Table 2.

Sequencing summary statistics showing number of reads and depth and breadth of coverages for MitoBait captures. * indicates samples with over 90% breadth of coverage that were used for comparisons with published mitogenomes

Sample site	Sample ID	Reads on‐target (%)	Unique reads on‐target (%)	Mean read depth (SD)	Mean % coverage
Tsingy de Beanka	BTS04	0.06	0.0015	1.56 (0.9)	59.3
Tsingy de Beanka	BTS27*	0.38*	0.0063*	13.0 (5.3)*	99.4*
Tsingy de Beanka	BTS38*	0.22*	0.027*	23.3 (5.9)*	98.0*
Tsingy de Beanka	BTS60	0.02	0.0005	1.8 (2.2)	45.6
Tsingy de Beanka	BTS68*	4.3*	0.0088*	8.5 (6.0)*	98.9*
Tsingy de Beanka	BTS102	0.26	0.0013	1.8 (1.4)	27.3
Tsingy de Beanka	BTS105	0.5	0.0005	1.7 (1.2)	22.1
Tsingy de Beanka	BTS108*	0.4*	0.014*	15.1 (5.6)*	99.5*
Tsingy de Beanka	BTS112	0.46	0.0056	1.3 (0.6)	10.9
Manombo Special Reserve	MSR01	0.05	0.0027	2.0 (1.4)	65.9
Manombo Special Reserve	MSR23	0.04	0.039	1.2 (0.4)	12.3
Manombo Special Reserve	MSR37	0.16	0.0002	1.1 (0.3)	11.1
Manombo Special Reserve	MSR39	27.54	0.0024	5.0 (11.83)	45.5
Manombo Special Reserve	MSR44	22.25	0.05	1.5 (1.2)	21.9
Manombo Special Reserve	MSR46	4.11	0.0019	1.3 (0.5)	10.8
Manombo Special Reserve	MSR50	12.19	0.025	2.5 (2.07)	70.9
Manombo Special Reserve	MSR56	0.024	0.0001	1.3 (0.6)	15.0
Manombo Special Reserve	MSR58*	2.71*	0.04*	12.4 (7.2)*	98.5*
Manombo Special Reserve	MSR62*	2.20*	0.015*	25.1 (8.8)*	99.8*