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. 2016 Oct 7;34(1):4–19. doi: 10.1093/molbev/msw214

Table 1.

Mantel’s Permutation Test for Similarity of FST Distance Matrices between HPV16 and Human Genome Sequence Data Sets.

Selection-filtered
 Including positions under selection
Taxa Loci Region/SNPs n Correlation (%)a P-valueb FDRc Correlation (%)a P-valueb FDRc
mtDNA 1 16 kb genome 875 12.4 0.037 0.017 15.8 0.026 0.018
NRY 1 5,000 kb 551 8.5 0.062 0.028 11.8 0.044 0.036
Europe chr1 6,353 773 8.8 0.062 0.029 12.7 0.033 0.026
Europe chr2 5,918 773 6.3 0.091 0.040 9.6 0.054 0.040
Europe chr3 5,325 773 8.8 0.063 0.032 12.7 0.037 0.030
Europe chr4 4,211 773 8.9 0.063 0.030 12.7 0.036 0.029
Europe chr5 4,743 773 5.6 0.104 0.047 8.7 0.061 0.047
Europe chr6 4,736 773 6.3 0.095 0.041 9.5 0.055 0.042
Europe chr7 4,162 773 5.2 0.112 0.048 8.1 0.062 0.048
Europe chr8 3,750 773 8.0 0.070 0.036 11.6 0.045 0.037
Europe chr9 3,222 773 8.8 0.064 0.033 12.7 0.038 0.033
Europe chr10 4,223 773 9.2 0.059 0.026 13.1 0.035 0.028
Europe chr11 3,850 773 5.9 0.099 0.046 9.2 0.058 0.046
Europe chr12 3,339 773 5.1 0.116 0.049 8.0 0.066 0.049
Europe chr13 2,234 773 5.8 0.098 0.045 9.2 0.057 0.045
Europe chr14 2,307 773 5.9 0.097 0.043 9.3 0.056 0.043
Europe chr15 2,346 773 6.2 0.096 0.042 9.3 0.054 0.041
Europe chr16 2,636 773 7.5 0.078 0.038 11.1 0.045 0.038
Europe chr17 2,109 773 6.8 0.084 0.039 10.1 0.045 0.039
Europe chr18 2,243 773 9.8 0.056 0.025 13.9 0.033 0.025
Europe chr19 1,175 773 3.9 0.139 0.050 6.5 0.085 0.050
Europe chr20 2,067 773 9.9 0.055 0.023 13.8 0.031 0.021
Europe chr21 973 773 10.0 0.055 0.024 14.1 0.031 0.022
Europe chr22 1,141 773 7.7 0.073 0.037 11.6 0.042 0.034

Note.—HPV16 sequence data (1,192 bp) encompassing LCR (735 bp) and E6 (457 bp) regions for 1,101 worldwide isolates were used in the correlations. mitochondrial DNA (mtDNA); nonrecombining part of the Y chosomosome (NRY); autosomal SNP data stratified by chromosome and ascertained using a European (Europe) ancestry data (autosomal SNP data ascertained using a sub-Saharan ancestry data is provided in supplementary table S8, supplementary material online). For both datasets nine geographic metapopulations were defined: North/East/West/Southern Africa, South Asia, East Asia, Europe, Central and South America (supplementary table S2 and S5. supplementary material online).

a

R2 of the correlation coefficient.

b

Mantel-test after 10,000 permutations.

c

False discovery rate controlling procedure (q = 0.05).