Table 1.

Summary of sequence matrices, tree inference strategies and best-fitting models in ML analyses. CP, complete plastomes; PCG, protein-coding genes; NPCG, non-protein coding genes; CP-slope, excluding saturated loci from CP based on slopes of the linear regression; CP-R², excluding saturated loci from CP based on R² of the linear regression; CP-gappy90, excluding sites with more than 90% gap percentage from CP; CP-gappy0, excluding all gap-containing sites from CP. Beat-fitting models of each locus under partitioned strategy for CP, PCG, and NPCG are not shown and indicated as “-”

Matrices	Alignment length (bp)	Parsimony informative sites	AT content of datasets (%)	Strategies	Models
CP / CP-p	141,881	1915	61.7	Unpartitioned / Partitioned	TVM+F+R5 / -
PCG / PCG-p	69,345	753	60.9	Unpartitioned / Partitioned	TVM+F+R2 / -
NPCG / NPCG-p	72,536	1162	62.4	Unpartitioned / Partitioned	K3Pu+F+R5 / -
CP-slope	99,898	1202	61.3	Unpartitioned	TVM+F+R2
CP-R2	101,321	1178	61.1	Unpartitioned	TVM+F+R2
CP-gappy90	138,627	1910	61.7	Unpartitioned	TVM+F+R5
CP-gappy70	138,282	1894	61.6	Unpartitioned	TVM+F+R5
CP-gappy50	138,133	1881	61.6	Unpartitioned	TVM+F+R5
CP-gappy25	137,808	1858	61.6	Unpartitioned	TVM+F+R4
CP-gappy15	137,738	1855	61.6	Unpartitioned	TVM+F+R4
CP-gappy13	137,726	1853	61.6	Unpartitioned	TVM+F+R4
CP-gappy12	137,716	1851	61.6	Unpartitioned	TVM+F+R4
CP-gappy10	135,865	1837	61.6	Unpartitioned	TVM+F+R4
CP-gappy09	131,254	1829	61.6	Unpartitioned	TVM+F+R4
CP-gappy07	130,998	1816	61.6	Unpartitioned	TVM+F+R4
CP-gappy05	130,948	1814	61.6	Unpartitioned	TVM+F+R4
CP-gappy04	130,658	1798	61.5	Unpartitioned	TVM+F+R4
CP-gappy02	127,918	1735	61.5	Unpartitioned	TVM+F+R4
CP-gappy0	112,034	1476	61.2	Unpartitioned	TVM+F+R3