Universität zu Köln

Rauscher, Martina (2018). Topology of genealogical trees - theory and application. PhD thesis, Universität zu Köln.

All available versions of this item

• Topology of genealogical trees - theory and application. (deposited 30 Nov 2018 11:21) [Currently Displayed]

Preview

PDF MRauscher_DissTwosided.pdf Download (9MB) | Preview

Abstract

Still today, identifying loci, which underwent recent selective sweeps is a difficult task, since traces are typically obscured by other evolutionary and demographic factors, such as genetic drift or population bottleneck events. To detect candidate loci of selective sweeps, we take here an approach which considers the genealogical relationships among individuals and the topological properties of the inferred coalescent tree. Selective sweeps can produce highly unbalanced coalescent tree topologies in region close to a selective sweep site. Building on a previously known test statistic called T3, which detects bias in the balance of binary genealogical trees, we derive a new test statistic based on a log likelihood approach and we call it the LR_T3-test. We present the results of genome wide screens of the LR_T3-test applied to the 26 populations of the phase 3 data set of the human 1,000 genomes project. Furthermore, we present a measure of topological linkage disequilibrium (tLD), which is based on clustering individuals with respect to their position in the genealogy rather than clustering alleles and haplotypes. We demonstrate its application to the beforehand processed human data.

Item Type:	Thesis (PhD thesis)
Creators:	Creators Email ORCID ORCID Put Code Rauscher, Martina martina.rauscher@uni-koeln.de UNSPECIFIED UNSPECIFIED
URN:	urn:nbn:de:hbz:38-90303
Date:	2018
Language:	English
Faculty:	Faculty of Mathematics and Natural Sciences
Divisions:	Faculty of Mathematics and Natural Sciences > Department of Biology > Institute for Genetics
Subjects:	Data processing Computer science Life sciences
Uncontrolled Keywords:	Keywords Language human population genetics; 1k genomes project; selective sweep; positive selection; coalescent tree topology; likelihood method; linkage disequilibrium; topological linkage disequilibrium; English
Date of oral exam:	26 October 2018
Referee:	Name Academic Title Wiehe, Thomas Prof. Dr. Nothnagel, Michael Prof. Dr.
Refereed:	Yes
URI:	http://kups.ub.uni-koeln.de/id/eprint/9030