Table 1

Glossary of terms

SymbolMeaning
s Number of replicates
k Number of sequences at a given generation
n Sample size
l Sequence length
N Effective population size
μMutation rate per site per generation
θ= 4Nμl = Population mutation parameter (per gene)
p Average pairwise sequence divergence
r Recombination rate per site per generation
ρ= 4Nrl = Population recombination parameter (per gene)
R(n)Expected number of recombination events
G Number of potential locations for recombination to occur
κTransition/transversion rate
πBase frequencies
αShape of gamma distribution
ΓGamma distribution
JCJukes–Cantor 1969 (49)
K80Kimura-2-parameters (50)
F81Felsenstein 1981 (51)
HKYHasegawa–Kishino–Yano 1985 (52)
x Power to detect recombination