Using the stringent criteria defined above, a total of five putative recombinant isolates were detected ( Figure 2 ). Four of these isolates, AY562985, EU167540, AY562989, AY225110, were those that showed discordant phylogenies described above ( Figure 1C ), and in each case, some recombinant regions were derived from genotype II sequences. Isolate AY562985 is predominantly genotype VII and had evidence of two recombination events based on RDP3 predictions. We confirmed that regions 508 to 926 (in NP) and 927 to 1511 (NP and P) are related to genotypes V and II, respectively by partitioning the data sets at the predicted break points and reconstructing a ML phylogeny ( Figure 3 ). In the region 927 to 1511, AY562985 had seven unique synonymous substitution sites compared to the other sixteen genotype II sequences in our dataset. Isolate AY562989, which is predominantly of genotype VI origin, also contained a putative recombinant region spanning positions 2039 to 3225, which was derived from genotype II and had three unique non-synonymous substitution sites compared to other genotype II sequences. Isolate AY225110 is a chimera of genotype I and II sequences. Compared to genotype II sequences, there were seven unique sites, four of which were non-synonymous substitutions, from the 59 end of NP to position 2702; two synonymous and two non-synonymous substitution sites in the 3757-7149 fragment; and two synonymous and seven non-synonymous substitution sites within the region from 13758 to the 39 end of L. For isolate EU167540, a putative recombination region between position 3753 and 4345 was affiliated with genotype II and had one non-synonymous substitution site compared to other strains. Thus, genotype II, which is used in vaccines globally, has recombined with at least three other class II aPMV-1 strains and the recombinant viruses have been isolated from both domestic and wild birds.