N |
Population size |
τf |
Time of fixation of selected allele |
t |
Time in generations |
x(t) |
Frequency of the selected allele |
h(t) |
Relative heterozygosity at the neutral locus among selected chromosomes |
ql |
Minor allele frequency at site l
|
l0
|
Length of neutral region |
L |
Flanking sequence length |
π |
Nucleotide diversity,
|
π0
|
Nucleotide diversity under neutrality |
πN |
Nucleotide diversity in a population of size N
|
p(t) |
Probability of common ancestry at the neutral locus |
n |
Number of sampled sequences |
μ |
Mutation rate per generation per chromosome per base pair |
θ = 4Nμ
|
Population-scaled mutation rate |
s |
Selection coefficient |
α = 2Ns
|
Population-scaled selection strength |
r |
Recombination rate per generation per chromosome per base pair |
ρ = 4Nr
|
Population-scaled recombination rate |
rf |
Recombination fraction (probability of productive recombination, per generation per chromosome) |
λ |
Rate of positively selected substitutions per site per generation |
kh |
Rate of common ancestry induced by sweep events [see (4)] |
Rc
|
Total rate of common ancestry induced by sweep and coalescent events |
Iα,s
|
The integral [see (4)] |
|
The integral [see (14)] |
I = 0.075 |
A constant approximating Iα,s
|