Table 2.

List of mutations and their impact on homoplasy at different levels.

						Homoplasy created in same
Locus	Population	Individualsa	Nature of mutation	Fragment length score also present in other individuals	No. of individuals with same score	Population	Species	Across species
PolyB08	L 108 + all P	All	Substitution	414, 418	74 out of 100 scored L	No	No	Yes
	P 102	All	Substitution	414	5 P + 74 L	No	Yes	Yes
Poly1	P 805, 1301, 102, L 108	All	Substitutions (3 separate)	214, 226, 230, 224	21 P + 100 L	No	Yes	Yes
	P + L 108	All	Substitutions (3 separate)	215, 226, 232	101 L	No	No	Yes
	P 805, 1301, L 108	All	Substitution	214, 226, 230, 224	28 P + 100 L	No	Yes	Yes
	L 120	1	Indel	216	1 L	No	Yes	No
	L 105	1	Indel	214	99 L + 18 P	Yes	Yes	Yes
	L 124	1	Indel	214	99 L + 18 P	Yes	Yes	Yes
PolyE01	P 1801, 601, 602	All	Substitutions (2 separate)	472, 474, 478, 416	20 L + 70 P	No	Yes	Yes
	L 108	1	Indel	474	10 L + 65 P	Yes	Yes	Yes
	L 102, 115	3	Indel + substitution	470, 476, 478	102 L + 2 P	Yes	Yes	Yes
	P 805	All	Substitutions (2 separate)	474	10 L + 58 P	No	Yes	Yes
	P + L 108	All	Substitutions (2 separate)	474, 416, 482, 468, 464, 470, 472, 478, 488	17 L	No	No	Yes
	L 105	1	Substitution	476	101 L	Yes	Yes	No
	L (but 102)	All but 2	Insert (×2 for 107)	470, 476, 470, 474, 472, 478, 456, 480, 434	In text and Fig. 3	Yes	Yes	Yes

Note: L = Polygala lewtonii; P = Polygala polygama.

^aNot all mutations apply to all individuals in the population at all loci and mutations.