Table 2.
Recombination events detected in the alignment of 122 whole CDV genome sequences using seven algorithms in the Recombination Detection Program (RDP).
| Acc. No. | # | Species | Country | Year | Clade | RDP pval | GC pval | BS pval | MC pval | Ch pval | SS pval | 3Seq pval |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| AB462810 | 1 ^ | CFA | Japan | nd | Asia-2 | 9.95 × 10−28 | 4.86 × 10−26 | 4.93 × 10−23 | 4.67 × 10−8 | 8.28 × 10−8 | 0.000173 | 1.32 × 10−11 |
| AB462810 | 2 | CFA | Japan | nd | Asia-3 | 7.74 × 10−28 | 1.01 × 10−26 | 3.87 × 10−21 | 5.43 × 10−7 | 5.32 × 10−7 | 3.00 × 10−8 | 1.32 × 10−11 |
| AB474397 | 1 ^ | CFA | Japan | nd | Asia-4 | 9.95 × 10−28 | 4.86 × 10−26 | 4.93 × 10−23 | 4.67 × 10−8 | 8.28 × 10−8 | 0.000173 | 1.32 × 10−11 |
| AB474397 | 2 | CFA | Japan | nd | Asia-5 | 7.74 × 10−28 | 1.01 × 10−26 | 3.87 × 10−21 | 5.43 × 10−7 | 5.32 × 10−7 | 3.00 × 10−8 | 1.32 × 10−11 |
| AY443350 | 1 ^ | PLO | USA | 2000 | Amer-2 | 3.23 × 10−12 | 5.27 × 10−18 | 4.42 × 10−16 | 1.00 × 10−11 | 7.02 × 10−13 | 3.73 × 10−16 | 2.21 × 10−16 |
| AY443350 | 2 ^ | PLO | USA | 2000 | Amer-2 | 2.34 × 10−12 | 0.007073 | 2.08 × 10−11 | 3.85 × 10−15 | 0.000116 | 4.74 × 10−7 | 6.62 × 10−12 |
| AY445077 | 1 ^ | PLO | USA | 1998 | Amer-1 * | 3.16 × 10−19 | 6.42 × 10−13 | 1.90 × 10−16 | 1.32 × 10−9 | 3.47 × 10−9 | 1.09 × 10−10 | 6.62 × 10−12 |
| AY445077 | 2 ~ | PLO | USA | 1998 | Amer-1 * | 6.21 × 10−8 | 8.26 × 10−8 | 4.02 × 10−5 | 0.020799 | 0.005608 | NS | 1.04 × 10−5 |
| AY466011 | 1 | PLO | USA | 1998 | Amer-1 * | 3.16 × 10−19 | 6.42 × 10−13 | 1.90 × 10−16 | 1.32 × 10−9 | 3.47 × 10−9 | 1.09 × 10−10 | 6.62 × 10−12 |
| AY466011 | 2 ~ | PLO | USA | 1998 | Amer-1 * | 6.21 × 10−8 | 8.26 × 10−8 | 4.02 × 10−5 | 0.020799 | 0.005608 | NS | 1.04 × 10−5 |
| AY542312 | 1 ^ | PLO | USA | 1998 | Amer-1 * | 3.16 × 10−19 | 6.42 × 10−13 | 1.90 × 10−16 | 1.32 × 10−9 | 3.47 × 10−9 | 1.09 × 10−10 | 6.62 × 10−12 |
| AY542312 | 2 ~ | PLO | USA | 1998 | Amer-1 * | 6.21 × 10−8 | 8.26 × 10−8 | 4.02 × 10−5 | 0.020799 | 0.005608 | NS | 1.04 × 10−5 |
| AY649446 | 1 ^ | PLO | USA | 2001 | Amer-2 | 4.64 × 10−11 | 1.04 × 10−14 | 1.03 × 10−8 | 0.000218 | 0.000172 | 0.01701 | 9.42 × 10−9 |
| AY649446 | 2 ^~ | PLO | USA | 2001 | Amer-2 | NS | 0.003004 | 0.004893 | 9.18 × 10−5 | 0.000131 | 8.85 × 10−16 | NS |
| HQ540293 | 1 | FOX | China | 2006 | Asia-1 | 3.89 × 10−71 | 4.39 × 10−69 | 4.91 × 10−63 | 4.81 × 10−18 | 1.78 × 10−17 | 2.67 × 10−17 | 1.99 × 10−11 |
| JX681125 | 1 | FOX | China | 2006 | Asia-1 | 3.89 × 10−71 | 4.39 × 10−69 | 4.91 × 10−63 | 4.81 × 10−18 | 1.78 × 10−17 | 2.67 × 10−17 | 1.99 × 10−11 |
| KJ123771 | 1 ~ | CFA | USA | 2004 | Amer-2 | NS | 0.000126 | 2.35 × 10−9 | 2.23 × 10−7 | 2.14 × 10−8 | 1.41 × 10−15 | 2.58 × 10−10 |
| KJ994343 | 1 | NPR | Canada | 2013 | Asia-1 | 7.52 × 10−33 | 1.95 × 10−31 | 1.98 × 10−26 | 1.42 × 10−5 | 1.12 × 10−5 | 3.55 × 10−6 | 1.99 × 10−11 |
| KJ994343 | 2 ^~ | NPR | Canada | 2013 | Asia-1 | 1.06 × 10−9 | 1.69 × 10−10 | 2.39 × 10−6 | 5.91 × 10−8 | 1.80 × 10−8 | 2.53 × 10−5 | 9.47 × 10−8 |
| KJ994343 | 3 ~ | NPR | Canada | 2013 | Asia-1 | 1.31 × 10−7 | 0.000298 | 1.72 × 10−5 | 0.012219 | 0.040604 | NS | 6.46 × 10−5 |
| KJ994343 | 4 | NPR | Canada | 2013 | Asia-1 | 0.003985 | NS | 0.012217 | 2.17 × 10−6 | 2.50 × 10−6 | NS | 7.89 × 10−8 |
| KJ994343 | 5 ~ | NPR | Canada | 2013 | Asia-1 | 2.93 × 10−5 | 5.18 × 10−5 | 6.73 × 10−7 | 0.003271 | 0.001688 | 0.000122 | 0.039698 |
^ The recombinant sequence may have been misidentified (one of the identified parents might be the recombinant). ~ It is possible that this apparent recombination signal could have been caused by an evolutionary process other than recombination. * Lineage is conventionally determined by hemagglutinin (H) gene diversity. In this case, the H gene sequence was the recombinant portion of the genome and thus defined the genotype; however, the majority of genome is America-2. Abbreviations: Acc. no. = Accession number, # = recombination event per sequence, GC = GENECONV, BS = BootScan, MC = MaxChi, Ch = Chimaera, SS = SiScan, CFA = domestic dog, PLO = raccoon, FOX = red fox, NPR = raccoon dog.