Tables
Table 1. Analysis of Variance using alpha diversity indices: Chao1 and Shannon indices. Nested ANOVAs were constructed using Cross, Sire (nested within Cross), and Pen (nested within Sire within cross) as main factors. Significant differences were found for Pen effects (P < 0.05) using Shannon's index.
 
Alpha diversity
Factor
Df
SS
MS
F-value
P-value
Chao1
Cross
7
14345
2049
1.88
0.080
Sire
56
61401
1096
1.00
0.48
Pen
43
72081
1676
1.54
0.038
Residuals
113
123390
1092
 
 
Shannon
Cross
7
5.99
0.86
1.14
0.34
Sire
56
32.0
0.57
0.76
0.87
Pen
43
25.2
0.59
0.78
0.82
Residuals
113
85.0
0.75
 
 
 
Table 2. Microbiome community composition analysis results using nested-PERMANOVA. Sires were nested in crosses, and replicate pens were nested in sires (nested in crosses).
Distance metric
Factor
Df
SS
MS
Pseudo-F
R2
P-value
Bray-Curtis
Cross
7
4.10
0.59
1.74
0.05
0.0025
Sire
56
20.0
0.36
1.06
0.26
0.23
Pen
43
13.6
0.32
0.94
0.18
0.76
Residuals
114
38.4
0.34
 
0.50
 
Total
220
76.1
 
 
1.00
 
Jaccard
Cross
7
4.06
0.58
1.55
0.05
0.00040
Sire
56
22.2
0.40
1.06
0.26
0.065
Pen
43
16.4
0.38
1.02
0.19
0.31
Residuals
114
42.7
0.37
 
0.50
 
Total
220
85.4
 
1.00
 
 
 
Table 3. Multiple pairwise PERMANOVA comparisons between hybrid-crosses based on Bray-Curtis and Jaccard distances (FDR P-values). The number of permutations used in the analysis was 9999. P-values are corrected to two significant figures.
 
Distance-metric
Cross
BQ
CAP
CHILL
NIT
PUNT
QUIN
RC
Bray-Curtis
CAP
0.86
CHILL
0.12
0.047
NIT
0.71
0.79
0.20
PUNT
0.86
0.86
0.19
0.86
QUIN
0.86
0.86
0.19
0.86
0.86
RC
0.86
0.86
0.19
0.86
0.86
0.86
YIAL
0.0028
0.0028
0.66
0.017
0.017
0.0056
0.017
Jaccard
CAP
0.63
CHILL
0.040
0.029
NIT
0.52
0.41
0.17
PUNT
0.63
0.52
0.10
0.65
QUIN
0.63
0.41
0.079
0.70
0.65
RC
0.78
0.70
0.11
0.78
0.52
0.63
YIAL
0.0021
0.0021
0.22
0.0047
0.0021
0.0021
0.0047