Table 1. All 12 populations acquired mutations while foreign DNA acquisition is restricted to those evolved in the presence of closely related other-Bacillus donors.

DNA donor	Biological repetition	# of mismatches	# of insertions	# of deletions	# of foreign DNA fragments	# of mismatches not in foreign fragments	# of insertions not in foreign fragments	# of deletions not in foreign fragments
No DNA	1	9	0	0	0	9	0	0
	2	2	0	0	0	2	0	0
	3	4	0	1	0	4	0	1
other-Bacillus	1	246	3	1	1	0	0	1
	2	103	0	1	1	2	0	0
	3	5585	39	44	36	12	0	1
Bacteria	1	2	1	0	0	2	1	0
	2	6	0	2	0	6	0	2
	3	10	1	0	0	10	1	0
Archaea	1	6	0	0	0	6	0	0
	2	17	1	0	0	17	1	0
	3	7	1	1	0	7	1	1

Deep sequencing results of all 12 evolved populations (indicated in the DNA donor and biological repetition columns) and the ancestor following 504 generations of evolution. The number of single-nucleotide mismatches and small insertions and deletions detected in each population (compared to the ancestor) is shown on the third to fifth columns respectively. The number of foreign DNA fragments detected in each population is shown in the sixth column. The seventh to ninth columns depict the number of single-nucleotide mismatches and small insertions and deletions that cannot be ascribed to a foreign DNA fragment, thus likely to result from mutations (for details on bioinformatic analysis see Material and Methods).