Genetic relationships among native americans based on β-globin gene cluster haplotype frequencies

The distribution of β-globin gene haplotypes was studied in 209 Amerindians from eight tribes of the Brazilian Amazon: Asurini from Xingú, Awá-Guajá, Parakanã, Urubú-Kaapór, Zoé, Kayapó (Xikrin from the Bacajá village), Katuena, and Tiriyó. Nine different haplotypes were found, two of which (n. 11 and 13) had not been previously identified in Brazilian indigenous populations. Haplotype 2 (+ -) was the most common in all groups studied, with frequencies varying from 70% to 100%, followed by haplotype 6 (+ + +), with frequencies between 7% and 18%. The frequency distribution of the β-globin gene haplotypes in the eighteen Brazilian Amerindian populations studied to date is characterized by a reduced number of haplotypes (average of 3.5) and low levels of heterozygosity and intrapopulational differentiation, with a single clearly predominant haplotype in most tribes (haplotype 2). The Parakanã, Urubú-Kaapór, Tiriyó and Xavante tribes constitute exceptions, presenting at least four haplotypes with relatively high frequencies. The closest genetic relationships were observed between the Brazilian and the Colombian Amerindians (Wayuu, Kamsa and Inga), and, to a lesser extent, with the Huichol of Mexico. North-American Amerindians are more differentiated and clearly separated from all other tribes, except the Xavante, from Brazil, and the Mapuche, from Argentina. A restricted pool of ancestral haplotypes may explain the low diversity observed among most present-day Brazilian and Colombian Amerindian groups, while interethnic admixture could be the most important factor to explain the high number of haplotypes and high levels of diversity observed in some South-American and most North-American tribes.


Introduction
The molecular polymorphism of the β-globin gene cluster was the first nuclear DNA segment widely studied for the analysis of evolutionary relationships among human populations (Wainscoat et al., 1986).The distribution of haplotypes associated with the βA gene is now known for a large number of populations.The data indicate that Africans are the most divergent group, and that the first split separated an African group from an Eurasian one (Wainscoat et al., 1986;Oehme et al., 1985;Antonarakis et al., 1985;Maggio et al., 1986;Kulozik et al., 1986;Ramsay and Jenkins, 1987;Hundrieser et al., 1988a,b;Yongvanit et al., 1989;Chen et al., 1990;Long et al., 1990;Trent et al., 1990;Shimizu, 1987;Shimizu et al., 1989;Varawalla et al., 1992;Penaloza et al., 1995;Hewitt et al., 1996;Castro-de-Guerra et al., 1997;Fucharoen et al., 1997;Kaufman et al., 1998;Villalobos-Arámbula et al., 2000).The distribution of βA haplotypes in Brazilian Amerindian populations was investigated in ten tribes of the Amazon region by Guerreiro et al. (1992Guerreiro et al. ( , 1994) ) and Bevilacqua et al. (1995), who obtained similar results.Haplotypes 2 and 6 were the most common, and heterozygosity was reduced, as compared to Europeans and Africans.The results also showed that Brazilian Amerindians are closely related to Asians, Polynesians and Micronesians.However, genetic studies of Brazilian Amerindians based on tandemly repeated minisatellite loci have shown that, although heterozygosity and the mean number of alleles are low, there is a marked heterogeneity among populations, with distinct patterns of allele distribution in different tribes.This suggests that the study of a small number of tribes may not adequately sample the whole range of genetic variability in Brazilian Amerindians (Zago et al., 1996).Here, we report on the distribution of the β-globin gene haplotypes in eight new Amerindian tribes from the Amazon region of Brazil, and compare our results with those reported previously for Native American and other human populations.
Blood samples were collected using the anticoagulant EDTA, and genomic DNA was isolated from whole blood by phenol-chloroform extraction and ethanol precipitation (Old and Higgs, 1983).β-globin gene haplotypes were identified by analyzing the following polymorphic restriction sites: 1. HincII 5'; 2. HindIII G; 3. HindII A; 4. HincII-β; 5. HincII-3'β.Typing was done by PCR amplification, followed by restriction digestion and agarose gel electrophoresis, according to Guerreiro et al. (1992) for site HincII 5', and to Sutton et al. (1989) for the remaining sites.Haplotype identification was made using the likelihood method described by Excoffier and Slatkin (1995).Haplotype diversity, the gene differentiation coefficient (Nei, 1973(Nei, , 1978;;Livshits and Nei, 1990), and genetic distances (DA distance, as described by Nei et al., 1983) between Brazilian Amerindians and other populations were estimated using the DISPAN program (Ota, 1993).A neighbor-joining tree (Saitou and Nei, 1987) was obtained from DA genetic distances using the same program.Comparisons of the haplotype distribution in different populations were made with Pearson's Chi-square statistic using the Biosys-1 program (Swofford and Selander, 1981).

Results
Nine different haplotypes were found, two of which (n. 11 and 13) had not been previously identified in Brazilian indigenous populations (Table 1).The number of identified haplotypes per tribe ranged from one in the Awá-Guajá to eight in the Urubú-Kaapór.Haplotype 2 (+ ----) was the most common in all groups studied, with frequencies varying from 70% to 100%, followed by haplo-230 Mousinho-Ribeiro et al.
Table 1 β-globin gene haplotypes in Brazilian Amerindians and other native Americans.
Haplotype 5 (-+ -+ +) was identified in five of the eight tribes, with frequencies between 3.6% and 7%, while haplotype 4 ( -+ --+) was observed in three tribes, with frequencies varying from 1% to 7%.The remaining haplotypes were identified in only one or two tribes, although with polymorphic frequencies in some cases.

Discussion
The most common β-globin gene haplotypes found in Brazilian Amerindians (haplotypes 2, 6, and 5) are considered to be first-order haplotypes in the phylogenetic scheme proposed by Chen et al. (1990) and Long et al. (1990).These haplotypes were probably brought to America by the first settlers of the continent, given that they are also common in Asia, the probable place of origin of the first migrants, and in the islands of the South Pacific, from where additional immigrants may have come (Salzano and Callegari-Jacques, 1988;Nei and Roychoudhury, 1993;Ward et al., 1991;Horai et al., 1993;Neves et al., 1998).According to this scheme, haplotypes 2, 5, and 6 would have originated directly from the ancestral type, possibly haplotype 1 (Chen et al., 1990 andLong et al., 1990) or haplotype 3 (Vincek et al., 1994), or from another firstorder haplotype (1 or 4).First-order haplotypes are separated by at least two mutation or gene conversion events (Long et al., 1990), making it unlikely that they arose in na-tive Americans from other first-order haplotypes, which are virtually absent in these populations.Second-order haplotypes (7, 9, 11, and 13), derived by recombination from first-order haplotypes, were also found in Brazilian natives at frequencies varying from 1.4% to 10.0.As they are rare or absent in Asians, they probably appeared during the colonization of the American continent.Three other first-order haplotypes (3, 4, and 16) were also found at low frequencies in Brazilian Amerindians.The presence of haplotype 3 can be attributed to admixture with people of African ancestry, since this haplotype is very common in Africans, but rare or absent in all other populations.The presence of the other first-order haplotypes (4 and 16) may also be due to admixture with non-Amerindians, although, as they are also found in Asian and Oceanic populations, they may have been present in the ancestral population.
The distribution of β-globin haplotypes in native Americans is shown in Table 1.To date, eleven different haplotypes have been identified in Brazilian tribes, although most of them have a reduced number of haplotypes (average of 3.5, minimum of 1, and maximum of 8).The highest value was observed in the Urubú-Kaapór, a tribe with significant levels of admixture with non-Amerindians.The haplotype distribution among tribes is generally homogeneous, haplotype 2 accounting for more than 78% of haplotypes.Haplotype 6 accounts for the majority of the remainder, followed by haplotype 5, also found in most of the eighteen tribes studied.Awá-Guajá, Parakanã, Urubú-Kaapór, Tiriyó and Xavante are the exceptions.Haplotype 2 is fixed in the former tribe, while the others present alternative haplotypes with relatively high frequencies.
Genetic variability measured by haplotype diversity and the coefficient of gene differentiation in native American and other ethnic groups is shown in Table 2. Total diversity (Ht) and intrapopulational variation (Hs) observed in Brazilian Amerindians are similar to those estimated for Asians, corroborating the results of Guerreiro et al. (1994) and Mattevi et al. (2000), but they are higher than those es-β-globin gene haplotypes in Native Americans 231 timated for Colombian Amerindians and, as expected, lower than those of North-American natives, Africans and Europeans.The interpopulational diversity (Dst) of Brazilian Amerindians is also higher than that observed in Colombian Amerindians, but a little lower than estimated for native North-Americans and Asians.Some of the Brazilian tribes, such as the Urubú-Kaapór and Tiriyó, and probably the Xavante, present evidence of interethnic admixture and exhibit high levels of heterozygosity, which may account for at least part of these differences.However, Callegari-Jacques and Salzano (1999) estimated interethnic admixture in the Xavante as being only about 2%.Anyway, when these tribes are excluded from diversity analyses, interpopulational diversity in Brazilian Amerindians is reduced to 0.8%, a value lower than those observed in other populations, except for Colombian Amerindians.
The genetic distances (DA) between Brazilian Amerindians and other American natives based on haplotype frequencies are shown in Table 3, and their relationship pattern is presented as a dendrogram (Figure 1).As a rule, the genetic distances between Brazilian Amerindians are low, except for the Urubú-Kaapór and Tiriyó, and the genetic affinities among tribes show no clear linguistic or geographic pattern.At a continental level, the lowest values of genetic distances from Brazilian Amerindians were observed in Colombian Amerindians (Wayuu, Kamsa and Inga) and Huichol (Mexico), who cluster in the upper part of the dendrogram (Figure 1).Mvskoke, Carrier-Sekani and Mapuche are the more differentiated groups, and form a separate cluster.
In summary, the results obtained through analysis of the β-globin haplotype in a relatively large number of Brazilian Amerindian populations agree with those of the first studies, indicating a homogeneous distribution of haplo-types in most tribes, characterized by a reduced number of haplotypes, and low levels of heterozygosity and differentiation.Haplotype 2 accounts for more than 78% of the total, the rest being mainly accounted for by haplotypes 5 and 6.The Parakanã, Urubú-Kaapór, Tiriyó and Xavante constitute exceptions by presenting at least one other haplotype with a relatively high frequency.The pattern of genetic affinities among Brazilian Amerindians indicates that most groups are closely related to each other, and to Colombian Amerindians, whereas North-American Amerindians are 232 Mousinho-Ribeiro et al.
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Table 2 -
β-globin gene haplotype diversity in American natives and other human populations.