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Table 3 Analysis of molecular variance (AMOVA) under four criteria of classification of populations, based on the 870 bp long NAT2 coding exon

From: Variation in NAT2 acetylation phenotypes is associated with differences in food-producing subsistence modes and ecoregions in Africa

    

Percentage of variation

    

Dataset1

Categories grouping2

Number of population samples

Number of groups

Between groups

Between populations within groups

Fixation indexes

      

ΦCT

P-value3

ΦSC

P-value4

AFR

Geo5

37

3

−0.016

3.23

−0.000126

0.3722

0.03230

<0.0001 (0.0004)

 

Lang

38

4

0.43

3.04

0.00425

0.1323

0.03053

<0.0001 (0.0004)

 

Subsist

38

4

1.82

2.02

0.01819

0.0003 (0.0012)

0.02055

<0.0001 (0.0004)

 

Clim

38

2

2.35

2.11

0.02345

0.0001 (0.0004)

0.02161

<0.0001 (0.0004)

FP

Geo5

28

3

−0.046

2.21

−0.000376

0.4572

0.02207

<0.0001 (0.0004)

 

Lang

29

3

−0.216

2.30

−0.002076

0.6201

0.02297

<0.0001 (0.0004)

 

Subsist

29

3

1.16

1.58

0.01156

0.0251 (0.1004)

0.01600

0.0001 (0.0004)

 

Clim

29

2

3.57

0.71

0.03572

<0.0001 (0.0004)

0.00739

0.0170 (0.0680)

FPLS

Geo

13

3

−0.536

2.99

−0.005276

0.7238

0.02974

<0.0001 (0.0004)

 

Lang7

12

2

−0.456

2.84

−0.004476

0.5612

0.02832

<0.0001 (0.0004)

 

Subsist

13

2

1.20

1.99

0.01202

0.0530

0.02016

<0.0001 (0.0004)

 

Clim

13

2

5.40

0.54

0.05403

0.0035 (0.0140)

0.00568

0.0462 (0.1848)

  1. 1 As described in Methods, the three population data subsets are AFR: 38 samples, excluding the Americans of African ancestry (ASW of [53], see Table 1); FP: 29 samples of African food-producing populations; FPLS: 13 samples of African food-producing populations with sample size ≥ 20 individuals. Thus, the ASW sample was not considered in any of the AMOVA analyses
  2. 2 Categories as in Table 1 : classification according to geographical region (Geo), subsistence mode (Subsist), linguistic affiliation (Lang), and ecoregion (Clim), namely climatic zone and biome, which defines the fourth categorization criterion that considers whether populations live within the dry savanna biome or outside of it
  3. 3 Significance of the ΦCT index and of the corresponding percentage of variation due to differences between groups. Significant P-values (i.e., <5 %) are shown in bold, and adjusted P-values after Bonferroni correction for multiple testing (here, four tests) are provided in brackets
  4. 4 Significance of the ΦSC index and of the corresponding percentage of variation due to differences between populations within groups. Significant P-values (i.e., <5%) are shown in bold, and adjusted P-values after Bonferroni correction for multiple testing (here, four tests) are provided in brackets
  5. 5 Only three geographical regions are considered here (Western, Central and Eastern, Table 1) because the fourth region (Northern) is represented by one population sample only (EGY)
  6. 6 Because variance components in AMOVA are actually defined as covariances, negative values can occur [95]. A negative ΦCT value would be expected if gene copies were more correlated between groups than between populations within groups. However, none of the negative ΦCT values in the table are statistically significant, thus indicating that they are equal to zero
  7. 7 Only two linguistic families are considered here (Niger-Congo and Nilo-Saharan, Table 1) because the third family (Afro-Asiatic) is represented by one population sample only (SOM)
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BMC Ecology and Evolution

ISSN: 2730-7182

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