Likelihood mapping of the Fsp (A) and H (B) datasets.

<p>The probabilities close to the triangle corners represent tree-like topologies (well-resolved). Those in the center and on the sides represent star-like (unresolved) and network-like signals (partially unresolved), respectively.</p

Phylogenetic analysis of CDV isolates.

<p>Thirty-seven nucleotide sequences of the Fsp (left) and H (right) datasets were used. Maximum likelihood trees were constructed using the Hasegawa-Kishino-Yano (G) substitution model for both datasets and were inferred through 500 replicates. Branch lengths are measured in the number of substitutions per site, as shown by the scale bars. Unrooted trees were depicted facing each other for comparison. AS1, Asia 1; AS2, Asia 2; EU1/SA1, Europe 1/South America 1; EU2, Europe 2; EU3, Europe 3; NA1, North America 1; NA2, North America 2; SA2, South America 2; Onder, Onderstepoort strain; Snyder, Snyder-Hill strain.</p

Inter- and intra-lineage amino acid divergences (p-distances).

<p>The upper values represent the divergence for Fsp; the lower values represent the divergence for the H protein. AS1, Asia 1; AS2, Asia 2; EU1/SA1, Europe 1/South America 1; EU2, Europe 2; EU3, Europe 3; NA1, North America 1; NA2, North America 2; SA2, South America 2.</p

Deep-sequencing profile of the distinguishing nucleotides between CPV-2a (KM457143) and 364-rec recombinant (KM457139) strains in sample 364.

a<p> The left fragment (NS gene) of the 364-rec strain was derived from a CPV-2c strain, and the right fragment was from a CPV-2a strain.</p>b<p> Coverage: number of times a nucleotide is read during the sequencing process.</p>c<p> The recombination breakpoint in the 364-rec recombinant strain falls in a 117-nt region between two constant parental markers (positions 2433 and 2549).</p>d<p> The difference in the 2907 position corresponds to a single-nucleotide polymorphism in the 2a homologous region of the co-infecting strains.</p><p>Deep-sequencing profile of the distinguishing nucleotides between CPV-2a (KM457143) and 364-rec recombinant (KM457139) strains in sample 364.</p

CPV recombination network.

<p>The phylogenetic network was generated from alignment of 42 complete CPV genome sequences. There are two main clades encompassing CPV-2c and CPV-2a strains (circles), and an edge (split) that reveals a possible recombination event involving strain 364-rec (KM457139). The Phi test for recombination was significant at p = 0.003.</p

Deep-sequencing profile of the distinguishing nucleotides between CPV-2a (KM457141) and CPV-2c (KM457142) strains in sample 370.

a<p>Coverage: number of times a nucleotide is read during the sequencing process.</p><p>Deep-sequencing profile of the distinguishing nucleotides between CPV-2a (KM457141) and CPV-2c (KM457142) strains in sample 370.</p

Uruguayan dog fecal samples used in this study.

a<p> (C) Capital city (Montevideo); (P) Periphery: cities/regions located in or near (within 15 km) the boundary of Montevideo; (I) Interior (remainder of the country). The VP2 gene sequences for some of these strains have been previously reported <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0111779#pone.0111779-Maya1" target="_blank">[31]</a>.</p><p>Uruguayan dog fecal samples used in this study.</p

Phylogenetic incongruence analysis.

<p>Phylogenetic reconstructions were performed with non-recombinant fragments of the 4269-bp CPV coding region containing nt 1–2500 (A), and nt 2501–4269 (B). The 364-rec strain (arrowhead) associates with both the CPV-2c (A) and CPV-2a (B) clades. 2a-UY: Uruguayan CPV-2a clade; 2c-UY: Uruguayan CPV-2c clade; FPV-US.06: feline panleukopenia virus (EU659115); MEV-CH.09: mink enteritis virus (FJ592174); CPV2-US.79: Canine parvovirus type 2 (M38245); CPV2a-15 United States 2a isolate (M24003); CPV2a-s5/2010 Chinese 2a isolate (KF638400.1). CPV2c-56/00 Italian 2c isolate. CH: China; US: United States; UY: Uruguay.</p

Nucleotide and amino acid differences along the coding sequences of all the Uruguayan CPV-2c and CPV-2a strains, and recombinant 364-rec strain (KM457139).

a<p>VP1 Intron. Nucleotides in bold represent identical sequences. Amino acids before and after positions correspond to the CPV-2a and CPV-2c strains, respectively.</p><p>Nucleotide and amino acid differences along the coding sequences of all the Uruguayan CPV-2c and CPV-2a strains, and recombinant 364-rec strain (KM457139).</p