TABLE 2.
HMM PBP convergent and homoplasic codon sitesa
| PBP | No. of codon site(s) (%) |
No. of convergent and homoplasic sites | ||
|---|---|---|---|---|
| Substituted (assemblies, alleles) | Convergent (assembly based) | Homoplasic (allele based) | ||
| 1A | 148, 141 | 56/148 (37.8) | 43/141 (30.5) | 41 |
| 1B | 156, 154 | 58/1567 (37.2) | 37/154 (24.0) | 31 |
| 2A | 185, 175 | 76/185 (41.1) | 86/175 (49.1) | 66 |
| 2X | 161, 168 | 44/161 (27.3) | 35/168 (20.8) | 28 |
a
Convergent codon sites (sites with amino acid substitutions identified in multiple genetic lineages), were determined by correlating SNPs derived from comparing the 26,456 WGS assemblies with the genetic lineages defined by HDBSCAN. Homoplasic codon sites were determined among 1,248 unique concatenated PBP alleles using SNPPar. The different input sets evaluated, and methods used are responsible for the modest difference in total substituted codon sites identified. The recombinant genetic outliers (pbp1b-143 and pbp2x-286) with SDSE-like sequences were excluded from both analyses.