Xenologs

Xenologs are homologous genes that have originated in different species through horizontal gene transfer rather than vertical descent from a common ancestor. In the study of genome evolution, xenologs are distinguished from orthologs, which arise by speciation, and paralogs, which arise by gene duplication within a lineage. Xenologs can be single genes or entire gene clusters that move between genomes, reshaping metabolic capabilities and ecological strategies in their hosts.

Horizontal gene transfer can occur through several mechanisms, including transformation (uptake of free DNA), transduction (gene transfer by viruses), and conjugation (transfer via cell-to-cell contact). Xenologous relationships often produce gene trees that do not mirror the species tree, and transferred genes may carry signatures such as atypical nucleotide composition, divergent codon usage, or association with plasmids and mobile genetic elements. Detecting xenologs relies on phylogenetic incongruence analyses, genome-wide comparisons, and, when possible, examination of gene synteny; challenges include convergent sequence changes, gene loss after transfer, and limited sampling.

Xenologs play a central role in rapid adaptation, enabling organisms to acquire new metabolic functions, stress responses, or antibiotic resistance. They are especially prominent in bacteria and archaea but have been observed in eukaryotes as well. The study of xenologs informs understanding of genome evolution, the dynamics of gene exchange across lineages, and the complex history underlying present-day gene repertoires.