Compensatory evolution for a gene deletion is not limited to its immediate functional network

Table 1 Functional locations of strictly compensatory changes for deletion of phage DNA ligase

Phage element	T3Δ1.3 A_E	T3Δ1.3 B_E	T7Δ1.3_E
DNA metabolism
ss DNA binding (2.5)	+¹
endonuclease (3)	+*	+	+
helicase/primase (4A, B)	+	+	+
DNA polymerase (5)		+	+
Exonuclease (6)		+
Virion
major capsid (10)		+
tail A (11)	+*		+²
tail B (12)	+
internal core (16)		+*
tail fiber (17)	+*	+
Other
protein kinase (0.7)	+
1.05 (unknown)	+*	+	A
1.5 (unknown)	+	+	+
1.6 (unknown)	+
host RNAP inhibition (2)		+
2.8 (unknown)	A	A	+
lysozyme (3.5)		+
5.3 (unknown)		+
RNase III site (6.5)	+		+
Ribosomal binding site (5)	+
Packaging (19)/19.2 (unknown)		+

+ = a gene that acquired at least one compensatory mutation. A = a gene that is absent from the respective genome. T3 data from Additional files 1 and 2; T7 data are from Rokyta et al. [7]; except for the tail mutation which was from the T7Δ1.3 adaptation done for this study. Omitted are changes that were not strictly compensatory and changes that were polymorphic in the endpoint, evolved populations. Changes in T3Δ1.3 A_E and T3Δ1.3 B_E indicated with an asterisk (*) were detected in the initial isolates, prior to exposure to the ligase-host.
¹ Consensus sequence was indicative of apparent fixation, but only 1 of 2 isolates carried this change. Designation as compensatory is based on the consensus sequence profile.
² 24559 A->G D111G; observed in a T7Δ1.3 adaptation done for this study; compensatory.

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