Estimation of genetic distances from human and mouse introns

Table 1 Correlation of distances measured in concatenated introns and exons of human and mouse orthologous genes

		K_i – K_s correlation		K_i – K_a correlation
Exon distance measurement^*	Intron alignment/selection method^†	Correlation coefficient (r)	Significance probability (p)	Correlation coefficient (r)	Significance probability (p)
ML (CF = 2)	Gap 1, Gblocks 1	0.34	0.0057	0.33	0.0081
ML (CF = 2)	Gap 1, Gblocks 2	0.32	0.0111	0.33	0.0079
ML (CF = 2)	Gap 2, Gblocks 1	0.35	0.0045	0.32	0.0108
ML (CF = 2)	Gap 2, Gblocks 2	0.33	0.0075	0.33	0.0089
ML (CF = 2)	Gap 3, Gblocks 1	0.32	0.0105	0.31	0.0124
ML (CF = 2)	Gap 3, Gblocks 2	0.30	0.0153	0.30	0.0165
ML (CF = 3)	Gap 1, Gblocks 1	0.35	0.0044	0.34	0.0061
ML (CF = 3)	Gap 1, Gblocks 2	0.32	0.0108	0.34	0.0061
ML (CF = 3)	Gap 2, Gblocks 1	0.35	0.0047	0.32	0.0095
ML (CF = 3)	Gap 2, Gblocks 2	0.32	0.0098	0.33	0.0077
ML (CF = 3)	Gap 3, Gblocks 1	0.31	0.0121	0.32	0.0112
ML (CF = 3)	Gap 3, Gblocks 2	0.29	0.0207	0.31	0.0147
NG	Gap 1, Gblocks 1	0.34	0.0068	0.33	0.0082
NG	Gap 1, Gblocks 2	0.32	0.0109	0.33	0.0079
NG	Gap 2, Gblocks 1	0.35	0.0053	0.32	0.0099
NG	Gap 2, Gblocks 2	0.35	0.0052	0.33	0.0082
NG	Gap 3, Gblocks 1	0.26	0.0371	0.32	0.0110
NG	Gap 3, Gblocks 2	0.29	0.0236	0.30	0.0154

^*K_s and K_a were measured by maximum likelihood (ML) with codon frequencies taken from the data (CF = 2) or used as free parameters (CF = 3), or by the Nei-Gojobori method (NG). ^†Introns were aligned using the Gap program with the parameters GOP = 50 and GEP = 3 (Gap 1); GOP = 35 and GEP = 2 (Gap 2); or GOP = 20 and GEP = 2 (Gap 3), and the conserved segments extracted with the Gblocks program with 'maximum number of contiguous nonconserved positions' = 8 (Gblocks 1) or 4 (Gblocks 2).

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