Table 3.
Molecular Diversity.
| Population samples | Sample_size (n) | Number of haplotypes (k) | k/n | Number of polymorphic sites | Haplogroup diversity (Ĥ ± SE) | Nucleotide diversity (π ± SE) | Tajima’s D | Fu’s FS test | Sum of Square differences (SSD) | Mean number of pairwise differences (MNPd) | Geneflow exchanged between groups (M = Nem) | Raggedness index | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Taiwan Dataset (NAN_Tw) | Changhua (LL_Tw) | 71 | 66 | 0.93 | 157 | 0.8743 ± 0.0012 | 0.006 ± 0.003 | −1.90** | −24.14*** | 0.003 | 17.07 | 10581.82 | 0.002 |
| Chiayi (LL_Tw) | 23 | 23 | 1.00 | 78 | 0.8744 ± 0.0018 | 0.005 ± 0.002 | −1.37 | −12.25*** | 0.018 | 14.34 | 5457.94 | 0.013 | |
| Green_Island (LL_Tw) | 25 | 18 | 0.72 | 68 | 0.8449 ± 0.0031 | 0.006 ± 0.003 | −0.75 | −12.72** | 0.011 | 16.66 | 32.59 | 0.022 | |
| Heping_Island (LL_Tw) | 10 | 8 | 0.80 | 40 | 0.6954 ± 0.0245 | 0.005 ± 0.003 | −0.23 | −2.48 | 0.047 | 14.62 | 15.50 | 0.079 | |
| Kaohsiung (LL_Tw) | 71 | 63 | 0.89 | 154 | 0.8677 ± 0.0019 | 0.006 ± 0.003 | −1.88** | −24.13*** | 0.005 | 17.41 | 712.30 | 0.003 | |
| Miaoli (LL_Tw) | 18 | 17 | 0.94 | 73 | 0.7705 ± 0.0095 | 0.006 ± 0.003 | −1.34 | −7.11** | 0.014 | 16.40 | 445.13 | 0.003 | |
| Papura (LL_Tw) | 38 | 36 | 0.95 | 102 | 0.8322 ± 0.0048 | 0.005 ± 0.002 | −1.54* | −24.29*** | 0.002 | 15.27 | 615.56 | 0.003 | |
| Penghu Islan (LL_Tw) | 47 | 40 | 0.85 | 110 | 0.8414 ± 0.0031 | 0.005 ± 0.002 | −1.63* | −24.27*** | 0.004 | 15.71 | 145.58 | 0.004 | |
| PingTong (LL_Tw) | 12 | 12 | 1.00 | 42 | 0.7761 ± 0.0007 | 0.003 ± 0.001 | −1.45 | −5.14** | 0.020 | 9.48 | 5136.77 | 0.058 | |
| Taipei (Ur_Tw) | 98 | 83 | 0.85 | 154 | 0.8733 ± 0.0017 | 0.005 ± 0.002 | −1.83** | −24.10*** | 0.003 | 15.33 | 631.66 | 0.001 | |
| Xiaoliuqiu (LL_Tw) | 11 | 11 | 1.00 | 74 | 0.7521 ± 0.0000 | 0.007 ± 0.004 | −1.32 | −2.27 | 0.018 | 19.96 | 8687.13 | 0.033 | |
| YIlan (LL_Tw) | 25 | 20 | 0.80 | 79 | 0.7975 ± 0.0062 | 0.005 ± 0.003 | −1.25 | −13.12** | 0.009 | 15.98 | 45.53 | 0.012 | |
| Yunlin (LL_Tw) | 149 | 115 | 0.77 | 185 | 0.8866 ± 0.0014 | 0.005 ± 0.002 | −1.92*** | −23.92** | 0.003 | 15.98 | 340.13 | 0.002 | |
| Literature Dataset | Matsu (East Coast China) | 50 | 47 | 0.94 | 125 | 0.8449 ± 0.0031 | 0.005 ± 0.002 | −1.72* | −24.28*** | 0.041*** | 15.03 | 963.27 | 0.016 |
| Fujian (East Coast China) | 148 | 121 | 0.82 | 184 | 0.8744 ± 0.0018 | 0.005 ± 0.002 | −2.00** | −23.97*** | 0.002 | 14.90 | 794.96 | 0.002 | |
| East Coast China (Fujian & Matsu) | 198 | 159 | 0.80 | 213 | 0.9181 ± 0.0004 | 0.005 ± 0.002 | −2.04**− | 23.85** | 0.003 | 14.90 | 795.47 | 0.001 | |
| East Indonesia (ISEA) | 72 | 55 | 0.76 | 127 | 0.8230 ± 0.0048 | 0.006 ± 0.003 | −1.66* | −24.15*** | 0.002 | 14.90 | 138.04 | 0.003 | |
| Hakka_Ko (Ur_Tw) | 45 | 40 | 0.89 | 114 | 0.8290 ± 0.0049 | 0.006 ± 0.003 | −1.80** | −24.26*** | 0.007 | 16.11 | 340.39 | 0.003 | |
| Japan (NE_Asia) | 664 | 375 | 0.56 | 315 | 0.9037 ± 0.0008 | 0.004 ± 0.002 | −2.15*** | −23.60** | 0.002 | 12.12 | 124.91 | 0.001 | |
| Makatao (LL_Tw) | 50 | 36 | 0.72 | 106 | 0.8123 ± 0.0056 | 0.005 ± 0.002 | −1.60* | −24.28*** | 0.005 | 15.02 | 64.35 | 0.005 | |
| Malaysia (MSEA) | 86 | 32 | 0.37 | 92 | 0.6862 ± 0.0186 | 0.004 ± 0.002 | −1.096 | −24.31*** | 0.007 | 12.24 | 11.09 | 0.011 | |
| Minnan_Ko (Ur_Tw) | 50 | 48 | 0.96 | 112 | 0.8500 ± 0.0027 | 0.005 ± 0.002 | −1.79* | −24.29*** | 0.070*** | 14.77 | 6328.73 | 0.004 | |
| Northeast China (NE_Asia) | 257 | 250 | 0.97 | 280 | 0.9037 ± 0.0008 | 0.005 ± 0.002 | −2.17*** | −23.78** | 0.021*** | 14.26 | 1001.74 | 0.001 | |
| Philippines (ISEA) | 260 | 114 | 0.44 | 222 | 0.7706 ± 0.0078 | 0.006 ± 0.003 | −1.79** | −23.66** | 0.005 | 17.70 | 12.83 | 0.002 | |
| South China (Sth_China) | 65 | 60 | 0.92 | 133 | 0.8743 ± 0.0012 | 0.005 ± 0.002 | −1.75* | −24.29*** | 0.001 | 13.84 | 269.88 | 0.003 | |
| Taiwan Indigenous peoples (AN_Tw) | 426 | 128 | 0.30 | 164 | 0.8154 ± 0.0042 | 0.006 ± 0.003 | −1.42** | −23.53** | 0.004 | 16.24 | 34.70 | 0.003 | |
| Thailand (MSEA) | 560 | 333 | 0.59 | 326 | 0.8667 ± 0.0020 | 0.004 ± 0.002 | −2.18*** | −23.61** | 0.001 | 12.68 | 156.91 | 0.002 | |
| Vietnam (MSEA) | 603 | 260 | 0.43 | 280 | 0.8625 ± 0.0020 | 0.006 ± 0.003 | −1.95** | −23.43* | 0.006 | 16.82 | 145.19 | 0.001 | |
| West Indonesia (ISEA) | 326 | 227 | 0.70 | 259 | 0.8132 ± 0.0047 | 0.006 ± 0.003 | −2.05*** | −23.60* | 0.004 | 16.84 | 197.46 | 0.001 |
Complete mtDNA genomes from the litterature (Table 1) have been adjusted to match the partial sequence of the Taiwan dataset. Statistics were undertaken with Arlequin software using HVS-I (nps 16006 to 16569), and coding regions (nps 8001 to 9000 and 9801 to 10900).
Ur_Tw Urban Taiwanese (Taipei, Minnan and Hakka), LL_Tw (Lowland Taiwanese), MSEA Mainland Southeast Asia, ISEA Island Southeast Asia, NE_Asia Northeast Asia, Sth_China South China, AN_Tw Austronesian-speaking Taiwanese, H haplogroup/gene diversity (Nei M. Molecular evolutionary genetics. New York: Columbia University Press; 1987), π nucleotide diversity, MNPd mean pairwise difference, n sample size, M geneflow exchanged between demes, SE standard error.
*p ≤ 0.02, **p ≤ 0.01, ***p ≤ 0.001.