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

Table 1

Aerobic respiration.

Gene name	Gene	Linked to	Number of LGT events	Monophyletic clades
Cytochrome c oxidase subunit I and III	CoxA; CoxAC; SoxB; DoxB; SoxM	CoxB in Ferroplasma and Picrophilus linked to CoxAC; CoxB1 in the Halobacteriales linked to CoxA1; CoxB2 in the Halobacteriales linked to CoxA2; CoxB3 in the Halobacteriales linked to CoxA3; CoxB in Natronomonas; PoxH in Thermoproteales and Aeropyrum linked to CoxA; PoxB in Pyrobaculum spp. And Aeropyrum linked to CoxAC; SoxA in the Sulfolobales linked to SoxB; SoxH in the Sulfolobales linked to SoxM	12–14	(1) Ferroplasma, Picrophilus; (2) Halobacteriales (CoxA1); (3) Halobacteriales (CoxA2); (4) Halobacteriales (CoxA3); (5) Natronomonas; (6) Caldivirga; (7) P. spp. (CoxA); (8) P. spp., Thermoproteus uzoniensis (CoxAC); (9) Aeropyrum (CoxA); (10) Aeropyrum (CoxAC); (11) Sulfolobales (SoxB); [(12) Sulfolobales (DoxB)]^∧; [(13) Sulfolobales (FoxA)]^∧; (14) Sulfolobales (SoxM)
Cytochrome c oxidase subunit II	CoxB; PoxB; PoxH; SoxA; SoxH	CoxB in Ferroplasma and Picrophilus linked to CoxAC; CoxB1 in the Halobacteriales linked to CoxA1; CoxB2 in the Halobacteriales linked to CoxA2; CoxB3 in the Halobacteriales linked to CoxA3; CoxA3 in Natronomonas PoxH in Thermoproteales and Aeropyrum linked to CoxA; PoxB in Pyrobaculum spp. and Aeropyrum linked to CoxAC; SoxA in the Sulfolobales linked to SoxB; SoxH in the Sulfolobales linked to SoxM	(11)^∗	(1) Ferroplasma, Picrophilus; (2) Halobacteriales (CoxB1); (3) Halobacteriales (CoxB2); (4) Halobacteriales (CoxB3); (5) Caldivirga; (6) P. spp. (PoxH); (7) P. aerophilum spp.,; Thermoproteus uzoniensis (PoxB); (8) Aeropyrum (PoxH); (9) Aeropyrum (PoxB); (10) Sulfolobales (SoxA); (11) Sulfolobales (SoxH)
Quinol oxidase subunit I		Linked to quinol oxidase subunit II in Methanosarcina, Thermococcus, and Halobacteriales	8	(1) T. gammatolerans, T. sp. AM4; (2) Halobacteriales; (3) M. acetivorans, M. Barkeri; (4) Archaeoglobus (CydA1 and CydA2); (5) Ferroplasma, Picrophilus, Tp. acidophilum, Tp. Volcanium; (6) Thermoproteales (copy 1 and copy 2); (7) Hyperthermus and Acidilobus (copy 1 and copy 2); (8) Vulcanisaeta spp. (extra copy)
Quinol oxidase subunit II		Linked to quinol oxidase subunit I in Methanosarcina, Thermococcus, and Halobacteriales	(3)	(1) T. gammatolerans, T. sp. AM4; (2) M. acetivorans, M. Barkeri; (3) Halobacteriales

^*Numbers in brackets indicate that these genes are linked to the previously listed gene and therefore should not be counted as an independent LGT event.
^∧Taxa in brackets indicate that these genes may have arisen by ancient gene duplication, and not LGT.