Universität zu Köln

Mishra, Swastik ORCID: 0009-0000-4107-6384, Lercher, Martin J ORCID: 0000-0003-3940-1621 and Crandall, Keith (2025). Horizontal Gene Transfer Inference: Gene Presence–Absence Outperforms Gene Trees. Molecular Biology and Evolution, 42 (7). pp. 1-9. Oxford University Press. ISSN 0737-4038

PDF msaf166.pdf Bereitstellung unter der CC-Lizenz: Creative Commons Attribution. Download (672kB)

Abstract

Horizontal gene transfer is a fundamental driver of prokaryotic evolution, facilitating the acquisition of novel traits and adaptation to new environments. Despite its importance, methods for inferring horizontal gene transfer are rarely systematically compared, leaving a gap in our understanding of their relative strengths and limitations. Validating horizontal gene transfer inference methods is challenging due to the absence of a genomic fossil record that could confirm historical transfer events. Without an empirical gold standard, new inference methods are typically validated using simulated data; however, these simulations may not accurately capture biological complexity and often embed the same assumptions used in the inference methods themselves. Here, we leverage the tendency of horizontal gene transfer events to involve multiple neighboring genes to assess the accuracy of diverse horizontal gene transfer inference methods. We show that methods analyzing gene family presence/absence patterns across species trees consistently outperform approaches based on gene tree-species tree reconciliation. Our findings challenge the prevailing assumption that explicit phylogenetic reconciliation methods are superior to simpler implicit methods. By providing a comprehensive benchmark, we offer practical recommendations for selecting appropriate methods and indicate avenues for future methodological advancements.

Item Type:	Article
Creators:	Creators Email ORCID ORCID Put Code Mishra, Swastik UNSPECIFIED https://orcid.org/0009-0000-4107-6384 UNSPECIFIED Lercher, Martin J UNSPECIFIED https://orcid.org/0000-0003-3940-1621 UNSPECIFIED Crandall, Keith UNSPECIFIED UNSPECIFIED UNSPECIFIED
URN:	urn:nbn:de:hbz:38-811290
Identification Number:	10.1093/molbev/msaf166
Journal or Publication Title:	Molecular Biology and Evolution
Volume:	42
Number:	7
Page Range:	pp. 1-9
Number of Pages:	9
Date:	28 July 2025
Publisher:	Oxford University Press
ISSN:	0737-4038
Language:	English
Faculty:	Faculty of Mathematics and Natural Sciences
Divisions:	Faculty of Mathematics and Natural Sciences > Department of Physics > Institute for Theoretical Physics
Subjects:	Physics
Uncontrolled Keywords:	Keywords Language horizontal gene transfer ; HGT inference ; gene presence–absence profiles ; reconciliation models ; implicit phylogenetic methods ; explicit phylogenetic methods English
['eprint_fieldname_oa_funders' not defined]:	Publikationsfonds UzK
Refereed:	Yes
URI:	http://kups.ub.uni-koeln.de/id/eprint/81129