Universität zu Köln

Klassmann, Alexander ORCID: 0000-0002-0175-1397 and Gautier, Mathieu (2022). Detecting selection using extended haplotype homozygosity (EHH)-based statistics in unphased or unpolarized data. PLoS One, 17 (1). SAN FRANCISCO: PUBLIC LIBRARY SCIENCE. ISSN 1932-6203

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Abstract

Analysis of population genetic data often includes a search for genomic regions with signs of recent positive selection. One of such approaches involves the concept of extended haplotype homozygosity (EHH) and its associated statistics. These statistics typically require phased haplotypes, and some of them necessitate polarized variants. Here, we unify and extend previously proposed modifications to loosen these requirements. We compare the modified versions with the original ones by measuring the false discovery rate in simulated whole-genome scans and by quantifying the overlap of inferred candidate regions in empirical data. We find that phasing information is indispensable for accurate estimation of within-population statistics (for all but very large samples) and of cross-population statistics for small samples. Ancestry information, in contrast, is of lesser importance for both types of statistic. Our publicly available R package rehh incorporates the modified statistics presented here.

Item Type:	Journal Article
Creators:	Creators Email ORCID ORCID Put Code Klassmann, Alexander UNSPECIFIED orcid.org/0000-0002-0175-1397 UNSPECIFIED Gautier, Mathieu UNSPECIFIED UNSPECIFIED UNSPECIFIED
URN:	urn:nbn:de:hbz:38-681009
DOI:	10.1371/journal.pone.0262024
Journal or Publication Title:	PLoS One
Volume:	17
Number:	1
Date:	2022
Publisher:	PUBLIC LIBRARY SCIENCE
Place of Publication:	SAN FRANCISCO
ISSN:	1932-6203
Language:	English
Faculty:	Unspecified
Divisions:	Unspecified
Subjects:	no entry
Uncontrolled Keywords:	Keywords Language RECENT POSITIVE SELECTION; LACTASE-PERSISTENCE; NATURAL-SELECTION; R PACKAGE; SWEEPS; SCANS; GENOME; RECOMBINATION; ADAPTATION; SIGNATURES Multiple languages Multidisciplinary Sciences Multiple languages
URI:	http://kups.ub.uni-koeln.de/id/eprint/68100