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Suppl. Table 2: Consensus results from 4 tests for intragenic recombination within gene sequences in our psbD dataset.  The four tests included (1) RDP, (2) GeneConv, (3) MaxChi, (4) Chimaera (as described in methods), and recombination was only considered ‘detected’ when the following criteria were satisfied: (i) similar regions were detected by 2 or more methods, (ii) all such regions were significant at P<0.05 after a [NAME] correction for multiple tests, (iii) consensus breakpoints could be inferred from the results.  Thus, "No recombination detected" does not preclude that intragenic recombination could be occurring within the sequence, but rather indicates our stringent criteria have not identified such an event.  While we define phages as either Prochlorococcus or Synechococcus phages depending on the original host of isolation, we note that many of the myoviruses cross infect both genera (represented with a ‘Δ’ where known, a ‘?’ where unknown, and no symbol for isolates that do not cross-infect across genera).  Concensus breakpoints relative to nucleotide positions in Thermosynechococcus psbD. | Unnamed: 1 | Unnamed: 2 | Unnamed: 3 | Unnamed: 4 | Unnamed: 5 | Unnamed: 6
 | No. | Recipient Taxon | Recombination detected? | Method | Consensus breakpoints, start…end | Donor of foreign sequence
Prochlorococcus hosts | 1 | MIT9211 | No
 | 2 | SS120 | No
 | 3 | NATL2A | No
 | 4 | NATL1A | No
 | 5 | MIT9215 | No
 | 6 | [NAME] | No
 | 7 | MIT9302 | No
 | 8 | MIT9515 | No
 | 9 | MED4 | No
Pro Myo viruses | 10 | P-SSM4_NATL2A | Yes | 2, 3 | 714..822 | Unknown
 | 11 | P-RSM2_NATL2A Δ | Yes | 2, 3 | 714..823 | Unknown
 | 12 | P-RSM3_NATL2A Δ | Yes | 2, 3 | 714..824 | Unknown
Synechococcus myoviruses (plus P-SSM1*) | 13 | S-SSM2_8102 Δ | Yes | 1,2,3,4 | 192..369 | S-BM4 or P-SSM1_9303
 | 14 | S-ShM2_8102 Δ | Yes | 1,2,3,5 | 193..370 | S-BM4 or P-SSM1_9303
 | 15 | syn10_8017 Δ | Yes | 1,3 | 183..255 | Unknown
 |  |  |  | 1,3 | 624..871 | Unknown
 | 16 | syn26_8017 Δ | Yes | 1,3 | 183..255 | Unknown & MIT 9303(3)
 |  |  |  | 1,3 | 624..871 | Unknown
 | 17 | syn9_8012 Δ | Yes | 1,3 | 183..255 | Unknown
 |  |  |  | 1,3 | 624..871 | Unknown
 | 18 | S-BM4_7803 ? | Yes | 1,2,4 | 183..255 | Unknown
 |  |  |  | 1,3,4 | 372..432 | Unknown & S-SSM3_8018 (3)
 |  |  |  | 1,2,3,4 | 624..851 | Unknown
 | 19 | S-RSM2_7803 ? | No
 | 20 | P-SSM1_9303 | Yes | 1,2,4 | 183..253 | Unknown
 |  |  |  | 1,3,4 | 496..606 | Unknown & WH8017 & WH8101
 |  |  |  | 1,2,4 | 621..871 | Unknown
 | 21 | S-SM1_6501 | Yes | 3,4 | 189..300 | syn1_8101 & Unknown
 |  |  |  | 2,3,4 | 639..837 | P-SSM1_9303
 | 22 | syn19_8109 Δ | Yes | 1,3,4 | 189..300 | Unknown
 |  |  |  | 2,3 | 639..837 | S-RSM2_7808
 |  |  |  | 1,4 | 709..786 | P-SSM1_9303
 | 23 | S-SSM3_8018 Δ | Yes | 1,2,3,4 | 216..252 | S-BM4 & P-SSM1_9303 (2,3) & S-RSM2_7803
 |  |  |  | 3,4 | 357..465 | Unknown & S-WHM1_7803
 | 24 | syn30_8018 Δ | Yes | 1,2,3,4 | 216..252 | S-BM4 & P-SSM1_9303 (2,3) & S-RSM2_7803
 |  |  |  | 3,4 | 357..465 | Unknown & syn1_8101
 | 25 | S-SSM5_8102 Δ | Yes | 1,2,3,4 | 317..453 | Unknown
 |  |  |  | 1,3,4 | 459..618 | Unknown & S-SSM3_8018
 |  |  |  | 1,4 | 483..541 | syn33_7803
 |  |  |  | 2,3,4 | 639..837 | P-SSM1_9303
 | 26 | S-WHM1_7803 Δ | Yes | 2,4 | 369..483 | syn1_8101
 |  |  |  | 2,4 | 468..579 | Unknown & WH8017
 | 27 | syn1_8101 | Yes | 1,4 | 486..634 | Unknown
 | 28 | [NAME] | Yes | 1,2,3,4 | 601..864 | S-SSM2_8102 & S-ShM2_8102
 | 29 | S-PM2_7803 | No
 | 30 | Syn9605_1 , Syn9605_2 | No
Synechococcus hosts | 31 | WH6501 | Yes | 3,4 | 628..702 | Unknown
 | 32 | WH8109 | No
 | 33 | WH8102_1 , WH8102_2 | No
 | 34 | WH8103 | No
 | 35 | WH8012 | No
 | 36 | WH7803 | Yes | 3,4 | 567..639 | S-SSM5 & Unknown
 | 37 | WH8017, WH8018 | Yes | 3,4 | 624..701 | Unknown
 | 38 | WH8101 | No
 | 39 | Syn9902_1,  Syn9902_2 | No
 | 40 | WH8020 | No
 | 41 | MIT9313 | No
 | 42 | MIT9303 | No
* Prochlorococcus myovirus P-SSM1 has both a psbA and psbD gene sequence that clusters with Synechococcus myoviruses (see text)