudogenes, loss-of-function, gene regulation, Y chromosome
National Category
Genetics Evolutionary Biology
Research subject
Biology with Specialisation in Human Evolution and Genetics
Identifiers
urn:nbn:se:uu:diva-361125 (URN)978-91-513-0447-2 (ISBN)
Public defence
2018-11-08, Lindahlsalen, 05:01058, EBC, Norbyvägen 18A, Uppsala, 10:15 (English)
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Available from: 2018-10-16 Created: 2018-09-20 Last updated: 2018-11-19

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Naidoo, ThijessenVicente, MárioMalmström, HelenaJakobsson, MattiasSchlebusch, Carina

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