TABLE 1

Symbols and abbreviations used

ARGAncestral recombination graph
fThe relative contribution of gene conversion vs. crossing over, f = ρgc
Embedded ImageA composite-likelihood estimate of f (Hudson 2001)
Embedded ImageA pattern-matching-based estimate of f (cf. Padhukasahasram et al. 2004)
hObserved number of haplotypes
lLocus length
LTract length
LDLinkage disequilibrium
LPACThe PAC likelihood function (Li and Stephens 2003)
PACThe product of approximate conditionals (Li and Stephens 2003)
μThe per generation rate of mutation
nNumber of sampled chromosomes
rThe per generation rate of recombination
Embedded ImageLamarcAn estimate of the per generation rate of recombination (Kuhner et al. 2000)
RhAn estimate of the number of recombination events at a locus (Myers and Griffiths 2003)
RlAn estimate of the number of recombination events at a locus (Song et al. 2005)
RmAn estimate of the number of recombination events at a locus (Hudson and Kaplan 1985)
RsAn estimate of the number of recombination events at a locus (Myers and Griffiths 2003)
RuAn estimate of the number of recombination events at a locus (Song et al. 2005)
ρThe population recombination parameter, 4Ner
ρcThe population recombination parameter due to crossover
ρgThe population recombination parameter due to gene conversion
Embedded ImageFD02An approximate-likelihood estimate of ρ (Fearnhead and Donnelly 2002)
Embedded ImageH01A composite-likelihood estimate of ρ (Hudson 2001)
Embedded ImageLamarcA full-likelihood estimate of ρ (Kuhner et al. 2002)
Embedded ImageLS03The PAC-likelihood estimate of ρ (Li and Stephens 2003)
Embedded ImageMAF02A composite-likelihood estimate of ρ (McVean et al. 2002)
Embedded ImageT05A summary statistic-based estimate of ρ (Haddrill et al. 2005)
Embedded ImageW00A summary statistic-based estimate of ρ (Wall 2000)
sThe rate of self-fertilization
SNumber of segregating sites
SpNumber of parsimony informative segregating sites
TTajima's D (Tajima 1989)
θThe population mutation parameter, 4Neμ
Embedded ImageFD02θ coestimated with ρ (Fearnhead and Donnelly 2002)
Embedded ImageLamarcθ coestimated with ρ (Kuhner et al. 2002)
Embedded ImageπAn estimate of θ based on pairwise differences (Tajima 1983)
Embedded ImageT05θ coestimated with ρ (Haddrill et al. 2005)
Embedded ImageWAn estimate of θ based on the number segregating sites (Watterson 1975)