Table 3

Details of nucleotide diversity and neutrality tests for candidate genes in the wild collection
Gene Set Population P(C) h S Ts Tv Ka Ks ω π (E-3) S.D. π (E-3) θw(E-3) S.D. θW(E-3) TD DT 95% C.I. p-value DT R2 p-value R2 Max. K
Asr 1 Exon Global 0.95 3 3 3 3 0.0 2.2 0.6 2.4 1.5 −0.22 −1.72 2.07 0.47 1.1 0.46 2
M 0.85 3 3 3 3 0.0 2.2 1.1 3.4 2.2 −1.18 −1.45 1.72 0.08 1.3 <0,001 2
G 0.75 2 2 2 2 0.0 1.9 1.3 2.8 2.1 −1.24 −1.24 1.65 <0,001 3.5 0.87 2
E 0.67 2 2 2 2 0.0 2.7 1.6 3.3 2.6 −0.97 −0.97 1.46 0.46 4.0 0.85 2
Intron Global 0.95 3 2 1 1 3.9 1.0 4.2 3.1 −0.16 −1.49 2.09 0.48 1.1 0.36 2
M 0.86 2 1 1 4.1 1.0 2.9 2.9 0.95 −1.46 1.48 0.68 2.3 0.33 1
G 0.75 2 1 1 2.5 1.7 3.6 3.6 −1.01 −1.01 1.34 0.52 3.5 0.50 1
Asr 2 Global Global 0.97 4 3 3 1 0.0 4.1 0.3 2.6 1.2 2.18 0.97 −1.62 <0,001 2.0 0.97 4
M 0.94 3 3 3 1 0.0 4.0 0.4 2.5 1.4 1.43 0.94 −1.74 1.92 1.9 0.92 4
G 0.78 2 3 3 4.1 1.0 3.0 2.0 1.60 0.91 −1.45 1.73 2.7 0.85 3
C 0.78 3 3 3 4.3 0.7 3.0 2.0 1.85 0.99 −1.45 1.73 2.8 0.93 3
A 0.91 3 3 3 2.5 0.9 2.8 1.4 0.48 0.72 −1.73 2.02 1.6 0.69 3
Exon Global 0.97 2 1 1 1 0.0 0.7 0.3 1.1 1.1 −0.46 0.49 −1.06 1.78 0.6 0.28 1
M 0.94 2 1 1 1 0.0 0.3 0.3 1.4 1.4 −1.14 0.28 −1.14 1.64 1.7 0.69 1
UTR Global 0.97 3 2 2 23.1 1.3 9.8 6.0 1.61 0.99 −1.57 1.96 2.4 0.99 3
M 0.94 2 2 2 23.7 1.9 11.8 7.4 2.32 0.99 −1.73 2.14 2.5 0.99 3
G 0.78 2 2 2 25.5 5.9 18.4 12.4 1.60 0.92 −1.45 1.86 2.7 0.88 3
C 0.78 2 2 2 26.6 4.2 18.4 12.4 1.85 0.98 −1.45 1.73 2.8 0.93 3
A 0.91 2 2 2 15.7 5.3 17.7 8.4 0.48 0.73 −1.73 1.87 0.16 0.65 0.03

h: number of haplotypes, S: number of polymorphic sites.

Populations M: Mesoamerican, G: Guatemala, C: Colombia, E: Peru and Ecuador, A: Andean.

P(C): Probability of having captured the deepest coalescent event.

π: nucleotide diversity Ts: Transitions, Tv: Transversions, ω: Non synonymous, synonymous substitution ratio (Ka/Ks) (Only for protein coding regions).

TD: Tajima’s D, θw: Theta of Watterson (per site, from S), S.D.: Standard deviation.

p-Value: probability estimator ≠ 0 as determined by coalescent simulation.

R2: Ramos-Onsins & Rozas’ R2 (tests population growth), Max. K: Maximum number of nucleotide differences between any two sequences.

Empty cells: No applicable data (when h = 0).

Cortés et al.

Cortés et al. BMC Genetics 2012 13:58   doi:10.1186/1471-2156-13-58

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