Table 1.

Model Summary. When applicable, models were run using either a 1.2 Ga or 1.6 Ga akinete constraint along with the calibrations indicated in Figure 1 and Table 2

Cyanobacteria models	Root prior		Taxa included	Akinete calibration?	Great Oxidation Event calibration?
	Age	Shape
Gloeobacter Outgroup 1 (Schirrmeister et al., 2013, 2015)	3,800 to 2,450 Ma	Flat	Cyanobacteria	Yes	Yes (root)
Gloeobacter Outgroup 2 (Blank & Sanchez‐Baracaldo, 2010)	2,700 to 2,320 Ma	Flat	Cyanobacteria	Yes	Yes (root)
Gloeobacter Outgroup 3 (Sánchez‐Baracaldo, 2015)	2,500 ± 200 Ma	Normal	Cyanobacteria	Yes	No
Alphaproteobacteria Outgroup 1 (Shih et al., 2017)	3,800 to 2,400 Ma	Flat	Cyanobacteria, Melainabacteria, Alphaproteobacteria	Yes	Yes (crown Cyanobacteria)
Alphaproteobacteria Outgroup 2 (Shih et al., 2017)	3,800 to 2,400 Ma	Flat	Cyanobacteria, Melainabacteria, Alphaproteobacteria	Yes	Yes (stem Cyanobacteria)
Alphaproteobacteria Outgroup 3 (Shih et al., 2017)	3,800 to 2,400 Ma	Flat	Cyanobacteria, Melainabacteria, Alphaproteobacteria	Yes	No
Alphaproteobacteria Outgroup 4 (Shih et al., 2017)	3,800 to 2,400 Ma	Flat	Cyanobacteria, Melainabacteria, Alphaproteobacteria	No	No

Phototroph models	Root prior		Taxa included	SahH HGT?	BchH HGT?
	Age	Shape
(A) Phototroph Tree	3,900 ± 200 Ma	Normal	All	No	No
(B) SahH	3,900 ± 200 Ma	Normal	All	Yes	No
(C) BchH	3,900 ± 200 Ma	Normal	All	No	Yes
(D) SahH+BchH	3,900 ± 200 Ma	Normal	All	Yes	Yes