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Suppl. Table 1: Consensus results from 4 tests for intragenic recombination within gene sequences in our psbA 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 psbA. | 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
Pro myoviruses (plus S-ShM1, S-SSM1*) | 1 | P-RSM4_9303 | No
 | 2 | P-SSM12_NATL2A, P-SSM9_NATL2A | Yes | 1,2 | 591..741 | Unknown
 | 3 | P-SSM4_NATL2A, P-RSM2_NATL2A Δ, P-RSM3_NATL2A Δ | No
 | 4 | S-ShM1_6501 | No
 | 5 | S-SSM1_6501 | No
 | 6 | P-SSM10_NATL2A | No
HL Prochloro-coccus hosts | 7 | MED4 | No
 | 8 | MIT9515 | No
 | 9 | MIT9302 | No
 | 10 | [NAME] | No
 | 11 | MIT9116 | Yes | 1,2 | 689..714 | Unknown
Pro myoviruses | 12 | P-SSM2_NATL1A | No
 | 13 | P-SSM3_NATL2A | No
 | 14 | P-RSM5_NATL1A | No
 | 15 | P-SSM8_9211 | No
LL Prochloro-coccus hosts | 16 | MIT9211 | No
 | 17 | SS120 | No
 | 18 | NATL2A | No
Synechococcus myoviruses (plus P-SSM1*) | 19 | S-SSM2_8102 Δ | Yes | 2,3 | 253..561 | S-ShM2_8102
 |  |  |  | 1,2,3,4 | 565..668 | P-SSP7_MED4(1,3,4) or P-SSP3_9312(2)
 | 20 | S-ShM2_8102 Δ | Yes | 3,4 | 669..789 | Unknown & MED4
 | 21 | syn1_8101 | No
 | 22 | syn33_8018 Δ | Yes | 2,3 | 459..567 | syn10_8017 or syn9_8109
 |  |  |  | 2.3 | 655..828 | Unknown
 |  |  |  | 1,2 | 793..959 | S-ShM2_8102
 |  |  |  | 1,2,3,4 | 864..964 | Syn9902_1 or 2 or 3(1), [NAME]), WH8109(3), WH8017(4)
 | 23 | S-SSM5_8102 Δ, S-SSM3_8018 Δ | No
 | 24 | syn30_8018 Δ | No
 | 25 | syn19_8109 Δ | No
 | 26 | S-BM4_7803 ? | No
 | 27 | S-RSM28_7803 ? | No
 | 28 | S-WHM1_7803 Δ | No
 | 29 | syn10_8017 Δ, syn26_8017 Δ | No
 | 30 | syn9_8109 Δ | No
 | 31 | S-RSM2_7803 ? | Yes | 1,2,3,4 | 549..825 | P-SSP7_MED4(1,2) or S-SSM2_8102(3,4)
 | 32 | P-SSM1_9303 | No
 | 33 | S-PM2_7803 | No
 | 34 | S-RSM88_7803 | No
 | 35 | BAC9D04 | No
Synechococcus hosts | 36 | WH8102_A | Yes | 3,4 | 340..391 | Unknown
 |  |  |  | 3,4 | 450..528 | Syn9605_1
 | 37 | WH8103_B | Yes | 3,4 | 340..391 | Unknown
 |  |  |  | 3,4 | 450..528 | Syn9605_1
 | 38 | WH8103_C | Yes | 3,4 | 448..631 | Unknown
 |  |  |  | 1,3 | 405..548 | Unknown
 |  |  |  | 1,2 | 450..528 | Unknown
 | 39 | [NAME] | No
 | 40 | WH8102_D | No
 | 41 | WH8103_A | No
 | 42 | Syn9902_1, Syn9902_2, Syn9902_3 | No
 | 43 | SynBL107_1 | Yes | 2,3 | 830..951 | S-ShM2_8102 or Syn9605_psbA2
 | 44 | Syn9902_4 | No
 | 45 | WH8020_A | Yes | 1,2,3 | 961..976 | MED4 or P-SSP6_9515 or Unknown
 | 46 | WH8101_C | Yes | 1,2,3 | 961..977 | MED4 or P-SSP6_9515 or Unknown
 | 47 | WH8020_C | No
 | 48 | [NAME] | No
 | 49 | Syn9605_2, Syn9605_3 | No
 | 50 | SynRSS9907 | No
 | 51 | WH8109 | No
 | 52 | Syn9605_1 | Yes | 3,4 | 867..977 | Unknown
 | 53 | WH8012 | No
 | 54 | WH8017 | No
 | 55 | WH8018_A | No
 | 56 | WH8018_C | No
 | 57 | WH7803 | No
 | 58 | WH8018_B | No
 | 59 | SynRS9901_1 | No
 | 60 | Syn9920, SynRS9901 | Yes | 2,3 | 642..846 | WH8018_B  or  WH8017
 | 61 | SynBL3_2, SynBL3_1 | Yes | 2,3 | 642..847 | WH8018_B  or  WH8018
 | 62 | MIT9313 | No
 | 63 | MIT9303 | No
 | 64 | WH8101_B | No
 | 65 | WH8101_A | Yes | 3,4 | 869..929 | Unknown
Pro-chloro-coccus podo-viruses | 66 | PSSP5_9515 | No
 | 67 | PSSP7_MED4 | No
 | 68 | PGSP1_MED4 | No
 | 69 | PSSP3_9312 | No
 | 70 | PSSP6_9515 | No
* Prochlorococcus myovirus P-SSM1 and Synechococcus myoviruses S-ShM1 and S-SSM1 have psbA gene sequences that do not cluster as predicted (see text)