α | Factor by which the recombination rate at S loci is increased from the basal rate r |
\( {d}_{S_P,V} \) | Number of mismatching loci between S P and V |
E P | Allele at the E locus of a host genotype P; 0 for WT, 1 for beneficial allele |
f P | Fitness of prokaryotic genotype P |
f V | Fitness of virus genotype V |
J | Clonality at N locus defined as p N 2 + (1 − p N )2 |
J a | Clonality at N locus after selective sweep |
J b | Clonality at N locus before selective sweep |
J rel | Relative clonality at N locus after fixation defined as (J a  − J b )/(1 − J b ) |
l | Number of possible alleles per S locus |
n | Number of S loci in prokaryote genome |
N P | Allele at the N locus of a host genotype P (0 or 1) |
P | Integer representing a prokaryote genotype (0 ≤ P < 4l n) |
p E | Frequency of allele 1 at E locus in host population |
p N | Frequency of allele 1 at N locus in host population |
p P | Frequency of host genotype P |
p V | Frequency of virus genotype V |
r | Basal recombination rate per locus per generation at E and N loci in hosts |
r V | Rate at which allele changes per locus per generation in viral genomes |
s e | Selection coefficient of ecologically beneficial allele |
s i | Selection coefficient of NFDS imposed at S loci |
S P | Allelic pattern of S loci of a host genotype P (0 ≤ S P  < l n) |
V | Integer representing a virus genotype (0 ≤ V < l n) |