Complicating factors include claims that the relationship between eukaryotes and the archaeal phylum Crenarchaeota is closer than the relationship between the Euryarchaeota and the phylum Crenarchaeota and the presence of archaea-like genes in certain bacteria, such as Thermotoga maritima, from horizontal gene transfer.
Faktor yang memperrumit termasuk klaim bahwa hubungan antara eukariota dan filum arkea Crenarchaeota lebih dekat daripada hubungan antara Euryarchaeota dan filum Crenarchaeota dan adanya gen seperti-arkea pada bakteri tertentu, seperti Thermotoga maritima, dari transfer gen horizontal.