Universität zu Köln

Natsidis, Paschalis, Kapli, Paschalia ORCID: 0000-0001-8769-8779, Schiffer, Philipp H. and Telford, Maximilian J. (2021). Systematic errors in orthology inference and their effects on evolutionary analyses. iScience, 24 (2). CAMBRIDGE: CELL PRESS. ISSN 2589-0042

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Abstract

The availability of complete sets of genes from many organisms makes it possible to identify genes unique to (or lost from) certain clades. This information is used to reconstruct phylogenetic trees; identify genes involved in the evolution of clade specific novelties; and for phylostratigraphy-identifying ages of genes in a given species. These investigations rely on accurately predicted orthologs. Here we use simulation to produce sets of orthologs that experience no gains or losses. We show that errors in identifying orthologs increase with higher rates of evolution. We use the predicted sets of orthologs, with errors, to reconstruct phylogenetic trees; to count gains and losses; and for phylostratigraphy. Our simulated data, containing information only from errors in orthology prediction, closely recapitulate findings from empirical data. We suggest published downstream analyses must be informed to a large extent by errors in orthology prediction that mimic expected patterns of gene evolution.

Item Type:	Journal Article
Creators:	Creators Email ORCID ORCID Put Code Natsidis, Paschalis UNSPECIFIED UNSPECIFIED UNSPECIFIED Kapli, Paschalia UNSPECIFIED orcid.org/0000-0001-8769-8779 UNSPECIFIED Schiffer, Philipp H. UNSPECIFIED UNSPECIFIED UNSPECIFIED Telford, Maximilian J. UNSPECIFIED UNSPECIFIED UNSPECIFIED
URN:	urn:nbn:de:hbz:38-577728
DOI:	10.1016/j.isci.2021.102110
Journal or Publication Title:	iScience
Volume:	24
Number:	2
Date:	2021
Publisher:	CELL PRESS
Place of Publication:	CAMBRIDGE
ISSN:	2589-0042
Language:	English
Faculty:	Unspecified
Divisions:	Unspecified
Subjects:	no entry
Uncontrolled Keywords:	Keywords Language PHYLOGENETIC ANALYSIS; GENOME Multiple languages Multidisciplinary Sciences Multiple languages
URI:	http://kups.ub.uni-koeln.de/id/eprint/57772