Table 2. Descriptions of the plastome partitions analyzed.

Code	Data partition	Gapped sites stripped	Positively selected sites removed	Matrix length
A	rbcL, ndhF, matK	−	−	7,195
B	rbcL, ndhF, matK	+	−	3,476
C	rbcL, ndhF, matK	−	+	6,722
D	rbcL, ndhF, matK	+	+	5,077
E	Plastome coding	−	−	59,299
F	Plastome coding	+	−	46,707
G	Plastome coding	−	+	55,851
H	Plastome coding	+	+	44,975
Q	Plastome noncoding	−	n/a	143,401
R	Plastome noncoding	+	n/a	26,307
W	Complete plastome	−	−	197,529
X	Complete plastome	+	−	78,714
Y	Complete plastome	−	+	197,332
Z	Complete plastome	+	+	71,140

Note:

Partitions variously included a subset of coding regions, all coding regions, noncoding regions and the complete plastome, including coding and noncoding partitions. In the alignments of each of these four core partitions we variously included or excluded gapped sites and positively selected sites in partitions including coding regions.