Table 5.

Genetic distances summary

			Outgroup distances					Human interparalog distances
Duplicon location	Duplicon name	Base pairs analyzed	Mean K Hum to Bab	Mean K Bab to Para	Mean K Bab to Anc	Mean K Ancest to Para	Mean K all Para	Bab mya	Bab rate (X10^-9)	Baboon Seed (mya)	Baboon Swaps (mya)
11q14	11q	1074	0.081	0.082	0.078	0.063	0.016	23	1.70	17.9	4.5
12p11	12p	737	0.076	0.075	0.084	0.064	0.027	23	1.83	19.4	8.2
22q12	CHK2	804	0.067	0.068	0.064	0.031	0.022	23	1.39	10.6	7.6
4q24	4q24	806	0.055	0.055	0.053	0.036	0.015	23	1.15	15.1	6.3
Xq28	ALD	663	0.061	0.074	0.067	0.047	0.028	23	1.46	17.7	10.6
11q14	11q	1074	0.081	0.081	0.078	0.061	0.016	23	1.70	17.3	4.5
22q11	GGT1	770	0.079	0.079	0.074	0.041	0.025	23	1.61	11.9	7.3
1p13	IGSF3	758	0.053	0.053	0.054	0.031	0.008	23	1.17	13.5	3.5
7q34	MLL3	553	0.054	0.053	0.056	0.032	0.015	23	1.22	13.6	6.4
4p16.1	4p16.1	1057	0.052	0.052	0.052	0.041	0.007	23	1.13	18.1	3.1
11p15	LSP1	734	0.055	0.054	0.056	0.032	0.009	23	1.22	13.4	3.8
4p16.3	4p16.3	672	0.071	0.068	0.077	0.03	0.01	23	1.67	9.7	3.2

The average number of nucleotide substitutions per site (K, Kimura two-parameter model) and associated standard errors were calculated for three output comparisons: all human sequences to the baboon outgroup (Hum to Bab), all human nonancestral paralogs to the baboon outgroup (Bab to Para), and the ancestral human to the outgroup (Bab to Anc). These were compared with two human interparalog calculations: human ancestral to all human paralogs (Ancest to Para) and the average K of all human paralogs (all Para). Relative to the outgroup distance, these latter two estimates provide information for the initial duplication from the euchromatin to the pericentromeric region (pericentromeric seeding) and the secondary duplication events (pericentromeric swapping). Based on an estimated divergence time of 23 million years between the human and baboon lineages, we calculate the effective nucleotide substitution rates (r = K/2T) for each locus. Standard errors around K values were small (<20% of the K value) with few exceptions (paralog SE for IGSF3, MLL3, 4p16.1, LSP1, and 4p16.3; range between 27% and 40%) and are therefore not known.

Punctuated duplication seeding events during the evolution of human chromosome 2p11