Reciprocal best hits are not a logically sufficient condition for orthology

TL;DR

Reciprocal best hits are not a logically sufficient condition for orthology, challenging common assumptions and prompting a reevaluation of algorithms used for ortholog identification.

Contribution

The paper clarifies the logical limitations of reciprocal best hits as a criterion for orthology, highlighting the need for more rigorous methods.

Findings

Reciprocal best hits are not sufficient for orthology.

Common algorithms based on reciprocal best hits may be logically flawed.

Reevaluation of ortholog detection methods is necessary.

Abstract

It is common to use reciprocal best hits, also known as a boomerang criterion, for determining orthology between sequences. The best hits may be found by blast, or by other more recently developed algorithms. Previous work seems to have assumed that reciprocal best hits is a sufficient but not necessary condition for orthology. In this article, I explain why reciprocal best hits cannot logically be a sufficient condition for orthology. If reciprocal best hits is neither sufficient nor necessary for orthology, it would seem worthwhile to examine further the logical foundations of some unsupervised algorithms that are used to identify orthologs.