Spreadsheet: 06a10c4f-b7ee-4f13-87f9-be1eb73b580c
Sheet: Sheet1

Table S2. Recombination events detected in houskeeping genes (panel A) and inlA (panel B) | Unnamed: 1 | Unnamed: 2 | Unnamed: 3 | Unnamed: 4 | Unnamed: 5
Event nr. | Receptor isolates | Donor isolates | Significance by method (d) | Genomic | Affected
 | (Lineage) | (Lineage) |  | position | Genes
[NAME] genes (a)
1 | Lineage 3 | CLIP85 (3) | RDP: 1.382e-25 (14/19) | 2792 – 390 | abcZ, cat,
 | except CLIP85 (3) | [CLIP85544 (2)] | Geneconv: 8.690e-25 |  | ldh
 |  |  | MaxChi: 3.028e-14
 |  |  | Chimaera: 1.190e-14
2 | CLIP 27555 (2) | CLIP83082 (1) | RDP: 1.337e-9 | 936 – 1418 | blgA, lhkA
 | CLIP83283 (2) | [CLIP85 (3)] | Geneconv: 8.335e-9
 | CLIP81209 (2) |  | MaxChi: 1.193e-3
 |  |  | Chimaera: 2.244e-3
3 | CLIP85 (3) | CLIP454 (1) | RDP: 5.010e-1 | 391 – 961 | ldh, dapE
 |  | [CLIP85820 (3)] | Geneconv: 3.196e-3
 |  |  | MaxChi: 2.666e-5
 |  |  | Chimaera: 2.272e-3
4 | CLIP166 (2) | CLIP161 (2) | RDP: 6.069e-3 | 1419 – 1882 | lhkA, dat
 | CLIP83088 (2) | [CLIP79028 (3)] | Geneconv: -/-
 | CLIP98 (2) |  | MaxChi: 5.703e-4 (2/3)
 |  |  | Chimaera: 2.585e-2 (2/3)
5 | Lineage 3 | CLIP166 (2) | RDP: 6.080e-3 | 2354 – 2766 | abcZ
 |  | [CLIP23265 (2)] | Geneconv: -/-
 |  |  | MaxChi: 8.393e-3 (13/20)
 |  |  | Chimaera: 7.904e-3 (9/20)
6 | CLIP85 (3) | CLIP83206 (1) | RDP: 2.400e-5 (1/6) | 1296 – 1599 | bglA, lhkA
 | CLIP71987 (3) | [CLIP76 (2)] | Geneconv: 1.329e-2
 | CLIP79453 (3) |  | MaxChi: 3.322e-3
 | CLIP53 (3) |  | Chimaera: 1.341e-2
 | CLIP78025 (3)
 | CLIP71988 (3)
4 | CLIP83641 (2) | CLIP23256 (3) | RDP: 2.987e-3 | 2285 – 472 | abcZ, cat,
 | CLIP84803 (2) | [CLIP161(2)] | Geneconv: 4.280e-3 (3/5) |  | ldh
 | CLIP78845 (2) |  | MaxChi: 3.230e-3
 | CLIP21734 (2) |  | Chimaera: 1.130e-3 (3/5)
 | CLIP161 (2)
B.  Full-length inlA coding sequence (b)
1 | 19 | 21 | RDP: -/- | 1972 - 2357
 | 13 |  | GeneConv: 1.2e-4 | 1332 - 2177
 | 8 |  | MaxChi: 3.3e-3
 | 6 |  | Chimaera: 7.6e-5 | 1332 - 2403
 | 5
2 | 20 | 37 | RDP: 7.6e-4 | 59 - 1404
 | 21 |  | GeneConv: -/-
 |  |  | MaxChi: 4.9e-7
 |  |  | Chimaera: 4.6e-7
3 | 15 | 25 | RDP: 2.3e-2 | 1397 - 2175
 | 17 |  | GeneConv: 7.1e-4
 | 18 |  | MaxChi: 3.3e-3
 | 1 |  | Chimaera: 4.5e-3 | 1848 - 2175
 | 2
 | 3
 | 4 |  |  | 1972 - 2190
4 | 22 | ? | RDP: -/- | 234 - 1295
 | 23 |  | GeneConv: -/-
 | 24 |  | MaxChi: 9.9e-4
 | 25 |  | Chimaera: 7.3e-3
 | 26
 | 27
 | 28
 | 29
 | 30
 | 31
 | 32
 | 33
(a). Recombination events as detected by RDP based on the concatenated sequences of seven genes. Lineage numbers are given in parentheses. The column "receptor" specifies haplotypes incorporating the fragment, "donor" names the haplotype that is closest to the infered donor strain, if it could be identified, and otherwise contains a question mark. The minor donor strain of each event is given in square brackets. The number of strains involved in recombination events varied depending on the algorithms implemented in RDP, and are given in brackets if deviating from the detected maximum. Events 1 and 4 span the junction of the seventh gene (ldh) and the first one (abcZ), as the concatenate was considered circular for analysis.
(b) Sequence numbers correspond to inlA alleles (see Figure 4 and Table S1)
(d) Significance names the five methods implemented in RDP3, with the significance estimates of the respective recombination event. If one method failed to detect a recombination event, "-/-" was assigned.