Evolutionary directions of single nucleotide substitutions and structural mutations in the chloroplast genomes of the family Calycanthaceae

Table 5 Associations of nucleotide mutations (N) to structural mutations (S). gdN: the genetic distance of the regions without structural mutations; gdS: the genetic distance of the regions with structural mutations. The distances are based on SNPs. Ia: Idiospermum australiense; Cc: Calycanthus chinensis; Cf: Calycanthus floridus; Chn: Chimonanthus nitens; Chp: Chimonanthus praecox

Level	Comparison	Whole genome						Noncoding region			Coding region
Level	Comparison	N	S	N/S	gdS	gdN	gdS/gdN	gdS	gdN	gdS/gdN	gdS	gdN	gdS/gdN
Subfamily	Ia/Cc	2664	250	10.66	0.0317	0.0130	2.44	0.0315	0.0145	2.17	0.0323	0.0126	2.56
Subfamily	Ia/Cf	2614	249	10.50	0.0312	0.0129	2.42	0.0307	0.0137	2.24	0.0325	0.0127	2.56
Subfamily	Ia/Chn	2647	264	10.03	0.0313	0.0129	2.43	0.0307	0.0145	2.12	0.0329	0.0126	2.61
Subfamily	Ia/Chp	2587	260	9.95	0.0307	0.0127	2.42	0.0301	0.0137	2.20	0.0325	0.0125	2.60
Genus	Cc/Chn	715	46	15.54	0.0076	0.0037	2.05	0.0081	0.0059	1.37	0.0063	0.0032	1.97
Genus	Cc/Chp	667	41	16.27	0.0072	0.0033	2.18	0.0077	0.0048	1.60	0.0059	0.0030	1.97
Genus	Chn/Cf	687	49	14.02	0.0075	0.0035	2.14	0.0077	0.0049	1.57	0.0070	0.0032	2.19
Genus	Chp/Cf	617	44	14.02	0.0069	0.0032	2.16	0.0070	0.0040	1.75	0.0065	0.0030	2.17
Species	Cc/Cf	383	17	22.53	0.0043	0.0018	2.39	0.0044	0.0026	1.69	0.0040	0.0016	2.50
Species	Chp/Chn	334	16	20.88	0.0033	0.0019	1.74	0.0035	0.0028	1.25	0.0030	0.0017	1.76

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