Table 3.

Programs used to estimate genetic parameters and conduct statistical tests and procedures

Program	Version	Parameters 1 , tests and embedded procedures	References
Arlequin	3.5.1.3	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	3.7.1.1	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	1.3.0.0	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; F_ST, standardized molecular variance among populations; φ_ST, 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; θ_A, θ₁, θ₂, sizes of ancestral and descendant populations; m₁, m₂, immigration into descendant populations; K, number of genotypic clusters.