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Table 1 Notation

From: Gene-specific selective sweeps in bacteria and archaea caused by negative frequency-dependent selection

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)

  1. E locus, ecological locus; N locus, neutral locus; S loci, susceptibility loci; WT, wild type.