Table 1.

Support values of selected branches

	a	b	c	d	e	f
NJ
1	100	68.2	64.8	100	100	64.4
2	100	91.6	(85.4)	100	100	47.3
12	100	95.2	94.1	100	100	52.2
123	100	79.2	94.2	100	100	81.2
aa	100	100	74	100	100	94
MP
1	100	39.3	80.0	100	100	—
2	100	69.1	(77.5)	100	99.3	—
12	100	46.6	97.3	100	100	48.5
123	100	31.0	93.7	100	100	—
aa	100	77.5	80.5	100	100	56.2
ML/QP
1	96.0	94.3	(69.4)	100	95.1	74.7
2	98.7	96.9	(83.6)	99.0	99.1	—
12	98.4	94.8	(76.1)	100	98.3	70.3
123	97.6	95.8	(77.9)	100	99.0	67.7
aa	99.9	99.9	(64.6)	100	91.2	89.1

The numbers show bootstrap and support values in percent for selected branches (a–f) shown in Fig. 3. The analyses of the assembly of 25 taxa were carried out by NJ, MP, and ML/QP (maximum likelihood using the quartet puzzling) tree search algorithm for 1st (1) 2nd (2), 1st plus 2nd (12), 1st plus 2nd plus 3rd codon positions (123), as well as amino acid (aa), sequences. For 1st codon position all changes except transitions in leucine codons were used; for 2nd codon position all changes were included, and for 3rd codon position transversions were used (61). At the nucleotide level the NJ analysis was performed applying the HKY model of sequence evolution (62), whereas for amino acid sequences the Dayhoff matrix was used. For ML/QP, the TN model (63) for nucleotide sequences or the mtREV-22 model (42) for amino acid sequences were applied. Due to computational constraints bootstrap replications were limited to 100 in the case of NJ and MP analyses of amino acids, in other instances 1000 bootstrap replicates were performed. Dash (—) denotes unresolved relationship, and values in parentheses show the support for the separation between myomorph rodents and eutherians when the position of the guinea pig and the rabbit deviated from that shown in Fig. 3.