A Shift in Porcine Circovirus 3 (PCV‐3) History Paradigm: Phylodynamic Analyses Reveal an Ancient Origin and Prolonged Undetected Circulation in the Worldwide Swine Population

Figure 1. a) PCV‐3 tMRCA and evolutionary rate based on dataset1. Left figure: density plot of the MRCA posterior probability. Right figure: density plot of the mean evolutionary rate posterior probability. Evolutionary rates of different genomic regions have been color coded. The 95HPD intervals are reported for both figures. b) PCV‐3 tMRCA and evolutionary rate based on dataset3. Left figure: density plot of the MRCA posterior probability. Right figure: density plot of the mean evolutionary rate posterior probability. The 95HPD intervals are reported for both figures. c) PCV‐3 tMRCA and evolutionary rate based on dataset2. Upper figure: box plot (left) and density plot (right) of the MRCA posterior probability. Lower figure: box plot (left) and density plot (right) of the mean evolutionary rate posterior probability. Results have been estimated performing ten independent runs based on randomly sampled sequences. The 95HPD intervals are reported for both figures.

Figure 2. PCV‐3 genotype population dynamics reconstructed based on dataset2. Upper figure: mean relative genetic diversity (N e x t) of the worldwide PCV‐3 population overtime. The results of the ten independent runs have been color coded. Lower figure: median and upper and lower 95HPD values are reported for each run.

Figure 3. Ancestral location scatter plot. Scatter plot representing the posterior probability of each ancestral location (color coded) prediction over time. The results of ten independent BEAST run are reported.

Figure 4. Network reporting the well‐supported migration routes (BF > 10). PCV‐3 spreading path among different countries estimated using ten independent BEAST runs (color coded) based on dataset2. The arrows' size is proportional to the BF value.

Figure 5. Line graph reporting dN–dS values estimated for each codon position of ORF1 (upper figure) and ORF2 gene (lower figure) using different methods. Sites detected to be under statistically significant positive selection by MEME are reported as red circles.

Figure 6. a) Tertiary structure of the Rep protein estimated through homology model. When located on the protein surfaces, sites under pervasive and episodic diversifying selection have been highlighted in orange and red, respectively. b) Tertiary structure of the Cap protein estimated through homology model. When located on the protein surfaces, sites under pervasive and episodic diversifying selection have been highlighted in red.