Complete Characterization of Incorrect Orthology Assignments in Best Match Graphs

D. Schaller, M. Geiß, P. Stadler, M. Hellmuth. Complete Characterization of Incorrect Orthology Assignments in Best Match Graphs. Journal of Mathematical Biology, volume 82, pages 20, DOI 10.1007/s00285-021-01564-8, 2, 2021.

Autoren
  • David Schaller
  • Manuela Geiß
  • Peter F. Stadler
  • Marc Hellmuth
TypArtikel
JournalJournal of Mathematical Biology
VerlagSpringer
Band82
DOI10.1007/s00285-021-01564-8
Monat2
Jahr2021
Seiten20
Abstract

Genome-scale orthology assignments are usually based on reciprocal best matches. In the absence of horizontal gene transfer (HGT), every pair of orthologs forms a reciprocal best match. Incorrect orthology assignments therefore are always false positives in the reciprocal best match graph. We consider duplication/loss scenarios and characterize unambiguous false-positive (u-fp) orthology assignments, that is, edges in the best match graphs (BMGs) that cannot correspond to orthologs for any gene tree that explains the BMG. Moreover, we provide a polynomial-time algorithm to identify all u-fp orthology assignments in a BMG. Simulations show that at least 75%75% of all incorrect orthology assignments can be detected in this manner. All results rely only on the structure of the BMGs and not on any a priori knowledge about underlying gene or species trees.