Table 3

Programs used to estimate genetic parameters and conduct statistical tests and procedures
Program Version Parameters1, tests and embedded procedures References
ARLEQUIN Diversity indices (H, k, h, π, FST, φST) [40]
Fu’s Fs test [41]
Linkage disequilibrium (D, D’, R2) [42]
IBD: Pairwise ΦST, FST and [43]
Mantel test [44]
BEAGLE Recombination test [45]
BEAST 1.7.2 Estimation of divergence time [46]
CNDM Cytonuclear disequilibrium (D, D’) [47]
CODONCODE ALIGNER Proofreading sequences CodonCode Corp., Dedham, MA
GENEPOP 4.0.10 Multilocus data management [48]
HWE exact tests [49]
IMA2 8.26.11 Demographic parameters (τ, θA, θ1, θ2, m1, m2) [50]
GENEIOUS 5.6.2 Sequence editing [51]
NETWORK PUBLISHER Illustrating gene networks [52]
NEWHYBRIDS 1 Assignment of putative hybrids [53]
PHASE 2.1.1 Decomposing heterozygotes, recombination test [54,55]
STRUCTURE 2.3.3 Assignment test (K) [56,57]

1 Parameters: H, number of haplotypes; k, number of polymorphic sites; h, haplotype diversity; π, nucleotide diversity per site; FST, standardized molecular variance among populations; φST, standardized molecular variance among populations; D, nuclear linkage disequilibrium (LD); D’, standardized LD; R2, correlation measure of LD; estimators of nuclear linkage disequilibrium; τ, time to most recent common ancestor; θA, θ1, θ2, sizes of ancestral and descendant populations; m1, m2, immigration into descendant populations; K, number of genotypic clusters.

Johnson et al.

Johnson et al. BMC Evolutionary Biology 2013 13:21   doi:10.1186/1471-2148-13-21

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