The rarity of gene shuffling in conserved genes

Table 2 Estimating the incidence of gene shuffling

Organism (T)	Reference taxa 1 (R1)	Reference taxa 2 (R2)	Shuffled genes (40%)	Sequences with detectable homology (h)	Number of duplicates/R1 genes tested	Duplication Rate (d/g)	Average K_s*	Average K_a
M. jannaschii	P. horikoshii	A. fulgidus	1	661	7/418	0.017	7.7	0.44
P. horikoshii	M. jannaschii	A. fulgidus	2	661	5/449	0.011	7.7	0.44
B. anthracis	B. cereus	B. subtilis	17	4,155.5	3/2568	0.0012	0.24	0.01
B. cereus	B. anthracis	B. subtilis	19	4,155.5	4/2624	0.0015	0.24	0.01
E. coli	S. enterica	H. influenzae	1	3,183.5	1/2182	0.0005	0.98	0.06
S. enterica	E. coli	H. influenzae	2	3,183.5	9/2140	0.0042	0.98	0.06
S. cerevisiae	S. pombe	N. crassa	3	2,365	104/946	0.110	3.9	0.50
S. pombe	S. cerevisiae	N. crassa	3	2,365	25/955	0.026	3.9	0.50
D. melanogaster	C. elegans	N. crassa	20	5,864	74/1008	0.073	8.0	0.52
C. elegans	D. melanogaster	N. crassa	34	5,864	98/1120	0.088	8.0	0.52

*Note that to obtain shuffling events/per gene/K_s = 1.0 (Table 1) we divided the average K_s by 2.
This was done because K_s is a pairwise distance, meaning that it gives the sum of the divergences from the common ancestor to T and from the common ancestor to R1. The same was done for the K_a analysis.

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