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Table 1 Description of characters, parameters and variables.

From: Selection dramatically reduces effective population size in HIV-1 infection

Characters Description
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).
F ^ MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaGafmOrayKbaKaaaaa@2CFA@ 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 AA, 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 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 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 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.