Pygmy Populations Research Articles

HapMap tagSNP transferability in multiple populations: General guidelines

Linkage disequilibrium (LD) has received much attention recently because of its value in localizing disease-causing genes. Due to the extensive LD between neighboring loci in the human genome, it is believed that a subset of the single nucleotide polymorphisms in a region (tagSNPs) can be selected to capture most of the remaining SNP variants. In this study, we examined LD patterns and HapMap tagSNP transferability in more than 300 individuals. A South Indian sample and an African Mbuti Pygmy population sample were included to evaluate the performance of HapMap tagSNPs in geographically distinct and genetically isolated populations. Our results show that HapMap tagSNPs selected with r 2 >= 0.8 can capture more than 85% of the SNPs in populations that are from the same continental group. Combined tagSNPs from HapMap CEU and CHB+JPT serve as the best reference for the Indian sample. The HapMap YRI are a sufficient reference for tagSNP selection in the Pygmy sample. In addition to our findings, we reviewed over 25 recent studies of tagSNP transferability and propose a general guideline for selecting tagSNPs from HapMap populations.

Maternal traces of deep common ancestry and asymmetric gene flow between Pygmy hunter–gatherers and Bantu-speaking farmers

Two groups of populations with completely different lifestyles-the Pygmy hunter-gatherers and the Bantu-speaking farmers-coexist in Central Africa. We investigated the origins of these two groups and the interactions between them, by analyzing mtDNA variation in 1,404 individuals from 20 farming populations and 9 Pygmy populations from Central Africa, with the aim of shedding light on one of the most fascinating cultural transitions in human evolution (the transition from hunting and gathering to agriculture). Our data indicate that this region was colonized gradually, with an initial L1c-rich ancestral population ultimately giving rise to current-day farmers, who display various L1c clades, and to Pygmies, in whom L1c1a is the only surviving clade. Detailed phylogenetic analysis of complete mtDNA sequences for L1c1a showed this clade to be autochthonous to Central Africa, with its most recent branches shared between farmers and Pygmies. Coalescence analyses revealed that these two groups arose through a complex evolutionary process characterized by (i) initial divergence of the ancestors of contemporary Pygmies from an ancestral Central African population no more than approximately 70,000 years ago, (ii) a period of isolation between the two groups, accounting for their phenotypic differences, (iii) long-standing asymmetric maternal gene flow from Pygmies to the ancestors of the farming populations, beginning no more than approximately 40,000 years ago and persisting until a few thousand years ago, and (iv) enrichment of the maternal gene pool of the ancestors of the farming populations by the arrival and/or subsequent demographic expansion of L0a, L2, and L3 carriers.

Life history trade-offs explain the evolution of human pygmies

Explanations for the evolution of human pygmies continue to be a matter of controversy, recently fuelled by the disagreements surrounding the interpretation of the fossil hominin Homo floresiensis. Traditional hypotheses assume that the small body size of human pygmies is an adaptation to special challenges, such as thermoregulation, locomotion in dense forests, or endurance against starvation. Here, we present an analysis of stature, growth, and individual fitness for a large population of Aeta and a smaller one of Batak from the Philippines and compare it with data on other pygmy groups accumulated by anthropologists for a century. The results challenge traditional explanations of human pygmy body size. We argue that human pygmy populations and adaptations evolved independently as the result of a life history tradeoff between the fertility benefits of larger body size against the costs of late growth cessation, under circumstances of significant young and adult mortality. Human pygmies do not appear to have evolved through positive selection for small stature-this was a by-product of selection for early onset of reproduction.

Y-chromosome diversity in Bantu and Pygmy populations from Central Africa

Linguistic and archaeological data have placed the Bantu homeland near the border between Cameroon and Nigeria, where the Bantu farmers are thought to have migrated from approximately 5000 years ago, spreading out over most of sub-Saharan Africa. In order to provide genetic insights into the so-called Bantu expansion, we have typed 18 well-characterized Y-chromosome short tandem repeats (STRs) in 24 Bantu and 3 Pygmy populations from Gabon and Cameroon. The results have shown not only that Bantu populations are very homogenous, but also that they are statistically very different from Pygmies and other African and non-African populations. High frequencies of the modal Bantu haplotype and of its one-step neighbours previously described have been found in all the Bantu populations sampled. Some traces of these haplotypes have also been found in Pygmies, indicating a possible Bantu-to-Pygmy flow of paternal lineages. No evidence has been found of the Fang being non-Bantu, despite their claim of having a semitic origin in Egypt. They do, however, show an intermediate allele (13.2) for DYS 385, whose date of appearance (approximately 5500 years ago) happens to coincide with the Bantu expansion.

Kairn A. Klieman. “The Pygmies Were Our Compass”: Bantu and Batwa in the History of West Central Africa, Early Times to c. 1900 C.E. Portsmouth, N.H.: Heinemann, 2003. xxxiv + 253 pp. Maps. Figure. Tables. Bibliography. Index. $26.00. Paper.

Kairn A. Klieman. “The Pygmies Were Our Compass”: Bantu and Batwa in the History of West Central Africa, Early Times to c. 1900 C.E. Portsmouth, N.H.: Heinemann, 2003. xxxiv + 253 pp. Maps. Figure. Tables. Bibliography. Index. $26.00. Paper. - Volume 48 Issue 1

HPA polymorphism in sub‐Saharan African populations: Beninese, Cameroonians, Congolese, and Pygmies

The frequency of human platelet antigen-1 (HPA-1) to HPA-11w (excluding HPA-8w) and HPA-15 systems was studied in four sub-Saharan populations: Beninese, Congolese (Democratic Republic of Congo Kinshasa), Cameroonians, and Aka pygmies (Central African Republic). No report of HPA prevalence has previously been published concerning these populations which are characterized by the highest HPA-2b gene frequencies of any reported to date (Aka 0.393, Benin 0.292, Cameroon 0.237, and Congo 0.224) and at lesser degree HPA-5b (Aka 0.405, Congo 0.268, Cameroon 0.254, and Benin 0.182). This study is of great importance (i) particularly in the context of the diversity caused by the population migrations, we may observe today in our hospitals (ii) to confirm that the Pygmy population with distinctive frequencies (absence of the HPA-1b, HPA-2b, and HPA-5b highest frequencies) is an isolated population.

Pygmy Populations Seronegative for Marburg Virus

Pygmy Populations Seronegative for Marburg Virus

HLA-DPB1, -DQB1 and -DRB1 alleles in a Aka Pygmy population from the Central African Republic

HLA-DPB1, -DQB1 and -DRB1 alleles in a Aka Pygmy population from the Central African Republic

HLA class I variation in the West African Pygmies and their genetic relationship with other African populations.

We have studied the polymorphism of HLA class I in two West African Pygmy populations, namely, the Bakola from Cameroon and the Mbenzele from the Central African Republic. A unique number of HLA alleles and haplotypes showed specific patterns of these populations. In this study, we identify two alleles (B*37, B*41) and three haplotypes (A*30-B*37, A*66-B*41 and A*68-B*58) that appear to be 'private' or typical of Western Pygmies. These data reflect similarities with the AKA Pygmies from the Central African Republic. On the other hand, we failed to identify alleles that are found at high frequencies among other sub-Saharan populations (B*42, B*51). Allelic and haplotypic frequency distributions show differences between the two Pygmy groups, e.g. B*35 was very common in the Mbenzele but has been found to be absent in the Bakola. In contrast, B*53, which is found in the Bakola, has been found to be rare in the Mbenzele Pygmies. In order to analyse the genetic relationships of the Bakola and Mbenzele Pygmies with other sub-Saharan populations, HLA gene frequencies were subjected to the Neighbour-Joining tree analysis. The Mbenzele, Bakola and AKA were found to be relatively close to each other and isolated from other sub-African populations. However, both the genetic distances and the within-group variation suggests that the Bakola are more admixed with Bantu farmers than Mbenzele.

Growth hormone binding protein, insulin-like growth factor-I and short stature in two pygmy populations from the Philippines.

The molecular basis and biochemical mediators of genetic growth propensity and adult height achievement in the general population are largely unknown. Pygmies represent one extreme of the height spectrum that may provide important clues regarding this issue. Previous studies in pygmies from Africa and Papua-New Guinea have shown decreased serum levels of growth hormone binding protein (GHBP), the circulating ectodomain of the growth hormone receptor (GHR). By inference, a similar limitation in tissue GHR expression has been assumed to be responsible for the partial growth hormone (GH) resistance observed in African pygmies. It is not clear how generalizable this concept is to other populations. To address this question, we studied two pygmy populations from the Philippines (Aeta and Mamanwa people) that are unrelated to the African pygmies. Serum GHBP and IGF-I levels were significantly decreased in both pygmy populations, compared to normal-statured Philippino controls. The results, together with previous observations in African and New Guinean pygmies, indicate that short stature is associated with low serum GHBP levels in pygmy populations of diverse origins and in different parts of the world. This strengthens the tentative postulate that the GHBP/GHR system plays an important role in the genetic and perhaps nutritional determination of adult stature in humans. Molecular genetic studies of the GHR gene in various pygmy populations may shed further light on the mystery of pygmy short stature.

Ebola and Marburg virus antibody prevalence in selected populations of the Central African Republic

With the natural history of the filovirus family seemingly unknown, filovirus ecology in its natural environment remains a rudimentary field of research. In order to investigate the maintenance cycle of filovirus in Central Africa, a study was conducted within the rain forest of the Central African Republic. The epidemiological study determines the frequency and distribution of filovirus seroprevalence in a selected human population. Using an ELISA, serum samples from Pygmy and non-Pygmy populations were tested for Ebola-Zaire virus and Marburg (MBG) virus antibody. Filovirus antibody reacting sera were found in all zones investigated, and in all populations studied (Ebola virus IgG 5.3%; Marburg virus IgG 2.4%). Pygmies appeared to have a significantly higher seroprevalence ( P < 0.03) against Ebola-Zaire virus (7.02%) than non-Pygmies (4.2%). MBG virus or related unknown filovirus strains also seem to be present in the western part of Central Africa. MBG virus antibodies were present in different Pygmy groups (ranging from 0.7 to 5.6%, mean 2.05%) and in several non-Pygmy populations (ranging from 0.0 to 3.9%, mean 3.4%) without an overall significant difference between the two groups ( P = 0.14). The potentialities of nonpathogenic filovirus strains circulating in the Central African Republic are discussed.

Microsatellite variation in Central Africa: an analysis of intrapopulational and interpopulational genetic diversity.

As a part of a research project on molecular variation in Central Africa, we have analyzed 10 microsatellites (CD4, CSFO, D3S1358, D18S51, D21S11, F13A1, FES, TH01, TPOX, and VWA) in the Bamileke and Ewondo from Cameroon and the Sanga and Mbenzele Pygmies from the Central African Republic (a total of 390 chromosomes). A statistically significant trend towards heterozygote deficiency was detected in the Mbenzele Pygmies. This was established through the use of powerful exact tests for the Hardy-Weinberg equilibrium. A certain degree of isolation and a small effective size may explain this finding. However, the lack of any substantial reduction in allelic diversity in the Mbenzele does not support the possibility that this group has a smaller effective size in evolutionary terms. A possible explanation based on ethnographic studies suggests that the gene flow from non-Pygmies to Pygmies could have been interrupted only in relatively recent times. The analysis of association between genotypes at pairs of independent loci indicates that the level of subheterogeneity is markedly lower in the Bamileke than in other sampled populations. This may be explained by the combined effect of larger population size, more rigid respect of clanic exogamy, and higher matrimonial mobility of the Bamileke. Finally, we have analyzed interpopulational relationships among our sampled populations and other Central African populations. The results are consistent with a previous study of protein loci (Spedini et al. 1999), which suggests the recent history of the Bamileke and Ewondo has led them to aquire a substantial genetic similarity. Furthermore, the Mbenzele Pygmies diverge from Biaka Pygmies, despite their common origin and geographical proximity. This is probably due to the differentiating effect of genetic drift, which is enhanced by the small effective size of Pygmy populations.

A survey of blood pressure distribution in Pygmy and Bantu populations in Cameroon.

A blood pressure survey was performed in isolated Pygmy communities and Bantu population samples living either in close relationship with the Pygmies or in separate areas within the same region. The Pygmies are still living as hunter-gatherers, whereas the Bantus rely on agriculture for food provision. Mean blood pressures in Pygmies were 130/85 mm Hg in males and 126/80 mm Hg in females and in Bantus were 137/87 mm Hg in males and 136/84 mm Hg in females. In spot urine the mean urinary sodium concentration was higher in Bantus than Pygmies (86 versus 37 mmol/L in males; 95 versus 56 mmol/L in females). In the total population urinary potassium concentration was very high (150 mmol/L), calcium concentration very low (0.4 mmol/L), and urea concentration low (6.9 g/L). After adjustment for age, height, weight, and sex, no racial differences in blood pressure were present. Blood pressure increased with age but body mass index did not. Diastolic pressure correlated significantly but negatively with urinary sodium in multiple regression analysis. Our study demonstrates that blood pressure increases with age in hunter-gatherer populations on a low to moderately high sodium diet in the presence of a low urinary excretion of calcium coupled with a low protein intake.

What is the situation of human T cell lymphotropic virus type II (HTLV-II) in Africa? Origin and dissemination of genomic subtypes.

Human T cell lymphotropic virus type II (HTLV-II) and its two genomic subtypes, A and B, which differ by 3 to 6% at the nucleotide level (depending on the gene studied), were until recently considered to be endemic only in certain Indian tribes in the Americas and were therefore considered mainly as a "New World virus." First, the evidence of HTLV-II antibodies and later characterization of isolates from sex workers or individuals living in large West and Central African cities suggested that HTLV-II subtype A could have been imported recently in Africa. However, the findings of HTLV-II infection in two Pygmy populations living in remote areas of Zaire and Cameroon suggest that HTLV-II might have been in Africa for a very long time. Furthermore, the discovery of HTLV-II subtype B virus in some of these Pygmies, but also in other individuals from Zaire and within a family in Gabon for three generations, confirms the hypothesis of a very ancient presence of this HTLV-II subtype B on the African continent Recent data indicate also that there exist in Central Africa specific HTLV-II divergent strains including an HTLV-II B variant strain in Gabon. In the context of recent evidence for interspecies transmission in Central and West Africa of HTLV-I/simian T cell lymphotropic virus type I (STLV-I) strains, leading to the two major HTLV-I African subtypes, we would like to suggest that some STLV-II (closely related to HTLV-II subtype B) still exist or might have existed in Central/East Africa. The recent finding of quite divergent primate T cell lymphotropic viruses (PTLVs) in several Pygmy chimpanzees of Zairian origin (PTLV-PP1664 and STLV-PP) and in wild-caught baboons in Eritrea, Ethiopia (PTLV-L), also supports the complementary hypothesis of a yet to be discovered new HTLV-II-related virus in humans. Careful study of the indeterminate Western blot patterns present in some populations in Central Africa strongly suggests that such an exciting possibility exists, thus opening new avenues of research on both the history of primate retroviruses and that of early human groups.

The Y-specific p21A1/TaqI polymorphism occurs in four major population Oroups.

The p21A1/TaqI polymorphism was studied in 904 individuals in 23 African population groups, encompassing the Caucasoid, Negroid, Khoisan and Pygmy populations. The frequency of the polymorphism was higher than previously reported, with the rarer allele occurring at frequencies ranging up to 0.41. No distinct trends in population frequency were observed, suggesting that the polymorphism is of little value in anthropological population studies. The existence of several TaqI mutations, in both time and position within the repeat unit, is indicated.

The comparative growth of Efe pygmies and African farmers from birth to age 5 years

Recent studies of African pygmies have concluded that the pattern of pygmy growth is similar to that of other Africans up to the time of puberty and that the short stature of adult pygmies is due primarily, if not solely, to the absence of accelerated adolescent growth. These conclusions are thought to be consistent with biochemical studies showing pygmies to have low levels of insulin-like growth factor 1 (IGF-1). All previous pygmy-growth studies have been of subjects of estimated, not known age. This paper reports the results of a mixed longitudinal growth study of Efe pygmy children of known age from birth to age 5 years. The mean adult stature of Efe pygmies is the shortest of any human population known, including other pygmy populations of central Africa. At birth, Efe were significantly smaller than neighbouring Lese Sudanic-speaking farmers and other rural Africans. During the first 5 years of life, Efe not only remained shorter than Lese controls at all ages, but the difference in stature between them increased. Unlike the Lese, Efe children showed a trend of increasingly negative z scores compared with the American reference population, from -2.71 (SD = 0.93) at 6 months to -4.16 (SD = 0.46) at age 5 years. These results indicate that suppression of pygmy growth does not occur solely at puberty, but from birth onward. Furthermore, they suggest that conclusions concerning the lack of an adolescent pygmy growth spurt have been premature and must await studies of older pygmy sub-adults of known age.

Anthropological survey on red cell glutathione peroxidase (GPX1) polymorphism in central western Africa: a tentative hypothesis on the interaction between GPX1*2 and Hb beta *S allelic products.

Phenotype and allele frequencies for erythrocyte glutathione peroxidase (GPX1) polymorphism are reported in the Mbugu and Sango (Central African Republic), Goun (Benin), and Bamileke (Cameroon) ethnic groups. The GPX1*2 allele frequencies (from 0.012 in the Sango to 0.058 in the Bamileke) fit into the range of the data already known for the Subsaharan populations. The value of GPX1*2 for study of the genetic admixture between Negro and Pygmy populations is suggested. Three different unusual GPX1 electrotypes are described. Finally, we hypothesize an interaction between GPX1*2 and Hb beta*S allelic products occurring in the sickle cells infected by Plasmodium falciparum.

Anomalously low endemic goiter prevalence among Efe pygmies.

The existence of endemic goiter, caused by iodine deficiency and the presence of a dietary goitrogen, has been noted in eastern Zaire by a number of authors (De Visscher et al.: Journal of Clinical Endocrinology and Metabolism 21:175-188, 1961; Delange et al.: Journal of Clinical Endocrinology and Metabolism 34:1059, 1972). In the Ituri Forest of Huate-Zaire, two distinct populations, the Efe (pygmy) and Lese (Bantu), live in association with each other and have similar diets. The goiter survey reported here documents differences in goiter prevalence and severity between the nomadic pygmy and village-living Bantu populations. While the Efe have an overall goiter prevalence of 9.4%, the Lese have a goiter prevalence of 42.9%. Furthermore, Efe women living in Lese villages and subsisting on a Lese diet have a prevalence of goiter similar to that of forest-living Efe women. Village-living individuals born of Efe mothers and Lese fathers have a prevalence of goiter greater than that of pure Efe but less than that of Lese. While our data cannot exclude dietary explanations for the difference in goiter prevalence between the Efe and Lese, they do support the hypothesis that the Efe possess an adaptation to an iodine-deficient environment that does not result in the development of goiters.

Stature estimates for some African Plio-Pleistocene fossil hominids

To estimate stature in fossil hominids, researchers generally use the Trotter & Gleser (1952, 1958) equations. These equations are based on a sample whose individuals are larger than the fossil sample to which they are customarily applied. This results in significant overestimates of early hominid statures. We offer here revised stature estimates for 15 reasonably well-preserved African Plio-Pleistocene hominid femora and tibiae (including AL 288-1 and WT 15000) based on least squares and major axis regression equations we developed for contemporary South African black tribal populations. By using this smaller and more homogeneous extant African sample, we predict that most of these hominids were smaller than McHenry's (and those subsequent) estimates have suggested. In the case of AL 288-1, our Model II estimate matches almost exactly Schmid's (1983; 1986; Geissmann 1986 a) anatomical reconstruction, while it differs significantly from the estimates derived from analyses of Olivier's recommended pygmy population. Although there is some disproportionality in the AL 288-1 lower limb, evidence is provided here to indicate that its effect on our stature estimates is probably small. This permits greater confidence to be placed in our estimates of her stature. In the final analysis, we find that except for Homo erectus the various groups of early hominids have overlapping ranges and differ little from one another in stature.

Grouping patterns of wild pygmy chimpanzees (Pan paniscus) observed at a marsh grassland amidst the tropical rain forest of Yalosidi, Republic of Zaïre

Fixed point observation to ascertain the grouping patterns of wild pygmy chimpanzees was carried out at a marsh grassland known locally as Iyoko amidst the tropical rain forest of Yalosidi, Republic of Zaire. The chimpanzees were seen alone or in parties consisting of up to 32 individuals. The mean size of parties which arrived at Iyoko was 7.9 (N=67), although the modal party size was 2–5. The majority (76%) of all observed parties including those that reformed after joining/parting while staying at Iyoko (N=96) was of the mixed type, i.e., consisting of adult male(s), adult female(s), and dependent individual(s). There was a tendency for parties to be composed of approximately equal numbers of adult males and females. All “social” activities such as sexual behavior and branch-dragging displays were recorded only in mixed parties consisting of more than ten individuals. The joining of parties of pygmy chimpanzees after arriving separately at Iyoko was seen 13 times and the parting of those before departing from Iyoko occurred seven times in total. In contrast, antagonistic encounters between two parties were recorded twice. These observations suggest that the joining/parting between parties is an intra-unit-group phenomenon while antagonistic encounters between parties are inter-unit-group interactions. It was assumed that at least two such unit-groups of pygmy chimpanzees consisting of 80–90 individuals in total utilized Iyoko without intermingling with each other. A comparison on grouping patterns among three pygmy chimpanzee populations (Yalosidi, Wamba, and Lomako) indicates that in terms of basic social organization they show many similarities except for the mean unit-group size, the mean party size, and the modal party size. Perhaps differences in the unit-group size were simply reflected as a whole in the differences of the mean party size as well as the modal party size observed across the three populations.