Table S2.

Calibration of HGT calling methodology using prior works

Gene name	Species prior works noted	Prior works where noted	This work's AI score in prior noted species	Species this work notes	Phylogenetic support for HGT?	Within scope of this study?
CK	E. cuniculi	Marcet-Houben & Gabaldón (5); Cuomo et al. (26)	110.5241	E. cuniculi, E. hellem, No. ceranae, N. parisii	Yes	Yes
Hemolysin III-like protein	E. cuniculi	Marcet-Houben & Gabaldón (5);	24.92297	E. cuniculi, E. hellem	Yes	Yes
Phosphoribosyltransferase	E. hellem	Pombert et al. (11)	168.8619	E. hellem	Yes	Yes
GTP cyclohydrolase	E. hellem	Pombert et al. (11)	124.3396	E. hellem	Yes	Yes
PNPs	E. hellem	Selman et al. (29)	84.38472	E. hellem	Yes	Yes
Folylpolyglutamate synthase	E. hellem	Pombert et al. (11)	56.17833	E. hellem	Yes	Yes
ADP/ATP translocase	E. cuniculi	Katinka et al. (22); Tsaousis et al. (10)	61.4767–43.85448*	All	Yes	Yes
Aspartate-ammonia ligase	No. ceranae	Heinz et al. (28)	67.46811	No. ceranae	Yes	Yes
Cysteine-rich secretory proteins, antigen S, and pathogenesis-related 1 protein	E. cuniculi, N. parisii	Nakjang et al. (13)	3.1920, 14.5334	n/a	n/a	Yes
Mechanosensitive ion channel	E. cuniculi, E. hellem, No. ceranae, N. parisii	Nakjang et al. (13)	6.83, 9.90, 0.755, -0.315	n/a	n/a	Yes
Glycosyltransferase	N. parisii	Nakjang et al. (13)	7.1309	n/a	n/a	No
Folic acid synthase	E. hellem	Pombert et al. (11)	−17.50439	n/a	n/a	No
Dihydrofolate synthase	E. hellem	Pombert et al. (11)	−30.22129	n/a	n/a	No

n/a, not applicable.

^*These genes have been duplicated over time, and each one has a unique AI score.