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. 2012 Jul 16;13:58. doi: 10.1186/1471-2156-13-58

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).