Appendix 1

UNSUPPORTED SPLITS IN G&

Appendix 2

EXAMPLES OF INTRASPECIFIC DIAGNOSABILITY BASED ON GENETIC DAT

Hvilsom2013

Hvilsom201

SAT 1 Phylogenetic Tree.

<p>Markov Chain Monte Carlo phylogenetic tree generated using the combined SAT 1 data set including both chronologically sampled (CHR) data sets and temporal sample clusters (CLU). Temporal sample clusters are collapsed and coloured. Posterior probabilities are given for each node and the scale bar indicates a branch length corresponding to 25 years.</p

<i>dN/dS</i> ratios for all datasets.

<p>Single likelihood ancestor counting (SLAC) P < 0.1. Serotype sequences constituted 221 amino acids (SAT 1), 216 amino acids (SAT 2).</p><p><i>dN/dS</i> ratios for all datasets.</p

SAT 2 Phylogenetic Tree.

<p>Markov Chain Monte Carlo phylogenetic tree generated using the combined SAT 2 data set including both chronologically sampled (CHR) data sets and temporal sample clusters (CLU). Temporal sample clusters are collapsed and coloured. Posterior probabilities are given for each node and the scale bar indicates a branch length corresponding to 25 years.</p