Research Article :

Mitochondrial DNA Polymorphisms of the Saisiyat Indigenous Group of Taiwan, Search for a Negrito Signature

Lan-Rong Chen, Jean Alain Trejaut, Ying-Hui Lai, Zong-Sian Chen, Jin-Yuan Huang, Marie Lin and Jun-Hun Loo

Abstract

Abstract

The genetic profile of Negritos of the Philippines differs from the non-Negrito groups with mitochondrial DNA haplogroups B4b1a2, B5, D6a, M, M52a, and N11b. Although Negritos are not seen in Taiwan, the strong genetic affinity between the Philippines and Taiwan Mountain Tribe Aborigines (TwMtA), and Folks tales of TwMtA, Saisiyat and Atayal recounting past contacts with Negritos, warrant the search for a Negrito signature in Taiwan.

Material and Method: Discriminant Analysis of Principal Component (DAPC) was used to determine the genetic relationship between TwMtA, Filipino and non-TwMtA groups.

Results: The deep coalescence of B4b1a2 in the Philippine Negritos, Saisiyat, Atayal, Island Southeast Asia, and SEA (Southeast Asia) suggested a deeply rooted common ancestry, but could not support a past Negrito presence in Taiwan. Conversely, the sharing of cultural components and mtDNA (mitochondrial DNA) haplogroup D6a2 in Saisiyat, Atayal and Philippine Negritos may characterize a Negrito signature in Taiwan. Although the molecular variation of D6a2 determines its presence in Taiwan back to middle Neolithic, other markers, Y-SNP haplogroups C-M146 and K-M9, warrant further analysis.

Conclusion:

Most likely, the physical characteristics, languages, and the genetic makeup of the Negritos in Taiwan have been diluted as the result of heavy migration from the mainland in the last 400 years.

Full-Text

Demographic Analysis

A bimodal curve was observed between 11 and 21 basepair differences in the mismatch distribution analysis of Saisiyat for 88 mtDNA sequences (Figure 2). The bimodal mismatch curve may have been the result of admixture. Further, in contrast with the Fu s Fs test, the plot did not support population sudden expansion [28]. Similarly, the hypothesis of sudden expansion was rejected by two demographic indexes, the Sum of Squared Deviation (SSD) test (SSD=0.008, P<0.001) and the raggedness (r=0.011, P<0.001) (Harpending 1994) indicating that the data deviated from the simulation expected under the model of expansion (Figure 2, blue line). The analysis (Number of pairs vs. Base pair differences) was obtained from 88 mtDNA Saisiyat sequences using nucleotide positions (nps) 8,000-9,000, nps 10,000-11,000, and Hyper Variable Segment I (HVS-I) nps 16040-16390 [22,24]. Using the Bayesian Skyline method, patterns of historical demography can also be inferred from estimates of the effective population size over time.

 

Figure 2: Mismatch Distribution Analysis (MMDA) of Saisiyat. 

Accordingly, we constructed a Bayesian Skyline Plot (BSP) plot (Figure 3) from 88 Saisiyat sequences of the mtDNA Hyper Variable Segment I (HVS-I) data, with 20 million Markov Chain Monte Carlo (MCMC) iterations, sampled every 3,000 steps, using a relaxed molecular clock and a mutation rate of 2.2964 x 10-7 mutations per site per year. The BSP showed an early Neolithic signature of population expansion, followed by a long phase of relatively constant population size and a sudden steep population reduction around 500 years BP. The Saisiyat present-day effective population obtained in Figure 3 is approximately 340 women (CI 100 to 1120 women) [29].

Figure 3: Bayesian Coalescent Skyline analysis of the Saisiyat tribe. 

Bayesian Skyline Plot (BSP) plot based on the mtDNA obtained from 88 Saisiyat sequences for the HVS-I control region. BSP was calculated using a relaxed molecular clock and a mutation rate of 2.2964 x 10^-7 mutations per site per year and estimated with 20 million MCMC iterations sampled every 3,000 steps. The dark blue line represents the posterior median of the effective population size through Time (one generation=25 years). The light blue lines represent the 95% confidence interval. 

MtDNA Haplogroup Distribution

Out of 20 mitochondrial haplogroups seen in Saisiyat (Figure 4), 15 were uniquely shared with the other the Austronesian speaking groups of Taiwan, and five haplogroups (B5a2a2a2, E1a1a1, F4b1 , M7b1a2a and Y2) had a frequency greater than 8% representing 75% of the Saisiyat gene pool. Interestingly, haplogroups D6a2 was only seen in Saisiyat (1.1%), Atayal (4.6%), reported in a single individual of the Pazeh plain tribe, and the Mamanwa Negritos from the Philippines (3.3%) [14,24].

Figure 4: Haplogroup frequency in Saisiyat shared with other populations.

 

Distribution of shared mtDNA haplogroups of Saisiyat constructed using Taiwan data and other relevant populations [24]. Haplogroups with a shade of grey represent sharing with non-Indigenous groups of Taiwan (Minnan and Hakka). All haplogroups not seen in Saisiyat but present in other groups are represented by other .

 Population Differentiation

Discriminant Analysis of Principal Components (Figure 5) showed a clear geographic divide along the first Discriminant component (the X axis), which form a separates the Austronesian-speaking groups on the right, from the Han, the TwH, and MSEA (Indochina) on the left. Further, although individuals were not tightly grouped, the Northern and Central TwMtA form a cluster that clearly separates them from a lower cluster encompassing Southern TwMtA and the Philippines. Finally, we note that the Southern Austronesian cluster (Southern TwMtA and the Philippines) shows more admixtures with TwH than the Northern cluster.

Figure 5: Scatter plot from DAPC from SNPs of mitochondrial DNA of Taiwan and the East Asian populations.

 

The dots represents individual from eight different groups and locations whose inertia ellipses are characterized by a color as indicated in the insert on the left. Sampling locations are: NTwMtA: North Taiwan Mountain Tribe Aborigines (TwMtA); CTwMtA: Central TwMtA; STwMtA: Southern TwMtA; TwH: Taiwan Han (Minnan and Hakka); MSEA: Mainland Southeast Asia (Indochina); Ph: Philippines; Han: Fujian. 

Phylogenetic Analysis

A maximum-likelihood tree using mtDNA haplogroup frequencies was inferred with the TreeMix software (Figure 6A). The tree was consistent with the geographical distribution of populations in Taiwan; it places Saisiyat in a strong relationship with the Northern tribes (Atayal and Taroko). Further, migration arrows were first limited to 20 migration events in the analysis and only the three most significant gene flow events were retained for clarity of (Figure 6B). The relationship delineated between Saisiyat and the central TwMtA (Thao and Bunun) was expected from the DAPC clustering shown in Figure 5. More interesting, was a significant input from the Philippines to Taiwan, consistent with a previous study [20]. And here seen as gene flow to Saisiyat with a migration weight of ~ 0.65 (Figure 6). Most likely, this result is the effect of the sharing of haplogroups B4a2a, E2b, M7b1a2a, D6a2, R9c1a and Y2 between Saisiyat and the Philippines (Figure 4). 

6A: Maximum-Likelihood tree inferred by TreeMix for all Taiwan and SEA populations assuming 20 significant gene-flow events, only the three most significant gene-flow events are shown for clarity, they are colored according to their weight on a zero to one scale [30]. 6B: Residual fit from A. Shaded colored cells represent Standard error for admixture events across all pairs of populations. Population pairs with a residual above zero are more closely related and more likely to correspond to an admixture event.

Figure 6: Derived origin of admixture for Taiwan populations using TreeMix.

 Discussion 

In the first stage of this work, we examined the genetic variability using mitochondrial nucleotide positions (nps) 8000 to 9000 and nps 10,000 to 11,000 of the coding regions, and the HVS-I segment of the D-loop region to determine the genetic diversity and origin of the Saisiyat tribe of Taiwan. In the second stage, we investigated the general believed that Negrito groups predating the Lower Glacial Maximum period were associated with the first settlers of Sunderland/Island Southeast Asia (ISEA) [9]. 

Although there are some Chinese accounts of small, dark-skinned people with curly hair in Taiwan, to date, Taiwan has no archeological human remains supporting this hypothesis. Interestingly, most Taiwan Mountain tribes have kept folk tales describing past contacts with Negrito groups, most particularly the Saisiyat tribe of Hsinchu and Miaoli (Figure 1) who still perform solemn rites to commemorate this past. On the other hand, the presence of Negrito is still existent in the Philippines and other parts of peninsular East Asia, but not in Taiwan. If there is any truth in these TwMtA folk tales, then a small number of Negrito in Taiwan must have interacted with Neolithic agriculturalist migrants from the Southeast Asian mainland and most likely shaped their genetic diversity. In this regard, it is sensible to expect that these early contacts must have left some genetic traces. Here, our analysis of mtDNA polymorphisms tries to provide new insights into the history of the Saisiyat tribe [31,32]. 

Genetic Structure of Saisiyat

To investigate the mtDNA structure of Saisiyat, we first generated a mismatch distribution (Figure 3). A bimodal curve was obtained, and the two demographic indexes, the SSD test (SSD=0.008, P<0.001) and the raggedness (r=0.011, P<0.001) were significantly different to expectation. These results did not support expansion. Further, the Bayesian Skyline plot (Figure 4) along with previous results from Ko s research group did not reveal sufficient structure to visualize a recent population expansion. These results were in contrast with a highly significant Fu s Fs test for the Saisiyat tribe [22,28,33]. 

It possible these results are revealing a sign that the Saisiyat tribe experienced prehistorically a rapid population growth from an ancestral population with a small effective population size. Alternatively, the excess of rare mutations indicated by the significant negative Fu s Fs test could be the result of recent gene flow introduced by non-indigenous groups of Taiwan, such as the Minnan and Hakka. Finally, The BSP indicated an effective population of approximately 1400 women. This number may actually be inflated since our data set was collected by LM in 2004, but does not conflict with previously published BPSs, nor with the actual present-day number of Saisiyat women indicated in the last Census from the Taiwan Council of Indigenous Peoples [1,2,22]. 

Distribution

The mtDNA composition of the Saisiyat: Out of 21 different mtDNA haplogroups, 15 haplogroups were characterized as northern TwMtA haplogroups. Four haplogroups, F2a, E1a1a1, M7b1a2a and Y2 (Figure 4), constituted 75% of the Saisiyat genome. Consistent with other extant Taiwan Mountain tribes, the Saisiyat tribe 29% of its mtDNA genome was shared with Non-Taiwan Aborigines (Supplementary Table S1) and were most likely acquired from migrants of Mainland East Asia in the last 400 years. 

Most of the remaining haplogroups were commonly seen throughout Taiwan Northern tribes. Among them, B4a2a, E2b, M7b1a2a, R9c1a, and Y2 were also seen in the Philippines. They are thought to represent a plausible signal for a mid-Holocene out-of-Taiwan expansion or a signal for a bidirectional migration between Taiwan and the Philippines [18,20,22,24,34-37]. The distribution of haplogroup D6 was intriguing. With a coalescence time of 14,390 years BP (Supplementary Table S1 and Figure S1) haplogroup D6 was seen at low frequency as D6c in East Asia and Southeast Asia (SEA). The presence of D6a2 as a single individual in the Pazeh plain tribe, in Saisiyat (1.1%), in Atayal (4.6%) and in the Mamanwa Negrito group of Mindanao in the Philippines (3.03%) could represent a genetic indicator of a past Negrito presence in Taiwan. However, a coalescence age estimate of D6a2 (2,626 years BP, CI 0-5,850) makes this supposition doubtful. It is possible the sharing of D6a2 between Saisiyat/Atayal and the Mamanwa must be the result of more recent gene flow. 

It is conceivable that the bearers of D6a have experienced a bottleneck between 2,600 and 12,000 years BP, as suggested by the long stretch of nucleotide variation between D6a and D6a2 in their mtDNA genome (Supplementary Table S1andSupplementary Figure S1). Lastly, mtDNA haplogroup Y2 is also shared between the Mamanwa and the Saisiyat and Atayal tribes. Nonetheless, its distribution in the Philippines (Negritos and non-Negritos) and its coalescence age estimate (5216 years BP, CI: 529-10046), characterize Y2 as a signature of the Neolithic expansion of Austronesian agriculturists in insular East Asia rather than a Negrito signature [14,15,17-21,24,34,38,39]. 

Principal Component Analysis

To characterize population structure across Saisiyat, other Taiwan groups, and their relationship with neighboring populations in MSEA and the Philippines, we performed a DAPC (Figure 5). The first component captured a clear geographical divide between Austronesian speaking groups and non-TwA groups including Fujian, Minnan, and Hakka. Component 2 in Figure 5 disclosed a strong affinity between Northern and Central TwMtA, and between the Philippines and the Southern TwMtA, suggesting that all these Austronesian-speaking populations have a common origin. However, the mtDNA composition of the Saisiyat suggested evidence supporting genetic affinity between Saisiyat and Negrito and non-Negrito groups of the Philippines. 

Using Delfin mtDNA and our Taiwan data set we constructed a Multidimensional scaling plot to establish this relationship (Supplementary Figure S3). While the relationship between populations was the same as in the DAPC plot, the Aeta and Agta Negrito groups were outbound, most likely because of the conjoint results of drift, the presence of high frequency haplogroups such as P and M52 in Aeta and Agta, and long isolation [14]. On the other hand, haplogroup B4b1a2, E1a1a1, Y2, and D6a in the Mamawan group inferred strong affinity of the Mamanwa Negritos with other Austronesian groups, suggesting a more recent gene-flow of Austronesian-speakers in the Mamawa. 

Maximum Likelihood Tree from TreeMix

TreeMix results inferred mtDNA gene-flow events (Figure 6) potentially summarizing patterns of population in the history of Taiwan such as bottlenecks, isolation, consanguinity within populations, here Saisiyat was characterized as a northern Taiwan tribe. Further, the gene-flow from Saisiyat (or the Northern TwMtA) to the Central TwMtA (Bunun, Thao, and Tsou) was previously foreseen in Figure 4 and 5, and is confirmed in Figure 6 [30]. Moreover, the strong migration event depicted by TreeMix from the Philippines to Saisiyat indicates genetic interflow. The mtDNA haplogroups possibly associated with this event, and seen in Saisiyat/Atayal and the Mamanwa Negrito group of the Philippines, can only be attributed to subtypes of haplogroups B4b1a2, E1a1a1, Y2, and D6a2. 

These findings substantiate a possible past existence of Negritos in Taiwan. They suggest that the Mamanwa are intermediate between Austronesian and Negritos (Supplementary Figure S3) and possibly experienced several admixture events in the past. This option is nonetheless not supported by the age estimate of molecular variation obtained for any of the haplogroups of the same clade between Mamanwa and Saisiyat/Atayal. For example, D6a2 dates only to 2600 ± 1500 yrs BP (Supplementary figure S1) and Y2 dates 3956 ± 2455 yrs BP (Supplementary figure S2). One possible way to demonstrate a Negrito ancestry in Taiwan associated to D6 or Y2 would be to find sister branches of these haplogroups in Taiwan and/or the Philippines that would allow a coalescent node in the pre-Holocene period.

 

Other Gene Systems

Supporting this last observation, our previous Y chromosome analysis observed 4 Y-chromosome single nucleotide polymorphism (Y-SNP) haplogroups out of 24 unrelated Saisiyat males (Supplementary Table S1). Only one major haplogroup O1a1^* (P203) had a frequency of 87.5%, while all other haplogroups (O1a2 (M50/110, O3a1^* (KL1/122) and O3a2c1a (M133/M7/M134) were seen only once (4.2%) [21]. When compared to the Y haplogroup profile of the Philippines, O1a1^* (P203) was prevalent in all Filipino ethnolinguistisc groups, Negritos and non-Negrito and its presence in any Negrito groups was regarded as an admixture with the former. Most interestingly, Negrito groups in the Philippines invariably possessed, to various levels, haplogroup haplogroups C-RPS4Y/M216, K-M9, and O3-M122 [15]. These haplogroups have  not been seen in Saisiyat, but single observations of C-RPS4Y/M216 and K-M9 have been seen in the Taiwan plain tribes and could support a past presence of Negrito in Taiwan [15,21].

Lastly, to our knowledge, no previous studies associating the Filipino Negrito groups and the HLA gene system have yet been published; accordingly, no Negrito HLA inferences could be used for Taiwan. Nonetheless, several HLA^*A-B-DRB1 haplotypes were unique to Saisiyat and 1/3 of Saisiyat haplotypes were shared with Atayal (Supplementary Table S1). Lastly, the sharing of haplotype HLA A^*34:01-B^*56:01 or simply the sole presence of A^*34:01 between Amis, Papua New Guinea highlanders, Maoris of New Zealand, and Australian Aborigines is intriguing. These findings suggest that HLA A^*34:01 could be a genetic indicator of the pre-dispersal period of the Negrito throughout ISEA in the late Pleistocene era and should warrant further HLA analysis of the Philippines Negritos [3,6,40,41]. 

Summary 

This investigation has contributed substantially more insights into the population groups in Taiwan and the Philippines. Further, while the physical appearance of Negritos has never been seen in Taiwan, few Taiwan Mountain tribes, such as the Saisiyat and the Atayal tribes, have conserved folktales inferring prehistoric co-habitation with them, and to this day, still celebrate this period bi-annually. Among the few mtDNA haplogroups shared between Taiwan Northern tribes and the Mamanwa Negritos (B4b1a2, E1a1a1, Y2 and D6a) only D6a may represent a common Negrito genetic legacy of the Saisiyat and Atayal tribes. This finding must be taken with caution, as the mid-Neolithic coalescence age estimate of D6a is too shallow. Further, no support was given from the Y chromosome analysis for Saisiyat and Atayal. Although the apparent affinity between the Taiwan Northern tribes and the Mamanwa Negritos of the southern Philippines could be the result of gene flow brought upon by bidirectional population movements at the time of the out of Taiwan, the presence of C-RPS4Y/M216 and K-M9 in Taiwan were scarce, and warrant more extensive studies of the Taiwan gene pool in the future. 

Material and Method 

Samples

Whole blood or saliva specimens were collected from 2704 unrelated individuals (Table 2) comprising Austronesian speaking groups from the Philippines (n=372), 251 TwMtA consisting of Saisiyat (n=88), Atayal (n=109 ) and Taroko (n=54), 271 central TwMtA consisting of Thao (n=30), Tsou (n=60) and Bunun (n=181), and 732 southern TwMtA consisting of Rukai (n=77), Paiwan (n=168), Puyuma (n=107), Amis (n=92) and the Yami islanders (n=88). The sampling also included 752 Taiwanese of Han descent (TwH) namely Minnan (n=599) and Hakka (n=153). Samples from neighbor populations included Han individuals from the east coast of China (Fujian, n=149), groups from Mainland Southeast Asia (MSEA, n=177), namely Vietnam (n=58), Thailand (n=77) and Akka (n=42), and finally 372 individuals from the Philippines as described in Tabbada. All samples above were collected from volunteers with individual written informed consent during the period of 2001 to 2004 by ML under approval of the Ethics Committee of the Mackay memorial hospital after giving information regarding the origins of their parents and grandparents [3,6,20].

Table 2: Population samples. 

Data Analysis

All collected samples in our dataset were typed for Human Leukocyte Antigens (HLA-A, -B and -DRB1) and described in the Anthropology/HLA diversity component of the 13th international histocompatibility workshop. Specimen typed for mtDNA had haplogroups assigned according to Build 17 of Phylotree. Y haplogroups of the non-recombining part of the Y-chromosome (NRY) were determined using 81 Y-SNPs, and further analyzed using 17 Y-chromosome short tandem repeats (Y-STRs): DYS19, DYS385I, DYS385II, DYS389I, DYS389II, DYSS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, and Y GATA-H4. Additionally, we used corresponding mtDNA data from the literature including 24 complete mtDNA genome sequences representing Saisiyat [20-22,24,42,43].The partial mtDNA sequences are available in (Supplementary Table S2) The whole-mtDNA genome sequencing is available in Supplementary Text File S1. We deposited 2 new whole- mtDNA sequences in GenBank. 

Statistical Analysis

In order to test for past population expansion of Saisiyat, we used two statistical tests Tajima s D and Fu s Fs [33,44]. The analyses were implemented in Arlequin 3.5.2.2, and p-values were generated using 1,000 simulations under a model of selective neutrality [45]. 

In addition, a mismatch frequency graph was plotted by using the mtDNA data from Arlequin 3.5.2.2 to determine whether the population of Saisiyat exhibited evidence of spatial range expansion or a stationary population history [44]. Demographic variation through time was obtained from a BSP using Beast with a relaxed molecular clock and a mutation rate of the mtDNA HVS-I data of 2.2964 x 10^-7 mutations per site per year. Adegenet for R was used to perform DAPC with a number of Principal Components set to 273. The DAPC plot and inertia ellipses were produced using the poppr module of the R package. A maximum likelihood tree using mtDNA SNP frequencies was inferred with the TreeMix software. Admixture and direction of gene flow were inferred using the 20 most significant events [29,30,46-48]. 

Acknowledgements

We are grateful to the people of Taiwan for donating their blood. 

Authors contributions

The project was conceived and designed by JAT. JAT and LRC drafted the manuscript equally. LRC performed data analysis. The laboratory work was performed by ZSC and YHL. All authors have read and approved the final version of the manuscript.

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^*Corresponding author

Keywords

Molecular Anthropology, Negrito, Austronesian, Population genetics, Saisiyat, Taiwan aborigines, Mitochondrial DNA.