The fourth major cluster includes Dpls.
The third major cluster includes the tetrapode PrPs.
The first major cluster includes Shos, Sho2s and PrP-likes.
Another major cluster includes the Mediterranean-type breeds, i.e., ALE, ENT, RET, TOR, LAM, NPE and MJA, which share a common origin and a close geographical distribution, and are often considered as varieties of the "Iberico" group of pigs.
The first major cluster included Z. diploperennis (Tz09), Z. perennis (Tz01 and Tz02), Z. luxurians (Tz05 and Tz06) and Z. nicaraguensis (Tz10).
Cluster 6 was a major cluster, including four genes in the C1 class, seven in the S14 (Clp) class, two in the M1 class, and four other classes.
The second major cluster included hydrophobic amino acid metabolism (e.g., for tryptophan, phenylalanine, and tyrosine) and aromatic compound degradation (e.g., of xylene and dioxins).
PG7, the major cluster, included caudatums from countries in Africa, Asia, and the United States as well as guinea-caudatums and durra-caudatums.
An intriguing observation was that, using a 70% similarity cut-off value for cluster analysis (approximately equivalent to less than or equal to eight PFGE fragment differences) resulted in most infection isolates being grouped into one major cluster (including PFGE clusters B, C, D and E), with 68% of infection isolates and 17% of carriage isolates (P < 0.01).
Otherwise, the major anomaly was the apparent difficulty that taxonomists have in recognizing strains of S. mitis; strains assigned on standard taxonomic grounds to this species were found among several clusters, although the major cluster included the S. mitis type strain.
In contrast, the third major cluster included 15 strains that had been isolated from cheese in the United States, Australia, and Europe, and was predicted to reflect recent divergence of strains that were highly specialized for this relatively new ecological niche (manufacture of cheese is thought to have begun ~8,000 years ago) [ 30, 31].
