Editing Common descent (section)

===Gene exchange clouds phylogenetic analysis===
{{further|Horizontal gene transfer}}

Theobald noted that substantial [[horizontal gene transfer]] could have occurred during early evolution. Bacteria today remain capable of gene exchange between distantly-related lineages. This weakens the basic assumption of phylogenetic analysis, that similarity of genomes implies common ancestry, because sufficient gene exchange would allow lineages to share much of their genome whether or not they [[monophyly|shared an ancestor (monophyly)]]. This has led to questions about the single ancestry of life.<ref name="theobald" /> However, biologists consider it very unlikely that completely unrelated proto-organisms could have exchanged genes, as their different coding mechanisms would have resulted only in garble rather than functioning systems. Later, however, many organisms all derived from a single ancestor could readily have shared genes that all worked in the same way, and it appears that they have.<ref name="theobald" />