Table 3 Programs used to estimate genetic parameters and conduct statistical tests and procedures

Arlequin

3.5.1.3

Diversity indices (H, k, h, π, F _ST , φ _ST )

[40]

Fu’s Fs test

[41]

Linkage disequilibrium (D, D’, R²)

[42]

IBD: Pairwise Φ _ST , F _ST 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, θ_A, 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]