Table 2. The constraints and calibrations placed on clades so that the reconstructed topology and divergence time estimates of our tree is more concordant with published molecular phylogenies.

Constraint	Taxa	Divergence calibration
Ingroup	All taxa bar Tupaia	N/A
Lepus	L. californicus, L. timidus, L. europaeus, L. americanus	4.03–5.90 (Matthee et al., 2004)
Ochotona	O. pallasi, O. princeps	23.31–39.26 (Matthee et al., 2004)
Sylvilagus	S. bachmanii, S. audubonii	2.43–6.65 (Matthee et al., 2004)
Leporids	All Lepus sp., B. idahoensis, B. monticularis, C. hispidus, N. timminsi, P. furnessi, P. marjorita, R. diazi, P. crassicaudatus, O. cuniculus, S. audubonii, S. bachmanii	N/A
Clade_one	O. pallasi, O. princeps, P. sardus	N/A
Clade_two	N. timminsi, P. marjorita, P. crassicaudatus	N/A
Clade_three	C. hispidus, O. cuniculus, B. monticularis, P. furnessi	N/A
Clade_four	R. diazi, B. idahoensis, S. audubonii, S. bachmanii	N/A