TABLE 3.

Sites under directional selection

Lineage	Site	Overall site composition	MRCA residuea	Inferred substitutionb	EBFc
L1a	384	G25K22	G	G1⇆22K	G: >105; K: >105
	386	I25T22	I	I1⇆22T	T: >105
	391	V26A21	V	A21⇆1V	A: >105
	397	S31N14K2	N	N0⇆30S	S: >105
	403	L24F23	F	F0⇆24L	F: >105
	408	K24S15R8	K	K1⇆8R
	408	K24S15R8	K	K0⇆15S	S: >105
L1b	349	T44A26S3	T	A25⇆1T	A: >105
	384	G48R23K2	G	G0⇆23R	R: >105
	385	T43A23P7	T	A23⇆0T	A: >105
	385	T43A23P7	T	P6⇆1T
	392	A66P5V2	A	A0⇆5P	P: 238.3
	397	S29K25N17R2	N	K24⇆0N	K: >105
	397	S29K25N17R2	N	N0⇆28S
	398	H54R12N6Q1	H	H0⇆6N
	398	H54R12N6Q1	H	H0⇆12R	R: 601.7
	404	D43S15H7T5Q1A1N1	D	D0⇆7H
	404	D43S15H7T5Q1A1N1	D	D1⇆15S	S: >105
	404	D43S15H7T5Q1A1N1	D	D0⇆5T
	405	S32Y12F11P6A5V4T3	S	A5⇆0S
	405	S32Y12F11P6A5V4T3	S	F11⇆0S
	405	S32Y12F11P6A5V4T3	S	P6⇆0S
	405	S32Y12F11P6A5V4T3	S	S0⇆4V
	405	S32Y12F11P6A5V4T3	S	S0⇆12Y	Y: >105
L1c	363	C12S6	C	C0⇆6S	S: >105
	395	D12N6	D	D1⇆6N	N: 355.8
	397	K14N4	K	K0⇆4N	N: 301.6
	398	H13S4Q1	H	H0⇆4S	S: >105
	404	A14S4	A	A0⇆4S	S: 205.9
L2	342	S15G8	S	G8⇆0S	G: >105

^aMRCA, most recent common ancestor.

^bA_C⇆_DB indicates C substitutions from A to B and D substitutions from B to A.

^cSites with an empirical Bayes factor (EBF) > 100 with preferential evolution toward the given residue are reported.