Afrobatrachian mitochondrial genomes: genome reorganization, gene rearrangement mechanisms, and evolutionary trends of duplicated and rearranged genes

Table 3 Substitution rates of duplicated and rearranged mitochondrial genes compared to non–rearranged genes

No	Compared genes	Outgroups	Compared lineage 1	Compared lineage 2	Substitution rates		Probability	Significance
			Non–rearranged taxa	Rearranged taxa	Lineage 1	Lineage 2		*
1	12S rrn	Non–ranoid neobatrachians	Non– Breviceps ranoids	Breviceps	0.2364	0.2306	0.6882
2	16S rrn	Non–ranoid neobatrachians	Non– Breviceps ranoids	Breviceps	0.2187	0.2352	0.1495
3	nd5	Non–ranoid neobatrachians	Ranoides without nd5 rearrangement	Part of ranids (Babina)	0.4832	0.5118	0.1025
4	nd5	Non–ranoid neobatrachians	Ranoides without nd5 rearrangement	Trichobatrachus	0.4832	0.4303	0.0011	*
5	nd5	Non–ranoid neobatrachians	Non–Trichobatrachus afrobatrachians	Trichobatrachus	0.4668	0.4599	0.6581
6	nd5	Non–ranoid neobatrachians	Ranoides without nd5 rearrangement	Rhacophoroidea	0.4832	0.5296	5.40 × 10^–4	*
7	nd5	Non–ranoid neobatrachians	Ranoides without nd5 rearrangement	Part of dicroglossids (Fejervarya and Hoplobatrachus)	0.4832	0.6403	≤ 1.00 × 10^–7	*
8	nd2	Non–ranoid neobatrachians	Non– Hyperolius ranoids	Hyperolius	0.5064	0.6555	4.38 × 10^–7	*
9	All mt genes	Non–ranoid neobatrachians	Ranoides without nd5 rearrangement	Rhacophoroidea	0.3769	0.3874	0.0024	*
10	All mt genes	Non–ranoid neobatrachians	Ranoides without nd5 rearrangement	Part of dicroglossids (Fejervarya and Hoplobatrachus)	0.3769	0.4045	≤ 1.00 × 10^–7	*
11	All mt genes	Non–ranoid neobatrachians	Non– Hyperolius ranoids	Hyperolius	0.3741	0.4048	≤ 1.00 × 10^–7	*

Substitution rates is the mean weighted substitution rate of each lineage relative to the outgroups calculated by RRTree [81]. If the estimated P-value is less than 1 × 10^–7, RRTree returns 1.00 × 10^–7. These values are shown as ≤ 1.00 × 10^–7. In each comparison, the faster rate is shown in bold.

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