Table 3.

Relative breakpoint distance and sequence divergence for several intra-genus pairs of protochordates

	Genus	Species-1	Species-2	Breakpointa		Protein-genesb		Protein	rRNAd
				All	-tRNA	dN	dS	% idc	rrnS	rrnL
Ascidiacea	Phallusia	mammillata	fumigata	0.71	0.80	0.182	56.60	72.36	0.452	0.412
	Ciona	intestinalis sp. A	intestinalis sp. B	0.08	0	0.055	3.25	88.79	0.113	0.147
	Ciona	intestinalis sp. A	savignyi	0.33	0.20	0.156	129.21	72.66	0.403	0.295
	Ciona	intestinalis sp. B	savignyi	0.41	0.20	0.169	83.0	71.42	0.396	0.310
Cephalochordata	Branchiostoma	floridae	lanceolatum	0	0	0.087	3.12	85.84	0.269	0.287
	Branchiostoma	belcheri	lanceolatum	0	0	0.097	3.94	84.26	0.257	0.236
	Branchiostoma	floridae	belcheri	0	0	0.110	3.75	82.54	0.289	0.263
	Epigonichthys	lucayanus	maldivensis	0.22	0.33	0.171	10.29	74.87	0.405	0.402

^a Relative breakpoint distance calculated dividing the pairwise breakpoint distance by the number of genes shared by corresponding genomes, for a dataset including all mt genes (All), and a dataset without tRNA genes (-tRNA).

^b dN (nonsynonymous substitutions) and dS (synonymous substitutions) calculated on the 13 mt protein-coding genes according to the codon substitution model of Goldman and Yang [73].

^c Percentage of amino acid identity calculated on the 13 mt-encoded proteins

^d Substitutions per sites calculated according to the GTR model [75].