Table 3 Molecular Diversity.

From: Diversity and distribution of mitochondrial DNA in non-Austronesian-speaking Taiwanese individuals

	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 = N_em)	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.

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Table 3 Molecular Diversity.

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