Table 1. The arsenal of parameters for population genetics/genomics analyses: measures of nucleotide diversity, LD, and tests of selection.

Measure/test	Description	References
Nucleotide diversity measures (uni-dimensional measures)
S, s	Number of segregating sites (per DNA sequence or per site, respectively)	Nei (1987)
H, η	Minimum number of mutations (per DNA sequence or per site, respectively)	Tajima (1996)
k	Average number of nucleotide differences (per DNA sequence) between any two sequences	Tajima (1983)
π	Nucleotide diversity: average number of nucleotide differences per site between any two sequences	Jukes and Cantor (1969); Nei and Gojobori (1986); Nei (1987)
θ, θW	Nucleotide polymorphism: proportion of nucleotide sites that are expected to be polymorphic in any suitable sample	Watterson (1975); Tajima (1993, 1996)
SFS	Site/allele frequency spectrum: distribution of allele frequencies at a given set of loci in a population or sample	Ronen et al. (2013)
LD (multi-dimensional association among variable sites) and recombination
D	Coefficient of LD whose range depends of the allele frequencies	Lewontin and Kojima (1960)
D′	Normalized D, independent of allele frequencies	Lewontin (1964)
R, R2	Statistical correlation between pairs of sites	Hill and Robertson (1968)
ZnS	Average of R2 over all pairwise comparisons	Kelly (1997)
ZA/ZZ	ZA is the average of R2 only between adjacent polymorphic sites. ZZ is ZA minus ZnS, which is an estimate of the recombination parameter r	Rozas et al. (2001)
Four-gamete test	Measure of historical recombination under the infinite-sites model	Hudson and Kaplan (1985)
ρ	Population-scaled recombination rate ρ = 4Ner [computed, e.g., by LDhat (Auton and McVean 2007) and LDhelmet (Chan et al. 2012)]	Hudson (1987)
Selection tests based on the allele frequency spectrum and/or levels of variability
Tajima’s D	Number of nucleotide polymorphisms with the mean pairwise difference between sequences	Tajima (1989)
Fu and Li’s D, D*	Number of derived nucleotide variants observed only once in a sample with the total number of derived nucleotide variants	Fu and Li (1993)
Fu and Li’s F, F*	Number of derived nucleotide variants observed only once in a sample with the mean pairwise difference between sequences	Fu and Li (1993)
Fay and Wu’s H	Number of derived nucleotide variants at low and high frequencies with the number of variants at intermediate frequencies	Fay and Wu (2000)
Zeng’s E, θL, DH	Difference between θL and θW: the first is sensitive to changes in high-frequency variants. DH is a joint test including Tajima’s D and Fay and Wu’s H	Zeng et al. (2006)
Achaz’s Y	Unified framework for θ estimators on the basis of the allele frequency spectrum	Achaz (2009)
Fu’s FS	Test based on the allele frequency spectrum	Fu (1997)
Ramos-Onsins’ and Rozas’ R2, R3, R4, R2E, R3E, R4E	Tests based on the difference between the number of singleton mutations and the average number of nucleotide differences	Ramos-Onsins and Rozas (2002)
CL, CLR	Genome scan for candidate regions of selective sweeps based on aberrant allele frequency spectrum	Nielsen et al. (2005)
Selection tests based on comparisons of polymorphism and/or divergence between different classes of mutation
dN/dS, Ka/Ks	Ratio of nonsynonymous to synonymous nucleotide divergence/polymorphism (ω)	Li et al. (1985); Nei and Gojobori (1986)
HKA	Degree of polymorphism within and between species at two or more loci	Hudson et al. (1987)
MK	Ratios of synonymous and nonsynonymous nucleotide divergence and polymorphism	McDonald and Kreitman (1991)
Estimators derived from extensions of the MK test or the DFE
NI	Neutrality index that summarizes the four values in an MK test table as a ratio of ratios	Rand and Kann (1996)
DoS	Direction of selection: difference between the proportion of nonsynonymous divergence and nonsynonymous polymorphism	Stoletzki and Eyre-Walker (2011)
α	Proportion of substitutions that are adaptive	Charlesworth (1994); Smith and Eyre-Walker (2002)
DFE-α	Fraction of adaptive nonsynonymous substitutions, robust to low recombination	Eyre-Walker and Keightley (2009)
ωA	Rate of adaptive evolution relative to the mutation rate	Castellano et al. (2016); James et al. (2016)
Ka+	Rate of adaptive amino acid substitution (Ka+ = αKa)	Castellano et al. (2016)
$\widehat{d},$ $\widehat{b},$ $\widehat{f},$ $\widehat{\mathrm{\gamma }},$ $\widehat{\mathrm{\alpha }}$	Fractions of five different selection regimes derived from an extension of the MK test: $\widehat{d},$ fraction of new mutations that are strongly deleterious and do not segregate in the population; $\widehat{b},$ fraction of new mutations that are slightly deleterious and segregate at minor allele frequency (MAF) <5%; $\widehat{f},$ fraction of new mutations that are neutral, calculated after removing the excess of sites at MAF <5% due to slightly deleterious mutations; $\widehat{\gamma },$ subset of $\widehat{f}$ corresponding to recently neutral sites; $\widehat{\alpha },$ fraction of new mutations that are adaptive, calculated after removing slightly deleterious mutations	Mackay et al. (2012)
LHRi	Proportion of adaptive substitutions lost due to HRi	Castellano et al. (2016)
ropt	Optimal baseline recombination, above which the genome is free of the HRi and thus LHRi = 0	Mackay et al. (2012); Castellano et al. (2016)
Selection tests based on LD
Hudson’s haplotype test	Detection of derived and ancestral alleles on unusually long haplotypes	Hudson et al. (1994)
B/Q	Based on LD between adjacent pairs of segregating sites, under the coalescent model with recombination	Wall (1999)
iHS	Integrated haplotype score, based on the frequency of alleles in regions of high LD	Voight et al. (2006)
LRH	Long-range haplotype test, based on the frequency of alleles in regions of long-range LD	Sabeti et al. (2002)
HS	Haplosimilarity score: long-range haplotype similarity	Hanchard et al. (2006)
EHH	Extended haplotype homozygosity: measurement of the decay of LD between loci with distance	Sabeti et al. (2002)
LDD	LD decay: expected decay of adjacent SNP LD at recently selected alleles	Wang et al. (2006)
SGS	Shared genomic segment analysis: detection of shared regions across individuals within populations	Cai et al. (2011)
GIBDLD	Detection of genomic loci with excess of identity-by-descent sharing in unrelated individuals as signature of recent selection	Han and Abney (2013)
XP-EHH	Long-range haplotype method to detect recent selective sweeps	Sabeti et al. (2007)
H12, H2/H1	Haplotype homozygosity	Garud et al. (2015)
Population differentiation and associated selection tests
GST	Analysis of gene diversity (heterozygosity) within and between subpopulations	Nei (1973)
FST	Average levels of gene flow based on allele frequencies, under the infinite-sites model	Hudson et al. (1992b)
Bayesian FST	Probability that a locus is subject to selection based on locus-specific population differentiation, using a Bayesian method	Foll and Gaggiotti (2008)
GST, HST, KST	Different test statistics based on haplotype frequencies and/or the number of nucleotide differences between sequences	Hudson et al. (1992a)
Snn	Genetic differentiation of subpopulations based on haplotypic data	Hudson (2000)
PhiST	Correlation of haplotypic diversity at different levels of hierarchical subdivision	Excoffier et al. (1992)
Strobeck’s S	Measure of population structure based on the comparison of the observed number of alleles in a sample to that expected when θ is estimated from the average number of nucleotide differences	Strobeck (1987)
XP-CLR	Cross-population composite likelihood ratio test, based on allele frequency differentiation across populations	Chen et al. (2010)
TLK, TF-LK	Original Lewontin–Krakauer test (TLK) and an extension (TF-LK), aimed at detecting selection based on the variance of FST across loci	Lewontin and Krakauer (1973); Bonhomme et al. (2010)
LSBL	Locus-specific branch length, based on pairwise FST distances	Shriver et al. (2004)
hapFLK	Detecting of selection based on differences in haplotype frequencies among populations with a hierarchical structure	Fariello et al. (2013)