Population genetic study among the Orang Asli (Semai Senoi) of Malaysia: Malayan aborigines

Population genetic study among the Orang Asli (Semai Senoi) of Malaysia: Malayan aborigines

Saha, N

N. SAHA,(1) H.W. MAK,(2) J.S.H. TAY,(1) J.A.M.A. TAN,(1) P.S. LOW,(1) AND M. SINGH(3)

The aboriginal populations in the Malaysian peninsula are known as Orang Asli, meaning “original people.” The Senoi are one of the three main aboriginal groups, the others being Negrito and Proto-Malay. The Senoi Semai are the most numerous, numbering about 15,000 people living in about 200 settlements located in the hilly jungle areas of the Malayan peninsula, 4000-7000 ft above sea level (Dentan 1968; Carey 1976). The Semai speak an Austro-Asiatic language related to the Mon-Khmer group (Lebar et al. 1964). Each of the subgroups has its own dialect. The Senoi language differs considerably from the Malay language, although some Malay words have been incorporated. The Semai practice the swidden form of agriculture and cultivate rice, tapioca, millet, and banana. They also fish and hunt using blowpipes with poison darts. Each settlement has its own saka, or communal area. The Semai are normally exogamous with bilateral inheritance, and the society has strict taboos on violence (Dentan 1968; Carey 1976).

The Semai are shorter and darker than the Malays and have broader noses. They have been variously described as a mixed Mongoloid-Australoid population (Coon 1965) or related to the Veddah of Sri Lanka (Hughes 1965). Intermarriage between Semai women and Chinese men and rarely between Semai men and Malay or Indian women has been recorded in the more acculturated areas and is reflected in the physical diversity of the Semai.

The ethnohistory of the Semai is obscure, but it is generally believed that they are aboriginal inhabitants of the Malayan peninsula. The Semai have a long history of trade in forest produce and iron tools with other Orang Asli and with the Malays.

Although several studies have been carried out among the Orang Asli, mostly in the Semai, in the past no systematic population genetic study has included more recently described isoelectric variations of blood genetic markers. Most of the studies have been restricted to the distribution of blood groups (Polunin and Sneath 1953; Fix and Lie-Injo 1975; Lie-Injo 1976), hemoglobin, and glucose-6-phosphate dehydrogenase (G6PD) (Bolton and Lie-Injo 1969; Clegg et al. 1971; Fessas et al. 1972; Fix and Lie-Injo 1975; Lie-Injo 1965; Lie-Injo and Chin 1964; Lie-Injo and Ti 1964; Lie-Injo et al. 1971, 1972, 1973; Baer et al. 1976). Limited information is available on the distribution of red cell enzymes and serum proteins in Malayan aborigines (Lie-Injo and Welch 1972; Lie-Injo et al. 1967; Welch et al. 1972; Welch 1973). A detailed study on the different aspects of the population structure of the Semai has revealed a considerable degree of spatial heterogeneity (Fix 1971, 1975, 1982, 1984).

In view of the scanty information on blood genetic markers in general and no information on isoelectric variations in Malayan aborigines, we carried out this detailed study of red cell enzyme and plasma protein polymorphisms in a group of Senoi Semai from the Pahang State of Malaysia and carried out genetic distance and principal components analyses to establish genetic affiliation between the Semai and the neighboring populations .

Materials and Methods

Blood samples were collected from 349 male and female Senoi Semai, 5 to 70 years of age, in 11 settlements (villages) in the Pahang State of western Malaysia (Figure 1). (Figure 1 omitted) Five milliliters of blood was collected from each subject and brought to the Institute for Medical Research, Kuala Lumpur, Malaysia, at wet-ice temperature. Packed cell and plasma samples were separated and stored in liquid nitrogen until brought to Singapore packed in dry ice. Red cell enzyme and plasma protein typing was carried out by electrophoretic and isoelectric separation, following methods similar to those described earlier from this laboratory (Saha 1989). The gene frequencies at the polymorphic loci were calculated by the gene counting method. Hardy-Weinberg equilibrium was tested by chi-square tests.

The genetic relations between the Senoi Semai of the present series and 14 other neighboring or ethnohistorically related populations (Malay; Javanese; Chinese; Koreans; Japanese; Tamils of Malaya, India, and Sri Lanka; Sinhalese; Khmer; Veddah; Oraon; Irula; Toda) were studied by genetic distance and principal components analyses using gene frequency data (Nei 1972; Nei and Roychoudhury 1974). The main constraint in selection of the populations in the context of the ethnohistory was the availability of comparable data in the literature. By and large we have tried to use the data generated from our own laboratory for the sake of uniformity in methodology, with due regard to other publications. It was not possible to study the genetic relationships using all the loci in all populations. As such, the results are presented in two steps: first, an analysis using all 15 populations using 7 polymorphic loci, and, second, an analysis using 13 polymorphic loci in 11 populations.

Furthermore, analyses were carried out both with and without the hemoglobin and G6PD loci for supposed selection implications of these two loci. In both analyses the results and interpretation were similar. As such, in the final presentation the results on the basis of all the available loci are presented.

The data sources for gene frequencies are given as notes to Table 4. (Table 4 omitted) The dendrograms were derived from the distance matrix using the cluster and tree procedures employing the minimum variance method (Ward 1963). The eigenvector representation was derived from the first two principal components based on gene frequencies (Hotelling 1933; Mardia et al. 1979) using the SAS software package on an IBM 3090 computer.

Results and Discussion

Hemoglobin. The distribution of hemoglobin and red cell glucose-phosphate dehydrogenase (G6PD) in the Senoi Semai is presented in Table 1. (Table 1 omitted) The high frequency of HB*E (0. 19) observed in the present series is consistent with that reported in the Semai of Pahang and in Perak State of Malaysia (0.22 and 0.25, respectively). The Temiar had a still higher frequency of HB*E (0.32), whereas the Temuan had a low frequency of HB*E (0.02) (Baer et al. 1976). Similar high frequencies of HB*E have been observed in the Khmer of Thailand and Cambodia (Lie-Injo 1965, 1969; Livingstone 1985) and in the Veddah of Sri Lanka. However, the Malays, Indians, and Chinese have a low frequency of HB*E.

A low frequency of Hb sup CoSp (0.01) has been observed in the Senoi Semai of the present series, although it was not detected in earlier series of Senoi Semai. A low frequency of Hb sup CoSp has been reported among the aboriginal Malay (Temuan, Jakun), the Malays, and the Batak of northern Sumatra in frequencies ranging from 0.001 to 0.015. This allele was not reported in the Khmer, Thai, and Vietnamese (Bowman et al. 1971; Flatz 1967). However, because of instability and low concentration, Hb sup CoSp could have been missed in some of the earlier studies.

The frequency of HB*BO was low in the Senoi Semai of the present series, as reported earlier (Lie-Injo 1976).

Red Cell G6PD. The frequency of G6PD deficiency in males has been found to be 0.16. A similar high prevalence of G6PD deficiency has been reported in the Semai of Perak and the Temuan (0.22). The other aboriginal populations of Malaysia had a frequency of Gd– ranging from 0.08 to 0.18, although the Negrito had a very low frequency of Gd– (0.02).

A unique, nondeficient G6PD variant (Gd sup Orang Asli ; G6PD*OA) has been observed at a frequency of 0.03 with about half the mobility of the common G6PD*B allele in TEB buffer (pH 8.6). This variant may be a private allele of the Malayan aborigines. Another slow nondeficient G6PD variant also has been observed in the Semai at a frequency of 0.02. In the females three heterozygotes with both variants have been observed (results not shown). These two nondeficient variants have not been characterized by detailed biochemical studies. No study has been carried out on the distribution of electrophoretic variants of G6PD among the Orang Asli. A detailed molecular characterization of these two variants is in progress and will be reported separately.

A high frequency of G6PD deficiency has also been reported among the Javanese, Khmer, and Thai, whereas the frequency Gd– was low among the Malays (0.02), Chinese (0.01), and Veddah of Sri Lanka

Red Cell Enzymes. Table 2 shows the distribution of electrophoretic variation of four red cell enzymes [acid phosphatase (ACP), esterase D (ESD), glyoxalase I(GLO1), and 6-phosphogluconate dehydrogenase (PGD)] and the isoelectric variation of phosphoglucomutase-1 (PGM1).

Acid Phosphatase. The frequency of ACP*A was 0.35 in the Semai, similar to that in the Khmer, Malay, Javanese, and Thai, whereas it was lower in the Chinese, Tamils, and Oraon. No information on the distribution of ACP is available in other aboriginal populations of Malaysia or the Veddah of Sri Lanka.

The frequency of ACP*C in the Semai is O. 12. ACP*C is reported to be absent in the neighboring populations or of low frequency, as in the Khmer, Malay, and Chinese.

A low frequency of ACP*D (0.01) has been observed in the present Semai population.

Esterase D and Glyoxalase I. The frequency of ESD*1 was found to be lower in the Semai (0.56) than in the Malays, Javanese, Chinese, and Tamils. The Khmer and the Oraons had a frequency of ESD*1 intermediate between these two groups (0.62 and 0.60).

The frequency of GLO1*1 in the Semai was higher (0.35) than that in the Malays, Javanese, Tamils, Chinese, and Khmer but similar to that in the Oraons (0.36).

6-Phosphogluconate Dehydrogenase. The frequency of PGD*C was found to be 0.02, which is similar to that in Khmer, Javanese, Chinese, Tamils, and Oraon but significantly lower than that in Chinese, Koreans, and Japanese. A variant form (PGD*F) has been observed in polymorphic frequency in the Semai of the present series (0.03) and appears to be a private allele. The mobility of the variant band appears to be similar to that of PGD sup Sinapore described earlier, although it needs to be confirmed by direct comparison (Blake et al. 1974). However, this is the third variant form of PGD, besides PGD*C, present in polymorphic frequency that might be a private allele; the other two variants are PGD sup Elcho in Australian Aborigines and PGD sup Kadar in the Kadar tribe of India (Saha et al. 1974).

Phosphoglucomutase-1 . The frequency of PGM1*2+ in the present Semai population is significantly higher (0.33) and the frequencies of PGM1*2– and PGM1*1– are lower than the frequencies found in other neighboring populations, including the Khmer. The combined frequency of PGM1*2 (0.37) is similar to that reported in the earlier series of Semai (Lie-Injo et al. 1976). A low frequency of PGM1*6 was also observed in the Semai.

Plasma Proteins. The results of the analyses for haptoglobin, transferrin, and group-specific component are given in Table 3. (Table 3 omitted)

Haptoglobin. The Semai are characterized by a very high prevalence (36%) of ahaptoglobinemia (HP*O). A similar high frequency of HP*O (17%) has been reported in Temuan (Baer et al. 1976) and in proto-Malays (Kirk and Lai 1961). The high frequency of HP*O has been partly attributed to malaria. Ahaptoglobinemia is sometimes misinterpreted because of hemolytic manifestations in the presence of malaria, making it indiscernible on gels, or may be due to a lower level of haptoglobin in the plasma. In the present study all the ahaptoglobinemia plasma samples have been confirmed by electroimmunoassay of haptoglobin concentration with specific anti-human haptoglobin. None of the ahaptoglobinemic samples had detectable haptoglobin. This raises an important question of the physiological role of haptoglobin in compensating for alternative plasma proteins. Furthermore, studies on the etiological role of malarial infection in the low production or lack of plasma haptoglobins are in progress.

The frequency of 0.37 for HP*1, excluding the ahaptoglobinemic individuals, is rather high for Asian populations, in which it varies between 0.16 and 0.30. The Khmer, Veddah, and other tribes of India, with the exception of the Toda, have a much lower frequency of HP*1. A high frequency of HP*1 has also been reported in the Temuan and proto-Malays (Lie-Injo 1976).

Transferrin Subtypes. A very low frequency of TF*D,CHI (0.01) has been observed in the present Semai population in contrast to the frequencies of 0.04 observed in the Malays and 0.09 observed in the Javanese. The Khmer have a frequency of TF*D,CHI of 0.03, whereas the Veddah and Oraon have higher frequencies (0.08 and 0.07, respectively). The frequencies of TF*C1, TF*C2, and TF*C3 were 0.75, 0.24, and 0.05, respectively, and were similar to those in the Khmer, Javanese, and Chinese. The Tamils had a lower frequency of TF*C2, whereas the frequency was higher in the Oraon (0.28). No previous study of isoelectric variation of transferrin in Malayan aborigines has been done.

Group-Specific Component Subtypes. The frequency of GC*2 is found to be very low (0.06) in the Semai compared with the neighboring populations. The Khmer and Veddah have GC*2 frequencies of 0.24 and 0.26, respectively, and the Malays and Javanese have an intermediate frequency of 0.18. The plasma GC system has not been studied in the Malayan aborigines before.

The frequency of GC*1F in the Semai is significantly higher (0.63) than that in the Khmer (0.46) and other neighboring populations (0.40–0.53).

Monomorphic Systems. No variation was observed at the albumin, adenylate kinase, phosphoglucose isomerase, lactate dehydrogenase, malate dehydrogenase, phosphoglucomutase locus 2, and superoxide dismutase loci in the Semai investigated in this study.

Hardy-Weinberg Equilibrium. The phenotypic distribution of all the polymorphic loci in the Semai were at Hardy-Weinberg equilibrium.

Average Heterozygosity. The average heterozygosity in the Semai of the present series is found to be 0.31 +/- 0.07 or 0.4 +/- 0.04, based on 30 or 53 alleles (Tables 5 and 6), respectively. (Tables 5 and 6 omitted) The average heterozygosity shows a general trend of increase in all the populations studied when the estimates include isoelectric polymorphisms.

Genetic Distance of the Senoi Semai, The gene frequencies used for the genetic distance and principal components analyses are given in Table 4.

The genetic distance matrix of the Senoi Semai with the other 14 populations based on 30 alleles at 7 polymorphic loci is presented in Table 5, and the derived dendrogram is presented in Figure 2. (Figure 2 omitted) A second distance analysis of the Semai with 10 populations based on 53 alleles at 13 polymorphic loci is presented in Table 6 and Figure 3. (Figure 3 omitted)

The dendrogram in Figure 2 shows two major clusters. (Figure 2 omitted) The first cluster is formed by the Khmer and the Senoi Semai. The second major cluster comprises two subclusters, one of which is composed of the Veddah and Toda of South India; the other subcluster has three branches: the Tamils of Malaya, India, and Sri Lanka and the Sinhalese; the Koreans, Japanese, Malays, and Chinese; and the Javanese and Oraon.

The second genetic distance analysis produced similar results (Table 6; Figure 3). The dendrogram of Figure 3 shows two major clusters. The first cluster is composed of the Senoi Semai, Javanese, and Khmer. The second major cluster has two subclusters: (1) the Tamils of Malaysia, Sri Lanka, and India and the Sinhalese and (2) the Koreans, Japanese, Malays, and Chinese.

The relationships between the Senoi Semai and the relevant populations were also examined by principal components analysis. The eigenvector diagrams derived from the first two principal components are presented in Figures 4 and 5. (Figures 4 and 5 omitted) Both eigenvector diagrams confirm the relationships of the population established by the genetic distance estimates.

The conclusion derived from the present genetic study is compatible with linguistic evidence that the Semai language is affiliated with the Mon-Khmer group of Austro-Asiatic languages (Dentan 1968). The evidence for the alternative suggestion of affiliation of the Semai with the Veddah is completely lacking in the present study. The lack of an appreciable genetic relationship between the Semai and the neighboring Malays, Chinese, and Indians is quite interesting and suggests some genetic isolation of the Semai from their neighbors despite their geographic proximity and history of trade contacts. Roychoudhury and Nei (1985) also observed little genetic contribution to the Chinese and Malay of Southeast Asia from populations of India. However, from an analysis of mitochondrial DNA Ballinger et al. (1992) observed genetic continuity of ancient Mongoloid migration to Southeast Asian populations.

Acknowledgments We thank the participants for ready cooperation in this project. The excellent technical assistance of Jumiah Bte Basair of the Department of Paediatrics, National University Hospital, and the staff of the Biotechnology Centre of the Institute for Medical Research is recorded with gratitude. We would also like to thank Mohd Ali, Director of Gombak Hospital, for his support and M. Jegathesan, Director of the Institute for Medical Research, Kuala Lumpur, Malaysia, for his permission to publish the results. The study was generously supported by grants from the National University of Singapore and the Research and Development Fund, National Science Council, Ministry of Science, Technology, and Environment, Malaysia (Project 91-26). Secretarial assistance by Tay Siew Leng is gratefully recorded.

1. Department of Pediatrics, Division of Human Genetics, National University of Singapore, Singapore 0511.

2. Institute for Medical Research, Kuala Lumpur, Malaysia.

3. Department of Microbiology, National University of Singapore, Singapore 0511.

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