Universität zu Köln

Wirtz, Johannes, Rauscher, Martina and Wiehe, Thomas ORCID: 0000-0002-8932-2772 (2018). Topological linkage disequilibrium calculated from coalescent genealogies. Theor. Popul. Biol., 124. S. 41 - 51. SAN DIEGO: ACADEMIC PRESS INC ELSEVIER SCIENCE. ISSN 1096-0325

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Abstract

We revisit the classical, and introduce a novel, concept of two-locus linkage disequilibrium (LD). In contrast to defining haplotypes as allele combinations at two marker loci, we concentrate on the clustering of a sample of chromosomes induced by their coalescent genealogy. The root of a binary coalescent tree defines two clusters of chromosomes, each one of them containing the left and right descendants of the root. At two different loci this assignment may be different as a result of recombination. We show that the proportion of shared chromosomes among clusters at two different loci, measured by the squared correlation, constitutes a natural measure of LD. We call this topological LD (tLD) since it is induced by the topology of the coalescent tree. We find that it is, on average, larger than classical LD for any given distance between loci. Furthermore, tLD has a smaller coefficient of variation, which should provide an advantage, compared to the use of classical LD, for any kind of mapping purposes. We conclude with a practical application to the LCT region in human populations. (C) 2018 Elsevier Inc. All rights reserved.

Item Type:	Journal Article
Creators:	Creators Email ORCID ORCID Put Code Wirtz, Johannes UNSPECIFIED UNSPECIFIED UNSPECIFIED Rauscher, Martina UNSPECIFIED UNSPECIFIED UNSPECIFIED Wiehe, Thomas UNSPECIFIED orcid.org/0000-0002-8932-2772 UNSPECIFIED
URN:	urn:nbn:de:hbz:38-164412
DOI:	10.1016/j.tpb.2018.09.001
Journal or Publication Title:	Theor. Popul. Biol.
Volume:	124
Page Range:	S. 41 - 51
Date:	2018
Publisher:	ACADEMIC PRESS INC ELSEVIER SCIENCE
Place of Publication:	SAN DIEGO
ISSN:	1096-0325
Language:	English
Faculty:	Faculty of Mathematics and Natural Sciences
Divisions:	Faculty of Mathematics and Natural Sciences > Department of Biology > Institute for Genetics
Subjects:	no entry
Uncontrolled Keywords:	Keywords Language POPULATION; FREQUENCIES; MODEL Multiple languages Ecology; Evolutionary Biology; Genetics & Heredity; Mathematical & Computational Biology Multiple languages
Refereed:	Yes
URI:	http://kups.ub.uni-koeln.de/id/eprint/16441