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). |
$\widehat{F}$ | 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. |