Table 1 Description of characters, parameters and variables.

S

Locus under selection.

L

Neutral locus linked to locus S.

A

Advantageous allele at locus S.

a

Disadvantageous allele at locus S.

Parameters

N

Census population size.

s

Selection coefficient.

W

Fitness of the advantageous allele A, w = 1+s.

μ

Probability that locus S mutates from A to a per virion per generation.

ν

Probability that locus S mutates from a to A per virion per generation.

U

Probability that mutation occurs at locus L per virion per generation.

r

Probability of recombination between loci L and S per virion per generation.

Variables

N _e

Effective population size.

A _t

Frequency of allele A at locus S at generation t.

a _t

Frequency of allele a at locus S at generation t.

F _t

Probability that two alleles at locus L are identical by descent at generation t (equivalent to the inbreeding coefficient in classic population genetics).

$\widehat{F}$

Inbreeding coefficient at equilibrium.

F _{AA, t}

F of locus L between offspring with allele A, at generation t.

F _{aa, t}

F of locus L between offspring with allele a, at generation t.

F _{Aa, t}

F of locus L between offspring with alleles A and a, at generation t.

p _{A, t}

Probability that an offspring at generation t is derived from a parent with allele A at generation t-1.

p _{a, t}

Probability that an offspring at generation t is derived from a parent with allele a at generation t-1.

p _{A→A, t}

Probability that an offspring at generation t is derived from a parent with allele A, given that the offspring has allele A.

p _{A→a, t}

Probability that an offspring at generation t is derived from a parent with allele A, given that the offspring has allele a.

p _{a→a, t}

Probability that an offspring at generation t is derived from a parent with allele a, given that the offspring has allele a.

p _{a→A, t}

Probability that an offspring at generation t is derived from a parent with allele a, given that the offspring has allele A.

P _{AA, t}

Probability of an individual at generation t having alleles at loci L and S both being derived from individual(s) with allele A at locus S.

P _{Aa, t}

Probability of an individual at generation t having locus L derived from an individual with allele A at locus S and locus S derived from an individual with allele a at locus S.

P _{aa, t}

Probability of an individual at generation t having alleles at loci L and S both being derived from individual(s) with allele a at locus S.

P _{aA, t}

Probability of an individual at generation t having locus L derived from an individual with allele a at locus S and locus S derived from an individual with allele A at locus S.