Low Rates of Lateral Gene Transfer among Metabolic Genes Define the Evolving Biogeochemical Niches of Archaea through Deep Time

Table 4

Organic carbon degradation.

Gene name	Gene	Linked to	Number of LGT events	Monophyletic clades
Chitinase and chitin degradation	ChiA	GlmA, GlmD, and Dak in Thermococcales	2	(1) Thermococcales; (2) Halobacteriales
Phenol/toluene/xylene hydroxylases		S. islandicus-S. solfataricus catechol dioxygenase, P. arsenaticum class III extradiol dioxygenases	(2)	(1) S. islandicus, S. Solfataricus; (2) P. arsenaticum
Hydroxyphenylacetate hydroxylases	HpaH	Sulfolobales HpaD	(1)	(1) Sulfolobales; (2) P. oguniense
Class II extradiol dioxygenases	HpaD	Sulfolobales HpaH, S. islandicus-S. solfataricus class III extradiol dioxygenases; S. islandicus-S. solfataricus phenol/toluene hydroxylases	3	(1) Sulfolobales (HpaH and catechol dioxygenase); (2) P. oguniense
Class III extradiol dioxygenases		S. islandicus HpaD, P. arsenaticum phenol/toluene hydroxylases, and Sulfolobales hydroxyphenylacetate hydroxylases	6	(1) Sulfolobales; (2) Tp. Acidophilum; (3) P. arsenaticum, P. Aerophilum; (4) Methanobacterium sp. AL-21, SWAN; (5) Methanosphaera and Methanoregula; (6) Methanosarcina acetivorans, M. barkeri